WorldWideScience

Sample records for bacteroidetes

  1. Environmental and gut Bacteroidetes: the food connection

    Directory of Open Access Journals (Sweden)

    François eThomas

    2011-05-01

    Full Text Available Members of the diverse bacterial phylum Bacteroidetes have colonized virtually all types of habitats on Earth. They are among the major members of the microbiota of animals, especially in the gastro-intestinal tract, can act as pathogens and are frequently found in soils, oceans and freshwater. In these contrasting ecological niches, Bacteroidetes are increasingly regarded as specialists for the degradation of high molecular weight organic matter, i.e. proteins and carbohydrates. This review presents the current knowledge on the role and mechanisms of polysaccharide degradation by Bacteroidetes in their respective habitats. The recent sequencing of Bacteroidetes genomes confirms the presence of numerous carbohydrate-active enzymes covering a large spectrum of substrates from plant, algal and animal origin. Comparative genomics reveal specific Polysaccharide Utilization Loci shared between distantly related members of the phylum, either in environmental or gut-associated species. Moreover, Bacteroidetes genomes appear to be highly plastic and frequently reorganized through genetic rearrangements, gene duplications and lateral gene transfers, a feature that could have driven their adaptation to distinct ecological niches. Evidence is accumulating that the nature of the diet shapes the composition of the intestinal microbiota. We address the potential links between gut and environmental bacteria through food consumption. Lateral gene transfer can provide gut bacteria with original sets of utensils to degrade otherwise refractory substrates found in the diet. A more complete understanding of the genetic gateways between food associated environmental species and intestinal microbial communities sheds new light on the origin and evolution of Bacteroidetes as animals' symbionts. It also raises the question as to how the consumption of increasingly hygienic and processed food deprives our microbiota from useful environmental genes and possibly affects

  2. Diversity of Bacteroidetes in high altitude saline evaporitic basins in northern Chile

    OpenAIRE

    Dorador, Cristina; Meneses, D.; Urtuvia, V.; Demergasso, C.; Vila, I; Witzel, K.-P.; Imhoff, Johannes F.

    2009-01-01

    The phylum Bacteroidetes represents one of the most abundant bacterial groups of marine and freshwater bacterioplankton. We investigated the diversity of Bacteroidetes in water and sediment samples from three evaporitic basins located in the highlands of northern Chile. We used both 16S rRNA gene clone libraries created with targeted Bacteroidetes-specific primers and separation of specifically amplified gene fragments by denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed ...

  3. Distribution and culturability of the uncultivated 'AGG58 cluster' of the Bacteroidetes phylum in aquatic environments.

    Science.gov (United States)

    O'Sullivan, Louise A; Fuller, Katherine E; Thomas, Ellen M; Turley, Carol M; Fry, John C; Weightman, Andrew J

    2004-03-01

    Members of the Bacteroidetes phylum are abundant in aquatic habitats when assessed by fluorescent in situ hybridisation and in some 16S rRNA gene libraries. In this study 16S rRNA gene clone libraries were constructed with bacterial primers that amplify Bacteroidetes sequences well (27F, 1492R) from coastal seawater near Plymouth (UK) during a phytoplankton bloom. Most of the clones (66%, 106/160) affiliated with the Bacteroidetes phylum, and of these 62% (66/106; or 41% 66/160 of the entire library) clustered with marine bacterioplankton clones env.agg58, Arctic97A-17, CF17, CF96 and CF101. This phylogenetic branch of Bacteroidetes was designated the 'AGG58 cluster', and its presence in various aquatic environments was investigated. Two pairs of AGG58-specific 16S rRNA-gene-targeted polymerase chain reaction (PCR) primers were designed and successfully used to detect the cluster in DNA extracts from three UK coastal seawater sites, and from freshwater River Taff epilithon. In addition, 600 putative Bacteroidetes strains were isolated from these sites on relatively high-nutrient agar media. AGG58 cluster specific probes were used to screen the amplified 16S rRNA gene products from the isolates, but no members of the AGG58 cluster were discovered. The least specific probe hybridised with one River Taff water isolate (RW262 NCIMB 13979) which formed a monophyletic group with the genera Crocinitomix, Brumimicrobium and Cryomorpha of the family Cryomorphaceae in the Bacteroidetes phylum. RW262 probably represents the first isolate of a new genus within this family. This study provides new evidence that the uncultivated AGG58 group is abundant, globally distributed, and can be rapidly detected with the new PCR primers described. PMID:19712324

  4. Draft Genome Sequence of the Moderately Thermophilic Bacterium Schleiferia thermophila Strain Yellowstone (Bacteroidetes)

    OpenAIRE

    Thiel, Vera; Hamilton, Trinity L.; Tomsho, Lynn P.; Burhans, Richard; Gay, Scott E.; Ramaley, Robert F.; Stephan C Schuster; Steinke, Laurey; Bryant, Donald A.

    2014-01-01

    The draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone (Bacteroidetes), isolated from Octopus Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 2,617,694 bp in 35 contigs. The draft genome is predicted to encode 2,457 protein coding genes and 37 tRNA encoding genes and two rRNA operons.

  5. Diversity of Bacteroidetes in high-altitude saline evaporitic basins in northern Chile

    Science.gov (United States)

    Dorador, Cristina; Meneses, Daniela; Urtuvia, Viviana; Demergasso, Cecilia; Vila, Irma; Witzel, Karl-Paul; Imhoff, Johannes F.

    2009-06-01

    The phylum Bacteroidetes represents one of the most abundant bacterial groups of marine and freshwater bacterioplankton. We investigated the diversity of Bacteroidetes in water and sediment samples from three evaporitic basins located in the highlands of northern Chile. We used both 16S rRNA gene clone libraries created with targeted Bacteroidetes-specific primers and separation of specifically amplified gene fragments by denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed a reduced richness of these organisms in samples from Salar de Huasco (two to four DGGE bands) increasing in Salar de Ascotán (two to seven DGGE bands) and Laguna Tebenquiche at Salar de Atacama (four to eight DGGE bands). Cluster analysis (WPGMA) of DGGE bands showed that bands from Salar de Huasco and Salar de Ascotán grouped together and samples from Salar de Atacama formed separate clusters in water and sediment samples, reflecting different Bacteroidetes communities between sites. Most of the sequences analyzed belonged to the family Flavobacteriaceae and clustered with the genera Psychroflexus, Gillisia, Maribacter, Muricauda, Flavobacterium, and Salegentibacter. The most abundant phylotype was highly related to Psychroflexus spp. and was recovered from all three study sites. The similarity of the analyzed sequences with their closest relatives in GenBank was typically Culture efforts will be necessary to get a better description of the diversity of this group in saline evaporitic basins of northern Chile.

  6. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age

    Directory of Open Access Journals (Sweden)

    Mariat D

    2009-06-01

    Full Text Available Abstract Background In humans, the intestinal microbiota plays an important role in the maintenance of host health by providing energy, nutrients, and immunological protection. Applying current molecular methods is necessary to surmount the limitations of classical culturing techniques in order to obtain an accurate description of the microbiota composition. Results Here we report on the comparative assessment of human fecal microbiota from three age-groups: infants, adults and the elderly. We demonstrate that the human intestinal microbiota undergoes maturation from birth to adulthood and is further altered with ageing. The counts of major bacterial groups Clostridium leptum, Clostridium coccoides, Bacteroidetes, Bifidobacterium, Lactobacillus and Escherichia coli were assessed by quantitative PCR (qPCR. By comparing species diversity profiles, we observed age-related changes in the human fecal microbiota. The microbiota of infants was generally characterized by low levels of total bacteria. C. leptum and C. coccoides species were highly represented in the microbiota of infants, while elderly subjects exhibited high levels of E. coli and Bacteroidetes. We observed that the ratio of Firmicutes to Bacteroidetes evolves during different life stages. For infants, adults and elderly individuals we measured ratios of 0.4, 10.9 and 0.6, respectively. Conclusion In this work we have confirmed that qPCR is a powerful technique in studying the diverse and complex fecal microbiota. Our work demonstrates that the fecal microbiota composition evolves throughout life, from early childhood to old age.

  7. Phylogeny and molecular signatures (conserved proteins and indels that are specific for the Bacteroidetes and Chlorobi species

    Directory of Open Access Journals (Sweden)

    Lorenzini Emily

    2007-05-01

    Full Text Available Abstract Background The Bacteroidetes and Chlorobi species constitute two main groups of the Bacteria that are closely related in phylogenetic trees. The Bacteroidetes species are widely distributed and include many important periodontal pathogens. In contrast, all Chlorobi are anoxygenic obligate photoautotrophs. Very few (or no biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them. Results Systematic blast searches were performed on each open reading frame in the genomes of Porphyromonas gingivalis W83, Bacteroides fragilis YCH46, B. thetaiotaomicron VPI-5482, Gramella forsetii KT0803, Chlorobium luteolum (formerly Pelodictyon luteolum DSM 273 and Chlorobaculum tepidum (formerly Chlorobium tepidum TLS to search for proteins that are uniquely present in either all or certain subgroups of Bacteroidetes and Chlorobi. These studies have identified > 600 proteins for which homologues are not found in other organisms. This includes 27 and 51 proteins that are specific for most of the sequenced Bacteroidetes and Chlorobi genomes, respectively; 52 and 38 proteins that are limited to species from the Bacteroidales and Flavobacteriales orders, respectively, and 5 proteins that are common to species from these two orders; 185 proteins that are specific for the Bacteroides genus. Additionally, 6 proteins that are uniquely shared by species from the Bacteroidetes and Chlorobi phyla (one of them also present in the Fibrobacteres have also been identified. This work also describes two large conserved inserts in DNA polymerase III (DnaE and alanyl-tRNA synthetase that are distinctive characteristics of the Chlorobi species and a 3 aa deletion in ClpB chaperone that is mainly found in various Bacteroidales, Flavobacteriales and Flexebacteraceae, but generally not found in the homologs from other organisms. Phylogenetic analyses of the Bacteroidetes and Chlorobi species is also

  8. A protein secretion system linked to bacteroidete gliding motility and pathogenesis.

    Science.gov (United States)

    Sato, Keiko; Naito, Mariko; Yukitake, Hideharu; Hirakawa, Hideki; Shoji, Mikio; McBride, Mark J; Rhodes, Ryan G; Nakayama, Koji

    2010-01-01

    Porphyromonas gingivalis secretes strong proteases called gingipains that are implicated in periodontal pathogenesis. Protein secretion systems common to other Gram-negative bacteria are lacking in P. gingivalis, but several proteins, including PorT, have been linked to gingipain secretion. Comparative genome analysis and genetic experiments revealed 11 additional proteins involved in gingipain secretion. Six of these (PorK, PorL, PorM, PorN, PorW, and Sov) were similar in sequence to Flavobacterium johnsoniae gliding motility proteins, and two others (PorX and PorY) were putative two-component system regulatory proteins. Real-time RT-PCR analysis revealed that porK, porL, porM, porN, porP, porT, and sov were down-regulated in P. gingivalis porX and porY mutants. Disruption of the F. johnsoniae porT ortholog resulted in defects in motility, chitinase secretion, and translocation of a gliding motility protein, SprB adhesin, to the cell surface, providing a link between a unique protein translocation system and a motility apparatus in members of the Bacteroidetes phylum. PMID:19966289

  9. Contrasting genomic patterns and infection strategies of two co-existing Bacteroidetes podovirus genera.

    Science.gov (United States)

    Holmfeldt, Karin; Howard-Varona, Cristina; Solonenko, Natalie; Sullivan, Matthew B

    2014-08-01

    Bacterial viruses (phages) are abundant, ecologically important biological entities. However, our understanding of their impact is limited by model systems that are primarily not well represented in nature, e.g. Enterophages and their hosts. Here, we investigate genomic characteristics and infection strategies among six aquatic Bacteroidetes phages that represent two genera of exceptionally large (∼70-75 kb genome) podoviruses, which were isolated from the same seawater sample using Cellulophaga baltica as host. Quantitative host range studies reveal that these genera have contrasting narrow (specialist) and broad (generalist) host ranges, with one-step growth curves revealing reduced burst sizes for the generalist phages. Genomic comparisons suggest candidate genes in each genus that might explain this host range variation, as well as provide hypotheses about receptors in the hosts. One generalist phage, φ38:1, was more deeply characterized, as its infection strategy switched from lytic on its original host to either inefficient lytic or lysogenic on an alternative host. If lysogenic, this phage was maintained extrachromosomally in the alternative host and could not be induced by mitomycin C. This work provides fundamental knowledge regarding phage-host ranges and their genomic drivers while also exploring the 'host environment' as a driver for switching phage replication mode. PMID:24428166

  10. Isolation and classification of a novel marine Bacteroidetes as Frondibacter aureus gen. nov., sp. nov.

    Science.gov (United States)

    Yoon, Jaewoo; Adachi, Kyoko; Kasai, Hiroaki

    2015-02-01

    A facultatively anaerobic, Gram-stain negative, golden-yellow pigmented, non-motile and rod-shaped bacterium, designated strain A5Q-67(T) was isolated from leaf litter collected at the mangrove estuary of Nakama River, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (94.2 %) to Imtechella halotolerans K1(T). The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain A5Q-67(T) were identified as iso-C17:0 3-OH, summed feature 1 (iso-C15:1 H and/or C13:0 3-OH) and iso-C15:0 as defined by the MIDI system. The DNA G+C content was determined to be 36.7 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Frondibacter aureus gen. nov., sp. nov. is proposed. The type strain of F. aureus is A5Q-67(T) (=KCTC 32991(T) = NBRC 110021(T)). PMID:25385000

  11. A polysaccharide utilization locus from an uncultured Bacteroidetes phylotype suggests ecological adaptation and substrate versatility

    DEFF Research Database (Denmark)

    Mackenzie, A.K.; Naas, A.E.; Kracun, Stjepan Kresimir;

    2015-01-01

    an uncultured Bacteroidetes phylotype (SRM-1) that dominates the rumen microbiome of Arctic reindeer. CSaveharacterization of the three PUL-encoded outer membrane glycoside hydrolases was performed using chromogenic substrates for initial screening, followed by detailed analyses of products generated from......D-like lipoproteins previously characterized from the same PUL, binding to cellulose was not observed. Overall, these activities and binding specificities correlated well with the glycan content of the reindeer rumen, which was determined using comprehensive microarray polymer profiling and showed an abundance...

  12. Hydrogenotrophic culture enrichment reveals rumen Lachnospiraceae and Ruminococcaceae acetogens and hydrogen-responsive Bacteroidetes from pasture-fed cattle.

    Science.gov (United States)

    Gagen, Emma J; Padmanabha, Jagadish; Denman, Stuart E; McSweeney, Christopher S

    2015-07-01

    Molecular information suggests that there is a broad diversity of acetogens in the rumen, distinct from any currently isolated acetogens. We combined molecular analysis with enrichment culture techniques to investigate this diversity further. Methane-inhibited, hydrogenotrophic enrichment cultures produced acetate as the dominant end product. Acetyl-CoA synthase gene analysis revealed putative acetogens in the cultures affiliated with the Lachnospiraceae and Ruminococcaceae as has been found in other rumen studies. No formyltetrahydrofolate synthetase genes affiliating with acetogens or with 'homoacetogen similarity' scores >90% were identified. To further investigate the hydrogenotrophic populations in these cultures and link functional gene information with 16S rRNA gene identity, cultures were subcultured quickly, twice, through medium without exogenous hydrogen, followed by incubation without exogenous hydrogen. Comparison of cultures lacking hydrogen and their parent cultures revealed novel Lachnospiraceae and Ruminococcaceae that diminished in the absence of hydrogen, supporting the hypothesis that they were likely the predominant acetogens in the enrichments. Interestingly, a range of Bacteroidetes rrs sequences that demonstrated <86% identity to any named isolate also diminished in cultures lacking hydrogen. Acetogens or sulphate reducers from the Bacteroidetes have not been reported previously; therefore this observation requires further investigation. PMID:26109360

  13. Assessment of fecal pollution sources in a small northern-plains watershed using PCR and phylogenetic analyses of Bacteroidetes 16S rRNA gene

    Science.gov (United States)

    Lamendella, R.; Domingo, J.W.S.; Oerther, D.B.; Vogel, J.R.; Stoeckel, D.M.

    2007-01-01

    We evaluated the efficacy, sensitivity, host-specificity, and spatial/temporal dynamics of human- and ruminant-specific 16S rRNA gene Bacteroidetes markers used to assess the sources of fecal pollution in a fecally impacted watershed. Phylogenetic analyses of 1271 fecal and environmental 16S rRNA gene clones were also performed to study the diversity of Bacteroidetes in this watershed. The host-specific assays indicated that ruminant feces were present in 28-54% of the water samples and in all sampling seasons, with increasing frequency in downstream sites. The human-targeted assays indicated that only 3-5% of the water samples were positive for human fecal signals, although a higher percentage of human-associated signals (19-24%) were detected in sediment samples. Phylogenetic analysis indicated that 57% of all water clones clustered with yet-to-be-cultured Bacteroidetes species associated with sequences obtained from ruminant feces, further supporting the prevalence of ruminant contamination in this watershed. However, since several clusters contained sequences from multiple sources, future studies need to consider the potential cosmopolitan nature of these bacterial populations when assessing fecal pollution sources using Bacteroidetes markers. Moreover, additional data is needed in order to understand the distribution of Bacteroidetes host-specific markers and their relationship to water quality regulatory standards. ?? 2006 Federation of European Microbiological Societies.

  14. Larkinella insperata gen. nov., sp. nov., a bacterium of the phylum 'Bacteroidetes' isolated from water of a steam generator.

    Science.gov (United States)

    Vancanneyt, Marc; Nedashkovskaya, Olga I; Snauwaert, Cindy; Mortier, Stefanie; Vandemeulebroecke, Katrien; Hoste, Bart; Dawyndt, Peter; Frolova, Galina M; Janssens, Danielle; Swings, Jean

    2006-01-01

    A Gram-negative bacterium, designated strain LMG 22510T, was isolated from water of a pharmaceutical company steam generator. The cells had a ring-like and horseshoe-shaped morphology and possessed gliding motility. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain was a member of the Flexibacter group within the phylum 'Bacteroidetes'; its nearest neighbour was Spirosoma linguale (88.8 % sequence similarity). DNA base content, fatty acid composition and biochemical characteristics were determined. Genotypic and phenotypic data indicated that strain LMG 22510T could not be assigned to any recognized genus; therefore, a novel genus and species is proposed, Larkinella insperata gen. nov., sp. nov., with LMG 22510T (= NCIMB 14103T) as the type strain. PMID:16403892

  15. Distribution of two triamines, spermidine and homospermidine, and an aromatic amine, 2-phenylethylamine, within the phylum Bacteroidetes.

    Science.gov (United States)

    Hosoya, Ryuichi; Hamana, Koei

    2004-10-01

    Cellular polyamines of the newly additional 19 species belonging to the class Bacteroides of the phylum Bacteroidetes were analyzed by HPLC to display polyamine distribution as a chemotaxonomic marker within the total 41 species. Three profiles, the presence of spermidine, the presence of homospermidine and the absence of both triamines, corresponded to their phylogenetical positions within the four families of the class. The occurrence of an aromatic amine, 2-phenylethylamine, extracted into cellular polyamine fraction, was also determined within the 121 species distributed within the phylum. This aromatic amine was found in Cellulophaga lytica, Cytophaga latercula, Tenacibaculum amylolyticum, Tenacibaculum martimum, Tenacibaculum mesophilum and Psychroflexus torquis belonging to the family Flavobacteriaceae of the class Flavobacteria, and Flexibacter flexilis and Microscilla marina belonging to the family Flexibacteraceae of the class Sphingobacteria. PMID:15747230

  16. Occurrence of human-associated Bacteroidetes genetic source tracking markers in raw and treated wastewater of municipal and domestic origin and comparison to standard and alternative indicators of faecal pollution

    OpenAIRE

    Mayer, R. E.; Bofill-Mas, S.; Egle, L.; Reischer, G. H.; Schade, M.; Fernandez-Cassi, X.; Fuchs, W; Mach, R. L.; Lindner, G.; Kirschner, A.; Gaisbauer, M.; Piringer, H.; A. P. Blaschke; Girones, R; M. Zessner

    2015-01-01

    This was a detailed investigation of the seasonal occurrence, dynamics, removal and resistance of human-associated genetic Bacteroidetes faecal markers (GeBaM) compared with ISO-based standard faecal indicator bacteria (SFIB), human-specific viral faecal markers and one human-associated Bacteroidetes phage in raw and treated wastewater of municipal and domestic origin. Characteristics of the selected activated sludge wastewater treatment plants (WWTPs) from Austria and Germany were studied in...

  17. Dextrins from Maize Starch as Substances Activating the Growth of Bacteroidetes and Actinobacteria Simultaneously Inhibiting the Growth of Firmicutes, Responsible for the Occurrence of Obesity.

    Science.gov (United States)

    Barczynska, Renata; Kapusniak, Janusz; Litwin, Mieczyslaw; Slizewska, Katarzyna; Szalecki, Mieczyslaw

    2016-06-01

    Unarguably, diet has a significant impact on human intestinal microbiota. The role of prebiotics as substances supporting the maintenance of appropriate body weight and reducing the demand for energy via stimulation of the growth of beneficial microbiota of the gut and formation products such as short-chain fatty acids, is more and more often highlighted. The objective of this study was to evaluate whether dextrins from maize starch resistant to enzymatic digestion stimulate the growth of Bacteroidetes and Actinobacteria strains representing a majority of the population of colon microbiota in lean individuals and limit the growth of Firmicutes bacterial strains representing a majority of the population of colon microbiota in obese individuals. The study was conducted with the use of in vitro method, using isolates from faeces of children characterized by normal weight, overweight and obesity. It was demonstrated that dextrins from maize starch equally efficient stimulate the growth of the isolates derived from normal-weight, overweight and obese children, and therefore may be added to foods as a beneficial component stimulating growth of strains belonging to Actinobacteria and Bacteroidetes for both overweight, obese and normal-weight children. PMID:27155867

  18. Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes

    Directory of Open Access Journals (Sweden)

    Jennifer L. Edwards

    2010-10-01

    Full Text Available Polysaccharides are an important source of organic carbon in the marine environment and degradation of the insoluble and globally abundant cellulose is a major component of the marine carbon cycle. Although a number of species of cultured bacteria are known to degrade crystalline cellulose, little is known of the polysaccharide hydrolases expressed by cellulose-degrading microbial communities, particularly in the marine environment. Next generation 454 Pyrosequencing was applied to analyze the microbial community that colonizes and degrades insoluble polysaccharides in situ in the Irish Sea. The bioinformatics tool MG-RAST was used to examine the randomly sampled data for taxonomic markers and functional genes, and showed that the community was dominated by members of the Gammaproteobacteria and Bacteroidetes. Furthermore, the identification of 211 gene sequences matched to a custom-made database comprising the members of nine glycoside hydrolase families revealed an extensive repertoire of functional genes predicted to be involved in cellulose utilization. This demonstrates that the use of an in situ cellulose baiting method yielded a marine microbial metagenome considerably enriched in functional genes involved in polysaccharide degradation. The research reported here is the first designed to specifically address the bacterial communities that colonize and degrade cellulose in the marine environment and to evaluate the glycoside hydrolase (cellulase and chitinase gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques.

  19. Coarse, but not finely ground, dietary fibre increases intestinal Firmicutes:Bacteroidetes ratio and reduces diarrhoea induced by experimental infection in piglets.

    Science.gov (United States)

    Molist, Francesc; Manzanilla, Edgar Garcia; Pérez, José Francisco; Nyachoti, Charles Martin

    2012-07-14

    Using dietary fibre to control childhood diarrhoea has rarely been discussed. However, dietary fibre is being proposed to prevent diarrhoea in piglets. The present study aimed to study the effects of introducing fibre in the post-weaning piglet diet and its particle size on the intestinal ecosystem before and after an experimental infection with Escherichia coli. A total of thirty-six post-weaning piglets were assigned to four experimental diets: a negative control (NC) diet, the same diet with 4 % wheat bran coarse (WBc) particle size or finely milled (WBF) and a positive control (PC) diet with an antibiotic. On day 9, animals were challenged with E. coli. Faecal and digesta samples were obtained before and after the experimental infection and changes in the microbial ecosystem were measured. Animals fed the WBc and the PC diets showed a significant reduction in the faecal score compared with the NC diet. The inclusion of WBc in the diet increased total volatile fatty acid concentration, reduced Bacteroidetes in the faeces before and after the experimental infection compared with the NC diet and increased Firmicutes at the end of the experiment. Based on the results, diarrhoea scours and the composition of the pig gut microbial community are modified by the inclusion of a relatively small amount of wheat bran in the diet, being the physical presentation of the fibre a determinant of that difference. PMID:22018207

  20. Structure-Function Analysis of a Mixed-linkage β-Glucanase/Xyloglucanase from the Key Ruminal Bacteroidetes Prevotella bryantii B(1)4.

    Science.gov (United States)

    McGregor, Nicholas; Morar, Mariya; Fenger, Thomas Hauch; Stogios, Peter; Lenfant, Nicolas; Yin, Victor; Xu, Xiaohui; Evdokimova, Elena; Cui, Hong; Henrissat, Bernard; Savchenko, Alexei; Brumer, Harry

    2016-01-15

    The recent classification of glycoside hydrolase family 5 (GH5) members into subfamilies enhances the prediction of substrate specificity by phylogenetic analysis. However, the small number of well characterized members is a current limitation to understanding the molecular basis of the diverse specificity observed across individual GH5 subfamilies. GH5 subfamily 4 (GH5_4) is one of the largest, with known activities comprising (carboxymethyl)cellulases, mixed-linkage endo-glucanases, and endo-xyloglucanases. Through detailed structure-function analysis, we have revisited the characterization of a classic GH5_4 carboxymethylcellulase, PbGH5A (also known as Orf4, carboxymethylcellulase, and Cel5A), from the symbiotic rumen Bacteroidetes Prevotella bryantii B14. We demonstrate that carboxymethylcellulose and phosphoric acid-swollen cellulose are in fact relatively poor substrates for PbGH5A, which instead exhibits clear primary specificity for the plant storage and cell wall polysaccharide, mixed-linkage β-glucan. Significant activity toward the plant cell wall polysaccharide xyloglucan was also observed. Determination of PbGH5A crystal structures in the apo-form and in complex with (xylo)glucan oligosaccharides and an active-site affinity label, together with detailed kinetic analysis using a variety of well defined oligosaccharide substrates, revealed the structural determinants of polysaccharide substrate specificity. In particular, this analysis highlighted the PbGH5A active-site motifs that engender predominant mixed-linkage endo-glucanase activity vis à vis predominant endo-xyloglucanases in GH5_4. However the detailed phylogenetic analysis of GH5_4 members did not delineate particular clades of enzymes sharing these sequence motifs; the phylogeny was instead dominated by bacterial taxonomy. Nonetheless, our results provide key enzyme functional and structural reference data for future bioinformatics analyses of (meta)genomes to elucidate the biology of

  1. Prebiotic fibres dose-dependently increase satiety hormones and alter Bacteroidetes and Firmicutes in lean and obese JCR:LA-cp rats.

    Science.gov (United States)

    Parnell, Jill A; Reimer, Raylene A

    2012-02-01

    There is a growing interest in modulating gut microbiota with diet in the context of obesity. The purpose of the present study was to evaluate the dose-dependent effects of prebiotics (inulin and oligofructose) on gut satiety hormones, energy expenditure, gastric emptying and gut microbiota. Male lean and obese JCR:LA-cp rats were randomised to either of the following: lean 0 % fibre (LC), lean 10 % fibre (LF), lean 20 % fibre (LHF), obese 0 % fibre (OC), obese 10 % fibre (OF) or obese 20 % fibre (OHF). Body composition, gastric emptying, energy expenditure, plasma satiety hormone concentrations and gut microbiota (using quantitative PCR) were measured. Caecal proglucagon and peptide YY mRNA levels were up-regulated 2-fold in the LF, OF and OHF groups and 3-fold in the LHF group. Ghrelin O-acyltransferase mRNA levels were higher in obese v. lean rats and decreased in the OHF group. Plasma ghrelin response was attenuated in the LHF group. Microbial species measured in the Bacteroidetes division decreased, whereas those in the Firmicutes increased in obese v. lean rats and improved with prebiotic intake. Bifidobacterium and Lactobacillus increased in the OHF v. OC group. Bacteroides and total bacteria negatively correlated with percentage of body fat and body weight. Enterobacteriaceae increased in conjunction with glucose area under the curve (AUC) and glucagon-like peptide-1 AUC. Bacteroides and total bacteria correlated positively with ghrelin AUC yet negatively with insulin AUC and energy intake (P alterations in gut microbiota) are regulated in a dose-dependent manner. The combined effects of prebiotics may have therapeutic potential for obesity. PMID:21767445

  2. Ichthyobacterium seriolicida gen. nov., sp. nov., a member of the phylum 'Bacteroidetes', isolated from yellowtail fish (Seriola quinqueradiata) affected by bacterial haemolytic jaundice, and proposal of a new family, Ichthyobacteriaceae fam. nov.

    Science.gov (United States)

    Takano, Tomokazu; Matsuyama, Tomomasa; Sakai, Takamitsu; Nakamura, Yoji; Kamaishi, Takashi; Nakayasu, Chihaya; Kondo, Hidehiro; Hirono, Ikuo; Fukuda, Yutaka; Sorimachi, Minoru; Iida, Takaji

    2016-02-01

    A novel Gram-stain-negative, rod-shaped (0.3 × 4-6 μm), non-flagellated, aerobic strain with gliding motility, designated JBKA-6T, was isolated in 1991 from a yellowtail fish, Seriola quinqueradiata, showing symptoms of bacterial haemolytic jaundice. 16S rRNA gene sequence analysis showed that strain JBKA-6T was related most closely to members of the family Flavobacteriaceae in the phylum 'Bacteroidetes'. Furthermore, based on gyrB gene sequence analysis, JBKA-6T was classified into a single clade within the order Flavobacteriales, which was distinct from the known clades of the families Flavobacteriaceae, Blattabacteriaceae and Cryomorphaceae. The predominant isoprenoid quinone was identified as MK-6 (97.9 %), and the major cellular fatty acids (>10 %) were C14 : 0 and iso-C15 : 0. The main polar lipids were phosphatidylethanolamine, three unidentified phospholipids, two unidentified aminophospholipids and two unidentified polar lipids. The DNA G+C content of JBKA-6T, as derived from its whole genome, was 33.4 mol%. The distinct phylogenetic position and phenotypic traits of strain JBKA-6T distinguish it from all other described species of the phylum 'Bacteroidetes', and therefore it was concluded that strain JBKA-6T represents a new member of the phylum 'Bacteroidetes', and the name Ichthyobacterium seriolicida gen. nov., sp. nov. is proposed. The type strain of Ichthyobacterium seriolicida is JBKA-6T ( = ATCC BAA-2465T = JCM 18228T). We also propose that Icthyobacterium gen. nov. is the type genus of a novel family, Ichthyobacteriaceae fam. nov. PMID:26554606

  3. Occurrence of human-associated Bacteroidetes genetic source tracking markers in raw and treated wastewater of municipal and domestic origin and comparison to standard and alternative indicators of faecal pollution.

    Science.gov (United States)

    Mayer, R E; Bofill-Mas, S; Egle, L; Reischer, G H; Schade, M; Fernandez-Cassi, X; Fuchs, W; Mach, R L; Lindner, G; Kirschner, A; Gaisbauer, M; Piringer, H; Blaschke, A P; Girones, R; Zessner, M; Sommer, R; Farnleitner, A H

    2016-03-01

    This was a detailed investigation of the seasonal occurrence, dynamics, removal and resistance of human-associated genetic Bacteroidetes faecal markers (GeBaM) compared with ISO-based standard faecal indicator bacteria (SFIB), human-specific viral faecal markers and one human-associated Bacteroidetes phage in raw and treated wastewater of municipal and domestic origin. Characteristics of the selected activated sludge wastewater treatment plants (WWTPs) from Austria and Germany were studied in detail (WWTPs, n = 13, connected populations from 3 to 49000 individuals), supported by volume-proportional automated 24-h sampling and chemical water quality analysis. GeBaM were consistently detected in high concentrations in raw (median log10 8.6 marker equivalents (ME) 100 ml(-1)) and biologically treated wastewater samples (median log10 6.2-6.5 ME 100 ml(-1)), irrespective of plant size, type and time of the season (n = 53-65). GeBaM, Escherichia coli, and enterococci concentrations revealed the same range of statistical variability for raw (multiplicative standard deviations s* = 2.3-3.0) and treated wastewater (s* = 3.7-4.5), with increased variability after treatment. Clostridium perfringens spores revealed the lowest variability for raw wastewater (s* = 1.5). In raw wastewater correlations among microbiological parameters were only detectable between GeBaM, C. perfringens and JC polyomaviruses. Statistical associations amongst microbial parameters increased during wastewater treatment. Two plants with advanced treatment were also investigated, revealing a minimum log10 5.0 (10th percentile) reduction of GeBaM in the activated sludge membrane bioreactor, but no reduction of the genetic markers during UV irradiation (254 nm). This study highlights the potential of human-associated GeBaM to complement wastewater impact monitoring based on the determination of SFIB. In addition, human-specific JC polyomaviruses and adenoviruses seem to be a valuable support

  4. A protein secretion system linked to bacteroidete gliding motility and pathogenesis.

    OpenAIRE

    Sato, Keiko; Naito, Mariko; Yukitake, Hideharu; Hirakawa, Hideki; Shoji, Mikio; McBride, Mark J.; Rhodes, Ryan G; Nakayama, Koji

    2010-01-01

    Porphyromonas gingivalis secretes strong proteases called gingipains that are implicated in periodontal pathogenesis. Protein secretion systems common to other Gram-negative bacteria are lacking in P. gingivalis, but several proteins, including PorT, have been linked to gingipain secretion. Comparative genome analysis and genetic experiments revealed 11 additional proteins involved in gingipain secretion. Six of these (PorK, PorL, PorM, PorN, PorW, and Sov) were similar in sequence to Flavoba...

  5. A protein secretion system linked to bacteroidete gliding motility and pathogenesis

    OpenAIRE

    Sato, Keiko; Naito, Mariko; Yukitake, Hideharu; Hirakawa, Hideki; Shoji, Mikio; McBride, Mark J.; Rhodes, Ryan G; Nakayama, Koji

    2009-01-01

    Porphyromonas gingivalis secretes strong proteases called gingipains that are implicated in periodontal pathogenesis. Protein secretion systems common to other Gram-negative bacteria are lacking in P. gingivalis, but several proteins, including PorT, have been linked to gingipain secretion. Comparative genome analysis and genetic experiments revealed 11 additional proteins involved in gingipain secretion. Six of these (PorK, PorL, PorM, PorN, PorW, and Sov) were similar in sequence to Flavoba...

  6. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

    DEFF Research Database (Denmark)

    Bahl, Martin Iain; Bergström, Anders; Licht, Tine Rask

    2012-01-01

    Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study, DNA was extracted either directly or following freeze storage of three homogenized human fecal...

  7. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

    DEFF Research Database (Denmark)

    Bahl, Martin Iain; Bergström, Anders; Licht, Tine Rask

    Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study DNA was extracted either directly or following freeze storage of three homogenized human fecal...

  8. Low Taxon Richness of Bacterioplankton in High-Altitude Lakes of the Eastern Tibetan Plateau, with a Predominance of Bacteroidetes and Synechococcus spp.▿ †

    OpenAIRE

    Xing, Peng; Hahn, Martin W.; Wu, Qinglong L.

    2009-01-01

    Plankton samples were collected from six remote freshwater and saline lakes located at altitudes of 3,204 to 4,718 m and 1,000 km apart within an area of ca. 1 million km2 on the eastern Tibetan Plateau to comparatively assess how environmental factors influence the diversity of bacterial communities in high-altitude lakes. The composition of the bacterioplankton was investigated by analysis of large clone libraries of 16S rRNA genes. Comparison of bacterioplankton diversities estimated for t...

  9. The modular xylanase Xyn10A from Rhodothermus marinus is cell-attached, and its C-terminal domain has several putative homologues among cell-attached proteins within the phylum Bacteroidetes

    DEFF Research Database (Denmark)

    Karlsson, Eva Nordberg; Hachem, Maher Abou; Ramchuran, Santosh;

    2004-01-01

    the light of this, a revision of experimental data present on both Xyn10A and Man26A was performed, and the results all indicate a cell-anchoring role of the domain, suggesting that this domain represents a novel type of module that mediates cell attachment in proteins originating from members of the...

  10. Denaturing gradient gel electrophoresis profiling of bacterial communities composition in Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, S.K.; Ramaiah, N.

    and sequenced indicated the preponderance of gammaproteobacteria, bacteroidetes and cyanobacteria. Non-metric dimensional scaling of the DGGE gels indicated that the spatial variations in BCC were prominent among the sampling locations. Temporal variations...

  11. A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut

    DEFF Research Database (Denmark)

    Karlsson, Fredrik H.; Ussery, David; Nielsen, Jens;

    2011-01-01

    Bacteroidetes/Chlorobi genomes to elucidate their phylogenetic relationship and to gain insight into what is separating the gut living Bacteroides and Parabacteroides genera from other Bacteroidetes/Chlorobi species. A comprehensive analysis shows that Bacteroides species have a higher number of......The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105...... other Bacteroides species, based on analysis of 16S rRNA sequence, whole-genome protein families and functional content, 16S rRNA sequences of the two species suggest that they belong to the Firmicutes phylum. We have presented a more detailed and precise description of the phylogenetic relationships of...

  12. Intracolonial differences in gut bacterial community between worker and soldier castes of Coptotermes formosanus

    Institute of Scientific and Technical Information of China (English)

    Hui Xiang; Lei Xie; Jun Zhang; Yan-Hua Long; Ning Liu; Yong-Ping Huang; QianWang

    2012-01-01

    The establishment of symbiotic relationships with intestinal microorganisms enables termites to thrive on recalcitrant substrates such as cellulose and wood.A termite colony is composed of several different castes which have distinct feeding habits.The soldiers,for example,cannot feed by themselves and depend on workers,who feed them with digested or semi-digested foods.To investigate the influence of feeding habits on the bacterial symbionts,a comparative study of gut bacteria between worker and soldier castes of the termite Coptotermesformosanus was conducted.The bacterial communities of both castes were investigated using denaturing gradient gel electrophoresis (DGGE) and clonal analysis of 16S ribosomal DNA (rDNA).Both methods indicated Bacteroidetes was the common predominant group; the common dominant phylotype was affiliated with a reported uncultured Bacteroidetes phylotype (BCfl-03).There were significant differences in Bacteroidetes and Spirochaetes between two castes.Compared to the gut bacteria of workers,those of soldiers were lower in abundance and diversity of Bacteroidetes and slightly higher in Spirochaetes.Two phylotypes (W8,W11) affiliated to Bacteroidetes and two (W26,W29) affiliated to Spirochaetes were exclusively found in the DGGE profile of the worker caste.Bacteroidetes are assumed to be involved in fermentation of sugars and nitrogenous compounds as well as degradation of uric acid.Spirochaetes are supposed to aid in the functions of acetogenesis and N2-fixation.The different feeding habits between workers and soldiers of C.formosanus may explain the observed differences in the gut bacterial community.

  13. Comparative fermentation of insoluble carbohydrates in an in vitro human feces model spiked with Lactobacillus acidophilus NCFM

    DEFF Research Database (Denmark)

    Knudsen, Anne; van Zanten, Gabriella C.; Jensen, Susanne L.;

    2013-01-01

    maize starch granules, pectin‐rich potato fiber, and potato lintner starch tested with human fresh fecal microbiota spiked with the probiotic Lactobacillus acidophilus NCFM. Microbial quantification by real‐time polymerase chain‐reaction (qRT‐PCR) revealed that Bacteroidetes was specifically suppressed...... increase in lactic acid production. Potato lintner starch had the greatest effect. Insoluble carbohydrates also suppressed production of SCFAs as compared to the control medium. Importantly, potato lintner starch most efficiently suppressed the ratio between the Bacteroidetes and Firmicutes and suppressed...

  14. Gut microbiota contributes to the growth of fast-growing transgenic common carp (Cyprinus carpio L..

    Directory of Open Access Journals (Sweden)

    Xuemei Li

    Full Text Available Gut microbiota has shown tight and coordinated connection with various functions of its host such as metabolism, immunity, energy utilization, and health maintenance. To gain insight into whether gut microbes affect the metabolism of fish, we employed fast-growing transgenic common carp (Cyprinus carpio L. to study the connections between its large body feature and gut microbes. Metagenome-based fingerprinting and high-throughput sequencing on bacterial 16S rRNA genes indicated that fish gut was dominated by Proteobacteria, Fusobacteria, Bacteroidetes and Firmicutes, which displayed significant differences between transgenic fish and wild-type controls. Analyses to study the association of gut microbes with the fish metabolism discovered three major phyla having significant relationships with the host metabolic factors. Biochemical and histological analyses indicated transgenic fish had increased carbohydrate but decreased lipid metabolisms. Additionally, transgenic fish has a significantly lower Bacteroidetes:Firmicutes ratio than that of wild-type controls, which is similar to mammals between obese and lean individuals. These findings suggest that gut microbiotas are associated with the growth of fast growing transgenic fish, and the relative abundance of Firmicutes over Bacteroidetes could be one of the factors contributing to its fast growth. Since the large body size of transgenic fish displays a proportional body growth, which is unlike obesity in human, the results together with the findings from others also suggest that the link between obesity and gut microbiota is likely more complex than a simple Bacteroidetes:Firmicutes ratio change.

  15. Draft Genome Sequences of Seven Bacterial Strains Isolated from a Polymicrobial Culture of Coccolith-Bearing (C-Type) Emiliania huxleyi M217

    Science.gov (United States)

    Rosana, Albert Remus R.; Orata, Fabini D.; Xu, Yue; Simkus, Danielle N.; Bramucci, Anna R.; Boucher, Yan

    2016-01-01

    Strains of Rhodobacteraceae, Sphingomonadales, Alteromonadales, and Bacteroidetes were isolated from a polymicrobial culture of the coccolith-forming (C-type) haptophyte Emiliania huxleyi strain M217. The genomes encode genes for the production of algal growth factors and the consumption of their hosts’ metabolic by-products, suggesting that the polymicrobial culture harbors many symbiotic interactions. PMID:27417845

  16. Cultivation of hard-to-culture subsurface mercury-resistant bacteria and discovery of new merA gene sequences

    DEFF Research Database (Denmark)

    Rasmussen, L D; Zawadsky, C; Binnerup, S J;

    2008-01-01

    sequencing of merA of selected isolates led to the discovery of new merA sequences. With phylum-specific merA primers, PCR products were obtained for Alpha- and Betaproteobacteria and Actinobacteria but not for Bacteroidetes and Firmicutes. The similarity to known sequences ranged between 89 and 95%. One of...

  17. Molecular phylogeny of intracellular symbiotic Gammaproteobacteria in insects

    OpenAIRE

    HUSNÍK, Filip

    2010-01-01

    Many groups of insects harbor mutualistic intracellular bacteria. These bacteria originated mainly from two bacterial phyla: Bacteroidetes and Proteobacteria. The thesis is focused on phylogeny of Enterobacteriaceae - the most diverse group of endosymbiotic bacteria within Gammaproteobacteria. The study brings new phylogenetical data on "primary" symbionts and summarizes the current state of knowledge on their phylogeny, evolution and diversity.

  18. Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing

    OpenAIRE

    Mehetre, Gajanan T.; Paranjpe, Aditi; Dastager, Syed G.; Dharne, Mahesh S.

    2016-01-01

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche.

  19. Variations of both bacterial community and extracellular polymers: the inducements of increase of cell hydrophobicity from biofloc to aerobic granule sludge.

    Science.gov (United States)

    Guo, Feng; Zhang, Sheng-Hua; Yu, Xin; Wei, Bo

    2011-06-01

    To investigate the inducements of increase of cell hydrophobicity from aerobic biofloc (ABF) and granular sludge (AGS), in this study, as the first time the hydrophilic and hydrophobic bacterial communities were analyzed independently. Meanwhile, the effect of extracellular polymers (EPS) on the cell hydrophobicity is also studied. Few Bacteroidetes were detected (1.35% in ABF and 3.84% in AGS) in hydrophilic bacteria, whereas they are abundant in the hydrophobic cells (47.8% and 43% for ABF and AGS, respectively). The main species of Bacteroidetes changed from class Sphingobacteria to Flavobacteria in AGS. On the other hand, EPS is directly responsible to cell hydrophobicity. For AGS, cell hydrophobicity was sharply decreased after EPS extraction. Both quantity and property of the extracellular protein are related to hydrophobicity. Our results showed the variation of cell hydrophobicity was resulted from variations of both bacterial population and EPS. PMID:21482465

  20. Spatial distribution of marine airborne bacterial communities

    OpenAIRE

    Seifried, Jasmin S; Wichels, Antje; Gerdts, Gunnar

    2015-01-01

    The spatial distribution of bacterial populations in marine bioaerosol samples was investigated during a cruise from the North Sea to the Baltic Sea via Skagerrak and Kattegat. The analysis of the sampled bacterial communities with a pyrosequencing approach revealed that the most abundant phyla were represented by the Proteobacteria (49.3%), Bacteroidetes (22.9%), Actinobacteria (16.3%), and Firmicutes (8.3%). Cyanobacteria were assigned to 1.5% of all bacterial reads. A core of 37 bacterial ...

  1. Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii

    OpenAIRE

    Million, M; Maraninchi, M; Henry, M; Armougom, F; Richet, H.; Carrieri, P; Valero, R.; Raccah, D.; Vialettes, B; Raoult, D.

    2012-01-01

    Background: Obesity is associated with increased health risk and has been associated with alterations in bacterial gut microbiota, with mainly a reduction in Bacteroidetes, but few data exist at the genus and species level. It has been reported that the Lactobacillus and Bifidobacterium genus representatives may have a critical role in weight regulation as an anti-obesity effect in experimental models and humans, or as a growth-promoter effect in agriculture depending on the strains. Objectiv...

  2. Abundance of Broad Bacterial Taxa in the Sargasso Sea Explained by Environmental Conditions but Not Water Mass

    OpenAIRE

    Sjöstedt, Johanna; Martiny, Jennifer B. H.; Munk, Peter; Riemann, Lasse

    2014-01-01

    To explore the potential linkage between distribution of marine bacterioplankton groups, environmental conditions, and water mass, we investigated the factors determining the abundance of bacterial taxa across the hydrographically complex Subtropical Convergence Zone in the Sargasso Sea. Based on information from 16S rRNA gene clone libraries from various locations and two depths, abundances of the predominant taxa (eubacteria, Archaea, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes,...

  3. Bacterial ecology of abattoir wastewater treated by an anaerobic digestor

    OpenAIRE

    Linda Jabari; Hana Gannoun; Eltaief Khelifi; Jean-Luc Cayol; Jean-Jacques Godon; Moktar Hamdi; Marie-Laure Fardeau

    2016-01-01

    Abstract Wastewater from an anaerobic treatment plant at a slaughterhouse was analysed to determine the bacterial biodiversity present. Molecular analysis of the anaerobic sludge obtained from the treatment plant showed significant diversity, as 27 different phyla were identified. Firmicutes, Proteobacteria, Bacteroidetes, Thermotogae, Euryarchaeota (methanogens), and msbl6 (candidate division) were the dominant phyla of the anaerobic treatment plant and represented 21.7%, 18.5%, 11.5%, 9.4%,...

  4. Role of the normal gut microbiota

    OpenAIRE

    Jandhyala, Sai Manasa; Talukdar, Rupjyoti; Subramanyam, Chivkula; Vuyyuru, Harish; Sasikala, Mitnala; Reddy, D Nageshwar

    2015-01-01

    Relation between the gut microbiota and human health is being increasingly recognised. It is now well established that a healthy gut flora is largely responsible for overall health of the host. The normal human gut microbiota comprises of two major phyla, namely Bacteroidetes and Firmicutes. Though the gut microbiota in an infant appears haphazard, it starts resembling the adult flora by the age of 3 years. Nevertheless, there exist temporal and spatial variations in the microbial distributio...

  5. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts.

    OpenAIRE

    Martens, Eric C.; Lowe, Elisabeth C.; Herbert Chiang; Nicholas A Pudlo; Meng Wu; McNulty, Nathan P.; D Wade Abbott; Bernard Henrissat; Gilbert, Harry J.; Bolam, David N.; Jeffrey I Gordon

    2011-01-01

    Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for cat...

  6. How Bacteria Turn Fiber into Food

    OpenAIRE

    Martens, Eric C.; Lowe, Elisabeth C.; Chiang, Herbert; Nicholas A Pudlo; Wu, Meng; McNulty, Nathan P.; Abbott, D Wade; Henrissat, Bernard; Gilbert, Harry J.; Bolam, David N.; Jeffrey I Gordon

    2011-01-01

    Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for cat...

  7. The Microbial Community in the Feces of the White Rhinoceros (Ceratotherium simum) as Determined by Barcoded Pyrosequencing Analysis

    OpenAIRE

    Bian, Gaorui; Ma, Li; Su, Yong; Zhu, Weiyun

    2013-01-01

    As a non-ruminant herbivore, the white rhinoceros has the ability to utilize fibrous plant matter through microbial fermentation in the hindgut. So far, there has been no report using molecular techniques to study the gut microbiota of the white rhinoceros. We used barcoded pyrosequencing to characterize 105,651 sequences of 16S rRNA genes obtained from fecal samples from five white rhinoceroses. Results showed that Firmicutes and Bacteroidetes were the predominant phyla in the samples, which...

  8. The gut microbiota of Colombians differs from that of Americans, Europeans and Asians

    OpenAIRE

    Escobar, Juan S; Klotz, Bernadette; Valdes, Beatriz E; Agudelo, Gloria M

    2014-01-01

    Background The composition of the gut microbiota has recently been associated with health and disease, particularly with obesity. Some studies suggested a higher proportion of Firmicutes and a lower proportion of Bacteroidetes in obese compared to lean people; others found discordant patterns. Most studies, however, focused on Americans or Europeans, giving a limited picture of the gut microbiome. To determine the generality of previous observations and expand our knowledge of the human gut m...

  9. Quantitative Fluorescence In Situ Hybridization of Microbial Communities in the Rumens of Cattle Fed Different Diets▿

    OpenAIRE

    Kong, Yunhong; He, Maolong; McAlister, Tim; Seviour, Robert; Forster, Robert

    2010-01-01

    At present there is little quantitative information on the identity and composition of bacterial populations in the rumen microbial community. Quantitative fluorescence in situ hybridization using newly designed oligonucleotide probes was applied to identify the microbial populations in liquid and solid fractions of rumen digesta from cows fed barley silage or grass hay diets with or without flaxseed. Bacteroidetes, Firmicutes, and Proteobacteria were abundant in both fractions, constituting ...

  10. Prebiotic fiber modulation of the gut microbiota improves risk factors for obesity and the metabolic syndrome

    OpenAIRE

    Parnell, Jill A.; Reimer, Raylene A.

    2012-01-01

    Prebiotic fibers are non-digestible carbohydrates that promote the growth of beneficial bacteria in the gut. Prebiotic consumption may benefit obesity and associated co-morbidities by improving or normalizing the dysbiosis of the gut microbiota. We evaluated the dose response to a prebiotic diet on the gut microbiota, body composition and obesity associated risk factors in lean and genetically obese rats. Prebiotic fibers increased Firmicutes and decreased Bacteroidetes, a profile often assoc...

  11. Peptidoglycan from Bacillus cereus Mediates Commensalism with Rhizosphere Bacteria from the Cytophaga-Flavobacterium Group

    OpenAIRE

    Peterson, Snow Brook; Dunn, Anne K.; Klimowicz, Amy K.; Handelsman, Jo

    2006-01-01

    Previous research in our laboratory revealed that the introduction of Bacillus cereus UW85 can increase the populations of bacteria from the Cytophaga-Flavobacterium (CF) group of the Bacteroidetes phylum in the soybean rhizosphere, suggesting that these rhizosphere microorganisms have a beneficial relationship (G. S. Gilbert, J. L. Parke, M. K. Clayton, and J. Handelsman, Ecology 74:840-854, 1993). In the present study, we determined the frequency at which CF bacteria coisolated with B. cere...

  12. Capnocytophaga canimorsus: A Human Pathogen Feeding at the Surface of Epithelial Cells and Phagocytes

    OpenAIRE

    Mally, Manuela; Shin, Hwain; Paroz, Cécile; Landmann, Regine; Cornelis, Guy R

    2008-01-01

    Author Summary Capnocytophaga canimorsus is a commensal bacterium of dogs/cats oral flora, which causes rare but severe infections in humans that have been bitten or simply licked by a dog/cat. Fulminant septicemia and peripheral gangrene are most common symptoms. Although splenectomy has been identified as a predisposing factor, some 40% of the patients have no immunosuppression history. C. canimorsus belongs to the phylum Bacteroidetes, which includes many commensals of the human gut flora ...

  13. Analysis of composition and structure of coastal to mesopelagic bacterioplankton communities in the northern Gulf of Mexico

    OpenAIRE

    GaryMKing; BradleyTolar

    2013-01-01

    16S rRNA gene amplicons were pyrosequenced to assess bacterioplankton community composition, diversity and phylogenetic community structure for 17 stations in the northern Gulf of Mexico (nGoM) sampled in March 2010. Statistical analyses showed that samples from depths ≤ 100 m differed distinctly from deeper samples. SAR 11 α-Proteobacteria and Bacteroidetes dominated communities at depths ≤ 100 m, which were characterized by high α-Proteobacteria/γ-Proteobacteria ratios (α/γ > 1.7). Th...

  14. Firmicutes dominate the bacterial taxa within sugar-cane processing plants

    OpenAIRE

    Farhana Sharmin; Steve Wakelin; Flavia Huygens; Megan Hargreaves

    2013-01-01

    Sugar cane processing sites are characterised by high sugar/hemicellulose levels, available moisture and warm conditions, and are relatively unexplored unique microbial environments. The PhyloChip microarray was used to investigate bacterial diversity and community composition in three Australian sugar cane processing plants. These ecosystems were highly complex and dominated by four main Phyla, Firmicutes (the most dominant), followed by Proteobacteria, Bacteroidetes, and Chloroflexi. Signif...

  15. Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing.

    Science.gov (United States)

    Mehetre, Gajanan T; Paranjpe, Aditi; Dastager, Syed G; Dharne, Mahesh S

    2016-01-01

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. PMID:26950332

  16. Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce

    Science.gov (United States)

    Li, Jian-Gang; Shen, Min-Chong; Hou, Jin-Feng; Li, Ling; Wu, Jun-Xia; Dong, Yuan-Hua

    2016-04-01

    Pyrosequencing-based analyses revealed significant effects among low (N50), medium (N80), and high (N100) fertilization on community composition involving a long-term monoculture of lettuce in a greenhouse in both summer and winter. The non-fertilized control (CK) treatment was characterized by a higher relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi; however, the average abundance of Firmicutes typically increased in summer, and the relative abundance of Bacteroidetes increased in winter in the N-fertilized treatments. Principle component analysis showed that the distribution of the microbial community was separated by a N gradient with N80 and N100 in the same group in the summer samples, while CK and N50 were in the same group in the winter samples, with the other N-level treatments existing independently. Redundancy analysis revealed that available N, NO3‑-N, and NH4+-N, were the main environmental factors affecting the distribution of the bacterial community. Correlation analysis showed that nitrogen affected the shifts of microbial communities by strongly driving the shifts of Firmicutes, Bacteroidetes, and Proteobacteria in summer samples, and Bacteroidetes, Actinobacteria, and Acidobacteria in winter samples. The study demonstrates a novel example of rhizosphere bacterial diversity and the main factors influencing rizosphere microbial community in continuous vegetable cropping within an intensive greenhouse ecosystem.

  17. High fat diet drives obesity regardless the composition of gut microbiota in mice.

    Science.gov (United States)

    Rabot, Sylvie; Membrez, Mathieu; Blancher, Florence; Berger, Bernard; Moine, Déborah; Krause, Lutz; Bibiloni, Rodrigo; Bruneau, Aurélia; Gérard, Philippe; Siddharth, Jay; Lauber, Christian L; Chou, Chieh Jason

    2016-01-01

    The gut microbiota is involved in many aspects of host physiology but its role in body weight and glucose metabolism remains unclear. Here we studied the compositional changes of gut microbiota in diet-induced obesity mice that were conventionally raised or received microbiota transplantation. In conventional mice, the diversity of the faecal microbiota was weakly associated with 1(st) week weight gain but transferring the microbiota of mice with contrasting weight gain to germfree mice did not change obesity development or feed efficiency of recipients regardless whether the microbiota was taken before or after 10 weeks high fat (HF) feeding. Interestingly, HF-induced glucose intolerance was influenced by microbiota inoculation and improved glucose tolerance was associated with a low Firmicutes to Bacteroidetes ratio. Transplantation of Bacteroidetes rich microbiota compared to a control microbiota ameliorated glucose intolerance caused by HF feeding. Altogether, our results demonstrate that gut microbiota is involved in the regulation of glucose metabolism and the abundance of Bacteroidetes significantly modulates HF-induced glucose intolerance but has limited impact on obesity in mice. Our results suggest that gut microbiota is a part of complex aetiology of insulin resistance syndrome, individual microbiota composition may cause phenotypic variation associated with HF feeding in mice. PMID:27577172

  18. Elucidating the richness of bacterial groups in the gut of Nicobarese tribal community - Perspective on their lifestyle transition.

    Science.gov (United States)

    Anwesh, Maile; Kumar, K Vinod; Nagarajan, Muruganandam; Chander, M Punnam; Kartick, C; Paluru, Vijayachari

    2016-06-01

    Lifestyle and dietary habits are crucial features that can alter the gut microbiome of humans. Humans, along with their gut microbes, have coevolved in order to sustain themselves in different environments. They were able to adapt themselves to the dietary sources available in their environment. The relation between humans and their gut microbiota and the link with coevolution forms an interesting aspect of research. To understand this association, the participation of ancient communities with less exposure to urbanization is a prerequisite. The current study quantifies the richness of bacterial groups in the gut of Nicobarese. This group of population is an ethnic community of Nicobar group of islands, who have migrated from the remote to rural and urban areas. Alterations in the dominant bacterial groups in relation to their lifestyle transition were emphasized, by comparing the participants from remote, rural and urban settings. The remote cohort remains diverse and stable than the other two cohorts and had higher numbers of Bacteroidetes. Prevotella forms the dominant genus in the Bacteroidetes phylum, indicating the carbohydrate-rich diet of remote Nicobarese. Whereas, the urban cohort is dominated by Bifidobacterium group rather than the Bacteroidetes. Implications of dietary patterns, the transition to different lifestyles and their impact on the microbiota among these cohorts are discussed. PMID:26946360

  19. Bacterial diversity in surface water of the Yellow Sea duringand after a green alga tide in 2008

    Institute of Scientific and Technical Information of China (English)

    GUO Cong; LI Fuchao; JIANG Peng; LIU Zhaopu; QIN Song

    2011-01-01

    From May to August 2008,a large "green tide",consisting of the alga Ulva (Enteromorpha) prolifera,occurred in the Yellow Sea,China,affecting the local marine ecosystem and human activities.We investigated the influence of the green tide on the microbial community in the surface seawater,at four sites from July to August 2008,using bacterial 16S rRNA gene clone libraries.We sequenced 228clones of unique patterns identified by restriction fragment length polymorphism (RFLP) techniques.The results show that 228 sequenced clones fell into six bacterial phyla:Proteobacteria,Bacteroidetes,Cyanobacteria,Verrucomicrobia,Actinobacteria,and Planctomycetes.Alphaproteobacteria (33%),Gammaproteobacteria (25%),Bacteroidetes (23%) and Cyanobacteria (9%) dominated the assemblage.Comparison between samples collected in July (during the tide) and those collected in August (after the tide) showed that,in the microbial community,diversities of Alphaproteobacteria and Cyanobacteria increased after the tide,while those of Gammaproteobacteria and Bacteroidetes decreased.These results indicate that the green tide influenced the growth of some bacteria,and provide information for further studies on the interactions and relationships between U.prolifera and the bacterial community.This study suggests that microbial community analysis is a good approach to monitoring green tides.

  20. High fat diet drives obesity regardless the composition of gut microbiota in mice

    Science.gov (United States)

    Rabot, Sylvie; Membrez, Mathieu; Blancher, Florence; Berger, Bernard; Moine, Déborah; Krause, Lutz; Bibiloni, Rodrigo; Bruneau, Aurélia; Gérard, Philippe; Siddharth, Jay; Lauber, Christian L.; Chou, Chieh Jason

    2016-01-01

    The gut microbiota is involved in many aspects of host physiology but its role in body weight and glucose metabolism remains unclear. Here we studied the compositional changes of gut microbiota in diet-induced obesity mice that were conventionally raised or received microbiota transplantation. In conventional mice, the diversity of the faecal microbiota was weakly associated with 1st week weight gain but transferring the microbiota of mice with contrasting weight gain to germfree mice did not change obesity development or feed efficiency of recipients regardless whether the microbiota was taken before or after 10 weeks high fat (HF) feeding. Interestingly, HF-induced glucose intolerance was influenced by microbiota inoculation and improved glucose tolerance was associated with a low Firmicutes to Bacteroidetes ratio. Transplantation of Bacteroidetes rich microbiota compared to a control microbiota ameliorated glucose intolerance caused by HF feeding. Altogether, our results demonstrate that gut microbiota is involved in the regulation of glucose metabolism and the abundance of Bacteroidetes significantly modulates HF-induced glucose intolerance but has limited impact on obesity in mice. Our results suggest that gut microbiota is a part of complex aetiology of insulin resistance syndrome, individual microbiota composition may cause phenotypic variation associated with HF feeding in mice. PMID:27577172

  1. Changes in microbial diversity of brined green asparagus upon treatment with high hydrostatic pressure.

    Science.gov (United States)

    Toledo Del Árbol, Julia; Pérez Pulido, Rubén; La Storia, Antonietta; Grande Burgos, Maria José; Lucas, Rosario; Ercolini, Danilo; Gálvez, Antonio

    2016-01-01

    The application of high hydrostatic pressure (HHP, 600MPa, 8 min) on brined green asparagus and the changes in bacterial diversity after treatments and during storage at 4 °C (30 days) or 22 °C (10 days) were studied. HHP treatments reduced viable cell counts by 3.6 log cycles. The residual surviving population did not increase during storage at 4 °C. However, bacterial counts significantly increased at 22 °C by day 3, leading to rapid spoilage. The microbiota of green asparagus was composed mainly by Proteobacteria (mainly Pantoea and Pseudomonas), followed by Firmicutes (mainly Lactococcus and Enterococcus) and to a less extent Bacteroidetes and Actinobacteria. During chill storage of untreated asparagus, the relative abundance of Proteobacteria as well as Enterococcus and Lactococcus decreased while Lactobacillus increased. During storage of untreated asparagus at 22 °C, the abundance of Bacteroidetes decreased while Proteobacteria increased during late storage. The HHP treatment determined a reduction of the Proteobacteria both early after treatment and during chill storage. In the HHP treated samples stored at 22 °C, the relative abundance of Pseudomonas rapidly decreased at day 1, with an increase of Bacteroidetes. This was followed by a marked increase in Enterobacteriaceae (Escherichia) simultaneously with increase in viable counts and spoilage. Results from the study indicate that the effect of HHP treatments on the viability ofmicrobial populations in foods also has an impact on the dynamics of microbial populations during the storage of the treated foods. PMID:26372734

  2. Novelty and spatio-temporal heterogeneity in the bacterial diversity of hypersaline Lake Tebenquiche (Salar de Atacama).

    Science.gov (United States)

    Demergasso, Cecilia; Escudero, Lorena; Casamayor, Emilio O; Chong, Guillermo; Balagué, Vanessa; Pedrós-Alió, Carlos

    2008-07-01

    Lake Tebenquiche is one of the largest saline water bodies in the Salar de Atacama at 2,500 m above sea level in northeastern Chile. Bacteria inhabiting there have to deal with extreme changes in salinity, temperature and UV dose (i.e., high environmental dissimilarity in the physical landscape). We analyzed the bacterioplankton structure of this lake by 16S rRNA gene analyses along a spatio-temporal survey. The bacterial assemblage within the lake was quite heterogeneous both in space and time. Salinity changed both in space and time ranging between 1 and 30% (w/v), and total abundances of planktonic prokaryotes in the different sampling points within the lake ranged between two and nine times 10(6) cells mL(-1). Community composition changed accordingly to the particular salinity of each point as depicted by genetic fingerprinting analyses (denaturing gradient gel electrophoresis), showing a high level of variation in species composition from place to place (beta-diversity). Three selected sites were analyzed in more detail by clone libraries. We observed a predominance of Bacteroidetes (about one third of the clones) and Gammaproteobacteria (another third) with respect to all the other bacterial groups. The diversity of Bacteroidetes sequences was large and showed a remarkable degree of novelty. Bacteroidetes formed at least four clusters with no cultured relatives in databases and rather distantly related to any known 16S rRNA sequence. Within this phylum, a rich and diverse presence of Salinibacter relatives was found in the saltiest part of the lake. Lake Tebenquiche included several novel microorganisms of environmental importance and appeared as a large unexplored reservoir of unknown bacteria. PMID:18347752

  3. Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health

    Directory of Open Access Journals (Sweden)

    Montijn Roy C

    2011-03-01

    Full Text Available Abstract Background An understanding of the relation of commensal microbiota to health is essential in preventing disease. Here we studied the oral microbial composition of children (N = 74, aged 3 - 18 years in natural transition from their deciduous to a permanent dentition and related the microbial profiles to their oral health status. The microbial composition of saliva was assessed by barcoded pyrosequencing of the V5-V6 hypervariable regions of the 16 S rRNA, as well as by using phylogenetic microarrays. Results Pyrosequencing reads (126174 reads, 1045 unique sequences represented 8 phyla and 113 higher taxa in saliva samples. Four phyla - Firmicutes, Bacteriodetes, Proteobacteria and Actinobacteria - predominated in all groups. The deciduous dentition harboured a higher proportion of Proteobacteria (Gammaproteobacteria, Moraxellaceae than Bacteroidetes, while in all other groups Bacteroidetes were at least as abundant as Proteobacteria. Bacteroidetes (mainly genus Prevotella, Veillonellaceae family, Spirochaetes and candidate division TM7 increased with increasing age, reflecting maturation of the microbiome driven by biological changes with age. Microarray analysis enabled further analysis of the individual salivary microbiota. Of 350 microarray probes, 156 gave a positive signal with, on average, 77 (range 48-93 probes per individual sample. A caries-free oral status significantly associated with the higher signal of the probes targeting Porphyromonas catoniae and Neisseria flavescens. Conclusions The potential role of P. catoniae and N. flavescens as oral health markers should be assessed in large-scale clinical studies. The combination of both, open-ended and targeted molecular approaches provides us with information that will increase our understanding of the interplay between the human host and its microbiome.

  4. Short communication: Modulation of the small intestinal microbial community composition over short-term or long-term administration with Lactobacillus plantarum ZDY2013.

    Science.gov (United States)

    Xie, Qiong; Pan, Mingfang; Huang, Renhui; Tian, Ximei; Tao, Xueying; Shah, Nagendra P; Wei, Hua; Wan, Cuixiang

    2016-09-01

    The small intestinal (SI) microbiota has an essential role in the maintenance of human health. However, data about the indigenous bacteria in SI as affected by probiotics are limited. In our study, the short-term and long-term effects of a probiotic candidate, Lactobacillus plantarum ZDY2013, on the SI microbiota of C57BL/6J mice were investigated by the Illumina HiSeq (Novogene Bioinformatics Technology Co., Ltd., Tianjin, China) platform targeting the V4 region of the 16S rDNA. A total of 858,011 sequences in 15 samples were read. The α diversity analysis revealed that oral administration with L. plantarum ZDY2013 for 3 wk led to a significant increase in the richness and diversity of the SI bacterial community. Principal coordinate analysis and unweighted pair-group method with arithmetic means analysis showed a clear alteration in the SI microbiota composition after 3 wk of L. plantarum ZDY2013 treatment, although these changes were not found 6 wk after ceasing L. plantarum ZDY2013 administration. Species annotation showed that the dominant phyla in SI microbiota were Firmicutes, Bacteroidetes, Proteobacteria, and Verrucomicrobia. Interestingly, operational taxonomic unit cluster analysis showed that administration with L. plantarum ZDY2013 for 3 wk significantly increased the abundance of Proteobacteria, but decreased that of Bacteroidetes. Linear discriminant analysis coupled with effect size identified 18 bacterial taxa (e.g., Ruminococcus spp. and Clostridium spp.) that overgrew in the SI microbiota of the mice administered with L. plantarum ZDY2013 for 3 wk, and most of them belonged to the phyla Bacteroidetes and Proteobacteria. However, only one bacterial taxon (e.g., Nocardioides spp.) was over-represented in the SI microbiota of mice 6 wk after L. plantarum ZDY2013 administration. Overall, this study shows that oral administration with probiotic results in an important but transient alteration in the microbiota of SI. PMID:27320669

  5. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

    Energy Technology Data Exchange (ETDEWEB)

    Mahowald, Michael [Washington University, St. Louis; Rey, Frederico E. [Washington University, St. Louis; Seedorf, Henning [Washington University, St. Louis; Turnbaugh, Peter J. [Washington University, St. Louis; Fulton, Robert S. [Washington University, St. Louis; Wollam, Aye [Washington University, St. Louis; Shah, Neha [Washington University, St. Louis; Wang, Chunyan [Washington University, St. Louis; Magrini, Vincent [Washington University, St. Louis; Wilson, Richard K. [Washington University, St. Louis; Cantarel, Brandi L. [Centre National de la Recherche Scientifique, Unite Mixte de Recherche; Coutinho, Pedro M [Universite d' Aix-Marseille I & II; Henrissat, Bernard [Universite d' Aix-Marseille I & II; Crock, Lara W. [Washington University, St. Louis; Verberkmoes, Nathan C [ORNL; Hettich, Robert {Bob} L [ORNL; Erickson, Alison L [ORNL; Gordon, Jeffrey [Washington University, St. Louis

    2009-01-01

    The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here, we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from Eubacterium rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling, high-resolution proteomic analysis, and biochemical assays of microbial microbial and microbial host interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating expression of a variety of polysaccharide utilization loci encoding numerous glycoside hydrolases, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is used by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of its major bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.

  6. Oral imazalil exposure induces gut microbiota dysbiosis and colonic inflammation in mice.

    Science.gov (United States)

    Jin, Cuiyuan; Zeng, Zhaoyang; Fu, Zhengwei; Jin, Yuanxiang

    2016-10-01

    The fungicide imazalil (IMZ) is used extensively in vegetable and fruit plantations and as a post-harvest treatment to avoid rot. Here, we revealed that ingestion of 25, 50 and 100 mg IMZ kg(-1) body weight for 28 d induced gut microbiota dysbiosis and colonic inflammation in mice. The relative abundance of Bacteroidetes, Firmicutes and Actinobacteria in the cecal contents decreased significantly after exposure to 100 mg kg(-1) IMZ for 28 d. In feces, the relative abundance in Bacteroidetes, Firmicutes and Actinobacteria decreased significantly after being exposed to 100 mg kg(-1) IMZ for 1, 14 and 7 d, respectively. High throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene revealed a significant reduction in the richness and diversity of microbiota in cecal contents and feces of IMZ-treated mice. Operational taxonomic units (OTUs) analysis identified 49.3% of OTUs changed in cecal contents, while 55.6% of OTUs changed in the feces after IMZ exposure. Overall, at the phylum level, the relative abundance of Firmicutes, Proteobacteria and Actinobacteria increased and that of Bacteroidetes decreased in IMZ-treated groups. At the genus level, the abundance of Lactobacillus and Bifidobacterium decreased while those of Deltaproteobacteria and Desulfovibrio increased in response to IMZ exposure. In addition, it was observed that IMZ exposure could induce colonic inflammation characterized by infiltration of inflammatory cells, elevated levels of lipocalin-2 (lcn-2) in the feces, and increased mRNA levels of Tnf-α, IL-1β, IL-22 and IFN-γ in the colon. Our findings strongly suggest that ingestion of IMZ has some risks to human health. PMID:27393971

  7. Microbial community response during the iron fertilization experiment LOHAFEX

    Digital Repository Service at National Institute of Oceanography (India)

    Thiele, S.; Fuchs, B.M.; Ramaiah, N.; Amanna, R.

    in community compo- sition within the respective layer. There was no accumulation of cells in deeper layers, as one would expect from a sinking and decaying algae bloom (14, 56). Only for the Bacteroidetes could a slightly higher cell abundance be monitored... at a depth of 300 m on days�1 and 36 compared to days 14 and 18 (both IN), as well as day 16 (OUT). These higher numbers might result from Bacte- roidetes cells attached to marine snow particles from the hypoth- esized bloom prior to LOHAFEX (day �1...

  8. Human microbiome: From the bathroom to the bedside.

    Science.gov (United States)

    Malnick, Stephen; Melzer, Ehud

    2015-08-15

    The human gut contains trillions of bacteria, the major phylae of which include Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria. Fecal microbial transplantation (FMT) has been known of for many years but only recently has been subjected to rigorous examination. We review the evidence regarding FMT for recurrent Clostridium difficile infection which has resulted in it being an approved treatment. In addition there is some evidence for its use in both irritable bowel syndrome and inflammatory bowel disease. Further research is needed in order to define the indications for FMT and the most appropriate method of administration. PMID:26301122

  9. Acetate consumption in anoxic marine sediments: Identification of key players using mixed pure cultures and sediment incubations

    DEFF Research Database (Denmark)

    Na, Hyunsoo

    at 10 mM acetate-2 mM (low) sulfate and lower (0.1 and 1 mM) acetate-high sulfate conditions, as revealed by Ion Torrent sequencing of 16S rRNA gene sequences. At 0.1 and 1 mM acetate concentrations, members of the phyla Firmicutes (Fusibacter-related), Fusobacteria, and Bacteroidetes were...... here the flexibility of the microbial communities in response to different geochemical conditions, in high resolution, with biological replicates, using Ion Torrent sequencing. Secondly, we used two different sediment incubation techniques, dialysis tube batch and continuous flow-through bioreactors...

  10. Diversity and homogeneity of oral microbiota in healthy Korean pre-school children using pyrosequencing.

    Science.gov (United States)

    Lee, Soo Eon; Nam, Ok Hyung; Lee, Hyo-Seol; Choi, Sung Chul

    2016-07-01

    Objectives The purpose of this study was designed to identify the oral microbiota in healthy Korean pre-school children using pyrosequencing. Materials and methods Dental plaque samples were obtained form 10 caries-free pre-school children. The samples were analysed using pyrosequencing. Results The pyrosequencing analysis revealed that, at the phylum level, Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria showed high abundance. Also, predominant genera were identified as core microbiome, such as Streptococcus, Neisseria, Capnocytophaga, Haemophilus and Veilonella. Conclusions The diversity and homogeneity was shown in the dental plaque microbiota in healthy Korean pre-school children. PMID:26758186

  11. High-quality draft genome sequence of Flavobacterium suncheonense GH29-5T (DSM 17707T) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5T

    OpenAIRE

    Tashkandy, Nisreen; Sabban, Sari; Fakieh, Mohammad; Meier-Kolthoff, Jan P; Huang, Sixing; Tindall, Brian J.; Rohde, Manfred; Baeshen, Mohammed N; Baeshen, Nabih A.; Lapidus, Alla; Copeland, Alex; Pillay, Manoj; Reddy, T. B. K.; Huntemann, Marcel; Pati, Amrita

    2016-01-01

    Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5T (DSM 17707T) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5T is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5T has 117 genes encoding peptidases but a small number of genes encoding ca...

  12. Bisucaberin B, a Linear Hydroxamate Class Siderophore from the Marine Bacterium Tenacibaculum mesophilum

    Directory of Open Access Journals (Sweden)

    Ryuichi Sakai

    2013-04-01

    Full Text Available A siderophore, named bisucaberin B, was isolated from Tenacibaculum mesophilum bacteria separated from a marine sponge collected in the Republic of Palau. Using spectroscopic and chemical methods, the structure of bisucaberin B (1 was clearly determined to be a linear dimeric hydroxamate class siderophore. Although compound 1 is an open form of the known macrocyclic dimer bisucaberin (2, and was previously described as a bacterial degradation product of desferrioxamine B (4, the present report is the first description of the de novo biosynthesis of 1. To the best of our knowledge, compound 1 is the first chemically characterized siderophore isolated from a bacterium belonging to the phylum Bacteroidetes.

  13. Bisucaberin B, a linear hydroxamate class siderophore from the marine bacterium Tenacibaculum mesophilum.

    Science.gov (United States)

    Fujita, Masaki J; Nakano, Koji; Sakai, Ryuichi

    2013-01-01

    A siderophore, named bisucaberin B, was isolated from Tenacibaculum mesophilum bacteria separated from a marine sponge collected in the Republic of Palau. Using spectroscopic and chemical methods, the structure of bisucaberin B (1) was clearly determined to be a linear dimeric hydroxamate class siderophore. Although compound 1 is an open form of the known macrocyclic dimer bisucaberin (2), and was previously described as a bacterial degradation product of desferrioxamine B (4), the present report is the first description of the de novo biosynthesis of 1. To the best of our knowledge, compound 1 is the first chemically characterized siderophore isolated from a bacterium belonging to the phylum Bacteroidetes. PMID:23549298

  14. Digestive challenges for vertebrate animals: Microbial diversity, cardiorespiratory coupling, and dietary specialization

    DEFF Research Database (Denmark)

    Barboza, P.S.; Bennett, A.; Lignot, H.-H.;

    2010-01-01

    digestive functions, and (3) the evolution of dietary specialization. Herbivores consume, digest, and detoxify complex diets by using a wide variety of enzymes expressed by bacteria, predominantly in the phyla Firmicutes and Bacteroidetes. Carnivores, such as snakes that feed intermittently, sometimes...... process very large meals that require compensatory adjustments in blood flow, acid secretion, and regulation of acid‐base homeostasis. Snakes and birds that specialize in simple diets of prey or nectar retain their ability to digest a wider selection of prey. The digestive system continues to be of...

  15. The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos

    DEFF Research Database (Denmark)

    Sommer, Felix; Ståhlman, Marcus; Ilkayeva, Olga;

    2016-01-01

    microbiota of free-ranging brown bears during their active phase and hibernation. Compared to the active phase, hibernation microbiota had reduced diversity, reduced levels of Firmicutes and Actinobacteria, and increased levels of Bacteroidetes. Several metabolites involved in lipid metabolism, including...... triglycerides, cholesterol, and bile acids, were also affected by hibernation. Transplantation of the bear microbiota from summer and winter to germ-free mice transferred some of the seasonal metabolic features and demonstrated that the summer microbiota promoted adiposity without impairing glucose tolerance......, suggesting that seasonal variation in the microbiota may contribute to host energy metabolism in the hibernating brown bear....

  16. Tailored enzymatic production of oligosaccharides from sugar beet pectin and evidence of differential effects of a single DP chain length difference on human faecal microbiota composition after in vitro fermentation

    DEFF Research Database (Denmark)

    Holck, Jesper; Hjernø, K.; Lorentzen, A.;

    2011-01-01

    polymerization (DP) from 2 to 8 and six different rhamnogalacturonide (RGI) structures, ranging from DP4 to 6 with defined galactose substitutions were purified. Total recoveries of 200 mg homogalacturonides and 67 mg rhamnogalacturonides per gram sugar beet pectin were obtained. This integrated biorefining...... method provides an option for advanced upgrading of sugar beet pectin into HG and RGI oligosaccharides of defined size and structure. In vitro microbial fermentation by human faecal samples (n = 9) showed a different response to the DP4 and DP5 HG structures on the ratio between Bacteroidetes and...

  17. A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens)

    DEFF Research Database (Denmark)

    Hildebrand, Falk; Ebersbach, Tine; Nielsen, Henrik Bjørn;

    2012-01-01

    Background: Guinea pig (Cavia porcellus) is an important model for human intestinal research. We have characterized the faecal microbiota of 60 guinea pigs using Illumina shotgun metagenomics, and used this data to compile a gene catalogue of its prevalent microbiota. Subsequently, we compared...... the guinea pig microbiome to existing human gut metagenome data from the MetaHIT project. Results: We found that the bacterial richness obtained for human samples was lower than for guinea pig samples. The intestinal microbiotas of both species were dominated by the two phyla Bacteroidetes and Firmicutes...

  18. Shedding Light on the Microbial Community of the Macropod Foregut Using 454-Amplicon Pyrosequencing

    OpenAIRE

    Gulino, Lisa-Maree; Ouwerkerk, Diane; Alicia Y H Kang; Maguire, Anita J.; Kienzle, Marco; Klieve, Athol V.

    2013-01-01

    Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as ‘shared’ OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales)...

  19. Human microbiome: From the bathroom to the bedside

    Institute of Scientific and Technical Information of China (English)

    Stephen; Malnick; Ehud; Melzer

    2015-01-01

    The human gut contains trillions of bacteria, the major phylae of which include Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria. Fecal microbial transplantation(FMT) has been known of for manyyears but only recently has been subjected to rigorous examination. We review the evidence regarding FMT for recurrent Clostridium difficile infection which has resulted in it being an approved treatment. In addition there is some evidence for its use in both irritable bowel syndrome and inflammatory bowel disease. Further research is needed in order to define the indications for FMT and the most appropriate method of administration.

  20. The Family Saprospiraceae

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Nielsen, Per Halkjær

    2014-01-01

    The Saprospiraceae, a family within the order Sphingobacteriales and the phylum Bacteroidetes, embrace the genera Saprospira, Lewinella, Haliscomenobacter, Aureispira, ‘‘Rubidimonas,’’ and ‘‘Portibacter.’’ The composition of the family, and delineation of genera and species, is largely defined by...... associated with predation of other bacteria and algae. Family members are likely important in the breakdown of complex organic compounds in the environment. Such a role is at least demonstrated in situ for activated sludge wastewater treatment systems where these organisms are frequently observed in...

  1. Dietary long-chain n-3 PUFA, gut microbiota and fat mass in early postnatal piglet development—exploring a potential interplay

    DEFF Research Database (Denmark)

    Andersen, A.D.; Mølbak, Lars; Thymann, T.; Michaelsen, K.F.; Lauritzen, L.

    2011-01-01

    Dietary n-3PUFA and gut bacteria, particularly Bacteroidetes, have been suggested to be related to adiposity. We investigated if n-3PUFA affected fat storage and cecal bacteria in piglets. Twenty-four 4-day-old piglets were allocated to formula rich in n-3PUFA (∼3E%) from fish oil (FO) or n-6PUFA...... from sunflower oil (SO) for 14 days. We assessed body weight, fat accumulation by dual-energy X-ray absorptiometry and microbial molecular fingerprints. Dietary PUFA-composition was reflected in higher erythrocyte n-3PUFA in the FO- than the SO-group (P...

  2. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation

    Directory of Open Access Journals (Sweden)

    Annette K. Møller

    2013-04-01

    Full Text Available The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA genes and 16S rRNA gene sequencing of cultivated isolates. Both the pyrosequence and cultivation data indicated that the phylogenetic composition of the microbial assemblages was different within the snow layers and between snow and freshwater. The highest diversity was seen in snow. In the middle and top snow layers, Proteobacteria, Bacteroidetes and Cyanobacteria dominated, although Actinobacteria and Firmicutes were relatively abundant also. High numbers of chloroplasts were also observed. In the deepest snow layer, large percentages of Firmicutes and Fusobacteria were seen. In freshwater, Bacteroidetes, Actinobacteria and Verrucomicrobia were the most abundant phyla while relatively few Proteobacteria and Cyanobacteria were present. Possibly, light intensity controlled the distribution of the Cyanobacteria and algae in the snow while carbon and nitrogen fixed by these autotrophs in turn fed the heterotrophic bacteria. In the lake, a probable lower light input relative to snow resulted in low numbers of Cyanobacteria and chloroplasts and, hence, limited input of organic carbon and nitrogen to the heterotrophic bacteria. Thus, differences in the physicochemical conditions may play an important role in the processes leading to distinctive bacterial community structures in High-Arctic snow and freshwater.

  3. Identification of microbial communities in open and closed circuit bioelectrochemical MBRs by high-throughput 454 pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Jian Huang

    Full Text Available Two bioelectrochemical membrane bioreactors (MBRs developed by integrating microbial fuel cell and MBR technology were operated under closed-circuit and open-circuit modes, and high-throughput 454 pyrosequencing was used to investigate the effects of the power generation on the microbial community of bio-anode and bio-cathode. Microbes on the anode under open-circuit operation (AO were enriched and highly diverse when compared to those on the anode under closed-circuit operation (AC. However, among the cathodes the closed-circuit mode (CC had richer and more diverse microbial community compared to the cathode under open-circuit mode (CO. On the anodes AO and AC, Proteobacteria and Bacteroidetes were the dominant phyla, while Firmicutes was enriched only on AC. Deltaproteobacteria affiliated to Proteobacteria were also more abundant on AC than AO. Furthermore, the relative abundance of Desulfuromonas, which are well-known electrogenic bacteria, were much higher on AC (10.2% when compared to AO (0.11%, indicating that closed-circuit operation was more conducive for the growth of electrogenic bacteria on the anodes. On the cathodes, Protebacteria was robust on CC while Bacteroidetes was more abundant on CO. Rhodobacter and Hydrogenophaga were also enriched on CC than CO, suggesting that these genera play a role in electron transfer from the cathode surface to the terminal electron acceptors in the bioelectrochemical MBR under closed-circuit operation.

  4. The mercury resistance (mer) operon in a marine gliding flavobacterium, Tenacibaculum discolor 9A5.

    Science.gov (United States)

    Allen, Rachel C; Tu, Yen-Kuei; Nevarez, Michael J; Bobbs, Alexander S; Friesen, Joseph W; Lorsch, Jon R; McCauley, John A; Voet, Judith G; Hamlett, Nancy V

    2013-01-01

    Genes conferring mercury resistance have been investigated in a variety of bacteria and archaea but not in bacteria of the phylum Bacteroidetes, despite their importance in many environments. We found, however, that a marine gliding Bacteroidetes species, Tenacibaculum discolor, was the predominant mercury-resistant bacterial taxon cultured from a salt marsh fertilized with mercury-contaminated sewage sludge. Here we report characterization of the mercuric reductase and the narrow-spectrum mercury resistance (mer) operon from one of these strains - T. discolor 9A5. This mer operon, which confers mercury resistance when cloned into Flavobacterium johnsoniae, encodes a novel mercury-responsive ArsR/SmtB family transcriptional regulator that appears to have evolved independently from other mercury-responsive regulators, a novel putative transport protein consisting of a fusion between the integral membrane Hg(II) transporter MerT and the periplasmic Hg(II)-binding protein MerP, an additional MerP protein, and a mercuric reductase that is phylogenetically distinct from other known mercuric reductases. PMID:22816663

  5. PCR-DGGE研究臭氧耦合ASBR/SBR控氮磷污泥减量化工艺中的细菌多样性%Bacterial Diversity of the Combined Ozonation-ASBR/SBR Sludge Reduction with Simultaneous Nitrogen and Phosphorus Removal Process Using PCR-DGGE

    Institute of Scientific and Technical Information of China (English)

    赵林林; 王海燕; 杨慧芬; 何赞; 周岳溪; 张乐; 庞朝辉

    2011-01-01

    采用分子生物学手段PCR-DGGE技术对臭氧耦合ASBR/SBR控氮磷污泥减量化工艺中的ASBR和污泥减量化前后的SBR中的细菌多样性进行了研究.结果表明,ASBR中的主要细菌类群为Firmicutes类群,β-proteobacterium类群,γ-proteobacterium类群和Bacteroidetes类群;污泥减量化后SBR中细菌丰富度与减量前相比有所增加,但是相似性指数极高,为85%;臭氧施加进行污泥减量对SBR中的优势菌群多样性影响不大,污泥减量化前后SBR反应器内均存在Firmicutes bacterium,Candidate division TM7,ammonia-oxidizing bacterium,Bacteroidetes bacterium,β-proteobacterium,Denitrifying bacterium,Pseudomonas sp和Nitrosococcus halophilus Nc4,其中减量化后Bacteroidetes bacterium,β-proteobacterium,Denitrifying bacterium和Nitrosococcus halophilus Nc4的数量略高于污泥减量化之前.

  6. Prokaryotic community composition revealed by denaturing gradient gel electrophoresis in the East Sea

    Science.gov (United States)

    Jang, Gwang Il; Choi, Dong Han

    2015-12-01

    To understand the temporal and spatial variation of the prokaryotic community in the East Sea, their composition was determined by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE)-sequencing techniques. The investigations were conducted twice annually in 2007 and 2009 in coastal and offshore stations. Prokaryotic abundance (PA), leucine incorporation rate, and other environmental parameters were also measured. By using the DGGE approach, we obtained 283 bacterial sequences and 160 archaeal sequences. The most frequently detected bacterial phylotypes during the investigations belonged to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. However, their relative compositions differed in time and space. Although Alphaproteobacteria and Bacteroidetes were the dominant groups in the surface water in May 2007 and in May and October 2007, Gammaproteobacteria was dominant in mesopelagic samples. However, Gammaproteobacteria was overwhelmingly dominant in most samples in August 2009. Although Deltaproteobacteria was rarely found as a dominant bacterial group, it occupied the highest fraction in a mesopelagic sample in October 2007. Epsilonproteobacteria also showed a similar trend, although its maximal dominance was found in a mesopelagic sample in August 2009. The archaeal community was dominated overwhelmingly by members of the Euryarchaeota in most of the investigations. However, Nitrosopumilales was dominant in aphotic samples in August 2009. Further, their spatiotemporal composition at the family level changed more dynamically in the East Sea. These temporal and spatial distributions of the prokaryotic community were influenced mainly by seawater temperature and depth in the East Sea.

  7. Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2014-04-07

    Though microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, the diversity and complexity of natural systems and their intractability to in situ environmental manipulation makes elucidation of the principles governing these interactions challenging. Examination of primary succession during phototrophic biofilm assembly provides a robust means by which to elucidate the dynamics of such interactions and determine their influence upon recruitment and maintenance of phylogenetic and functional diversity in microbial communities. We isolated and characterized two unicyanobacterial consortia from the Hot Lake phototrophic mat, quantifying the structural and community composition of their assembling biofilms. The same heterotrophs were retained in both consortia and included members of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, taxa frequently reported as consorts of microbial photoautotrophs. Cyanobacteria led biofilm assembly, eventually giving way to a late heterotrophic bloom. The consortial biofilms exhibited similar patterns of assembly, with the relative abundances of members of Bacteroidetes and Alphaproteobacteria increasing and members of Gammaproteobacteria decreasing as colonization progressed. Despite similar trends in assembly at higher taxa, the consortia exhibited substantial differences in community structure at the species level. These similar patterns of assembly with divergent community structures suggest that, while similar niches are created by the metabolism of the cyanobacteria, the resultant webs of autotroph-heterotroph and heterotroph-heterotroph interactions driving metabolic exchange are specific to each primary producer. Altogether, our data support these Hot Lake unicyanobacterial consortia as generalizable model systems whose simplicity and tractability permit the deciphering of community assembly principles relevant to natural microbial communities.

  8. Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes.

    Science.gov (United States)

    Lopez-Fernandez, Margarita; Cherkouk, Andrea; Vilchez-Vargas, Ramiro; Jauregui, Ruy; Pieper, Dietmar; Boon, Nico; Sanchez-Castro, Ivan; Merroun, Mohamed L

    2015-11-01

    The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work, the bacterial population of bentonite formations of Almeria (Spain), selected as a reference material for bentonite-engineered barriers in the disposal of radioactive wastes, was studied. 16S ribosomal RNA (rRNA) gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina sequencing. Using both techniques, the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria, Nitrospirae, Verrucomicrobia and an unknown phylum. The dominant groups of the community were represented by Proteobacteria and Bacteroidetes. A high diversity was found in three of the studied samples. However, two samples were less diverse and dominated by Betaproteobacteria. PMID:26024740

  9. Correlation between diet and gut bacteria in a population of young adults.

    Science.gov (United States)

    Mayorga Reyes, Lino; González Vázquez, Raquel; Cruz Arroyo, Schahrasad M; Melendez Avalos, Araceli; Reyes Castillo, Pedro A; Chavaro Pérez, David A; Ramos Terrones, Idalia; Ramos Ibáñez, Norma; Rodríguez Magallanes, Magdalena M; Langella, Philippe; Bermúdez Humarán, Luis; Azaola Espinosa, Alejandro

    2016-06-01

    Dietary habits strongly influence gut microbiota. The aim of this study was to compare and correlated the abundance of Firmicutes and Bacteroidetes phyla, some representative bacteria of these phyla such as Bacteroides thetaiotaomicron, Prevotella, Faecalibacterium prausnitzii, Clostridium leptum and Bifidobacterium longum as a member of Actinobacteria phylum in young adults with their food intake. Faecal samples used came from lean subjects (BMI = 19.83 ± 0.94 kg/m(2)), overweight (BMI = 27.17 ± 0.51 kg/m(2)) and obese (BMI = 41.33 ± 5.25 kg/m(2)). There were significant differences in total studied gut microbiota between the overweight and lean groups. Members of the Firmicutes phylum, and Bifidobacterium longum, were more abundant in the lean group. The results suggest that diet rich in unsaturated fatty acids and fibre promote an abundant population of beneficial bacteria such as B. longum and Bacteroidetes. However, it has been considered that the results may be biased due to the size of the individuals studied; therefore the results could be only valid for the studied population. PMID:27018166

  10. Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake.

    Science.gov (United States)

    Woodhouse, Jason Nicholas; Kinsela, Andrew Stephen; Collins, Richard Nicholas; Bowling, Lee Chester; Honeyman, Gordon L; Holliday, Jon K; Neilan, Brett Anthony

    2016-06-01

    The frequency of freshwater cyanobacterial blooms is at risk of increasing as a consequence of climate change and eutrophication of waterways. It is increasingly apparent that abiotic data are insufficient to explain variability within the cyanobacterial community, with biotic factors such as heterotrophic bacterioplankton, viruses and protists emerging as critical drivers. During the Australian summer of 2012-2013, a bloom that occurred in a shallow ephemeral lake over a 6-month period was comprised of 22 distinct cyanobacteria, including Microcystis, Dolichospermum, Oscillatoria and Sphaerospermopsis. Cyanobacterial cell densities, bacterial community composition and abiotic parameters were assessed over this period. Alpha-diversity indices and multivariate analysis were successful at differentiating three distinct bloom phases and the contribution of abiotic parameters to each. Network analysis, assessing correlations between biotic and abiotic variables, reproduced these phases and assessed the relative importance of both abiotic and biotic factors. Variables possessing elevated betweeness centrality included temperature, sodium and operational taxonomic units belonging to the phyla Verrucomicrobia, Planctomyces, Bacteroidetes and Actinobacteria. Species-specific associations between cyanobacteria and bacterioplankton, including the free-living Actinobacteria acI, Bacteroidetes, Betaproteobacteria and Verrucomicrobia, were also identified. We concluded that changes in the abundance and nature of freshwater cyanobacteria are associated with changes in the diversity and composition of lake bacterioplankton. Given this, an increase in the frequency of cyanobacteria blooms has the potential to alter nutrient cycling and contribute to long-term functional perturbation of freshwater systems. PMID:26636552

  11. Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water.

    Science.gov (United States)

    Narciso-da-Rocha, Carlos; Manaia, Célia M

    2016-09-01

    The environment is the original and most ancient source of the antibiotic resistance determinants that threat the human health nowadays. In the environment, water is a privileged habitat and mode of dissemination of bacteria of different origins. Freshwater bodies that cross urban areas are supposed to hold a complex mixture of both human/animal origin and strictly environmental bacteria. In this study, we were interested in unveiling the bacterial diversity in urban river transects and, simultaneously, investigate the occurrence of antibiotic resistant bacteria, in particular the multidrug resistant (MDR). With this aim, water and sediments of two rivers were sampled from an urban transect and the bacterial diversity was assessed based on 16S rRNA gene-based community analysis and, simultaneously, total heterotrophic bacteria were isolated in the presence and in the absence of antibiotics. The three predominant phyla were Proteobacteria, Bacteroidetes and Actinobacteria, in water, or Acidobacteria, in sediments. MDR bacteria were observed to belong to the predominant phyla observed in water, mostly of the classes Gamma- and Betaproteobacteria (Proteobacteria) and Sphingobacteriia and Flavobacteriia (Bacteroidetes) and belonged to genera of ubiquitous (Pseudomonas, Acinetobacter, Stenotrophomonas) or mainly environmental (Chitinophaga, Chryseobacterium) bacteria. The observation that MDR bacteria are widespread in the environment and over distinct phylogenetic lineages has two relevant implications: i) the potential of environmental bacteria as source or facilitators for antibiotic resistance acquisition; ii) the need to complement culture-independent methods with culture-based approaches in order to identify major sources of MDR profiles. PMID:27131885

  12. Pyrosequencing analysis of bacterial communities in Lake Bosten, a large brackish inland lake in the arid northwest of China.

    Science.gov (United States)

    Zhang, Lei; Gao, Guang; Tang, Xiangming; Shao, Keqiang; Gong, Yi

    2016-06-01

    The bacteria inhabiting brackish lake environments are poorly known, and there are few studies on the microbial diversity of these environments. Lake Bosten, a large brackish inland lake, is the largest lake in Xinjiang Province in northwestern China. Because sediments record past limnic changes, the analysis of sedimentary bacteria in Lake Bosten may help elucidate bacterial responses to environmental change. We employed 454 pyrosequencing to investigate the diversity and bacterial community composition in Lake Bosten. A total of 48 230 high-quality sequence reads with 16 314 operational taxonomic units were successfully obtained from the 4 selected samples, and they were numerically dominated by members of the Deltaproteobacteria (17.1%), Chloroflexi (16.1%), Betaproteobacteria (12.6%), Bacteroidetes (6.6%), and Firmicutes (5.7%) groups, accounting for more than 58.1% of the bacterial sequences. The sediment bacterial communities and diversity were consistently different along the 2 geographic environmental gradients: (i) freshwater-brackish water gradient and (ii) oligotrophic-mesotrophic habitat gradient. Deltaproteobacteria, Chloroflexi, and Betaproteobacteria were amplified throughout all of the sampling sites. More Bacteroidetes and Firmicutes were found near the Kaidu River estuary (site 14). Our investigation showed that Proteobacteria did not display any systematic change along the salinity gradient, and numerous 16S rRNA sequences could not be identified at the genus level. Our data will provide a better understanding of the diversity and distribution of bacteria in arid region brackish lakes. PMID:27045804

  13. Common occurrence of antibacterial agents in human intestinal microbiota

    Directory of Open Access Journals (Sweden)

    Fatima eDrissi

    2015-05-01

    Full Text Available Laboratory experiments have revealed many active mechanisms by which bacteria can inhibit the growth of other organisms. Bacteriocins are a diverse group of natural ribosomally-synthesized antimicrobial peptides produced by a wide range of bacteria and which seem to play an important role in mediating competition within bacterial communities. In this study, we have identified and established the structural classification of putative bacteriocins encoded by 317 microbial genomes in the human intestine. On the basis of homologies to available bacteriocin sequences, mainly from lactic acid bacteria, we report the widespread occurrence of bacteriocins across the gut microbiota: 175 bacteriocins were found to be encoded in Firmicutes, 79 in Proteobacteria, 34 in Bacteroidetes and 25 in Actinobacteria. Bacteriocins from gut bacteria displayed wide differences among phyla with regard to class distribution, net positive charge, hydrophobicity and secondary structure, but the α-helix was the most abundant structure. The peptide structures and physiochemical properties of bacteriocins produced by the most abundant bacteria in the gut, the Firmicutes and the Bacteroidetes, seem to ensure low antibiotic activity and participate in permanent intestinal host defence against the proliferation of harmful bacteria. Meanwhile, the potentially harmful bacteria, including the Proteobacteria, displayed highly effective bacteriocins, probably supporting the virulent character of diseases. These findings highlight the eventual role played by bacteriocins in gut microbial competition and their potential place in antibiotic therapy.

  14. Influence of freshwater discharge on the microbial degradation processes of dissolved organic nitrogen in a subtropical estuary.

    Science.gov (United States)

    Garcia, Juan C; Ketover, Rheannon D J; Loh, Ai Ning; Parsons, Michael L; Urakawa, Hidetoshi

    2015-02-01

    River bacterioplankton communities, influenced by watershed usage, are responsible for water purification. Bacterioplankton may be critical in the degradation of dissolved organic nitrogen (DON), the major nitrogen pool in the Caloosahatchee River, Florida. We investigated how freshwater discharge influences estuarine bacterioplankton and how the freshwater-originated DON is utilized by estuarine bacterioplankton. Microcosm experiments were conducted during low and high discharge using two upstream freshwater samples: one site primarily influenced by Lake Okeechobee and the other site moderately influenced by an agricultural watershed. These freshwater samples were filtered to eliminate indigenous microbial populations, then mixed with estuarine bacterioplankton. High-throughput sequencing revealed that bacterioplankton differed between low and high discharge and were influenced by salinity. Alphaproteobacteria and Bacteroidetes dominated in low discharge while Bacteroidetes and Cyanobacteria dominated during high discharge. In the microcosm experiment, DON concentration decreased with increasing cell densities, suggesting that the DON was utilized as a carbon and nitrogen source. Band signals in denaturing gradient gel electrophoresis corresponding to Alphaproteobacteria and Actinobacteria decreased while Gammaproteobacteria increased during the 1 month incubation. This data suggests that estuarine bacterioplankton communities are influenced by variations in discharge patterns and use freshwater-originated DON as demonstrated by a shift in community structure. PMID:25542211

  15. Impaired carbohydrate digestion and transport and mucosal dysbiosis in the intestines of children with autism and gastrointestinal disturbances.

    Directory of Open Access Journals (Sweden)

    Brent L Williams

    Full Text Available Gastrointestinal disturbances are commonly reported in children with autism, complicate clinical management, and may contribute to behavioral impairment. Reports of deficiencies in disaccharidase enzymatic activity and of beneficial responses to probiotic and dietary therapies led us to survey gene expression and the mucoepithelial microbiota in intestinal biopsies from children with autism and gastrointestinal disease and children with gastrointestinal disease alone. Ileal transcripts encoding disaccharidases and hexose transporters were deficient in children with autism, indicating impairment of the primary pathway for carbohydrate digestion and transport in enterocytes. Deficient expression of these enzymes and transporters was associated with expression of the intestinal transcription factor, CDX2. Metagenomic analysis of intestinal bacteria revealed compositional dysbiosis manifest as decreases in Bacteroidetes, increases in the ratio of Firmicutes to Bacteroidetes, and increases in Betaproteobacteria. Expression levels of disaccharidases and transporters were associated with the abundance of affected bacterial phylotypes. These results indicate a relationship between human intestinal gene expression and bacterial community structure and may provide insights into the pathophysiology of gastrointestinal disturbances in children with autism.

  16. Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues

    Directory of Open Access Journals (Sweden)

    Jenny Chun-Yee Ng

    2015-10-01

    Full Text Available Corals are rapidly declining globally due to coral diseases. Skeletal growth anomalies (SGA or coral tumors are a group of coral diseases that affect coral reefs worldwide, including Hong Kong waters in the Indo-Pacific region. To better understand how bacterial communities may vary in corals with SGA, for the first time, we examined the bacterial composition associated with the apparently healthy and the diseased tissues of SGA-affected Platgyra carnosus using 16S ribosomal rRNA gene pyrosequencing. Taxonomic analysis revealed Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria as the main phyla in both the apparently healthy and the diseased tissues. A significant difference in the bacterial community composition was observed between the two conditions at the OTU level. Diseased tissues were associated with higher abundances of Acidobacteria and Gemmatimonadetes, and a lower abundance of Spirochaetes. Several OTUs belonging to Rhodobacteraceae, Rhizobiales, Gammaproteobacteria, and Cytophaga-Flavobacterium-Bacteroidetes (CFB were strongly associated with the diseased tissues. These groups of bacteria may contain potential pathogens involved with the development of SGA or opportunistic secondary or tertiary colonizers that proliferated upon the health-compromised coral host. We suggest that these bacterial groups to be further studied based on inoculation experiments and testing of Koch’s postulates in efforts to understand the etiology and progression of SGA.

  17. Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci.

    Directory of Open Access Journals (Sweden)

    Phillip B Pope

    Full Text Available Lignocellulosic biomass remains a largely untapped source of renewable energy predominantly due to its recalcitrance and an incomplete understanding of how this is overcome in nature. We present here a compositional and comparative analysis of metagenomic data pertaining to a natural biomass-converting ecosystem adapted to austere arctic nutritional conditions, namely the rumen microbiome of Svalbard reindeer (Rangifer tarandus platyrhynchus. Community analysis showed that deeply-branched cellulolytic lineages affiliated to the Bacteroidetes and Firmicutes are dominant, whilst sequence binning methods facilitated the assemblage of metagenomic sequence for a dominant and novel Bacteroidales clade (SRM-1. Analysis of unassembled metagenomic sequence as well as metabolic reconstruction of SRM-1 revealed the presence of multiple polysaccharide utilization loci-like systems (PULs as well as members of more than 20 glycoside hydrolase and other carbohydrate-active enzyme families targeting various polysaccharides including cellulose, xylan and pectin. Functional screening of cloned metagenome fragments revealed high cellulolytic activity and an abundance of PULs that are rich in endoglucanases (GH5 but devoid of other common enzymes thought to be involved in cellulose degradation. Combining these results with known and partly re-evaluated metagenomic data strongly indicates that much like the human distal gut, the digestive system of herbivores harbours high numbers of deeply branched and as-yet uncultured members of the Bacteroidetes that depend on PUL-like systems for plant biomass degradation.

  18. Phylum Level Change in the Cecal and Fecal Gut Communities of Rats Fed Diets Containing Different Fermentable Substrates Supports a Role for Nitrogen as a Factor Contributing to Community Structure

    Directory of Open Access Journals (Sweden)

    Martin Kalmokoff

    2015-05-01

    Full Text Available Fermentation differs between the proximal and distal gut but little is known regarding how the bacterial communities differ or how they are influenced by diet. In order to investigate this, we compared community diversity in the cecum and feces of rats by 16S rRNA gene content and DNA shot gun metagenomics after feeding purified diets containing different fermentable substrates. Gut community composition was dependent on the source of fermentable substrate included in the diet. Cecal communities were dominated by Firmicutes, and contained a higher abundance of Lachnospiraceae compared to feces. In feces, community structure was shifted by varying degrees depending on diet towards the Bacteroidetes, although this change was not always evident from 16S rRNA gene data. Multi-dimensional scaling analysis (PCoA comparing cecal and fecal metagenomes grouped by location within the gut rather than by diet, suggesting that factors in addition to substrate were important for community change in the distal gut. Differentially abundant genes in each environment supported this shift away from the Firmicutes in the cecum (e.g., motility towards the Bacteroidetes in feces (e.g., Bacteroidales transposons. We suggest that this phylum level change reflects a shift to ammonia as the primary source of nitrogen used to support continued microbial growth in the distal gut.

  19. Diversity rankings among bacterial lineages in soil.

    Science.gov (United States)

    Youssef, Noha H; Elshahed, Mostafa S

    2009-03-01

    We used rarefaction curve analysis and diversity ordering-based approaches to rank the 11 most frequently encountered bacterial lineages in soil according to diversity in 5 previously reported 16S rRNA gene clone libraries derived from agricultural, undisturbed tall grass prairie and forest soils (n=26,140, 28 328, 31 818, 13 001 and 53 533). The Planctomycetes, Firmicutes and the delta-Proteobacteria were consistently ranked among the most diverse lineages in all data sets, whereas the Verrucomicrobia, Gemmatimonadetes and beta-Proteobacteria were consistently ranked among the least diverse. On the other hand, the rankings of alpha-Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes and Chloroflexi varied widely in different soil clone libraries. In general, lineages exhibiting largest differences in diversity rankings also exhibited the largest difference in relative abundance in the data sets examined. Within these lineages, a positive correlation between relative abundance and diversity was observed within the Acidobacteria, Actinobacteria and Chloroflexi, and a negative diversity-abundance correlation was observed within the Bacteroidetes. The ecological and evolutionary implications of these results are discussed. PMID:18987677

  20. Succession and replacement of bacterial populations in the caecum of egg laying hens over their whole life.

    Directory of Open Access Journals (Sweden)

    Petra Videnska

    Full Text Available In this study we characterised the development of caecal microbiota in egg laying hens over their commercial production lifespan, from the day of hatching until 60 weeks of age. Using pyrosequencing of V3/V4 variable regions of 16S rRNA genes for microbiota characterisation, we were able to define 4 different stages of caecal microbiota development. The first stage lasted for the first week of life and was characterised by a high prevalence of Enterobacteriaceae (phylum Proteobacteria. The second stage lasted from week 2 to week 4 and was characterised by nearly an absolute dominance of Lachnospiraceae and Ruminococcaceae (both phylum Firmicutes. The third stage lasted from month 2 to month 6 and was characterised by the succession of Firmicutes at the expense of Bacteroidetes. The fourth stage was typical for adult hens in full egg production aged 7 months or more and was characterised by a constant ratio of Bacteroidetes and Firmicutes formed by equal numbers of the representatives of both phyla.

  1. The microbial community in the feces of the white rhinoceros (Ceratotherium simum as determined by barcoded pyrosequencing analysis.

    Directory of Open Access Journals (Sweden)

    Gaorui Bian

    Full Text Available As a non-ruminant herbivore, the white rhinoceros has the ability to utilize fibrous plant matter through microbial fermentation in the hindgut. So far, there has been no report using molecular techniques to study the gut microbiota of the white rhinoceros. We used barcoded pyrosequencing to characterize 105,651 sequences of 16S rRNA genes obtained from fecal samples from five white rhinoceroses. Results showed that Firmicutes and Bacteroidetes were the predominant phyla in the samples, which were comprised largely of unclassified bacteria. The microbiota of one animal treated with drug therapy differed from those in other healthy animals, and was dominated by Aerococcus -related bacteria. The core microbiota in the healthy rhinoceros were dominated by phyla Firmicutes and Bacteroidetes, represented by the Ruminococcaceae, Lachnospiraceae, Rikenellaceae and Prevotellaceae families. The present work provides a phylogenetic framework for understanding the complex microbial community of the rhinoceros; however, further studies are required to link the distinctive microbiota with their digestive role in the hindgut of the white rhinoceros.

  2. Microbial community analysis of anaerobic reactors treating soft drink wastewater.

    Directory of Open Access Journals (Sweden)

    Takashi Narihiro

    Full Text Available The anaerobic packed-bed (AP and hybrid packed-bed (HP reactors containing methanogenic microbial consortia were applied to treat synthetic soft drink wastewater, which contains polyethylene glycol (PEG and fructose as the primary constituents. The AP and HP reactors achieved high COD removal efficiency (>95% after 80 and 33 days of the operation, respectively, and operated stably over 2 years. 16S rRNA gene pyrotag analyses on a total of 25 biofilm samples generated 98,057 reads, which were clustered into 2,882 operational taxonomic units (OTUs. Both AP and HP communities were predominated by Bacteroidetes, Chloroflexi, Firmicutes, and candidate phylum KSB3 that may degrade organic compound in wastewater treatment processes. Other OTUs related to uncharacterized Geobacter and Spirochaetes clades and candidate phylum GN04 were also detected at high abundance; however, their relationship to wastewater treatment has remained unclear. In particular, KSB3, GN04, Bacteroidetes, and Chloroflexi are consistently associated with the organic loading rate (OLR increase to 1.5 g COD/L-d. Interestingly, KSB3 and GN04 dramatically decrease in both reactors after further OLR increase to 2.0 g COD/L-d. These results indicate that OLR strongly influences microbial community composition. This suggests that specific uncultivated taxa may take central roles in COD removal from soft drink wastewater depending on OLR.

  3. The effect of anaerobic-aerobic and feast-famine cultivation pattern on bacterial diversity during poly-β-hydroxybutyrate production from domestic sewage sludge.

    Science.gov (United States)

    Liu, Changli; Liu, Di; Qi, Yingjie; Zhang, Ying; Liu, Xi; Zhao, Min

    2016-07-01

    The main objective of this work was to investigate the influence of different oxygen supply patterns on poly-β-hydroxybutyrate (PHB) yield and bacterial community diversity. The anaerobic-aerobic (A/O) sequencing batch reactors (SBR1) and feast-famine (F/F) SBR2 were used to cultivate activated sludge to produce PHB. The mixed microbial communities were collected and analyzed after 3 months cultivation. The PHB maximum yield was 64 wt% in SBR1 and 53 wt% in SBR2. Pyrosequencing analysis 16S rRNA gene of two microbial communities indicated there were nine and four bacterial phyla in SBR1 and SBR2, respectively. Specifically, Proteobacteria (36.4 % of the total bacterial community), Actinobacteria (19.7 %), Acidobacteria (14.1 %), Firmicutes (4.4 %), Bacteroidetes (1.7 %), Cyanobacteria/Chloroplast (1.5 %), TM7 (0.8 %), Gemmatimonadetes (0.2 %), and Nitrospirae (0.1 %) were present in SBR1. Proteobacteria (94.2 %), Bacteroidetes (2.9 %), Firmicutes (1.9 %), and Actinobacteria (0.7 %) were present in SBR2. Our results indicated the SBR1 fermentation system was more stable than that of SBR2 for PHB accumulation. PMID:26996908

  4. Longitudinal shifts in bacterial diversity and fermentation pattern in the rumen of steers grazing wheat pasture.

    Science.gov (United States)

    Pitta, D W; Pinchak, W E; Dowd, S; Dorton, K; Yoon, I; Min, B R; Fulford, J D; Wickersham, T A; Malinowski, D P

    2014-12-01

    Grazing steers on winter wheat forage is routinely practiced in the Southern Great Plains of the US. Here, we investigated the dynamics in bacterial populations of both solid and liquid ruminal fractions of steers grazing on maturing wheat forage of changing nutritive quality. The relationship between bacterial diversity and fermentation parameters in the liquid fraction was also investigated. During the first 28 days, the wheat was in a vegetative phase with a relatively high crude protein content (CP; 21%), which led to the incidence of mild cases of frothy bloat among steers. Rumen samples were collected on days 14, 28, 56 and 76, separated into solid and liquid fractions and analyzed for bacterial diversity using 16S pyrotag technology. The predominant phyla identified were Bacteroidetes (59-77%) and Firmicutes (20-33%) across both ruminal fractions. Very few differences were observed in the rumen bacterial communities within solid and liquid fractions on day 14. However, by day 28, the relatively high CP content complemented a distinct bacterial and chemical composition of the rumen fluid that was characterized by a higher ratio (4:1) of Bacteroidetes:Firmicutes and a corresponding lower acetate:propionate (3:1) ratio. Further, a greater accumulation of biofilm (mucopolysaccharide complex) on day 28 was strongly associated with the abundance of Firmicutes lineages such as Clostridium, Ruminococcus, Oscillospira and Moryella (Pbloat-prone) and reproductive stages of wheat forage. PMID:25086244

  5. Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16S rRNA gene.

    Directory of Open Access Journals (Sweden)

    Marcio C Costa

    Full Text Available The intestinal tract houses one of the richest and most complex microbial populations on the planet, and plays a critical role in health and a wide range of diseases. Limited studies using new sequencing technologies in horses are available. The objective of this study was to characterize the fecal microbiome of healthy horses and to compare the fecal microbiome of healthy horses to that of horses with undifferentiated colitis. A total of 195,748 sequences obtained from 6 healthy horses and 10 horses affected by undifferentiated colitis were analyzed. Firmicutes predominated (68% among healthy horses followed by Bacteroidetes (14% and Proteobacteria (10%. In contrast, Bacteroidetes (40% was the most abundant phylum among horses with colitis, followed by Firmicutes (30% and Proteobacteria (18%. Healthy horses had a significantly higher relative abundance of Actinobacteria and Spirochaetes while horses with colitis had significantly more Fusobacteria. Members of the Clostridia class were more abundant in healthy horses. Members of the Lachnospiraceae family were the most frequently shared among healthy individuals. The species richness reported here indicates the complexity of the equine intestinal microbiome. The predominance of Clostridia demonstrates the importance of this group of bacteria in healthy horses. The marked differences in the microbiome between healthy horses and horses with colitis indicate that colitis may be a disease of gut dysbiosis, rather than one that occurs simply through overgrowth of an individual pathogen.

  6. Bacterial diversity in the foreland of the Tianshan No. 1 glacier, China

    International Nuclear Information System (INIS)

    There is compelling evidence that glaciers are retreating in many mountainous areas of the world due to global warming. With this glacier retreat, new habitats are being exposed that are colonized by microorganisms whose diversity and function are less well studied. Here, we characterized bacterial diversity along the chronosequences of the glacier No. 1 foreland that follows glacier retreat. An average of 10 000 sequences was obtained from each sample by 454 pyrosequencing. Using non-parametric and rarefaction estimated analysis, we found bacterial phylotype richness was high. The bacterial species turnover rate was especially high between sites exposed for 6 and 10 yr. Pyrosequencing showed tremendous bacterial diversity, among which the Acidobacteria, Actinobacteria, Bacteroidetes and Proteobacteria were found to be present at larger numbers at the study area. Meanwhile, the proportion of Bacteroidetes and Proteobacteria decreased and the proportion of Acidobacteria increased along the chronosequences. Some known functional bacterial genera were also detected and the sulfur- and sulfate-reducing bacteria were present in a lower proportion of sequences. These findings suggest that high-throughput pyrosequencing can comprehensively detect bacteria in the foreland, including rare groups, and give a deeper understanding of the bacterial community structure and variation along the chronosequences. (letter)

  7. Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium

    Science.gov (United States)

    Shen, Ting-Chin David; Chehoud, Christel; Ni, Josephine; Hsu, Evelyn; Chen, Ying-Yu; Bailey, Aubrey; Laughlin, Alice; Bittinger, Kyle; Bushman, Frederic D; Wu, Gary D

    2016-01-01

    We have recently reported that Altered Schaedler Flora (ASF) can be used to durably engineer the gut microbiota to reduce ammonia production as an effective modality to reduce morbidity and mortality in the setting of liver injury. Here we investigated the effects of a low protein diet on ASF colonization and its ability to engineer the microbiota. Initially, ASF inoculation was similar between mice fed a normal protein diet or low protein diet, but the outgrowth of gut microbiota differed over the ensuing month. Notable was the inability of the dominant Parabacteroides ASF taxon to exclude other taxa belonging to the Bacteroidetes phylum in the setting of a low protein diet. Instead, a poorly classified yet highly represented Bacteroidetes family, S24-7, returned within 4 weeks of inoculation in mice fed a low protein diet, demonstrating a reduction in ASF resilience in response to dietary stress. Nevertheless, fecal ammonia levels remained significantly lower than those observed in mice on the same low protein diet that received a transplant of normal feces. No deleterious effects were observed in host physiology due to ASF inoculation into mice on a low protein diet. In total, these results demonstrate that low protein diet can have a pronounced effect on engineering the gut microbiota but modulation of ammonia is preserved. PMID:27176607

  8. A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean

    Institute of Scientific and Technical Information of China (English)

    WANG Jing; KAN Jinjun; BORECKI Laura; ZHANG Xiaodong; WANG Dongxiao; SUN Jun

    2016-01-01

    Besides being critical components of marine food web, microorganisms play vital roles in biogeochemical cycling of nutrients and elements in the ocean. Currently little is known about microbial population structure and their distributions in the eastern Indian Ocean. In this study, we applied molecular approaches including polymerase chain reaction-denaturant gradient gel electrophoresis (PCR-DGGE) and High-Throughput next generation sequencing to investigate bacterial 16S rRNA genes from the equatorial regions and the adjacent Bay of Bengal in the eastern Indian Ocean. In general,Bacteroidetes,Proteobacteria (mainlyAlpha, andGamma),Actinobacteria, Cyanobacteria andPlanctomycetes dominated the microbial communities. Horizontally distinct spatial distribution of major microbial groups was observed from PCR-DGGE gel image analyses. However, further detailed characterization of community structures by pyrosequencing suggested a more pronounced stratified distribution pattern:Cyanobacteria andActinobacteria were more predominant at surface water (25 m);Bacteroidetes dominated at 25 m and 150 m whileProteobacteria (mainlyAlphaproteobacteria) occurred more frequently at 75 m water depth. With increasing water depth, the bacterial communities from different locations tended to share high similarity, indicating a niche partitioning for minor groups of bacteria recovered with high throughput sequencing approaches. This study provided the first “snapshot” on biodiversity and spatial distribution ofBacteria in water columns in the eastern Indian Ocean, and the findings further emphasized the potential functional roles of these microbes in energy and resource cycling in the eastern Indian Ocean.

  9. Distribution, diversity and abundance of bacterial laccase-like genes in different particle size fractions of sediments in a subtropical mangrove ecosystem.

    Science.gov (United States)

    Luo, Ling; Zhou, Zhi-Chao; Gu, Ji-Dong

    2015-10-01

    This study investigated the diversity and abundance of bacterial lacasse-like genes in different particle size fractions, namely sand, silt, and clay of sediments in a subtropical mangrove ecosystem. Moreover, the effects of nutrient conditions on bacterial laccase-like communities as well as the correlation between nutrients and, both the abundance and diversity indices of laccase-like bacteria in particle size fractions were also studied. Compared to bulk sediments, Bacteroidetes, Caldithrix, Cyanobacteria and Chloroflexi were dominated in all 3 particle-size fractions of intertidal sediment (IZ), but Actinobacteria and Firmicutes were lost after the fractionation procedures used. The diversity index of IZ fractions decreased in the order of bulk > clay > silt > sand. In fractions of mangrove forest sediment (MG), Verrucomicrobia was found in silt, and both Actinobacteria and Bacteroidetes appeared in clay, but no new species were found in sand. The declining order of diversity index in MG fractions was clay > silt > sand > bulk. Furthermore, the abundance of lacasse-like bacteria varied with different particle-size fractions significantly (p clay > silt in both IZ and MG fractions. Additionally, nutrient availability was found to significantly affect the diversity and community structure of laccase-like bacteria (p carbon contents were positively related to the abundance of bacterial laccase-like genes in particle size fractions (p < 0.05). Therefore, this study further provides evidence that bacterial laccase plays a vital role in turnover of sediment organic matter and cycling of nutrients. PMID:25822201

  10. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae

    Directory of Open Access Journals (Sweden)

    Narit Thaochan

    2015-12-01

    Full Text Available The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering and Bactrocera tryoni (Froggatt, was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria which was prominent in all clones. The total bacterial community consisted of Proteobacteria (more than 75% of clones, except in the crop of B. cacuminata where more than 50% of clones belonged to Firmicutes. Firmicutes gave the number of the secondary community structure in the fly’s gut. Four orders, Alpha-, Beta-, Delta- and Gammaproteobacteria and the phyla Firmicutes and Actinobacteria were found in both fruit fly species, while the order Epsilonproteobacteria and the phylum Bacteroidetes were found only in B. tryoni. Two phyla, Actinobacteria and Bacteroidetes, were rare and less frequent in the flies. There was a greater diversity of bacteria in the crop of the two fruit fly species than in the midgut. The midgut of B. tryoni females and the midgut of B. cacuminata males had the lowest bacterial diversity.

  11. The bacterial community associated with the leech Myzobdella lugubris Leidy 1851 (Hirudinea: Piscicolidae from Lake Erie, Michigan, USA

    Directory of Open Access Journals (Sweden)

    Schulz C.

    2010-06-01

    Full Text Available Leeches are widespread in the Great Lakes Basin, yet their potential to harbor disease-causing agents has not been investigated. The purpose of this study was to identify the bacterial community of the commonly occurring leech, Myzobdella lugubris, within the Lake Erie Watershed. Leech samples were collected from the pectoral fins of channel catfish, Ictalurus punctatus, and freshwater drum, Aplodinotus grunniens, from Lake Erie in commercial trap nets and pooled into two samples based on host attachment. Bacteria from within the viscera of M. lugubris were identified by sequencing their 16S rRNA (rDNA gene of amplified community bacterial DNA extracted from pooled leech homogenate samples and were checked for similarity in two public databases: the Ribosomal Database Project and BLAST. Bacteria belonging to the phylum Bacteroidetes, β-proteobacteria, Verrucomicrobia, and unclassified Bacteria were present in the leech samples. A large number of bacteria found within leeches attached to channel catfish consisted of sequences that could not be classified beyond the Domain Bacteria. However, many of these sequences were homologous (< 45 % to the phylum Bacteroidetes. One of the five genera detected in the leech homogenates was Flavobacterium psychrophilum, a serious fish pathogen that causes Bacterial Cold Water Disease. While the occurrence of genera varies, bacteria associated with the two fish species were similar.

  12. Impact of manufactured TiO2 nanoparticles on planktonic and sessile bacterial communities

    International Nuclear Information System (INIS)

    In the present study, we conducted a 2 week microcosm experiment with a natural freshwater bacterial community to assess the effects of titanium dioxide nanoparticles (TiO2-NPs) at various concentrations (0, 1, 10 and 100 mg/L) on planktonic and sessile bacteria under dark conditions. Results showed an increase of planktonic bacterial abundance at the highest TiO2-NP concentration, concomitant with a decrease from that of sessile bacteria. Bacterial assemblages were most affected by the 100 mg/L TiO2-NP exposure and overall diversity was found to be lower for planktonic bacteria and higher for sessile bacteria at this concentration. In both compartments, a 100 mg/L TiO2-NPs exposure induced a decrease in the ratio between the Betaproteobacteria and Bacteroidetes. For planktonic communities, a decrease of Comamonadaceae was observed concomitant with an increase of Oxalobacteraceae and Cytophagaceae (especially Emticicia). For sessile communities, results showed a strong decrease of Betaproteobacteria and particularly of Comamonadaceae. - Highlights: • Microcosm experiments with natural water exposed to TiO2-NPs. • Toxicity of TiO2-NPs assessed on both planktonic and sessile bacteria. • Effects on bacterial community structure and diversity. • Shift occurs in the Betaproteobacteria/Bacteroidetes repartition in communities. - TiO2-NPs increase abundance of planktonic bacteria, decrease that of sessile bacteria, and affect diversity and structure of communities in both cases

  13. Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium.

    Directory of Open Access Journals (Sweden)

    Ting-Chin David Shen

    Full Text Available We have recently reported that Altered Schaedler Flora (ASF can be used to durably engineer the gut microbiota to reduce ammonia production as an effective modality to reduce morbidity and mortality in the setting of liver injury. Here we investigated the effects of a low protein diet on ASF colonization and its ability to engineer the microbiota. Initially, ASF inoculation was similar between mice fed a normal protein diet or low protein diet, but the outgrowth of gut microbiota differed over the ensuing month. Notable was the inability of the dominant Parabacteroides ASF taxon to exclude other taxa belonging to the Bacteroidetes phylum in the setting of a low protein diet. Instead, a poorly classified yet highly represented Bacteroidetes family, S24-7, returned within 4 weeks of inoculation in mice fed a low protein diet, demonstrating a reduction in ASF resilience in response to dietary stress. Nevertheless, fecal ammonia levels remained significantly lower than those observed in mice on the same low protein diet that received a transplant of normal feces. No deleterious effects were observed in host physiology due to ASF inoculation into mice on a low protein diet. In total, these results demonstrate that low protein diet can have a pronounced effect on engineering the gut microbiota but modulation of ammonia is preserved.

  14. Biomethane production and dynamics of microflora in response to copper treatments during mesophilic anaerobic digestion.

    Science.gov (United States)

    Ke, Xin; Wang, Chunyong; Li, Rundong; Zhang, Yun; Zhang, Haijun; Gui, Shaofeng

    2014-08-01

    This study discussed the effects of different concentrations (0.625, 1.875 and 3.125 mM) of copper (Cu) in the form of CuSO4 on biomethane production and on the dynamics of microbial communities during the mesophilic anaerobic digestion (AD) of cow manure. The effects on biomethane production were found to depend on CuSO4 concentrations. After 50 days of AD, treatment A3 (3.125 mM) had lower cumulative biomethane production than the no-Cu control. The maximum value of cumulative biomethane production was detected under treatment A2 (1.875 mM). These results suggested that the stimulation or inhibition to biomethane production might be related to the concentration and chemical forms of Cu. Moreover, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to discuss the dynamics of microbial communities. Results revealed that different concentrations of CuSO4 had effects on the richness and diversity of bacterial and archaeal communities. The predominance of Bacteroidetes bacterium (GU339485.1) was verified through the sequencing of the dominant DGGE bands. Furthermore, Bacteroidetes bacterium could be detected during the whole AD process and is adaptable to a certain concentration range of CuSO4. PMID:25092381

  15. PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, T.A.; Holmes, S.; Alekseyenko, A.V.; Shenoy, M.; DeSantis, T.; Wu, C.H.; Andersen, G.L.; Winston, J.; Sonnenburg, J.; Pasricha, P.J.; Spormann, A.

    2010-12-01

    Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease. Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS. Our results revealed a significantly increased compositional difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species. The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.

  16. Gut Microbiota and Host Reaction in Liver Diseases

    Directory of Open Access Journals (Sweden)

    Hiroshi Fukui

    2015-10-01

    Full Text Available Although alcohol feeding produces evident intestinal microbial changes in animals, only some alcoholics show evident intestinal dysbiosis, a decrease in Bacteroidetes and an increase in Proteobacteria. Gut dysbiosis is related to intestinal hyperpermeability and endotoxemia in alcoholic patients. Alcoholics further exhibit reduced numbers of the beneficial Lactobacillus and Bifidobacterium. Large amounts of endotoxins translocated from the gut strongly activate Toll-like receptor 4 in the liver and play an important role in the progression of alcoholic liver disease (ALD, especially in severe alcoholic liver injury. Gut microbiota and bacterial endotoxins are further involved in some of the mechanisms of nonalcoholic fatty liver disease (NAFLD and its progression to nonalcoholic steatohepatitis (NASH. There is experimental evidence that a high-fat diet causes characteristic dysbiosis of NAFLD, with a decrease in Bacteroidetes and increases in Firmicutes and Proteobacteria, and gut dysbiosis itself can induce hepatic steatosis and metabolic syndrome. Clinical data support the above dysbiosis, but the details are variable. Intestinal dysbiosis and endotoxemia greatly affect the cirrhotics in relation to major complications and prognosis. Metagenomic approaches to dysbiosis may be promising for the analysis of deranged host metabolism in NASH and cirrhosis. Management of dysbiosis may become a cornerstone for the future treatment of liver diseases.

  17. Evaluation of microbial population dynamics in the co-composting of cow manure and rice straw using high throughput sequencing analysis.

    Science.gov (United States)

    Ren, Guangming; Xu, Xiuhong; Qu, Juanjuan; Zhu, Liping; Wang, Tingting

    2016-06-01

    Microbial population dynamics in co-composting of cow manure and rice straw were evaluated using 16S high throughput sequencing technology. Physicochemical factors, including temperature, pH, nitrogen contents, the ratio of carbon and nitrogen, and germination index, were also determined in this study. 16S high throughput sequencing results showed that bacterial community structure and composition significantly varied in each phase of composting. The major phyla included Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria and Planctomycetes, respectively. Bacteroidetes and Proteobacteria were the most abundant phyla in all phases, and Actinobacteria was just dominant in the mesophilic phase, while Firmicutes and Planctomycetes were ubiquitous. At the genus level, Simiduia, Flavobacterium, unclassified Chitinophagaceae and Flexibacter notably changed in each phase of composting. Bacterial community diversity in the mesophilic phase was higher than that in others based on the Shannon-Wiener index and Simpson diversity index. The ratio of carbon and nitrogen and germination index indicated that the co-composting of cow manure and rice straw reached maturation. The result of nitrogen contents showed that nitrogen loss mainly occurred in the thermophilic phase. In addition, the differences in the distributions of key OTUs between in the late thermophilic phase and the cooling and maturation phase were unobvious compared with other phase's base on the principal component analysis. Redundancy analysis revealed that the changes of nitrogen played a predominant role in the distributions of OTUs during the composting process. PMID:27116967

  18. Interferon Tau Affects Mouse Intestinal Microbiota and Expression of IL-17.

    Science.gov (United States)

    Ren, Wenkai; Chen, Shuai; Zhang, Liwen; Liu, Gang; Hussain, Tarique; Hao, Xiao; Yin, Jie; Duan, Jielin; Tan, Bie; Wu, Guoyao; Bazer, Fuller W; Yin, Yulong

    2016-01-01

    This study was conducted to explore the effects of interferon tau (IFNT) on the intestinal microbiota and expression of interleukin 17 (IL-17) in the intestine of mice. IFNT supplementation increased microbial diversity in the jejunum and ileum but decreased microbial diversity in the feces. IFNT supplementation influenced the composition of the intestinal microbiota as follows: (1) decreasing the percentage of Firmicutes and increasing Bacteroidetes in the jejunum and ileum; (2) enhancing the percentage of Firmicutes but decreasing Bacteroidetes in the colon and feces; (3) decreasing Lactobacillus in the jejunum and ileum; (4) increasing the percentage of Blautia, Bacteroides, Alloprevotella, and Lactobacillus in the colon; and (5) increasing the percentage of Lactobacillus, Bacteroides, and Allobaculum, while decreasing Blautia in the feces. Also, IFNT supplementation decreased the expression of IL-17 in the intestines of normal mice and of an intestinal pathogen infected mice. In conclusion, IFNT supplementation modulates the intestinal microbiota and intestinal IL-17 expression, indicating the applicability of IFNT to treat the intestinal diseases involving IL-17 expression and microbiota. PMID:27610003

  19. Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows.

    Science.gov (United States)

    Pitta, Dipti W; Indugu, Nagaraju; Kumar, Sanjay; Vecchiarelli, Bonnie; Sinha, Rohini; Baker, Linda D; Bhukya, Bhima; Ferguson, James D

    2016-04-01

    The microbial ecology of the rumen microbiome is influenced by the diet and the physiological status of the dairy cow and can have tremendous influence on the yield and components of milk. There are significant differences in milk yields between first and subsequent lactations of dairy cows, but information on how the rumen microbiome changes as the dairy cow gets older has received little attention. We characterized the rumen microbiome of the dairy cow for phylogeny and functional pathways by lactation group and stage of lactation using a metagenomics approach. Our findings revealed that the rumen microbiome was dominated by Bacteroidetes (70%), Firmicutes (15-20%) and Proteobacteria (7%). The abundance of Firmicutes and Proteobacteria were independently influenced by diet and lactation. Bacteroidetes contributed to a majority of the metabolic functions in first lactation dairy cows while the contribution from Firmicutes and Proteobacteria increased incrementally in second and third lactation dairy cows. We found that nearly 70% of the CAZymes were oligosaccharide breaking enzymes which reflect the higher starch and fermentable sugars in the diet. The results of this study suggest that the rumen microbiome continues to evolve as the dairy cow advances in lactations and these changes may have a significant role in milk production. PMID:26700882

  20. Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points

    Energy Technology Data Exchange (ETDEWEB)

    Handley, Kim M.; Wrighton, Kelly C.; Miller, Christopher S.; Wilkins, Michael J.; Kantor, Rose S.; Thomas, Brian C.; Williams, Kenneth H.; Gilbert, Jack A.; Long, Philip E.; Banfield, Jillian F.

    2015-03-01

    We explored the impact of the starting community composition and structure on ecosystem response to perturbations using organic carbon amendment experiments. Subsurface sediment was partitioned into flow-through columns, and the microbial communities were initially stimulated in situ by addition of acetate as a carbon and electron donor source. This drove community richness and evenness down, and pushed the system into a new biogeochemical state characterized by iron reduction. Reconstructed near-full-length 16S rRNA gene sequence analysis indicated a concomitant enrichment of Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After 10 to 12 days, acetate was exchange for lactate in a subset of columns. Following the clear onset of sulfate reduction (35 days after acetate-amendment), acetate was substituted for lactate in additional columns. Acetatestimulated communities differed markedly during each biogeochemical regime and at each lactate-switch. Regardless, however, of when communities were switched to lactate, they followed comparable trajectories with respect to composition and structure, with convergence evident one week after each switch, and marked after one month of lactate amendment. During sulfate reduction all treatments were enriched in Firmicutes and a number of species likely involved in sulfate reduction (notably Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum). Lactate treatments were distinguished by substantially lower relative abundances of Desulfotomaculum and Bacteroidetes, and enrichments of Psychrosinus and Clostridiales species. Results imply that the structure of the starting community was not significant in controlling organism selection in community succession.

  1. Mining of luxS genes from rumen microbial consortia by metagenomic and metatranscriptomic approaches.

    Science.gov (United States)

    Ghali, Ines; Shinkai, Takumi; Mitsumori, Makoto

    2016-05-01

    Although rumen bacterial communities vary depending on many factors such as diet, age and physiological conditions, a core microbiota exists within the rumen. In many natural environments, some bacteria use a quorum-sensing (QS) system to regulate their physiological activities. However, very limited information is available about QS systems in rumen. To investigate the autoinducer 2 (AI-2)-mediated QS system in rumen, we detected genes (luxS) encoding the AI-2 synthase (LuxS), from three datasets embedded in metagenomics RAST server (MG-RAST) and from a metatranscriptome dataset. We collected 135 luxS genes from the metagenomic datasets, which were presumed to originate from Bacteroidetes, Firmicutes, Fusobacteria and Actinobacteria, and 34 luxS genes from the metatranscriptome dataset, which probably originated from Bacteroidetes, Firmicutes and Spirochaetes. Because the essential amino acids for LuxS activity were conserved in the LuxS homologues predicted from luxS gene sequences from both datasets, the LuxS homologues probably function in the rumen. Since the largest number of sequences of luxS genes were collected from the genera Prevotella, Ruminococcus and Eubacterium, which include many fibrolytic bacteria and constituent members of biofilm on feed particles, an AI-2-mediated QS system is likely involved in biofilm formation and fibrolytic activity in the rumen. PMID:26277986

  2. Mechanism and Effect of Temperature on Variations in Antibiotic Resistance Genes during Anaerobic Digestion of Dairy Manure

    Science.gov (United States)

    Sun, Wei; Qian, Xun; Gu, Jie; Wang, Xiao-Juan; Duan, Man-Li

    2016-07-01

    Animal manure comprises an important reservoir for antibiotic resistance genes (ARGs), but the variation in ARGs during anaerobic digestion at various temperatures and its underlying mechanism remain unclear. Thus, we performed anaerobic digestion using dairy manure at three temperature levels (moderate: 20 °C, mesophilic: 35 °C, and thermophilic: 55 °C), to analyze the dynamics of ARGs and bacterial communities by quantitative PCR and 16S rRNA gene sequencing. We found that 8/10 detected ARGs declined and 5/10 decreased more than 1.0 log during thermophilic digestion, whereas only four and five ARGs decreased during moderate and mesophilic digestion, respectively. The changes in ARGs and bacterial communities were similar under the moderate and mesophilic treatments, but distinct from those in the thermophilic system. Potential pathogens such as Bacteroidetes, Proteobacteria, and Corynebacterium were removed by thermophilic digestion but not by moderate and mesophilic digestion. The bacterial community succession was the dominant mechanism that influenced the variation in ARGs and integrons during anaerobic digestion. Thermophilic digestion decreased the amount of mesophilic bacteria (Bacteroidetes and Proteobacteria) carrying ARGs. Anaerobic digestion generally decreased the abundance of integrons by eliminating the aerobic hosts of integrons (Actinomycetales and Bacilli). Thermophilic anaerobic digestion is recommended for the treatment and reuse of animal manure.

  3. Juvenile ferric iron prevents microbiota dysbiosis and colitis in adult rodents

    Institute of Scientific and Technical Information of China (English)

    Chourouk Ettreiki; Pascale Gadonna-Widehem; Irène Mangin; Mo(i)se Co(e)ffier; Carine Delayre-Orthez; Pauline M Anton

    2012-01-01

    AIM:To assess whether juvenile chronic ferric iron ingestion limit colitis and dysbiosis at adulthood in rats and mice.METHODS:Two sets of experiments were designed.In the first set,recently weaned mice were either orally administered ferrous (Fe2+) iron salt or ferric (Fe3+) microencapsulated iron for 6 wk.The last week of experiments trinitrobenzene sulfonic acid (TNBS) colitis was induced.In the second set,juvenile rats received the microencapsulated ferric iron for 6 wk and were also submitted to TNBS colitis during the last week of experiments.In both sets of experiments,animals were sacrificed 7 d after TNBS instillation.Severity of the inflammation was assessed by scoring macroscopic lesions and quantifying colonic myeloperoxidase (MPO) activity.Alteration of the microflora profile was estimated using quantitative polymerase chain reaction (qPCR) by measuring the evolution of total caecal microflora,Bacteroidetes,Firmicutes and enterobacteria.RESULTS:Neither ferrous nor ferric iron daily exposures at the juvenile period result in any effect in control animals at adulthood although ferrous iron repeated administration in infancy limited weight gain.Ferrous iron was unable to limit the experimental colitis (1.71 ± 0.27MPO U/mg protein vs 2.47 ± 0.22 MPO U/mg protein in colitic mice).In contrast,ferric iron significantly prevented the increase of MPO activity (1.64 ± 0.14 MPO U/mg protein) in TNBS-induced colitis.Moreover,this positive effect was observed at both the doses of ferric iron used (75 and 150 mg/kg per day po-6 wk).In the study we also compared,in both rats and mice,the consequences of chronic repeated low level exposure to ferric iron (75 mg/kg per day po-6 wk) on TNBS-induced colitis and its related dysbiosis.We confirmed that ferric iron limited the TNBS-induced increase of MPO activity in both the rodent species.Furthermore,we assessed the ferric iron incidence on TNBS-induced intestinal microbiota dysbiosis.At first,we needed to optimize the

  4. Should we build "obese" or "lean" anaerobic digesters?

    Directory of Open Access Journals (Sweden)

    Aurelio Briones

    Full Text Available Conventional anaerobic digesters (ADs treating dairy manure are fed with raw or fermented manure rich in volatile fatty acids (VFAs. In contrast, pre-fermented AD (PF-AD is fed with the more recalcitrant, fiber-rich fraction of manure that has been pre-fermented and depleted of VFAs. Thus, the substrate of PF-AD may be likened to a lean diet rich in fibers while the pre-fermentation stage fermenter is fed a relatively rich diet containing labile organic substances. Previous results have shown that conventional and pre-fermented ADs fed with raw or pre-fermented manure, respectively, produced comparable methane yields. The primary objective of this study was to characterize, using next-generation DNA sequencing, the bacterial communities in various bioreactors (pre-fermentation stage fermenter; various operational arrangements PF-AD; conventional single-stage AD; and a full scale AD and compare the Firmicutes to Bacteroidetes (F/B ratios in these different systems. Firmicutes and Bacteroidetes constituted the two most abundant phyla in all AD samples analyzed, as well as most of the samples analyzed in the fermenters and manure samples. Higher relative abundance of Bacteroidetes, ranging from 26% to 51% of bacteria, tended to be associated with PF-AD samples, while the highest relative abundance of Firmicutes occurred in the fermenter (maximum of 76% of bacteria and manure (maximum of 66% of bacteria samples. On average, primary stage fermenters exhibited microbiological traits linked to obesity: higher F/B ratios and a 'diet' that is less fibrous and more labile compared to that fed to PF-AD. On the other hand, microbial characteristics associated with leanness (lower F/B ratios combined with fibrous substrate were associated with PF-AD. We propose that bacterial communities in AD shift depending on the quality of substrate, which ultimately results in maintaining VFA yields in PF-AD, similar to the role of bacterial communities and a high fiber

  5. Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon.

    Directory of Open Access Journals (Sweden)

    Anthony A Devine

    Full Text Available Ileocecal resection (ICR is a commonly required surgical intervention in unmanageable Crohn's disease and necrotizing enterocolitis. However, the impact of ICR, and the concomitant doses of antibiotic routinely given with ICR, on the intestinal commensal microbiota has not been determined. In this study, wild-type C57BL6 mice were subjected to ICR and concomitant single intraperitoneal antibiotic injection. Intestinal lumen contents were collected from jejunum and colon at 7, 14, and 28 days after resection and compared to non-ICR controls. Samples were analyzed by 16S rRNA gene pyrosequencing and quantitative PCR. The intestinal microbiota was altered by 7 days after ICR and accompanying antibiotic treatment, with decreased diversity in the colon. Phylogenetic diversity (PD decreased from 11.8 ± 1.8 in non-ICR controls to 5.9 ± 0.5 in 7-day post-ICR samples. There were also minor effects in the jejunum where PD values decreased from 8.3 ± 0.4 to 7.5 ± 1.4. PCoA analysis indicated that bacterial populations 28 days post-ICR differed significantly from non-ICR controls. Moreover, colon and jejunum bacterial populations were remarkably similar 28 days after resection, whereas the initial communities differed markedly. Firmicutes and Bacteroidetes were the predominant phyla in jejunum and colon before ICR; however, Firmicutes became the vastly predominant phylum in jejunum and colon 28 days after ICR. Although the microbiota returned towards a homeostatic state, with re-establishment of Firmicutes as the predominant phylum, we did not detect Bacteroidetes in the colon 28 days after ICR. In the jejunum Bacteroidetes was detected at a 0.01% abundance after this time period. The changes in jejunal and colonic microbiota induced by ICR and concomitant antibiotic injection may therefore be considered as potential regulators of post-surgical adaptive growth or function, and in a setting of active IBD, potential contributors to post

  6. Effects of apples and specific apple components on the cecal environment of conventional rats: role of apple pectin

    Directory of Open Access Journals (Sweden)

    Markowski Jaroslaw

    2010-01-01

    Full Text Available Abstract Background Our study was part of the large European project ISAFRUIT aiming to reveal the biological explanations for the epidemiologically well-established health effects of fruits. The objective was to identify effects of apple and apple product consumption on the composition of the cecal microbial community in rats, as well as on a number of cecal parameters, which may be influenced by a changed microbiota. Results Principal Component Analysis (PCA of cecal microbiota profiles obtained by PCR-DGGE targeting bacterial 16S rRNA genes showed an effect of whole apples in a long-term feeding study (14 weeks, while no effects of apple juice, purée or pomace on microbial composition in cecum were observed. Administration of either 0.33 or 3.3% apple pectin in the diet resulted in considerable changes in the DGGE profiles. A 2-fold increase in the activity of beta-glucuronidase was observed in animals fed with pectin (7% in the diet for four weeks, as compared to control animals (P Bacteroidetes, whereas bands that became more prominent represented mainly Gram-positive anaerobic rods belonging to the phylum Firmicutes, and specific species belonging to the Clostridium Cluster XIVa. Quantitative real-time PCR confirmed a lower amount of given Bacteroidetes species in the pectin-fed rats as well as in the apple-fed rats in the four-week study (P Clostridium coccoides (belonging to Cluster XIVa, as well as of genes encoding butyryl-coenzyme A CoA transferase, which is involved in butyrate production, was detected by quantitative PCR in fecal samples from the pectin-fed animals. Conclusions Our findings show that consumption of apple pectin (7% in the diet increases the population of butyrate- and β-glucuronidase producing Clostridiales, and decreases the population of specific species within the Bacteroidetes group in the rat gut. Similar changes were not caused by consumption of whole apples, apple juice, purée or pomace.

  7. Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines

    Directory of Open Access Journals (Sweden)

    Charlotte Dafni Vavourakis

    2016-02-01

    Full Text Available Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first ‘metagenomic snapshots’ of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha- and Gammaproteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter and Rhodobaca and chemolithotrophic sulfur oxidizers (Thioalkalivibrio were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermaceae-related draft genome were indicative of a

  8. Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

    Science.gov (United States)

    Vavourakis, Charlotte D.; Ghai, Rohit; Rodriguez-Valera, Francisco; Sorokin, Dimitry Y.; Tringe, Susannah G.; Hugenholtz, Philip; Muyzer, Gerard

    2016-01-01

    Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first “metagenomic snapshots” of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermaceae-related draft genome were indicative of a “salt-in” strategy of

  9. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation

    DEFF Research Database (Denmark)

    Møller, Annette; Søborg, Ditte Andreasen; Al-Soud, Waleed Abu;

    2013-01-01

    controlled the distribution of the Cyanobacteria and algae in the snow while carbon and nitrogen fixed by these autotrophs in turn fed the heterotrophic bacteria. In the lake, a probable lower light input relative to snow resulted in low numbers of Cyanobacteria and chloroplasts and, hence, limited input......The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA genes and 16S rRNA gene sequencing of cultivated isolates. Both the pyrosequence and cultivation data indicated that the phylogenetic composition...... of the microbial assemblages was different within the snow layers and between snow and freshwater. The highest diversity was seen in snow. In the middle and top snow layers, Proteobacteria, Bacteroidetes and Cyanobacteria dominated, although Actinobacteria and Firmicutes were relatively abundant also. High numbers...

  10. Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis.

    Science.gov (United States)

    Dubin, Krista; Callahan, Margaret K; Ren, Boyu; Khanin, Raya; Viale, Agnes; Ling, Lilan; No, Daniel; Gobourne, Asia; Littmann, Eric; Huttenhower, Curtis; Pamer, Eric G; Wolchok, Jedd D

    2016-01-01

    The composition of the intestinal microbiota influences the development of inflammatory disorders. However, associating inflammatory diseases with specific microbial members of the microbiota is challenging, because clinically detectable inflammation and its treatment can alter the microbiota's composition. Immunologic checkpoint blockade with ipilimumab, a monoclonal antibody that blocks cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) signalling, is associated with new-onset, immune-mediated colitis. Here we conduct a prospective study of patients with metastatic melanoma undergoing ipilimumab treatment and correlate the pre-inflammation faecal microbiota and microbiome composition with subsequent colitis development. We demonstrate that increased representation of bacteria belonging to the Bacteroidetes phylum is correlated with resistance to the development of checkpoint-blockade-induced colitis. Furthermore, a paucity of genetic pathways involved in polyamine transport and B vitamin biosynthesis is associated with an increased risk of colitis. Identification of these biomarkers may enable interventions to reduce the risk of inflammatory complications following cancer immunotherapy. PMID:26837003

  11. Screening of a microbial consortium for highly simultaneous degradation of lignocellulose and chlorophenols.

    Science.gov (United States)

    Liang, Jiajin; Peng, Xiang; Yin, Dexing; Li, Beiyin; Wang, Dehan; Lin, Yunqin

    2015-08-01

    In this work, spent mushroom substrates were utilized for screening a microbial consortium with highly simultaneous degradation of lignocellulose and chlorophenols. The desired microbial consortium OEM1 was gained through successive cultivation for about 50 generations and its stability of composition was verified by denaturing gradient gel electrophoresis (DGGE) during screening process. It could degrade lignocellulose and chlorophenols at around 50% and 100%, respectively, within 7days. The diversity analysis and the growth characteristics of OEM1 during degradation process were investigated by PCR-DGGE combined with clone and sequence. The results indicated that OEM1 consisted of 31 strains. Proteobacteria and Bacteroidetes were the predominant bacterial groups. The dynamic change of OEM1 illustrated that consortium community structure was effected by pH and substrate alteration and tended to be stable after 6days' cultivation. Furthermore, bacteria (11 strains) and actinomycetes (2 strains) were obtained based on plate isolation and identified via 16S rDNA sequence. PMID:25974352

  12. Unravelling the microbiome of eggs of the endangered sea turtle Eretmochelys imbricata identifies bacteria with activity against the emerging pathogen Fusarium falciforme.

    Directory of Open Access Journals (Sweden)

    Jullie M Sarmiento-Ramírez

    Full Text Available Habitat bioaugmentation and introduction of protective microbiota have been proposed as potential conservation strategies to rescue endangered mammals and amphibians from emerging diseases. For both strategies, insight into the microbiomes of the endangered species and their habitats is essential. Here, we sampled nests of the endangered sea turtle species Eretmochelys imbricata that were infected with the fungal pathogen Fusarium falciforme. Metagenomic analysis of the bacterial communities associated with the shells of the sea turtle eggs revealed approximately 16,664 operational taxonomic units, with Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes as the most dominant phyla. Subsequent isolation of Actinobacteria from the eggshells led to the identification of several genera (Streptomyces, Amycolaptosis, Micromomospora Plantactinospora and Solwaraspora that inhibit hyphal growth of the pathogen F. falciforme. These bacterial genera constitute a first set of microbial indicators to evaluate the potential role of microbiota in conservation of endangered sea turtle species.

  13. Simultaneous microbial and electrochemical reductions of vanadium (V) with bioelectricity generation in microbial fuel cells.

    Science.gov (United States)

    Zhang, Baogang; Tian, Caixing; Liu, Ying; Hao, Liting; Liu, Ye; Feng, Chuanping; Liu, Yuqian; Wang, Zhongli

    2015-03-01

    Simultaneous microbial and electrochemical reductions of vanadium (V) with bioelectricity generation were realized in microbial fuel cells (MFCs). With initial V(V) concentrations of 75 mg/l and 150 mg/l in anolyte and catholyte, respectively, stable power output of 419±11 mW/m(2) was achieved. After 12h operation, V(V) concentration in the catholyte decreased to the value similar to that of the initial one in the anolyte, meanwhile it was nearly reduced completely in the anolyte. V(IV) was the main reduction product, which subsequently precipitated, acquiring total vanadium removal efficiencies of 76.8±2.9%. Microbial community analysis revealed the emergence of the new species of Deltaproteobacteria and Bacteroidetes as well as the enhanced Spirochaetes mainly functioned in the anode. This study opens new pathways to successful remediation of vanadium contamination. PMID:25536507

  14. Bacteria and archaea paleomicrobiology of the dental calculus: a review.

    Science.gov (United States)

    Huynh, H T T; Verneau, J; Levasseur, A; Drancourt, M; Aboudharam, G

    2016-06-01

    Dental calculus, a material observed in the majority of adults worldwide, emerged as a source for correlating paleomicrobiology with human health and diet. This mini review of 48 articles on the paleomicrobiology of dental calculus over 7550 years discloses a secular core microbiota comprising nine bacterial phyla - Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, TM7, Synergistetes, Chloroflexi, Fusobacteria, Spirochetes - and one archaeal phylum Euryarchaeota; and some accessory microbiota that appear and disappear according to time frame. The diet residues and oral microbes, including bacteria, archaea, viruses and fungi, consisting of harmless organisms and pathogens associated with local and systemic infections have been found trapped in ancient dental calculus by morphological approaches, immunolabeling techniques, isotope analyses, fluorescent in situ hybridization, DNA-based approaches, and protein-based approaches. These observations led to correlation of paleomicrobiology, particularly Streptococcus mutans and archaea, with past human health and diet. PMID:26194817

  15. Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment

    DEFF Research Database (Denmark)

    Otani, Saria; Hansen, Lars Hestbjerg; Sørensen, Søren J;

    2016-01-01

    Fungus-growing termites (subfamily Macrotermitinae) mix plant forage with asexual spores of their plant-degrading fungal symbiont Termitomyces in their guts and deposit this blend in fungus comb structures, within which the plant matter is degraded. As Termitomyces grows, it produces nodules with...... asexual spores, which the termites feed on. Since all comb material passes through termite guts, it is inevitable that gut bacteria are also deposited in the comb, but it has remained unknown which bacteria are deposited and whether distinct comb bacterial communities are sustained. Using high......-throughput sequencing of the 16S rRNA gene, we explored the bacterial community compositions of 33 fungus comb samples from four termite species (three genera) collected at four South African geographic locations in 2011 and 2013. We identified 33 bacterial phyla, with Firmicutes, Bacteroidetes, Proteobacteria...

  16. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T)

    Energy Technology Data Exchange (ETDEWEB)

    Han, Cliff; Spring, Stefan; Lapidus, Alla; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Saunders, Elizabeth; Chertkov, Olga; Brettin, Thomas; Goker, Markus; Rohde, Manfred; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Detter, John C.

    2009-05-20

    Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome.

    Directory of Open Access Journals (Sweden)

    Scott T Kelley

    Full Text Available Women with polycystic ovary syndrome (PCOS have reproductive and metabolic abnormalities that result in an increased risk of infertility, diabetes and cardiovascular disease. The large intestine contains a complex community of microorganisms (the gut microbiome that is dysregulated in humans with obesity and type 2 diabetes. Using a letrozole-induced PCOS mouse model, we demonstrated significant diet-independent changes in the gut microbial community, suggesting that gut microbiome dysbiosis may also occur in PCOS women. Letrozole treatment was associated with a time-dependent shift in the gut microbiome and a substantial reduction in overall species and phylogenetic richness. Letrozole treatment also correlated with significant changes in the abundance of specific Bacteroidetes and Firmicutes previously implicated in other mouse models of metabolic disease in a time-dependent manner. Our results suggest that the hyperandrogenemia observed in PCOS may significantly alter the gut microbiome independently of diet.

  18. Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome and metatranscriptome

    Directory of Open Access Journals (Sweden)

    Vimac Nolla-Ardevol

    2015-06-01

    Full Text Available A haloalkaline anaerobic microbial community obtained from soda lake sediments was used to inoculate anaerobic reactors for the production of methane rich biogas. The microalga Spirulina was successfully digested by the haloalkaline microbial consortium at alkaline conditions (pH 10, 2.0 M Na+. Continuous biogas production was observed and the obtained biogas was rich in methane, up to 96 %. Alkaline medium acted as a CO2 scrubber which resulted in low amounts of CO2 and no traces of H2S in the produced biogas. A hydraulic retention time of 15 days and 0.25 g Spirulina L-1 day-1 organic loading rate were identified as the optimal operational parameters. Metagenomics and metatranscriptomics analysis showed that the hydrolysis of the supplied substrate was mainly carried out by Bacteroidetes of the ML635J-40 aquatic group while the hydrogenotrophic pathway was the main producer of methane in a methanogenic community dominated by Methanocalculus.

  19. Having older siblings is associated with gut microbiota development during early childhood

    DEFF Research Database (Denmark)

    Laursen, Martin Frederik; Zachariassen, Gitte; Bahl, Martin Iain;

    2015-01-01

    Evidence suggests that early life infections, presence of older siblings and furred pets in the household affect the risk of developing allergic diseases through altered microbial exposure. Recently, low gut microbial diversity during infancy has also been linked with later development of allergies....... Bacterial compositions and diversity indices were determined in fecal samples collected from 114 infants in the SKOT I cohort at age 9 and 18 months by 16S rRNA gene sequencing. These were compared to the presence of older siblings, furred pets and early life infections and the cumulative prevalence of...... diagnosed asthmatic bronchitis and self-reported eczema at 3 years of age. The number of older siblings correlated positively with bacterial diversity (p = 0.030), diversity of the phyla Firmicutes (p = 0.013) and Bacteroidetes (p = 0.004) and bacterial richness (p = 0.006) at 18 months. Further, having...

  20. Las degradation in a fluidized bed reactor and phylogenetic characterization of the biofilm

    Directory of Open Access Journals (Sweden)

    L. L. Oliveira

    2013-09-01

    Full Text Available A fluidized bed reactor was used to study the degradation of the surfactant linear alkylbenzene sulfonate (LAS. The reactor was inoculated with anaerobic sludge and was fed with a synthetic substrate supplemented with LAS in increasing concentrations (8.2 to 45.8 mg l-1. The removal efficiency of 93% was obtained after 270 days of operation. Subsequently, 16S rRNA gene sequencing and phylogenetic analysis of the sample at the last stage of the reactor operation recovered 105 clones belonging to the domain Bacteria. These clones represented a variety of phyla with significant homology to Bacteroidetes (40%, Proteobacteria (42%, Verrucomicrobia (4%, Acidobacteria (3%, Firmicutes (2%, and Gemmatimonadetes (1%. A small fraction of the clones (8% was not related to any phylum. Such phyla variety indicated the role of microbial consortia in degrading the surfactant LAS.

  1. Microbial Community Analysis of a Single Chamber Microbial Fuel Cell Using Potato Wastewater

    Energy Technology Data Exchange (ETDEWEB)

    Zhen Li; Rishika Haynes; Eugene Sato; Malcolm Shields; Yoshiko Fujita; Chikashi Sato

    2014-04-01

    Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bioelectrochemical reactions mediated by microorganisms. We investigated the diversity of the microbial community in an air cathode single chamber MFC that utilized potato-process wastewater as substrate. Terminal Restriction Fragment Length Polymorphism (T-RFLP) results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S rDNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopy results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that utilize potato wastewater.

  2. Microbial community structure and dynamics during co-digestion of whey permeate and cow manure in continuous stirred tank reactor systems.

    Science.gov (United States)

    Hagen, Live Heldal; Vivekanand, Vivekanand; Linjordet, Roar; Pope, Phillip B; Eijsink, Vincent G H; Horn, Svein J

    2014-11-01

    Microbial community profiles in two parallel CSTR biogas reactors fed with whey permeate and cow manure were investigated. The operating conditions for these two reactors were identical, yet only one of them (R1) showed stable performance, whereas the other (R2) showed a decrease in methane production accompanied by accumulation of propionic acid and, later, acetic acid. This gave a unique opportunity to study the dynamics of the microbial communities in two biogas reactors apparently operating close to the edge of stability. The microbial community was dominated by Bacteroidetes and Firmicutes, and the methanogens Methanobacteriales and Methanomicrobiales in both reactors, but with larger fluctuations in R2. Correlation analyses showed that the depletion of propionic acid in R1 and the late increase of acetic acid in R2 was related to several bacterial groups. The biogas production in R1 shows that stable co-digestion of manure and whey can be achieved with reasonable yields. PMID:25222739

  3. Isolation and characterization of the microbial community of a freshwater distribution system

    International Nuclear Information System (INIS)

    This investigation provides generic information on culturable and non-culturable microbial community of a freshwater distribution system. Culture based and culture independent (16S rRNA gene sequencing) techniques were used to identify the resident microbial community of the system. Selective isolation of the fouling bacteria such as biofilm formers and corrosion causing bacteria was also attempted. Denaturing gradient gel electrophoresis (DGGE) was carried out and the bands were sequenced to obtain the diversity of the total bacterial types. Pseudomonas aeruginosa was predominantly observed in most of the samples. A variety of bacteria, related to groups such as Cyanobacteria, Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were identified. The study highlights the relevance of the observed microbial diversity with respect to material deterioration in a freshwater distribution system, which can aid in designing effective control methods. (author)

  4. Changes in the gut microbiota of cloned and non-cloned control pigs during development of obesity: gut microbiota during development of obesity in cloned pigs

    DEFF Research Database (Denmark)

    Pedersen, Rebecca; Andersen, Anders Daniel; Mølbak, Lars;

    2013-01-01

    Background Obesity induced by a high-caloric diet has previously been associated with changes in the gut microbiota in mice and in humans. In this study, pigs were cloned to minimize genetic and biological variation among the animals with the aim of developing a controlled metabolomic model...... suitable for a diet-intervention study. Cloning of pigs may be an attractive way to reduce genetic influences when investigating the effect of diet and obesity on different physiological sites. The aim of this study was to assess and compare the changes in the composition of the gut microbiota of cloned vs....... non-cloned pigs during development of obesity by a high-fat/high-caloric diet. Furthermore, we investigated the association between diet-induced obesity and the relative abundance of the phyla Firmicutes and Bacteroidetes in the fecal-microbiota. The fecal microbiota from obese cloned (n = 5) and non-cloned...

  5. Molecular analysis of microbial diversity in corrosion samples from energy transmission towers.

    Science.gov (United States)

    Oliveira, Valéria M; Lopes-Oliveira, Patrícia F; Passarini, Michel R Z; Menezes, Claudia B A; Oliveira, Walter R C; Rocha, Adriano J; Sette, Lara D

    2011-04-01

    Microbial diversity in corrosion samples from energy transmission towers was investigated using molecular methods. Ribosomal DNA fragments were used to assemble gene libraries. Sequence analysis indicated 10 bacterial genera within the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. In the two libraries generated from corroded screw-derived samples, the genus Acinetobacter was the most abundant. Acinetobacter and Clostridium spp. dominated, with similar percentages, in the libraries derived from corrosion scrapings. Fungal clones were affiliated with 14 genera belonging to the phyla Ascomycota and Basidiomycota; of these, Capnobotryella and Fellomyces were the most abundant fungi observed. Several of the microorganisms had not previously been associated with biofilms and corrosion, reinforcing the need to use molecular techniques to achieve a more comprehensive assessment of microbial diversity in environmental samples. PMID:21563009

  6. Application of a new purification method of West-Kazakhstan chestnut soil microbiota DNA for metagenomic analysis

    Science.gov (United States)

    Sergaliev, N. Kh.; Kakishev, M. G.; Zhiengaliev, A. T.; Volodin, M. A.; Andronov, E. E.; Pinaev, A. G.

    2015-04-01

    A method for the extraction of soil microbial DNA has been tested on chestnut soils (Kastanozems) of the West Kazakhstan region. The taxonomic analysis of soil microbiome libraries has shown that the phyla Actinobacteria and Proteobacteria constitute the largest part of microbial communities in the analyzed soils. The Archaea form an appreciable part of the microbiome in the studied samples. In the underdeveloped dark chestnut soil, their portion is higher than 11%. This is of interest, as the proportion of Archaea in the soil communities of virgin lands usually does not exceed 5%. In addition to the phyla mentioned above, there are representatives of the phyla Acidobacteria, Bacteroidetes, Firmicutes, Gemmatimonadales, Planctomycetes, and Verrucomicrobia, which are all fairly common in soil communities.

  7. The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome.

    Science.gov (United States)

    Kelley, Scott T; Skarra, Danalea V; Rivera, Alissa J; Thackray, Varykina G

    2016-01-01

    Women with polycystic ovary syndrome (PCOS) have reproductive and metabolic abnormalities that result in an increased risk of infertility, diabetes and cardiovascular disease. The large intestine contains a complex community of microorganisms (the gut microbiome) that is dysregulated in humans with obesity and type 2 diabetes. Using a letrozole-induced PCOS mouse model, we demonstrated significant diet-independent changes in the gut microbial community, suggesting that gut microbiome dysbiosis may also occur in PCOS women. Letrozole treatment was associated with a time-dependent shift in the gut microbiome and a substantial reduction in overall species and phylogenetic richness. Letrozole treatment also correlated with significant changes in the abundance of specific Bacteroidetes and Firmicutes previously implicated in other mouse models of metabolic disease in a time-dependent manner. Our results suggest that the hyperandrogenemia observed in PCOS may significantly alter the gut microbiome independently of diet. PMID:26731268

  8. Who is actively denitrifying in activated sludge?

    DEFF Research Database (Denmark)

    Hansen, Aviaja Anna; Nielsen, Jeppe Lund

    -scale wastewater treatment plant the transcripts (mRNA) of the nirS, nirK and nosZ denitrification genes expressed under acetate or amino acid consumption were amplified, sequenced and identified. This revealed that the majority of the denitrifiers belonged to Alpha- and Betaproteobacteria, while only few...... genetic diversity was observed from the nirS transcripts and not the nosZ transcripts. Likewise, denitrifying cultures obtained from the activated sludge affiliated with the same Alpha- and Betaproteobacteria as detected with the denitrification genes, except one culture, which affiliated with...... Bacteroidetes. Furthermore, potential denitrifying genera of Alpha- and Betaproteobacteria were quantified in the activated sludge with 16S rRNA gene probes for fluorescence in situ hybridization (FISH). This revealed that Aquaspirillum-related bacteria were dominant followed by bacteria related to Azoarcus...

  9. Diet type dictates the gut microbiota and the immune response against Yersinia ruckeri in rainbow trout (Oncorhynchus mykiss)

    DEFF Research Database (Denmark)

    Ingerslev, Hans-Christian; Strube, Mikael Lenz; Jørgensen, Louise von Gersdorff;

    2014-01-01

    rainbow trout. The plant-based diet gave rise to an intestinal microbiota dominated by the genera Streptococcus, Leuconostoc and Weissella from phylum Firmicutes whereas phylum Proteobacteria/Bacteroidetes/Actinobacteria dominated the community in the marine fed fish. In connection to the Y. ruckeri bath...... challenge there was no effect of the diet type on the cumulative survival, but the number of Y. ruckeri positive fish as measured by plate count and the number of fish with a 'high' number of reads belonging to genus Yersinia as measured by 16S rRNA next-generation sequencing was higher for marine diet fed...... fish. Furthermore, the two experimental groups of fish showed a differential immune response, where Y. ruckeri challenged marine fed fish had a higher transcription of IL-1β and MBL-2 relative to challenged plant diet fed fish. The data suggest that the plant diet gave rise to a prebiotic effect...

  10. Bacterial reduction of mercury in the high arctic

    DEFF Research Database (Denmark)

    Møller, Annette Klæstrup

    It is well-established that mercury (Hg) from lower latitudes is transferred to and pollutes the Arctic environment. One mechanism of Hg transfer is through the atmosphere where Hg is deposited in the Arctic in the spring time during Atmospheric Mercury Depletion Events (AMDE): large amounts of Hg...... is believed to be depleted from the atmosphere and deposited onto snow and sea-ice through photochemical reactions. The faith of mercury after deposition is poorly understood and while bacteria are known to play an important role in the bio-geochemical Hg cycle in various temperate environments, their role......, Bacteroidetes, Actinobacteria and Planctomycetes in freshwater. The bacteria identified in this study both included phylotypes commonly found in cold environments as well as rare phylotypes. During the time of sampling atmospheric ozone measurements and total Hg measurements in the snow indicated...

  11. Complete genome sequence of Hymenobacter sp. strain PAMC26554, an ionizing radiation-resistant bacterium isolated from an Antarctic lichen.

    Science.gov (United States)

    Oh, Tae-Jin; Han, So-Ra; Ahn, Do-Hwan; Park, Hyun; Kim, Augustine Yonghwi

    2016-06-10

    A Gram-negative, rod-shaped, red-pink in color, and UV radiation-resistant bacterium Hymenobacter sp. strain PAMC26554 was isolated from Usnea sp., an Antarctic lichen, and belongs to the class of Cytophagia and the phylum of Bacteroidetes. The complete genome of Hymenobacter sp. PAMC26554 consists of one chromosome (5,244,843bp) with two plasmids (199,990bp and 6421bp). The genomic sequence indicates that Hymenobacter sp. strain PAMC26554 possesses several genes involved in the nucleotide excision repair pathway that protects damaged DNA. This complete genome information will help us to understand its adaptation and novel survival strategy in the Antarctic extreme cold environment. PMID:27063139

  12. The Gut Microbiome and Obesity.

    Science.gov (United States)

    John, George Kunnackal; Mullin, Gerard E

    2016-07-01

    The gut microbiome consists of trillions of bacteria which play an important role in human metabolism. Animal and human studies have implicated distortion of the normal microbial balance in obesity and metabolic syndrome. Bacteria causing weight gain are thought to induce the expression of genes related to lipid and carbohydrate metabolism thereby leading to greater energy harvest from the diet. There is a large body of evidence demonstrating that alteration in the proportion of Bacteroidetes and Firmicutes leads to the development of obesity, but this has been recently challenged. It is likely that the influence of gut microbiome on obesity is much more complex than simply an imbalance in the proportion of these phyla of bacteria. Modulation of the gut microbiome through diet, pre- and probiotics, antibiotics, surgery, and fecal transplantation has the potential to majorly impact the obesity epidemic. PMID:27255389

  13. Effects of apples and specific apple components on the cecal environment of conventional rats: Role of apple pectin

    DEFF Research Database (Denmark)

    Licht, Tine Rask; Hansen, Max; Bergström, Anders;

    2010-01-01

    Background: Our study was part of the large European project ISAFRUIT aiming to reveal the biological explanations for the epidemiologically well-established health effects of fruits. The objective was to identify effects of apple and apple product consumption on the composition of the cecal...... study (14 weeks), while no effects of apple juice, puree or pomace on microbial composition in cecum were observed. Administration of either 0.33 or 3.3% apple pectin in the diet resulted in considerable changes in the DGGE profiles. A 2-fold increase in the activity of beta-glucuronidase was observed......-glucuronidase producing Clostridiales, and decreases the population of specific species within the Bacteroidetes group in the rat gut. Similar changes were not caused by consumption of whole apples, apple juice, puree or pomace....

  14. [Metagenomic Analysis of Microbial Communities of the Sediments of the Kara Sea Shelf and the Yenisei Bay].

    Science.gov (United States)

    Mamaeva, E V; Galach'yants, Yu P; Khabudaev, K V; Petrova, D P; Pogodaeva, T V; Khodzher, T B; Zemskaya, T I

    2016-01-01

    Microbial diversity in the sediments of the Kara Sea shelf and the southern Yenisei Bay, differing in pore water mineralization, was studied using massive parallel pyrosequencing according to the 454 (Roche) technology. Members of the same phyla (Cyanobacteria, Verrucomicrobia, Actinobacteria, Proteobacteria, and Bacteroidetes) predominated in bacterial communities of the sediments, while their ratio and taxonomic composition varied within the phyla and depended on pore water mineralization. Increasing salinity gradient was found to coincide with increased share of the γ-Proteobacteria and decreased abundance of α- and β-Proteo- bacteria, as well as of the phyla Verrucomicrobia, Chloroflexi, Chlorobi, and Acidobacteria. Archaeal diversity was lower, with Thaumarchaeota predominant in the sediments with high and low mineralization, while Crenarchaeota predominated in moderately mineralized sediments. Microbial communities of the Kara Sea shelf and Yenisei Gulf sediments were found to contain the organisms capable of utilization of a broad spectrum of carbon sources, including gaseous and petroleum hydrocarbons. PMID:27476207

  15. Complete genome sequence of Weeksella virosa type strain (9751T)

    Energy Technology Data Exchange (ETDEWEB)

    Lang, Elke [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kopitz, marcus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

    2011-01-01

    Weeksella virosa Holmes et al. 1987 is the sole member and type species of the genus Weeksella which belongs to the family Flavobacteriaceae of the phylum Bacteroidetes. Twenty-nine isolates, collected from clinical specimens provided the basis for the taxon description. While the species seems to be a saprophyte of the mucous membranes of healthy man and warm-blooded animals a causal relationship with disease has been reported in a few instances. Except for the ability to produce indole and to hydrolyze Tween and proteins such as casein and gelatin, this aerobic, non-motile, non-pigmented bacterial species is metabolically inert in most traditional biochemical tests. The 2,272,954 bp long genome with its 2,105 protein-coding and 76 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  16. Metagenomic characterization of biodiversity in the extremely arid desert soils of Kazakhstan

    Science.gov (United States)

    Kutovaya, O. V.; Lebedeva, M. P.; Tkhakakhova, A. K.; Ivanova, E. A.; Andronov, E. E.

    2015-05-01

    For the first time, the composition of microbiomes in the biological crust (AKL) horizons of extremely arid desert soils (Aridic Calcisols) developed from saline and nonsaline alluvial deposits in the Ili Depression (eastern Kazakhstan) was analyzed. To describe the diversity of microorganisms in the soil samples, a novel method of pyrosequencing (Roche/454 Life Sciences) was applied. It was shown that bacteria from the Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, Acidobacteria, and Bacteroidetes phyla predominate in all the samples; these are typical representatives of the microbiome of soil crusts. A distinctive feature of the extremely arid soils is the high contribution of cyanobacteria (25-30%) to the total DNA. In the soils developed from saline sediments, representatives from the Rubrobacteraceae, Streptococcaceae, and Caulobacteraceae families and from the Firmicutes phylum predominated. In the soils developed from nonsaline gypsiferous deposits, bacteria from the class of Acidobacteria, subgroup Gp3, of the Methylobacteriaceae family and the class of Subdivision 3 from the Verrucomicrobia phylum predominated.

  17. Evolution of microbial community along with increasing solid concentration during high-solids anaerobic digestion of sewage sludge.

    Science.gov (United States)

    Liu, Can; Li, Huan; Zhang, Yuyao; Si, Dandan; Chen, Qingwu

    2016-09-01

    High-solids anaerobic digestion (HSAD), a promising method with smaller reactor and less heating energy consumption, showed relatively lower digestion efficiency sometimes and higher tolerance to some inhibitors. To investigate the phenomena, the archaeal and bacterial communities in four anaerobic digesters treating sewage sludge with total solids (TS) of 10-19% were investigated. Although acetoclastic methanogenesis conducted mainly by genus Methanosarcina was still the main pathway producing methane, the total ratio of acetoclastic methanogens decreased along with the increased TS. In contrary, the relative abundance of hydrogenotrophic methanogens increased from 6.8% at TS 10% to 22.3% at TS 19%, and methylotrophic methanogens from 10.4% to 20.9%. The bacterial community was dominated by five phyla. Acidogenic and acetogenic bacteria affiliated to Firmicutes decreased following the increase of TS; while the proteolysis phylum Bacteroidetes increased, with a tolerant family ST-12K33 notably existing in the digesters at TS 17% and 19%. PMID:27235970

  18. Global patterns of marine bacterioplankton diversity and characterisation of bioactive Vibrionaceae isolates

    DEFF Research Database (Denmark)

    Wietz, Matthias

    The purpose of the present study was to analyze the composition of marine bacterial communities around the world, and to investigate bacterial isolates regarding the production of antibiotics. This included molecular analyses of marine bacterioplankton, as well as culture-based studies of marine....... Quantitative community analyses showed latitudinal patterns in bacterial distribution, revealing significantly different relative abundances of Bacteroidetes, unclassified Bacteria and Vibrio between warmer and colder oceans. Absolute cell numbers of most bacterial groups were positively correlated...... bacterial isolates with antagonistic activity. The work was based on samples collected during the Galathea 3 and LOMROG-II marine research expeditions that have explored many different oceanic regions worldwide. A molecular survey of marine bacterioplankton at 24 worldwide stations investigated...

  19. Metagenomic analysis of a desulphurisation system used to treat biogas from vinasse methanisation.

    Science.gov (United States)

    Dias, Marcela França; Colturato, Luis Felipe; de Oliveira, João Paulo; Leite, Laura Rabelo; Oliveira, Guilherme; Chernicharo, Carlos Augusto; de Araújo, Juliana Calabria

    2016-04-01

    We investigated the response of microbial community to changes in H2S loading rate in a microaerated desulphurisation system treating biogas from vinasse methanisation. H2S removal efficiency was high, and both COD and DO seemed to be important parameters to biomass activity. DGGE analysis retrieved sequences of sulphide-oxidising bacteria (SOB), such as Thioalkalimicrobium sp. Deep sequencing analysis revealed that the microbial community was complex and remained constant throughout the experiment. Most sequences belonged to Firmicutes and Proteobacteria, and, to a lesser extent, Bacteroidetes, Chloroflexi, and Synergistetes. Despite the high sulphide removal efficiency, the abundance of the taxa of SOB was low, and was negatively affected by the high sulphide loading rate. PMID:26803795

  20. Molecular characterization of an endolithic microbial community in dolomite rock in the central Alps (Switzerland).

    Science.gov (United States)

    Horath, Thomas; Bachofen, Reinhard

    2009-08-01

    Endolithic microorganisms colonize the pores in exposed dolomite rocks in the Piora Valley in the Swiss Alps. They appear as distinct grayish-green bands about 1-8 mm below the rock surface. Based on environmental small subunit ribosomal RNA gene sequences, a diverse community driven by photosynthesis has been found. Cyanobacteria (57 clones), especially the genus Leptolyngbya, form the functional basis for an endolithic community which contains a wide spectrum of so far not characterized species of chemotrophic Bacteria (64 clones) with mainly Actinobacteria, Alpha-Proteobacteria, Bacteroidetes, and Acidobacteria, as well as a cluster within the Chloroflexaceae. Furthermore, a cluster within the Crenarchaeotes (40 clones) has been detected. Although the eukaryotic diversity was outside the scope of the study, an amoeba (39 clones), and several green algae (51 clones) have been observed. We conclude that the bacterial diversity in this endolithic habitat, especially of chemotrophic, nonpigmented organisms, is considerable and that Archaea are present as well. PMID:19172216

  1. The human vaginal bacterial biota and bacterial vaginosis.

    Science.gov (United States)

    Srinivasan, Sujatha; Fredricks, David N

    2008-01-01

    The bacterial biota of the human vagina can have a profound impact on the health of women and their neonates. Changes in the vaginal microbiota have been associated with several adverse health outcomes including premature birth, pelvic inflammatory disease, and acquisition of HIV infection. Cultivation-independent molecular methods have provided new insights regarding bacterial diversity in this important niche, particularly in women with the common condition bacterial vaginosis (BV). PCR methods have shown that women with BV have complex communities of vaginal bacteria that include many fastidious species, particularly from the phyla Bacteroidetes and Actinobacteria. Healthy women are mostly colonized with lactobacilli such as Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus iners, though a variety of other bacteria may be present. The microbiology of BV is heterogeneous. The presence of Gardnerella vaginalis and Atopobium vaginae coating the vaginal epithelium in some subjects with BV suggests that biofilms may contribute to this condition. PMID:19282975

  2. Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments.

    Science.gov (United States)

    Eyice, Özge; Schäfer, Hendrik

    2016-01-01

    One-carbon compounds such as methanol, dimethylsulfide (DMS) and dimethylsulfoxide (DMSO) are significant intermediates in biogeochemical cycles. They are suggested to affect atmospheric chemistry and global climate. Methylotrophic microorganisms are considered as a significant sink for these compounds; therefore, we analyzed the diversity of terrestrial bacteria that utilize methanol, DMS and DMSO as carbon and energy source using culture-dependent and culture-independent methods. The effect of habitat type on the methylotrophic community structure was also investigated in rhizosphere and bulk soil. While thirteen strains affiliated to the genera Hyphomicrobium, Methylobacterium, Pseudomonas, Hydrogenophaga, Rhodococcus, Flavobacterium and Variovorax were isolated, denaturing gradient gel electrophoresis revealed the dominance of Thiobacillus, Rhodococcus, Flavobacterium and Bacteroidetes species. Furthermore, methylotrophic communities that degrade methanol or DMS are not shaped by terrestrial habitat type. Rhizosphere and soil samples showed dominance of Methylophilus spp. and Methylovorus spp. for methanol enrichments; Cytophaga spp., Pseudomonas tremae and Thiobacillus thioparus for DMS enrichments. PMID:26475353

  3. Wheat straw: An inefficient substrate for rapid natural lignocellulosic composting.

    Science.gov (United States)

    Zhang, Lili; Jia, Yangyang; Zhang, Xiaomei; Feng, Xihong; Wu, Jinjuan; Wang, Lushan; Chen, Guanjun

    2016-06-01

    Composting is a promising method for the management of agricultural wastes. However, results for wheat straw composts with different carbon-to-nitrogen ratios revealed that wheat straw was only partly degraded after composting for 25days, with hemicellulose and cellulose content decreasing by 14% and 33%, respectively. No significant changes in community structure were found after composting according to 454-pyrosequencing. Bacterial communities were represented by Proteobacteria and Bacteroidetes throughout the composting process, including relatively high abundances of pathogenic microbes such as Pseudomonas and Flexibacter, suggesting that innocent treatment of the composts had not been achieved. Besides, the significant lignocellulose degrader Thermomyces was not the exclusively dominant fungus with relative abundance only accounting for 19% of fungal communities. These results indicated that comparing with maize straw, wheat straw was an inefficient substrate for rapid natural lignocellulose-based composting, which might be due to the recalcitrance of wheat straw. PMID:26980627

  4. New and Rare Carotenoids Isolated from Marine Bacteria and Their Antioxidant Activities

    Directory of Open Access Journals (Sweden)

    Kazutoshi Shindo

    2014-03-01

    Full Text Available Marine bacteria have not been examined as extensively as land bacteria. We screened carotenoids from orange or red pigments-producing marine bacteria belonging to rare or novel species. The new acyclic carotenoids with a C30 aglycone, diapolycopenedioc acid xylosylesters A–C and methyl 5-glucosyl-5,6-dihydro-apo-4,4′-lycopenoate, were isolated from the novel Gram-negative bacterium Rubritalea squalenifaciens, which belongs to phylum Verrucomicrobia, as well as the low-GC Gram-positive bacterium Planococcus maritimus strain iso-3 belonging to the class Bacilli, phylum Firmicutes, respectively. The rare monocyclic C40 carotenoids, (3R-saproxanthin and (3R,2′S-myxol, were isolated from novel species of Gram-negative bacteria belonging to the family Flavobacteriaceae, phylum Bacteroidetes. In this review, we report the structures and antioxidant activities of these carotenoids, and consider relationships between bacterial phyla and carotenoid structures.

  5. Hydrolyzed polyacrylamide biodegradation and mechanism in sequencing batch biofilm reactor.

    Science.gov (United States)

    Yan, Miao; Zhao, Lanmei; Bao, Mutai; Lu, Jinren

    2016-05-01

    An investigation was performed to study the performance of a sequencing batch biofilm reactor (SBBR) to treat hydrolyzed polyacrylamides (HPAMs) and to determine the mechanisms of HPAM biodegradation. The mechanisms for the optimized parameters that significantly improved the degradation efficiency of the HPAMs were investigated by a synergistic effect of the co-metabolism in the sludge and the enzyme activities. The HPAM and TOC removal ratio reached 54.69% and 70.14%. A significant decrease in the total nitrogen concentration was measured. The carbon backbone of the HPAMs could be degraded after the separation of the amide group according to the data analysis. The HPLC results indicated that the HPAMs could be converted to polymer fragments without the generation of the acrylamide monomer intermediate. The results from high-throughput sequencing analysis revealed proteobacterias, bacteroidetes and planctomycetes were the key microorganisms involved in the degradation. PMID:26896716

  6. Characterisation of the gut microbiota in three porcine models of obesity and metabolic syndrome

    DEFF Research Database (Denmark)

    Pedersen, Rebecca

    ‐dynamic array. The faecal, colonic and ileal microbiota of lean and obese, cloned and non‐cloned pigs was investigated by T‐RFLP and the results showed that the gut microbiota was affected by high‐fat/high‐energy diet and obesity. A positive correlation was observed between body‐weight and percentage of body‐fat......Obesity is increasing worldwide at an alarming rate which has reached epidemic proportions. Obesity and its co‐morbidities such as cardiovascular disease, type‐2 diabetes and cancer are of great economical burden to the countries affected. Efforts have been made to identify the causal factors that...... over time in both the lean and obese group. The colon microbiota of lean cloned pigs contained relatively more of bacteria belonging to the phylum Firmicutes and less bacteria belonging to the phylum Bacteroidetes than obese cloned pigs. In the obese group, body‐weight correlated positively with the...

  7. Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.

    Science.gov (United States)

    Jeanbille, M; Buée, M; Bach, C; Cébron, A; Frey-Klett, P; Turpault, M P; Uroz, S

    2016-02-01

    Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences. PMID:26370112

  8. Contrasting soil bacterial community structure between the phyla Acidobacteria and Proteobacteria in tropical Southeast Asian and temperate Japanese forests.

    Science.gov (United States)

    Miyashita, Naohiko T

    2015-01-01

    Soil bacterial community structures of six dominant phyla (Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, Bacteroidetes and Actinobacteria) and unclassified bacteria detected in tropical Sarawakian and temperate Japanese forests were compared based on 16S rRNA gene sequence variation. The class composition in each phylum was similar among the studied forests; however, significant heterogeneities of class frequencies were detected. Acidobacteria and Proteobacteria were the most dominant phyla in all six forests, but differed in the level of bacterial species diversity, pattern of species occurrence and association pattern of species composition with physicochemical properties in soil. Species diversity among Acidobacteria was approximately half that among Proteobacteria, based on the number of clusters and the Chao1 index, even though a similar number of sequence reads were obtained for these two phyla. In contrast, species diversity within Planctomycetes and Bacteroidetes was nearly as high as within Acidobacteria, despite many fewer sequence reads. The density of species (the number of sequence reads per cluster) correlated negatively with species diversity, and species density within Acidobacteria was approximately twice that within Proteobacteria. Although the percentage of forest-specific species was high for all bacterial groups, sampling site-specific species varied among bacterial groups, indicating limited inter-forest migration and differential movement of bacteria in forest soil. For five of the seven bacterial groups, including Acidobacteria, soil pH appeared to strongly influence species composition, but this association was not observed for Proteobacterial species. Topology of UPGMA trees and pattern of NMDS plots among the forests differed among the bacterial groups, suggesting that each bacterial group has adapted and evolved independently in each forest. PMID:26399766

  9. Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil

    International Nuclear Information System (INIS)

    Highlights: • Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided. • A failure of exogenous white rot fungi to colonize the polluted soil is shown by DGGE and pyrosequencing. • Surfactant Brij 30 hampers 4-ring PAHs degradation due to toxicity over Actinobacteria and Bacteroidetes populations. • A high prevalence of Fusarium and Scedosporium populations is revealed during soil bioremediation. • Cupriavidus, Mycobacterium and Chithinophagaceae are potential HMW–PAH degraders in the soil. - Abstract: Bacterial and fungal biodiversity throughout different biostimulation and bioaugmentation treatments applied to an industrial creosote-polluted soil were analyzed by means of polyphasic approach in order to gain insight into the microbial community structure and dynamics. Pyrosequencing data obtained from initial creosote polluted soil (after a biopiling step) revealed that Alpha and Gammaproteobacteria were the most abundant bacterial groups, whereas Fusarium and Scedosporium were the main fungal genera in the contaminated soil. At the end of 60-days laboratory scale bioremediation assays, pyrosequencing and DGGE data showed that (i) major bacterial community shifts were caused by the type of mobilizing agent added to the soil and, to a lesser extent, by the addition of lignocellulosic substrate; and (ii) the presence of the non-ionic surfactant (Brij 30) hampered the proliferation of Actinobacteria (Mycobacteriaceae) and Bacteroidetes (Chitinophagaceae) and, in the absence of lignocellulosic substrate, also impeded polycyclic aromatic hydrocarbons (PAHs) degradation. The results show the importance of implementing bioremediation experiments combined with microbiome assessment to gain insight on the effect of crucial parameters (e.g. use of additives) over the potential functions of complex microbial communities harbored in polluted soils, essential for bioremediation success

  10. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Handley, KM [University of California, Berkeley; Verberkmoes, Nathan C [ORNL; Steefel, Carl I [Lawrence Berkeley National Laboratory (LBNL); Sharon, I [University of California, Berkeley; Williams, Ken [Lawrence Berkeley National Laboratory (LBNL); Miller, CS [University of California, Berkeley; Frischkorn, Kyle C [University of California, Berkeley; Chourey, Karuna [ORNL; Thomas, Brian [University of California, Berkeley; Shah, Manesh B [ORNL; Long, Phil [Pacific Northwest National Laboratory (PNNL); Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley

    2013-01-01

    Stimulation of subsurface microorganisms to induce reductive immobilization of metals is a promising approach for bioremediation, yet the overall microbial community response is typically poorly understood. Here we used community proteogenomics to test the hypothesis that excess input of acetate activates syntrophic interactions among autotrophs and heterotrophs. A flow-through sediment column was incubated in a groundwater well of an acetate-amended aquifer. Genomic sequences from the community recovered during microbial sulfate reduction were used to econstruct, de novo, near-complete genomes for Desulfobacter (Deltaproteobacteria) and relatives of Sulfurovum and Sulfurimonas (Epsilonproteobacteria), and Bacteroidetes. Partial genomes were obtained for Clostridiales (Firmicutes) and Desulfuromonadales-like Deltaproteobacteria. The majority of proteins identified by mass spectrometry corresponded to Desulfobacter-like species, and demonstrate the role of this organism in sulfate reduction (Dsr and APS), nitrogen-fixation (Nif) and acetate oxidation to CO2 during amendment. Results suggest less abundant Desulfuromonadales and Bacteroidetes also actively contributed to CO2 production via the TCA cycle. Proteomic data indicate that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfide oxidation (using Nap, Nir, Nos, SQR and Sox), with CO2 fixed using the reverse TCA cycle. Modeling shows that this reaction was thermodynamically possible, and kinetically favorable relative to acetate-dependent denitrification. We conclude that high-levels of carbon amendment aimed to stimulate anaerobic heterotrophy led to carbon fixation in co-dependent chemoautotrophs. These results have implications for understanding complex ecosystem behavior, and show that high levels of organic carbon supplementation can expand the range of microbial functionalities accessible for ecosystem manipulation.

  11. Relationship of Enhanced Butyrate Production by Colonic Butyrate-Producing Bacteria to Immunomodulatory Effects in Normal Mice Fed an Insoluble Fraction of Brassica rapa L.

    Science.gov (United States)

    Tanaka, Sachi; Yamamoto, Kana; Yamada, Kazuki; Furuya, Kanon; Uyeno, Yutaka

    2016-05-01

    This study was performed to determine the effects of feeding a fiber-rich fraction of Brassica vegetables on the immune response through changes in enteric bacteria and short-chain fatty acid (SCFA) production in normal mice. The boiled-water-insoluble fraction of Brassica rapa L. (nozawana), which consists mainly of dietary fiber, was chosen as a test material. A total of 31 male C57BL/6J mice were divided into two groups and housed in a specific-pathogen-free facility. The animals were fed either a control diet or the control diet plus the insoluble B. rapa L. fraction for 2 weeks and sacrificed to determine microbiological and SCFA profiles in lower-gut samples and immunological molecules. rRNA-based quantification indicated that the relative population of Bacteroidetes was markedly lower in the colon samples of the insoluble B. rapa L. fraction-fed group than that in the controls. Populations of the Eubacterium rectale group and Faecalibacterium prausnitzii, both of which are representative butyrate-producing bacteria, doubled after 2 weeks of fraction intake, accompanying a marginal increase in the proportion of colonic butyrate. In addition, feeding with the fraction significantly increased levels of the anti-inflammatory cytokine interleukin-10 (IL-10) and tended to increase splenic regulatory T cell numbers but significantly reduced the population of cells expressing activation markers. We demonstrated that inclusion of the boiled-water-insoluble fraction of B. rapa L. can alter the composition of the gut microbiota to decrease the numbers of Bacteroidetes and to increase the numbers of butyrate-producing bacteria, either of which may be involved in the observed shift in the production of splenic IL-10. PMID:26921420

  12. Distribution of endophytic bacteria in Alopecurus aequalis Sobol and Oxalis corniculata L. from soils contaminated by polycyclic aromatic hydrocarbons.

    Directory of Open Access Journals (Sweden)

    Anping Peng

    Full Text Available The distributions of endophytic bacteria in Alopecurus aequalis Sobol and Oxalis corniculata L. grown in soils contaminated with different levels of polycyclic aromatic hydrocarbons (PAHs were investigated with polymerase chain reaction followed by denaturing gradient gel electrophoresis technology (PCR-DGGE and cultivation methods. Twelve types of PAHs, at concentrations varying from 0.16 to 180 mg·kg(-1, were observed in the roots and shoots of the two plants. The total PAH concentrations in Alopecurus aequalis Sobol obtained from three different PAH-contaminated stations were 184, 197, and 304 mg·kg(-1, and the total PAH concentrations in Oxalis corniculata L. were 251, 346, and 600 mg·kg(-1, respectively. The PCR-DGGE results showed that the endophytic bacterial communities in the roots and shoots of the two plants were quite different, although most bacteria belonged to Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. A total of 68 endophytic bacterial strains were isolated from different tissues of the two plants and classified into three phyla: Firmicutes, Proteobacteria and Bacteroidetes. In both plants, Bacillus spp. and Pseudomonas spp. were the dominant cultivable populations. With an increase in the PAH pollution level, the diversity and distribution of endophytic bacteria in the two plants changed correspondingly, and the number of cultivable endophytic bacterial strains decreased rapidly. Testing of the isolated endophytic bacteria for tolerance to each type of PAH showed that most isolates could grow well on Luria-Bertani media in the presence of different PAHs, and some isolates were able to grow rapidly on a mineral salt medium with a single PAH as the sole carbon and energy source, indicating that these strains may have the potential to degrade PAHs in plants. This research provides the first insight into the characteristics of endophytic bacterial populations under different PAH pollution levels and provides a

  13. Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis)

    Science.gov (United States)

    Gruninger, Robert J.; McAllister, Tim A.; Forster, Robert J.

    2016-01-01

    The North American Beaver (Castor canadensis) is the second largest living rodent and an iconic symbol of Canada. The beaver is a semi-aquatic browser whose diet consists of lignocellulose from a variety of plants. The beaver is a hindgut fermenter and has an enlarged ceacum that houses a complex microbiome. There have been few studies examining the microbial diversity in gastrointestinal tract of hindgut fermenting herbivores. To examine the bacterial and archaeal communities inhabiting the gastrointestinal tract of the beaver, the microbiome of the ceacum and feaces was examined using culture-independent methods. DNA from the microbial community of the ceacum and feaces of 4 adult beavers was extracted, and the16S rRNA gene was sequenced using either bacterial or archaeal specific primers. A total of 1447 and 1435 unique bacterial OTUs were sequenced from the ceacum and feaces, respectively. On average, the majority of OTUs within the ceacum were classified as Bacteroidetes (49.2%) and Firmicutes (47.6%). The feaces was also dominated by OTUs from Bacteroidetes (36.8%) and Firmicutes (58.9%). The composition of bacterial community was not significantly different among animals. The composition of the ceacal and feacal microbiome differed, but this difference is due to changes in the abundance of closely related OTUs, not because of major differences in the taxonomic composition of the communities. Within these communities, known degraders of lignocellulose were identified. In contrast, to the bacterial microbiome, the archaeal community was dominated by a single species of methanogen, Methanosphaera stadtmanae. The data presented here provide the first insight into the microbial community within the hindgut of the beaver. PMID:27227334

  14. The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation

    Directory of Open Access Journals (Sweden)

    Zhou Bai-Cheng

    2010-04-01

    Full Text Available Abstract Background Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes. Results The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins. Conclusion Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.

  15. Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes ▿ †

    Science.gov (United States)

    Will, Christiane; Thürmer, Andrea; Wollherr, Antje; Nacke, Heiko; Herold, Nadine; Schrumpf, Marion; Gutknecht, Jessica; Wubet, Tesfaye; Buscot, François; Daniel, Rolf

    2010-01-01

    The diversity of bacteria in soil is enormous, and soil bacterial communities can vary greatly in structure. Here, we employed a pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to characterize the overall and horizon-specific (A and B horizons) bacterial community compositions in nine grassland soils, which covered three different land use types. The entire data set comprised 752,838 sequences, 600,544 of which could be classified below the domain level. The average number of sequences per horizon was 41,824. The dominant taxonomic groups present in all samples and horizons were the Acidobacteria, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes. Despite these overarching dominant taxa, the abundance, diversity, and composition of bacterial communities were horizon specific. In almost all cases, the estimated bacterial diversity (H′) was higher in the A horizons than in the corresponding B horizons. In addition, the H′ was positively correlated with the organic carbon content, the total nitrogen content, and the C-to-N ratio, which decreased with soil depth. It appeared that lower land use intensity results in higher bacterial diversity. The majority of sequences affiliated with the Actinobacteria, Bacteroidetes, Cyanobacteria, Fibrobacteres, Firmicutes, Spirochaetes, Verrucomicrobia, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were derived from A horizons, whereas the majority of the sequences related to Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospira, TM7, and WS3 originated from B horizons. The distribution of some bacterial phylogenetic groups and subgroups in the different horizons correlated with soil properties such as organic carbon content, total nitrogen content, or microbial biomass. PMID:20729324

  16. Novel gut-based pharmacology of metformin in patients with type 2 diabetes mellitus.

    Directory of Open Access Journals (Sweden)

    Antonella Napolitano

    Full Text Available Metformin, a biguanide derivate, has pleiotropic effects beyond glucose reduction, including improvement of lipid profiles and lowering microvascular and macrovascular complications associated with type 2 diabetes mellitus (T2DM. These effects have been ascribed to adenosine monophosphate-activated protein kinase (AMPK activation in the liver and skeletal muscle. However, metformin effects are not attenuated when AMPK is knocked out and intravenous metformin is less effective than oral medication, raising the possibility of important gut pharmacology. We hypothesized that the pharmacology of metformin includes alteration of bile acid recirculation and gut microbiota resulting in enhanced enteroendocrine hormone secretion. In this study we evaluated T2DM subjects on and off metformin monotherapy to characterize the gut-based mechanisms of metformin. Subjects were studied at 4 time points: (i at baseline on metformin, (ii 7 days after stopping metformin, (iii when fasting blood glucose (FBG had risen by 25% after stopping metformin, and (iv when FBG returned to baseline levels after restarting the metformin. At these timepoints we profiled glucose, insulin, gut hormones (glucagon-like peptide-1 (GLP-1, peptide tyrosine-tyrosine (PYY and glucose-dependent insulinotropic peptide (GIP and bile acids in blood, as well as duodenal and faecal bile acids and gut microbiota. We found that metformin withdrawal was associated with a reduction of active and total GLP-1 and elevation of serum bile acids, especially cholic acid and its conjugates. These effects reversed when metformin was restarted. Effects on circulating PYY were more modest, while GIP changes were negligible. Microbiota abundance of the phylum Firmicutes was positively correlated with changes in cholic acid and conjugates, while Bacteroidetes abundance was negatively correlated. Firmicutes and Bacteroidetes representation were also correlated with levels of serum PYY. Our study suggests that

  17. Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania

    Science.gov (United States)

    Coman, Cristian; Chiriac, Cecilia M.; Robeson, Michael S.; Ionescu, Corina; Dragos, Nicolae; Barbu-Tudoran, Lucian; Andrei, Adrian-Ştefan; Banciu, Horia L.; Sicora, Cosmin; Podar, Mircea

    2015-01-01

    Modern mineral deposits play an important role in evolutionary studies by providing clues to the formation of ancient lithified microbial communities. Here we report the presence of microbialite-forming microbial mats in different microenvironments at 32°C, 49°C, and 65°C around the geothermal spring from an abandoned oil drill in Ciocaia, Romania. The mineralogy and the macro- and microstructure of the microbialites were investigated, together with their microbial diversity based on a 16S rRNA gene amplicon sequencing approach. The calcium carbonate is deposited mainly in the form of calcite. At 32°C and 49°C, the microbialites show a laminated structure with visible microbial mat-carbonate crystal interactions. At 65°C, the mineral deposit is clotted, without obvious organic residues. Partial 16S rRNA gene amplicon sequencing showed that the relative abundance of the phylum Archaea was low at 32°C (1%. The dominant bacterial groups at 32°C were Cyanobacteria, Gammaproteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Thermi, Actinobacteria, Planctomycetes, and Defferibacteres. At 49°C, there was a striking dominance of the Gammaproteobacteria, followed by Firmicutes, Bacteroidetes, and Armantimonadetes. The 65°C sample was dominated by Betaproteobacteria, Firmicutes, [OP1], Defferibacteres, Thermi, Thermotogae, [EM3], and Nitrospirae. Several groups from Proteobacteria and Firmicutes, together with Halobacteria and Melainabacteria were described for the first time in calcium carbonate deposits. Overall, the spring from Ciocaia emerges as a valuable site to probe microbes-minerals interrelationships along thermal and geochemical gradients. PMID:25870594

  18. Metabolic responses of novel cellulolytic and saccharolytic agricultural soil Bacteria to oxygen.

    Science.gov (United States)

    Schellenberger, Stefanie; Kolb, Steffen; Drake, Harold L

    2010-04-01

    Cellulose is the most abundant biopolymer in terrestrial ecosystems and is degraded by microbial communities in soils. However, relatively little is known about the diversity and function of soil prokaryotes that might participate in the overall degradation of this biopolymer. The active cellulolytic and saccharolytic Bacteria in an agricultural soil were evaluated by 16S rRNA (13)C-based stable isotope probing. Cellulose, cellobiose and glucose were mineralized under oxic conditions in soil slurries to carbon dioxide. Under anoxic conditions, these substrates were converted primarily to acetate, butyrate, carbon dioxide, hydrogen and traces of propionate and iso-butyrate; the production of these fermentation end-products was concomitant with the apparent reduction of iron(III). [(13)C]-cellulose was mainly degraded under oxic conditions by novel family-level taxa of the Bacteroidetes and Chloroflexi, and a known family-level taxon of Planctomycetes, whereas degradation under anoxic conditions was facilitated by the Kineosporiaceae (Actinobacteria) and cluster III Clostridiaceae and novel clusters within Bacteroidetes. Active aerobic sub-communities in oxic [(13)C]-cellobiose and [(13)C]-glucose treatments were dominated by Intrasporangiaceae and Micrococcaceae (Actinobacteria) whereas active cluster I Clostridiaceae (Firmicutes) were prevalent in anoxic treatments. A very large number (i.e. 28) of the detected taxa did not closely affiliate with known families, and active Archaea were not detected in any of the treatments. These collective findings suggest that: (i) a large uncultured diversity of soil Bacteria was involved in the utilization of cellulose and products of its hydrolysis, (ii) the active saccharolytic community differed phylogenetically from the active cellulolytic community, (iii) oxygen availability impacted differentially on the activity of taxa and (iv) different redox guilds (e.g. fermenters and iron reducers) compete or interact during

  19. Microbial characterization of microbial ecosystems associated to evaporites domes of gypsum in Salar de Llamara in Atacama desert.

    Science.gov (United States)

    Rasuk, Maria Cecilia; Kurth, Daniel; Flores, Maria Regina; Contreras, Manuel; Novoa, Fernando; Poire, Daniel; Farias, Maria Eugenia

    2014-10-01

    The Central Andes in northern Chile contains a large number of closed basins whose central depression is occupied by saline lakes and salt crusts (salars). One of these basins is Salar de Llamara (850 m a.s.l.), where large domed structures of seemingly evaporitic origin forming domes can be found. In this work, we performed a detailed microbial characterization of these domes. Mineralogical studies revealed gypsum (CaSO(4)) as a major component. Microbial communities associated to these structures were analysed by 454 16S rDNA amplicon sequencing and compared between winter and summer seasons. Bacteroidetes Proteobacteria and Planctomycetes remained as the main phylogenetic groups, an increased diversity was found in winter. Comparison of the upper air-exposed part and the lower water-submerged part of the domes in both seasons showed little variation in the upper zone, showing a predominance of Chromatiales (Gammaproteobacteria), Rhodospirillales (Alphaproteobacteria), and Sphingobacteriales (Bacteroidetes). However, the submerged part showed marked differences between seasons, being dominated by Proteobacteria (Alpha and Gamma) and Verrucomicrobia in summer, but with more diverse phyla found in winter. Even though not abundant by sequence, Cyanobacteria were visually identified by scanning electron microscopy (SEM), which also revealed the presence of diatoms. Photosynthetic pigments were detected by high-performance liquid chromatography, being more diverse on the upper photosynthetic layer. Finally, the system was compared with other endoevaporite, mats microbialite and Stromatolites microbial ecosystems, showing higher similitude with evaporitic ecosystems from Atacama and Guerrero Negro. This environment is of special interest for extremophile studies because microbial life develops associated to minerals in the driest desert all over the world. Nevertheless, it is endangered by mining activity associated to copper and lithium extraction; thus, its

  20. Diversified microbiota of meconium is affected by maternal diabetes status.

    Directory of Open Access Journals (Sweden)

    Jianzhong Hu

    Full Text Available This study was aimed to assess the diversity of the meconium microbiome and determine if the bacterial community is affected by maternal diabetes status.The first intestinal discharge (meconium was collected from 23 newborns stratified by maternal diabetes status: 4 mothers had pre-gestational type 2 diabetes mellitus (DM including one mother with dizygotic twins, 5 developed gestational diabetes mellitus (GDM and 13 had no diabetes. The meconium microbiome was profiled using multi-barcode 16S rRNA sequencing followed by taxonomic assignment and diversity analysis.All meconium samples were not sterile and contained diversified microbiota. Compared with adult feces, the meconium showed a lower species diversity, higher sample-to-sample variation, and enrichment of Proteobacteria and reduction of Bacteroidetes. Among the meconium samples, the taxonomy analyses suggested that the overall bacterial content significantly differed by maternal diabetes status, with the microbiome of the DM group showing higher alpha-diversity than that of no-diabetes or GDM groups. No global difference was found between babies delivered vaginally versus via Cesarean-section. Regression analysis showed that the most robust predictor for the meconium microbiota composition was the maternal diabetes status that preceded pregnancy. Specifically, Bacteroidetes (phyla and Parabacteriodes (genus were enriched in the meconium in the DM group compared to the no-diabetes group.Our study provides evidence that meconium contains diversified microbiota and is not affected by the mode of delivery. It also suggests that the meconium microbiome of infants born to mothers with DM is enriched for the same bacterial taxa as those reported in the fecal microbiome of adult DM patients.

  1. TCDD modulation of gut microbiome correlated with liver and immune toxicity in streptozotocin (STZ)-induced hyperglycemic mice.

    Science.gov (United States)

    Lefever, Daniel E; Xu, Joella; Chen, Yingjia; Huang, Guannan; Tamas, Nagy; Guo, Tai L

    2016-08-01

    An increasing body of evidence has shown the important role of the gut microbiome in mediating toxicity following environmental contaminant exposure. The goal of this study was to determine if the adverse metabolic effects of chronic 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure would be sufficient to exacerbate hyperglycemia, and to further determine if these outcomes were attributable to the gut microbiota alteration. Adult male CD-1 mice were exposed to TCDD (6μg/kg body weight biweekly) by gavage and injected (i.p.) with STZ (4×50mg/kg body weight) to induced hyperglycemia. 16S rRNA sequencing was used to characterize the changes in the microbiome community composition. Glucose monitoring, flow cytometry, histopathology, and organ characterization were performed to determine the deleterious phenotypic changes of TCDD exposure. Chronic TCDD treatment did not appear to exacerbate STZ-induced hyperglycemia as blood glucose levels were slightly reduced in the TCDD treated mice; however, polydipsia and polyphagia were observed. Importantly, TCDD exposure caused a dramatic change in microbiota structure, as characterized at the phylum level by increasing Firmicutes and decreasing Bacteroidetes while at the family level most notably by increasing Lactobacillaceae and Desulfovibrionaceae, and decreasing Prevotellaceae and ACK M1. The changes in microbiota were further found to be broadly associated with phenotypic changes seen from chronic TCDD treatment. In particular, the phylum level Bacteroidetes to Firmicutes ratio negatively correlated with both liver weight and liver pathology, and positively associated with %CD3(+)NK(+) T cells, a key mediator of host-microbial interactions. Collectively, these findings suggest that the dysregulated gut microbiome may contribute to the deleterious effects (e.g., liver toxicity) seen with TCDD exposure. PMID:27221631

  2. Impact of water quality on bacterioplankton assemblage along Cértima River Basin (central western Portugal) assessed by PCR-DGGE and multivariate analysis.

    Science.gov (United States)

    de Figueiredo, Daniela R; Ferreira, Raquel V; Cerqueira, Mário; de Melo, Teresa Condesso; Pereira, Mário J; Castro, Bruno B; Correia, António

    2012-01-01

    The information on bacterial community composition (BCC) in Portuguese water bodies is very scarce. Cértima River (central western Portugal) is known to have high levels of pollution, namely organic. In the present work, the BCC from a set of 16 water samples collected from Cértima River Basin and its main tributaries was characterized using 16S rDNA-denaturing gradient gel electrophoresis, a culture-independent molecular approach. Molecular data were related to environmental parameters through multivariate analysis to investigate potential impact of water pollution along the river. Principal component analysis using environmental data showed a water quality gradient from more pristine waters (at the mountain tributaries) to waters with increasingly eutrophic potential (such as Fermentelos Lake). This gradient was mainly defined by factors such as organic and inorganic nutrient sources, electrical conductivity, hydrogen carbonate concentration, and pH. Molecular results showed variations in BCC along Cértima River Basin but in the main river section, a Bacteroidetes phylotype (Flavobacterium sp.) proved to be dominant throughout the river course. Multivariate analysis suggests that spatial variation of BCC along the Cértima River Basin depended mainly on parameters such as Chl a, total suspended solid (TSS), total organic carbon, electrical conductivity, and HCO[Formula: see text] levels. Bacteroidetes phylotypes were all related to higher electrical conductivity and HCO[Formula: see text] levels although some of these were also correlated with high SO[Formula: see text] and others with high soluble reactive phosphorus, nitrate, TN, and Kjeld-N levels. The Gammaproteobacteria occurrence was correlated with high SO[Formula: see text] levels. One of the Betaproteobacteria phylotypes showed to correlate with low redox potential (E(h)) and high temperature, pH, TSS, and Chl a levels while another one showed a negative correlation with Chl a values. PMID:21431313

  3. Low temperature geomicrobiology follows host rock composition along a geochemical gradient in Lau Basin

    Directory of Open Access Journals (Sweden)

    JasonBSylvan

    2013-03-01

    Full Text Available The East Lau Spreading Center (ELSC and Valu Fa Ridge (VFR comprise a ridge segment in the southwest Pacific Ocean where rapid transitions in the underlying mantle chemistry manifest themselves as gradients in seafloor rock geochemistry. We studied the geology and microbial diversity of three silicate rock samples and three inactive sulfide chimney samples collected, from north to south, at the vent fields Kilo Moana, ABE, Tui Malila and Mariner. This is the first study of microbial populations on basaltic andesite, which was sampled at Mariner vent field. Silicate rock geochemistry exhibits clear latitudinal trends that are mirrored by changes in bacterial community composition. α-proteobacteria, ε-proteobacteria and Bacteroidetes are most common on a silicate collected from Kilo Moana and their proportions decrease linearly on silicates collected further south. Conversely, a silicate from Mariner vent field hosts high proportions of a unique lineage of Chloroflexi unrelated (<90% sequence similarity to previously recovered environmental clones or isolates, which decrease at ABE and are absent at Kilo Moana. The exteriors of inactive sulfide structures are dominated by lineages of sulfur oxidizing α-proteobacteria, γ-proteobacteria and ε-proteobacteria while the interior of one chimney is dominated by putative sulfur-reducing δ-proteobacteria. A comparison of bacterial communities on inactive sulfides from this and previous studies reveals the presence of a clade of uncultured Bacteroidetes exclusive to sulfidic environments, and a high degree of heterogeneity in bacterial community composition from one sulfide structure to another. In light of the heterogeneous nature of bacterial communities observed here and in previous studies of both active and inactive hydrothermal sulfide structures, the presence of numerous niches may be detected on these structures in the future by finer scale sampling and analysis.

  4. Screening and degrading characteristics and community structure of a high molecular weight polycyclic aromatic hydrocarbon-degrading bacterial consortium from contaminated soil

    Institute of Scientific and Technical Information of China (English)

    Run Sun; Jinghua Jin; Guangdong Sun; Ying Liu; Zhipei Liu

    2010-01-01

    Inoculation with efficient microbes had been proved to be the most important way for the bioremediation of polluted environments.For the treatment of abandoned site of Beijing Coking Chemical Plant contaminated with high level of high-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs),a bacterial consortium capable of degrading HMW-PAHs,designated 1-18-1,was enriched and screened from HMW-PAHs contaminated soil.Its degrading ability was analyzed by high performance liquid chromatography (HPLC),and the community structure was investigated by construction and analyses of the 16S rRNA gene clone libraries (A,B and F) at different transfers.The results indicated that 1-18-1 was able to utilize pyrene,fluoranthene and benzo[a]pyrene as sole carbon and energy source for growth.The degradation rate of pyrene and fluoranthene reached 82.8% and 96.2% after incubation for 8 days at 30℃,respectively;while the degradation rate of benzo[a]pyrene was only 65.1% after incubation for 28 days at 30℃.Totally,108,100 and 100 valid clones were randomly selected and sequenced from the libraries A,B,and E Phylogenetic analyses showed that all the clones could be divided into 5 groups,Bacteroidetes,α-Proteobacteria,Actinobacteria,β-Proteobacteria and γ-Proteobacteria.Sequence similarity analyses showed total 39 operational taxonomic units (OTUs) in the libraries.The predominant bacterial groups were α-Proteobacteria (19 OTUs,48.7%),γ-Proteobacteria (9 OTUs,23.1%) and β-Protcobacteria (8 OTUs,20.5%).During the transfer process,the proportions of α-Proteobacteria and β-Proteobacteria increased greatly (from 47% to 93%),while γ-Proteobacteria decreased from 32% (library A) to 6% (library F);and Bacteroidetes group disappeared in libraries B and F.

  5. Faecal microbiome in new-onset juvenile idiopathic arthritis.

    Science.gov (United States)

    Tejesvi, M V; Arvonen, M; Kangas, S M; Keskitalo, P L; Pirttilä, A M; Karttunen, T J; Vähäsalo, P

    2016-03-01

    Alterations in the intestinal microbial flora have been linked with autoimmune diseases. Our objective was to analyse the composition of the faecal microbiome of children with new-onset juvenile idiopathic arthritis (JIA) compared to healthy controls, and to identify specific gut bacteria associated with JIA. Stool samples from patients were taken at the time of diagnosis of JIA. The microbiome profiles of samples of 30 children with JIA (mean age 6.2 years, 22 girls) were analysed with 16S region-based sequencing profiling and compared to the stool samples of healthy controls (n = 27, mean age 5.4 years, 18 girls). The proportion of bacteria belonging to the phylum Firmicutes was significantly lower in children with JIA [21 % (95 % confident interval [CI]: 17-25 %)] compared to controls [33 % (95 % CI: 26-41 %), p = 0.009]. Bacteria belonging to Bacteroidetes were significantly more abundant in JIA [78 % (95 % CI: 74-82 %)] than in control samples [65 % (95 % CI: 57-73 %), p = 0.008]. Shared operational taxonomic units (OTUs) between the groups revealed that genera Actinobacteria and Fusobacteria were present only in JIA patients and Lentisphaerae only in controls. In summary, faecal flora in JIA is characterised by a low level of Firmicutes and an abundance of Bacteroidetes, resembling the aberration reported in type 1 diabetes. We suggest that alterations in the intestinal microbial flora may challenge the mucosal immune system of genetically susceptible subjects predisposing to local proinflammatory cascades, thus contributing to the development of JIA. PMID:26718942

  6. Identifying the microbial communities and operational conditions for optimized wastewater treatment in microbial fuel cells.

    Science.gov (United States)

    Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M; Wu, Angela; Yamanaka, Yuko; Nealson, Kenneth H; Bretschger, Orianna

    2013-12-01

    Microbial fuel cells (MFCs) are devices that exploit microorganisms as "biocatalysts" to recover energy from organic matter in the form of electricity. MFCs have been explored as possible energy neutral wastewater treatment systems; however, fundamental knowledge is still required about how MFC-associated microbial communities are affected by different operational conditions and can be optimized for accelerated wastewater treatment rates. In this study, we explored how electricity-generating microbial biofilms were established at MFC anodes and responded to three different operational conditions during wastewater treatment: 1) MFC operation using a 750 Ω external resistor (0.3 mA current production); 2) set-potential (SP) operation with the anode electrode potentiostatically controlled to +100 mV vs SHE (4.0 mA current production); and 3) open circuit (OC) operation (zero current generation). For all reactors, primary clarifier effluent collected from a municipal wastewater plant was used as the sole carbon and microbial source. Batch operation demonstrated nearly complete organic matter consumption after a residence time of 8-12 days for the MFC condition, 4-6 days for the SP condition, and 15-20 days for the OC condition. These results indicate that higher current generation accelerates organic matter degradation during MFC wastewater treatment. The microbial community analysis was conducted for the three reactors using 16S rRNA gene sequencing. Although the inoculated wastewater was dominated by members of Epsilonproteobacteria, Gammaproteobacteria, and Bacteroidetes species, the electricity-generating biofilms in MFC and SP reactors were dominated by Deltaproteobacteria and Bacteroidetes. Within Deltaproteobacteria, phylotypes classified to family Desulfobulbaceae and Geobacteraceae increased significantly under the SP condition with higher current generation; however those phylotypes were not found in the OC reactor. These analyses suggest that species

  7. Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252)

    KAUST Repository

    Koo, Hyunmin

    2014-09-10

    The indigenous bacterial communities in sediment microcosms from Dauphin Island (DI), Petit Bois Island (PB) and Perdido Pass (PP) of the coastal Gulf of Mexico were compared following treatment with Macondo oil (MC252) using pyrosequencing and culture-based approaches. After quality-based trimming, 28,991 partial 16S rRNA sequence reads were analyzed by rarefaction, confirming that analyses of bacterial communities were saturated with respect to species diversity. Changes in the relative abundances of Proteobacteria, Bacteroidetes and Firmicutes played an important role in structuring bacterial communities in oil-treated sediments. Proteobacteria were dominant in oil-treated samples, whereas Firmicutes and Bacteroidetes were either the second or the third most abundant taxa. Tenericutes, members of which are known for oil biodegradation, were detected shortly after treatment, and continued to increase in DI and PP sediments. Multivariate statistical analyses (ADONIS) revealed significant dissimilarity of bacterial communities between oil-treated and untreated samples and among locations. In addition, a similarity percentage analysis showed the contribution of each species to the contrast between untreated and oil-treated samples. PCR amplification using DNA from pure cultures of Exiguobacterium,  Pseudoalteromonas,  Halomonas and Dyadobacter, isolated from oil-treated microcosm sediments, produced amplicons similar to polycyclic aromatic hydrocarbon-degrading genes. In the context of the 2010 Macondo blowout, the results from our study demonstrated that the indigenous bacterial communities in coastal Gulf of Mexico sediment microcosms responded to the MC252 oil with altered community structure and species composition. The rapid proliferation of hydrocarbonoclastic bacteria suggests their involvement in the degradation of the spilt oil in the Gulf of Mexico ecosystem.

  8. Comparative fecal metagenomics unveils unique functional capacity of the swine gut

    Directory of Open Access Journals (Sweden)

    Martinson John

    2011-05-01

    Full Text Available Abstract Background Uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health as well as to food and water safety due to the presence of human pathogens in pig feces. Nonetheless, limited information on the functional diversity of the swine gut microbiome is available. Results Analysis of 637, 722 pyrosequencing reads (130 megabases generated from Yorkshire pig fecal DNA extracts was performed to help better understand the microbial diversity and largely unknown functional capacity of the swine gut microbiome. Swine fecal metagenomic sequences were annotated using both MG-RAST and JGI IMG/M-ER pipelines. Taxonomic analysis of metagenomic reads indicated that swine fecal microbiomes were dominated by Firmicutes and Bacteroidetes phyla. At a finer phylogenetic resolution, Prevotella spp. dominated the swine fecal metagenome, while some genes associated with Treponema and Anareovibrio species were found to be exclusively within the pig fecal metagenomic sequences analyzed. Functional analysis revealed that carbohydrate metabolism was the most abundant SEED subsystem, representing 13% of the swine metagenome. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Virulence factors associated with antibiotic resistance genes with highest sequence homology to genes in Bacteroidetes, Clostridia, and Methanosarcina were numerous within the gene families unique to the swine fecal metagenomes. Other abundant proteins unique to the distal swine gut shared high sequence homology to putative carbohydrate membrane transporters. Conclusions The results from this metagenomic survey demonstrated the presence of genes associated with resistance to antibiotics and carbohydrate metabolism suggesting that the swine gut microbiome may be shaped by husbandry practices.

  9. Impact of solar radiation on bacterioplankton in Laguna Vilama, a hypersaline Andean lake (4650 m)

    Science.gov (United States)

    FaríAs, MaríA. Eugenia; FernáNdez-Zenoff, Verónica; Flores, Regina; OrdóñEz, Omar; EstéVez, Cristina

    2009-06-01

    Laguna Vilama is a hypersaline Lake located at 4660 m altitude in the northwest of Argentina high up in the Andean Puna. The impact of ultraviolet (UV) radiation on bacterioplankton was studied by collecting samples at different times of the day. Molecular analysis (DGGE) showed that the bacterioplankton community is characterized by Gamma-proteobacteria (Halomonas sp., Marinobacter sp.), Alpha-proteobacteria (Roseobacter sp.), HGC (Agrococcus jenensis and an uncultured bacterium), and CFB (uncultured Bacteroidetes). During the day, minor modifications in bacterial diversity such as intensification of Bacteroidetes' signal and an emergence of Gamma-proteobacteria (Marinobacter flavimaris) were observed after solar exposure. DNA damage, measured as an accumulation of Cyclobutane Pyrimidine Dimers (CPDs), in bacterioplankton and naked DNA increased from 100 CPDs MB-1 at 1200 local time (LT) to 300 CPDs MB-1 at 1600 LT, and from 80 CPDs MB-1 at 1200 LT to 640 CPDs MB-1 at 1600 LT, respectively. In addition, pure cultures of Pseudomonas sp. V1 and Brachybacterium sp. V5, two bacteria previously isolated from this environment, were exposed simultaneously with the community, and viability of both strains diminished after solar exposure. No CPD accumulation was observed in either of the exposed cultures, but an increase in mutagenesis was detected in V5. Of both strains only Brachybacterium sp. V5 showed CPD accumulation in naked DNA. These results suggest that the bacterioplankton community is well adapted to this highly solar irradiated environment showing little accumulation of CPDs and few changes in the community composition. They also demonstrate that these microorganisms contain efficient mechanisms against UV damage.

  10. Marine microbial community response to inorganic and organic sediment amendments in laboratory mesocosms.

    Science.gov (United States)

    Kan, Jinjun; Wang, Yanbing; Obraztsova, Anna; Rosen, Gunther; Leather, James; Scheckel, Kirk G; Nealson, Kenneth H; Arias-Thode, Y Meriah

    2011-10-01

    Sediment amendments provide promising strategies of enhancing sequestration of heavy metals and degradation of organic contaminants. The impacts of sediment amendments for metal and organic remediation including apatite, organoclay (and apatite and organoclay in geotextile mats), acetate, and chitin on environmental microbial communities in overlying water and sediment profiles are reported here. These experiments were performed concurrent with an ecotoxicity evaluation (data submitted in companion paper) and X-ray absorption spectroscopy of zinc speciation post apatite amendments. X-ray absorption spectra showed that a modest modification of zinc speciation occurred in amended treatments. Significant changes in both bacterial cell densities and populations were observed in response to amendments of apatite+organoclay, chitin, and acetate. The enriched bacteria and breakdown of these amendments were likely attributed to water quality degradation (e.g. ammonia and dissolved oxygen). Molecular fingerprints of bacterial communities by denaturant gradient gel electrophoresis (DGGE) showed that distinct bacterial populations occurred in overlying waters from different amendments: apatite+organoclay led to the dominance of Gammaproteobacteria, acetate enriched Alphaproteobacteria, and chitin treatment led to a dominance of Bacteroidetes and Alphaproteobacteria. In amended sediments, Firmicutes, Bacteroidetes, and Deltaproteobacteria (Desulfovibrio) were commonly found with chitin and apatite+chitin treatments. Finally, sulfate-reducing bacteria (e.g. Desulfovibrio) and metal-reducing bacteria were also recovered with most probable number (MPN) analyses in treatments with acetate, chitin, and apatite+chitin. These geochemically important bacteria were stimulated by amendments and may play critical functional roles in the metal and organic contaminant remediation process for future investigations of contaminated sediments. PMID:21784523

  11. Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing.

    Directory of Open Access Journals (Sweden)

    Changin Oh

    Full Text Available The oral microbiome, which is closely associated with many diseases, and the resident pathogenic oral bacteria, which can be transferred by close physical contact, are important public health considerations. Although the dog is the most common companion animal, the composition of the canine oral microbiome, which may include human pathogenic bacteria, and its relationship with that of their owners are unclear. In this study, 16S rDNA pyrosequencing was used to compare the oral microbiomes of 10 dogs and their owners and to identify zoonotic pathogens. Pyrosequencing revealed 246 operational taxonomic units in the 10 samples, representing 57 genera from eight bacterial phyla. Firmicutes (57.6%, Proteobacteria (21.6%, Bacteroidetes (9.8%, Actinobacteria (7.1%, and Fusobacteria (3.9% were the predominant phyla in the human oral samples, whereas Proteobacteria (25.7%, Actinobacteria (21%, Bacteroidetes (19.7%, Firmicutes (19.3%, and Fusobacteria (12.3% were predominant in the canine oral samples. The predominant genera in the human samples were Streptococcus (43.9%, Neisseria (10.3%, Haemophilus (9.6%, Prevotella (8.4%, and Veillonella (8.1%, whereas the predominant genera in the canine samples were Actinomyces (17.2%, Unknown (16.8, Porphyromonas (14.8, Fusobacterium (11.8, and Neisseria (7.2%. The oral microbiomes of dogs and their owners were appreciably different, and similarity in the microbiomes of canines and their owners was not correlated with residing in the same household. Oral-to-oral transfer of Neisseria shayeganii, Porphyromonas canigingivalis, Tannerella forsythia, and Streptococcus minor from dogs to humans was suspected. The finding of potentially zoonotic and periodontopathic bacteria in the canine oral microbiome may be a public health concern.

  12. Abundant intergenic TAACTGA direct repeats and putative alternate RNA polymerase β´ subunits in marine Beggiatoaceae genomes: possible regulatory roles and origins

    Directory of Open Access Journals (Sweden)

    Barbara J. MacGregor

    2015-12-01

    Full Text Available The genome sequences of several giant marine sulfur-oxidizing bacteria present evidence of a possible post-transcriptional regulatory network that may have been transmitted to or from two distantly related bacteria lineages. The draft genome of a Cand. Maribeggiatoa filament from the Guaymas Basin (Gulf of California, Mexico seafloor contains 169 sets of TAACTGA direct repeats and one indirect repeat, with two to six copies per set. Related heptamers are rarely or never found as direct repeats. TAACTGA direct repeats are also found in some other Beggiatoaceae, Thiocystis violascens, a range of Cyanobacteria, and five Bacteroidetes. This phylogenetic distribution suggests they may have been transmitted horizontally, but no mechanism is evident. There is no correlation between total TAACTGA occurrences and repeats per genome. In most species the repeat units are relatively short, but longer arrays of up to 43 copies are found in several Bacteroidetes and Cyanobacteria. The majority of TAACTGA repeats in the Cand. Maribeggiatoa Orange Guaymas (BOGUAY genome are within several nucleotides upstream of a putative start codon, suggesting they may be binding sites for a post-transcriptional regulator. Candidates include members of the ribosomal protein S1, Csp (cold shock protein, and Csr (carbon storage regulator families. No pattern was evident in the predicted functions of the open reading frames (ORFs downstream of repeats, but some encode presumably essential products such as ribosomal proteins. Among these is an ORF encoding a possible alternate or modified RNA polymerase beta prime subunit, predicted to have the expected subunit interaction domains but lacking most catalytic residues. A similar ORF was found in the Thioploca ingrica draft genome, but in no others. In both species they are immediately upstream of putative sensor kinase genes with nearly identical domain structures. In the marine Beggiatoaceae, a role for the TAACTGA repeats in

  13. Abundant Intergenic TAACTGA Direct Repeats and Putative Alternate RNA Polymerase β' Subunits in Marine Beggiatoaceae Genomes: Possible Regulatory Roles and Origins.

    Science.gov (United States)

    MacGregor, Barbara J

    2015-01-01

    The genome sequences of several giant marine sulfur-oxidizing bacteria present evidence of a possible post-transcriptional regulatory network that may have been transmitted to or from two distantly related bacteria lineages. The draft genome of a Cand. "Maribeggiatoa" filament from the Guaymas Basin (Gulf of California, Mexico) seafloor contains 169 sets of TAACTGA direct repeats and one indirect repeat, with two to six copies per set. Related heptamers are rarely or never found as direct repeats. TAACTGA direct repeats are also found in some other Beggiatoaceae, Thiocystis violascens, a range of Cyanobacteria, and five Bacteroidetes. This phylogenetic distribution suggests they may have been transmitted horizontally, but no mechanism is evident. There is no correlation between total TAACTGA occurrences and repeats per genome. In most species the repeat units are relatively short, but longer arrays of up to 43 copies are found in several Bacteroidetes and Cyanobacteria. The majority of TAACTGA repeats in the Cand. "Maribeggiatoa" Orange Guaymas (BOGUAY) genome are within several nucleotides upstream of a putative start codon, suggesting they may be binding sites for a post-transcriptional regulator. Candidates include members of the ribosomal protein S1, Csp (cold shock protein), and Csr (carbon storage regulator) families. No pattern was evident in the predicted functions of the open reading frames (ORFs) downstream of repeats, but some encode presumably essential products such as ribosomal proteins. Among these is an ORF encoding a possible alternate or modified RNA polymerase beta prime subunit, predicted to have the expected subunit interaction domains but lacking most catalytic residues. A similar ORF was found in the Thioploca ingrica draft genome, but in no others. In both species they are immediately upstream of putative sensor kinase genes with nearly identical domain structures. In the marine Beggiatoaceae, a role for the TAACTGA repeats in translational

  14. Diversity of the bacterial community in the rice rhizosphere managed under conventional and no-tillage practices.

    Science.gov (United States)

    Aslam, Zubair; Yasir, Muhammad; Yoon, Hwan Sik; Jeon, Che Ok; Chung, Young Ryun

    2013-12-01

    Bacterial diversity in the rice rhizosphere at different rice growth stages, managed under conventional and no-tillage practices, was explored using a culture-based approach. Actinobacteria are among the bacterial phyla abundant in the rice rhizosphere. Their diversity was further examined by constructing metagenomic libraries based on the 16S rRNA gene, using actinobacterial- and streptomycete-specific polymerase chain reaction (PCR) primers. The study included 132 culturable strains and 125 clones from the 16S rRNA gene libraries. In conventional tillage, there were 38% Proteobacteria, 22% Actinobacteria, 33% Firmicutes, 5% Bacteroidetes, and 2% Acidobacteria, whereas with no-tillage management there were 63% Proteobacteria, 24% Actinobacteria, 6% Firmicutes, and 8% Bacteroidetes as estimated using the culture-dependent method during the four stages of rice cultivation. Principal coordinates analysis was used to cluster the bacterial communities along axes of maximal variance. The different growth stages of rice appeared to influence the rhizosphere bacterial profile for both cultivation practices. Novel clones with low similarities (89-97%) to Actinobacteria and Streptomyces were retrieved from both rice fields by screening the 16S rRNA gene libraries using actinobacterial- and streptomycete-specific primers. By comparing the actinobacterial community retrieved by culture-dependent and molecular methods, it was clear that a more comprehensive assessment of microbial diversity in the rice rhizosphere can be obtained using a combination of both techniques than by using either method alone. We also succeeded in culturing a number of bacteria that were previously described as unculturable. These were in a phylogenetically deep lineage when compared with related cultivable genera. PMID:24385351

  15. High-intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity.

    Science.gov (United States)

    Denou, Emmanuel; Marcinko, Katarina; Surette, Michael G; Steinberg, Gregory R; Schertzer, Jonathan D

    2016-06-01

    Diet and exercise underpin the risk of obesity-related metabolic disease. Diet alters the gut microbiota, which contributes to aspects of metabolic disease during obesity. Repeated exercise provides metabolic benefits during obesity. We assessed whether exercise could oppose changes in the taxonomic and predicted metagenomic characteristics of the gut microbiota during diet-induced obesity. We hypothesized that high-intensity interval training (HIIT) would counteract high-fat diet (HFD)-induced changes in the microbiota without altering obesity in mice. Compared with chow-fed mice, an obesity-causing HFD decreased the Bacteroidetes-to-Firmicutes ratio and decreased the genetic capacity in the fecal microbiota for metabolic pathways such as the tricarboxylic acid (TCA) cycle. After HFD-induced obesity was established, a subset of mice were HIIT for 6 wk, which increased host aerobic capacity but did not alter body or adipose tissue mass. The effects of exercise training on the microbiota were gut segment dependent and more extensive in the distal gut. HIIT increased the alpha diversity and Bacteroidetes/Firmicutes ratio of the distal gut and fecal microbiota during diet-induced obesity. Exercise training increased the predicted genetic capacity related to the TCA cycle among other aspects of metabolism. Strikingly, the same microbial metabolism indexes that were increased by exercise were all decreased in HFD-fed vs. chow diet-fed mice. Therefore, exercise training directly opposed some of the obesity-related changes in gut microbiota, including lower metagenomic indexes of metabolism. Some host and microbial pathways appeared similarly affected by exercise. These exercise- and diet-induced microbiota interactions can be captured in feces. PMID:27117007

  16. Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

    Science.gov (United States)

    Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

    2016-10-01

    Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (P<0.001) higher in all water samples than sediment, where as Acidobacteria and Actinobacteria where significantly higher (P<0.05) in all the sediment samples than surface water. Overall results, using the β diversity measures, coupled with PCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (P<0.001). Also, there were differences in bacterial community composition between agricultural runoff and urban runoff based on parsimony tests using 454 pyrosequencing data. Fecal indicator bacteria in surface water along different creeks and channels were significantly correlated with pH (P<0.01), NO2 (P<0.03), and NH4N (P<0.005); and in the sediment with NO3 (P<0.015). Our results suggest that microbial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water

  17. Diversity and Temporal Dynamics of the Epiphytic Bacterial Communities Associated with the Canopy-Forming Seaweed Cystoseira compressa (Esper) Gerloff and Nizamuddin.

    Science.gov (United States)

    Mancuso, Francesco P; D'Hondt, Sofie; Willems, Anne; Airoldi, Laura; De Clerck, Olivier

    2016-01-01

    Canopy-forming seaweed species of the genus Cystoseira form diverse and productive habitats along temperate rocky coasts of the Mediterranean Sea. Despite numerous studies on the rich macrofauna and flora associated with Cystoseira spp., there is little knowledge about the epiphytic bacteria. We analyzed bacterial populations associated with canopies of Cystoseira compressa, over an annual vegetative cycle (May-October), and their relationships with the bacterial populations in the surrounding seawater, at intertidal rocky shores in Vasto (Chieti-Italy). The bacterial diversity was assessed using Illumina Miseq sequences of V1-V3 hypervariable regions of 16S rRNA gene. C. compressa bacterial community was dominated by sequences of Proteobacteria and Bacteroidetes, Verrucomicrobia, Actinobacteria, and Cyanobacteria especially of the Rhodobacteriaceae, Flavobacteriaceae, Sapropiraceae, Verrucomicrobiaceae, and Phyllobacteriaceae families. Seawater libraries were also dominated by Proteobacteria and Bacteroidetes sequences, especially of the Candidatus Pelagibacter (SAR11) and Rhodobacteriaceae families, but were shown to be clearly distinct from C. compressa libraries with only few species in common between the two habitats. We observed a clear successional pattern in the epiphytic bacteria of C. compressa over time. These variations were characterized by gradual addition of OTUs (Verrucomicrobia, Actinobacteria and SR1) to the community over a growing season, indicative of a temporal gradient, rather than a radical reorganization of the bacterial community. Moreover, we also found an increase in abundance over time of Rhodobacteraceae, comprising six potential pathogenic genera, Ruegeria, Nautella, Aquimarina, Loktanella, Saprospira, and Phaeobacter which seemed to be associated to aged thalli of C. compressa. These bacteria could have the potential to affect the health and ecology of the algae, suggesting the hypothesis of a possible, but still unexplored, role of

  18. Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray) analysis.

    Science.gov (United States)

    Patra, Amlan K; Yu, Zhongtang

    2015-01-01

    In a previous study origanum oil (ORO), garlic oil (GAO), and peppermint oil (PEO) were shown to effectively lower methane production, decrease abundance of methanogens, and change abundances of several bacterial populations important to feed digestion in vitro. In this study, the impact of these essential oils (EOs, at 0.50 g/L) on the rumen bacterial community composition and population was further examined using the recently developed RumenBactArray. Species richness (expressed as number of operational taxonomic units, OTUs) in the phylum Firmicutes, especially those in the class Clostridia, was decreased by ORO and GAO, but increased by PEO, while that in the phylum Bacteroidetes was increased by ORO and PEO. Species richness in the genus Butyrivibrio was lowered by all the EOs. Increases of Bacteroidetes OTUs mainly resulted from increases of Prevotella OTUs. Overall, 67 individual OTUs showed significant differences (P ≤ 0.05) in relative abundance across the EO treatments. The predominant OTUs affected by EOs were diverse, including those related to Syntrophococcus sucromutans, Succiniclasticum ruminis, and Lachnobacterium bovis, and those classified to Prevotella, Clostridium, Roseburia, Pseudobutyrivibrio, Lachnospiraceae, Ruminococcaceae, Prevotellaceae, Bacteroidales, and Clostridiales. In total, 60 OTUs were found significantly (P ≤ 0.05) correlated with feed degradability, ammonia concentration, and molar percentage of volatile fatty acids. Taken together, this study demonstrated extensive impact of EOs on rumen bacterial communities in an EO type-dependent manner, especially those in the predominant families Prevotellaceae, Lachnospiraceae, and Ruminococcaceae. The information from this study may aid in understanding the effect of EOs on feed digestion and fermentation by rumen bacteria. PMID:25914694

  19. Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray analysis

    Directory of Open Access Journals (Sweden)

    Amlan Kumar Patra

    2015-04-01

    Full Text Available In a previous study origanum oil (ORO, garlic oil (GAO, and peppermint oil (PEO were shown to effectively lower methane production, decrease abundance of methanogens, and change abundances of several bacterial populations important to feed digestion in vitro. In this study, the impact of these essential oils (EOs, at 0.50 g/L, on the rumen bacterial community composition and population was further examined using the recently developed RumenBactArray. Species richness (expressed as number of operational taxonomic units, OTUs in the phylum Firmicutes, especially those in the class Clostridia, was decreased by ORO and GAO, but increased by PEO, while that in the phylum Bacteroidetes was increased by ORO and PEO. Species richness in the genus Butyrivibrio was lowered by all the EOs. Increases of Bacteroidetes OTUs mainly resulted from increases of Prevotella OTUs. Overall, 67 individual OTUs showed significant differences (P≤0.05 in relative abundance across the EO treatments. The predominant OTUs affected by EOs were diverse, including those related to Syntrophococcus sucromutans, Succiniclasticum ruminis, and Lachnobacterium bovis, and those classified to Prevotella, Clostridium, Roseburia, Pseudobutyrivibrio, Lachnospiraceae, Ruminococcaceae, Prevotellaceae, Bacteroidales, and Clostridiales. In total, 60 OTUs were found significantly (P≤0.05 correlated with feed degradability, ammonia concentration, and molar percentage of volatile fatty acids. Taken together, this study demonstrated extensive impact of EOs on rumen bacterial communities in an EO type-dependent manner, especially those in the predominant families Prevotellaceae, Lachnospiraceae and Ruminococcaceae. The information from this study may aid in understanding the effect of EOs on feed digestion and fermentation by rumen bacteria.

  20. Bacterial succession within an ephemeral hypereutrophic mojave desert playa lake

    Science.gov (United States)

    Navarro, J.B.; Moser, D.P.; Flores, A.; Ross, C.; Rosen, Michael R.; Dong, H.; Zhang, G.; Hedlund, B.P.

    2009-01-01

    Ephemerally wet playas are conspicuous features of arid landscapes worldwide; however, they have not been well studied as habitats for microorganisms. We tracked the geochemistry and microbial community in Silver Lake playa, California, over one flooding/desiccation cycle following the unusually wet winter of 2004-2005. Over the course of the study, total dissolved solids increased by 10-fold and pH increased by nearly one unit. As the lake contracted and temperatures increased over the summer, a moderately dense planktonic population of 1 ?????106 cells ml-1 of culturable heterotrophs was replaced by a dense population of more than 1????????109 cells ml-1, which appears to be the highest concentration of culturable planktonic heterotrophs reported in any natural aquatic ecosystem. This correlated with a dramatic depletion of nitrate as well as changes in the microbial community, as assessed by small subunit ribosomal RNA gene sequencing of bacterial isolates and uncultivated clones. Isolates from the early-phase flooded playa were primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet clone libraries were dominated by Betaproteobacteria and yet uncultivated Actinobacteria. Isolates from the late-flooded phase ecosystem were predominantly Proteobacteria, particularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, Hydrogenophaga, Alishwenella, and relatives of Thauera; however, clone libraries were composed almost entirely of Synechococcus (Cyanobacteria). A sample taken after the playa surface was completely desiccated contained diverse culturable Actinobacteria typically isolated from soils. In total, 205 isolates and 166 clones represented 82 and 44 species-level groups, respectively, including a wide diversity of Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, and Cyanobacteria. ?? 2008 Springer Science+Business Media, LLC.

  1. Response of bacterial community compositions to different sources of pollutants in sediments of a tributary of Taihu Lake, China.

    Science.gov (United States)

    Wang, Jing; Li, Yi; Wang, Peifang; Niu, Lihua; Zhang, Wenlong; Wang, Chao

    2016-07-01

    Sediment bacterial communities are sensitive to water conditions in river ecosystems. The objective of this study was to compare the influences of different pollution sources, including urban areas, wastewater treatment plants (WWTPs), suburban areas, and agricultural areas, on sediment bacterial communities along a typical tributary of Taihu Lake, China. The dominant composition of the sediment bacterial community was determined using a combination of terminal restriction fragment length polymorphism (T-RFLP) and a 16S rRNA clone library. The results showed that the sediment bacterial communities were distinctly affected by the four pollution sources. Alphaproteobacteria, Betaproteobacteria, and Actinobacteria (>50 % in total) were the predominant bacterial taxa across the sediment samples. Apart from those, the sediment bacterial community composition (BCC) affected by WWTP effluent was subsequently dominated by Nitrospira (12.4 %) and Bacteroidetes (11.5 %), agriculture was dominated by Firmicutes (13.2 %) and Deltaproteobacteria (7.2 %), while urban and suburban were dominated by Bacteroidetes (7.6 and 7.9 %, respectively) and Deltaproteobacteria (7.9 and 7.6 %, respectively). Cluster analysis indicated that the BCC affected by WWTP effluent was distinct from the BCC in urban, suburban, and agricultural areas. In addition, the bacterial community richness and evenness affected by WWTP effluent were much less than those by the other pollution sources. Redundancy analysis (RDA) indicated that the variation in BCC across the sediment samples was significantly associated with ammonium (17 %), organic matter (12 %), and cadmium (3 %) (p < 0.01). Overall, the results indicated that the four different pollution sources (WWTP, urban, suburban, and agriculture) have dissimilar impacts on the sediment BCC in the tributary of Taihu Lake, while WWTPs exhibited the greatest potential to lead to biotic homogenization in river sediments. PMID:27040536

  2. Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil

    Energy Technology Data Exchange (ETDEWEB)

    Lladó, S., E-mail: llado@biomed.cas.cz [Department of Microbiology, University of Barcelona, Diagonal 645, E-08028 Barcelona (Spain); Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 142 20 Prague 4 (Czech Republic); Covino, S., E-mail: covino@biomed.cas.cz [Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 142 20 Prague 4 (Czech Republic); Solanas, A.M., E-mail: asolanas@ub.edu [Department of Microbiology, University of Barcelona, Diagonal 645, E-08028 Barcelona (Spain); Petruccioli, M., E-mail: petrucci@unitus.it [Department for Innovation in Biological, Agro-Food and Forest Systems [DIBAF], University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo (Italy); D’annibale, A., E-mail: dannib@unitus.it [Department for Innovation in Biological, Agro-Food and Forest Systems [DIBAF], University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo (Italy); Viñas, M., E-mail: marc.vinas@irta.cat [GIRO Joint Research Unit IRTA-UPC, Institute of Research and Technology Food and Agriculture [IRTA], Torre Marimon, E-08140 Caldes de Montbui (Spain)

    2015-02-11

    Highlights: • Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided. • A failure of exogenous white rot fungi to colonize the polluted soil is shown by DGGE and pyrosequencing. • Surfactant Brij 30 hampers 4-ring PAHs degradation due to toxicity over Actinobacteria and Bacteroidetes populations. • A high prevalence of Fusarium and Scedosporium populations is revealed during soil bioremediation. • Cupriavidus, Mycobacterium and Chithinophagaceae are potential HMW–PAH degraders in the soil. - Abstract: Bacterial and fungal biodiversity throughout different biostimulation and bioaugmentation treatments applied to an industrial creosote-polluted soil were analyzed by means of polyphasic approach in order to gain insight into the microbial community structure and dynamics. Pyrosequencing data obtained from initial creosote polluted soil (after a biopiling step) revealed that Alpha and Gammaproteobacteria were the most abundant bacterial groups, whereas Fusarium and Scedosporium were the main fungal genera in the contaminated soil. At the end of 60-days laboratory scale bioremediation assays, pyrosequencing and DGGE data showed that (i) major bacterial community shifts were caused by the type of mobilizing agent added to the soil and, to a lesser extent, by the addition of lignocellulosic substrate; and (ii) the presence of the non-ionic surfactant (Brij 30) hampered the proliferation of Actinobacteria (Mycobacteriaceae) and Bacteroidetes (Chitinophagaceae) and, in the absence of lignocellulosic substrate, also impeded polycyclic aromatic hydrocarbons (PAHs) degradation. The results show the importance of implementing bioremediation experiments combined with microbiome assessment to gain insight on the effect of crucial parameters (e.g. use of additives) over the potential functions of complex microbial communities harbored in polluted soils, essential for bioremediation success.

  3. Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China.

    Science.gov (United States)

    Zhang, Bingchang; Kong, Weidong; Wu, Nan; Zhang, Yuanming

    2016-06-01

    Biological soil crusts (BSCs) are common and play critical roles in semi-arid and arid ecosystems. Bacteria, as an important community in BSCs, play critical roles in biochemical processes. However, how bacterial diversity and community change in different successional stages of BSCs is still unknown. We used 454 pyrosequencing of 16S rRNA to investigate the bacterial composition and community, and the relationships between bacterial composition and environmental factors were also explored. In different successional stages of BSCs, the number of bacteria operational taxonomic units (OTUs) detected in each sample ranged from 2572 to 3157. Proteobacteria, Cyanobacteria, Bacteroidetes were dominant in BSCs, followed by Firmicutes, Acidobacteria, and Actinobacteria. At the successional stages of BSCs, bacterial communities, OTU composition and their relative abundance notably differentiated, and Cyanobacteria, especially Microcoleus vaginatus, dominated algal crust and lichen crust, and were the main C-fixing bacteria in BSCs. Proteobacteria and Bacteroidetes increased with the development of BSCs. OTUs related to Planomicrobium Chinese, Desulfobulbus sp., Desulfomicrobium sp., Arthrobacter sp., and Ahhaerbacter sp. showed higher relative abundance in bare sand than other successional stages of BSCs, while relative abundance of Sphingomonas sp. Niastella sp., Pedobacter, Candidatus solobacter, and Streptophyta increased with the development of BSCs. In successional stages of BSCs, bacterial OTUs composition demonstrated strong correlations with soil nutrients, soil salts, and soil enzymes. Additionally, variation of bacterial composition led to different ecological function. In bare sand, some species were related with mineral metabolism or promoting plant growth, and in algal crust and lichen crust, C-fixing bacteria increased and accumulated C to the desert soil. In later developed stage of BSCs, bacteria related with decomposition of organic matter, such as

  4. Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing.

    Science.gov (United States)

    Lee, Da-Eun; Lee, Jinhwan; Kim, Young-Mog; Myeong, Jeong-In; Kim, Kyoung-Ho

    2016-04-01

    Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters. PMID:27033205

  5. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

    Energy Technology Data Exchange (ETDEWEB)

    Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.; Wong, J.; DeSantis, T.Z.; Brodie, E.L.; Hazen, T.C.; Holden, P.A.; Andersen, G.L.

    2010-03-01

    Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.

  6. High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet.

    Science.gov (United States)

    Wang, Wen; Cao, Jian; Yang, Fang; Wang, Xuelian; Zheng, Sisi; Sharshov, Kirill; Li, Laixing

    2016-04-01

    Elucidating the spatial dynamic and core gut microbiome related to wild bar-headed goose is of crucial importance for probiotics development that may meet the demands of bar-headed goose artificial breeding industries and accelerate the domestication of this species. However, the core microbial communities in the wild bar-headed geese remain totally unknown. Here, for the first time, we present a comprehensive survey of bar-headed geese gut microbial communities by Illumina high-throughput sequencing technology using nine individuals from three distinct wintering locations in Tibet. A total of 236,676 sequences were analyzed, and 607 OTUs were identified. We show that the gut microbial communities of bar-headed geese have representatives of 14 phyla and are dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The additive abundance of these four most dominant phyla was above 96% across all the samples. At the genus level, the sequences represented 150 genera. A set of 19 genera were present in all samples and considered as core gut microbiome. The top seven most abundant core genera were distributed in that four dominant phyla. Among them, four genera (Lactococcus, Bacillus, Solibacillus, and Streptococcus) belonged to Firmicutes, while for other three phyla, each containing one genus, such as Proteobacteria (genus Pseudomonas), Actinobacteria (genus Arthrobacter), and Bacteroidetes (genus Bacteroides). This broad survey represents the most in-depth assessment, to date, of the gut microbes that associated with bar-headed geese. These data create a baseline for future bar-headed goose microbiology research, and make an original contribution to probiotics development for bar-headed goose artificial breeding industries. PMID:26842811

  7. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

    Directory of Open Access Journals (Sweden)

    StephenRLindemann

    2014-04-01

    Full Text Available Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural

  8. Methane Inhibition Alters the Microbial Community, Hydrogen Flow, and Fermentation Response in the Rumen of Cattle

    Science.gov (United States)

    Martinez-Fernandez, Gonzalo; Denman, Stuart E.; Yang, Chunlei; Cheung, Jane; Mitsumori, Makoto; McSweeney, Christopher S.

    2016-01-01

    Management of metabolic hydrogen ([H]) in the rumen has been identified as an important consideration when reducing ruminant CH4 emissions. However, little is known about hydrogen flux and microbial rumen population responses to CH4 inhibition when animals are fed with slowly degradable diets. The effects of the anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology, and H2/CH4 production were investigated in vivo. Eight rumen fistulated Brahman steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate diet (60:40) with increasing levels (low, mid, and high) of chloroform in a cyclodextrin matrix. The increasing levels of chloroform resulted in an increase in H2 expelled as CH4 production decreased with no effect on dry matter intakes. The amount of expelled H2 per mole of decreased methane, was lower for the hay diet suggesting a more efficient redirection of hydrogen into other microbial products compared with hay:concentrate diet. A shift in rumen fermentation toward propionate and branched-chain fatty acids was observed for both diets. Animals fed with the hay:concentrate diet had both higher formate concentration and H2 expelled than those fed only roughage hay. Metabolomic analyses revealed an increase in the concentration of amino acids, organic, and nucleic acids in the fluid phase for both diets when methanogenesis was inhibited. These changes in the rumen metabolism were accompanied by a shift in the microbiota with an increase in Bacteroidetes:Firmicutes ratio and a decrease in Archaea and Synergistetes for both diets. Within the Bacteroidetes family, some OTUs assigned to Prevotella were promoted under chloroform treatment. These bacteria may be partly responsible for the increase in amino acids and propionate in the rumen. No significant changes were observed for abundance of fibrolytic bacteria, protozoa, and fungi, which suggests that fiber degradation was not impaired. The observed 30% decrease in

  9. 污水处理活性污泥微生物群落多样性研究%Microbial Population Diversity of Activated Sludge for Wastewater Treatment

    Institute of Scientific and Technical Information of China (English)

    金浩; 李柏林; 欧杰; 陈兰明

    2012-01-01

    为研究污水处理活性污泥微生物多样性,提取了活性污泥宏基因组DNA,并采用细菌通用引物27F和1492R扩增了上海污泥厂活性污泥细菌16S rDNA片段,构建了细菌16S rDNA克隆文库,并对该文库中的微生物群落进行了分析.共获得200条高质量序列并建立系统发育树,结果显示活性污泥主要的细菌类群为变形菌门(Proteobacteria)(91.9%)、厚壁菌门(Firmicures)(4.6%)、拟杆菌门(Bacteroidetes)(2%)、绿弯菌门(Chloroflexi)(0.5%)、硝化螺菌门(Nitrospirae)(1%).其中,明显的优势菌群为Alcaligenes feacalis(55%)、Pseudomonas aeruginosa(12.8%)和Stenotrophomonas(12.8%),优势菌的产酶能力在活性污泥中显示生态修复功能菌的作用.%In order to study the microbial diversity of activated sludge (AS) for wastewater treatment, the macro-ge-nomic DNA of the AS was extracted from a wastewater factory in Shanghai. The 16S rDNA of the AS bacteria was amplified using bacteria general primers 27F and 1492R to construct the bacterial 16S rDNA clone library, and analyzed the microbial population of the library. All together 200 bands of high quality sequences were obtained and established a phylogenetic tree. The results showed that the main bacterial population of the AS was the phyla of Proteobacteria (91.9% ) , Firmicutes (4.6% ) , Bacteroidetes (2% ) , Chloroflexi (0.5% ) , Nitrospirae (1% ). Among them Al-caligenes feacalis (55% ) , Pseudomonas aeruginosa ( 12. 8% ) , and Stenolrophomonas ( 12. 8% ) were noticeably dominant bacterial population, enzyme production capacity of the dominant bacteria showed the ecological restoration function in the AS.

  10. Internal and external influences on near-surface microbial community structure in the vicinity of the Cape Verde Islands.

    Science.gov (United States)

    Hill, Polly G; Heywood, Jane L; Holland, Ross J; Purdie, Duncan A; Fuchs, Bernhard M; Zubkov, Mikhail V

    2012-01-01

    Microbial community structure in the subtropical north-east Atlantic Ocean was compared between 2 years and variation attributed to environmental variables. Surface seawater communities were analysed by flow cytometry and fluorescence in situ hybridisation. Probes specific to Alphaproteobacteria, Cyanobacteria, Gammaproteobacteria and Bacteroidetes identified 67-100% of cells. Due to natural variation in the study region due to the occurrence of major currents and islands, data could not be pooled but were instead divided between distinct water masses. Community structure did not differ greatly around the Cape Verde Islands between sampling periods but varied substantially in the open ocean, suggesting different environmental perturbations favour specific bacterial groups. Wind speed varied significantly between years, with moderate to strong breeze in winter 2008 and gales in winter 2006 (8.9 ± 0.2 ms(-1) and 16.0 ± 0.4 ms(-1), respectively). Enhanced wind-driven turbulence was associated with domination by the SAR11 clade of Alphaproteobacteria, which were present at 2.4-fold in the abundance of Prochlorococcus (41.8 ± 1.6% cells, compared to 17.7 ± 7.1%). Conversely, the calmer conditions of 2008 seemed to favour Prochlorococcus (40.0 ± 1.2% cells). Prochlorococcus high-light adapted clade HLI were only numerous during wind-driven turbulence, whereas oligotrophic-adapted clade HLII dominated under calm conditions. Bacteroidetes were most prominent in turbulent conditions (9.5 ± 1.3% cells as opposed to 4.7 ± 0.3%), as were Synechococcus. In 2008, a considerable dust deposition event occurred in the region, which may have led to the substantial Gammaproteobacteria population (22.5 ± 4.0% cells compared to 4.6 ± 0.6% in 2006). Wind-driven turbulence may have a significant impact on microbial community structure in the surface ocean. Therefore, community change following dust storm events may be linked to associated

  11. Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

    Directory of Open Access Journals (Sweden)

    M.-C. Ciobanu

    2012-09-01

    Full Text Available An interdisciplinary study was conducted to evaluate the relationship between geological and paleoenvironmental parameters and the bacterial and archaeal community structure of two contrasting subseafloor sites in the Western Mediterranean Sea (Ligurian Sea and Gulf of Lion. Both depositional environments in this area are well-documented from paleoclimatic and paleooceanographic point of views. Available data sets allowed us to calibrate the investigated cores with reference and dated cores previously collected in the same area, and notably correlated to Quaternary climate variations. DNA-based fingerprints showed that the archaeal diversity was composed by one group, Miscellaneous Crenarchaeotic Group (MCG, within the Gulf of Lion sediments and of nine different lineages (dominated by MCG, South African Gold Mine Euryarchaeotal Group (SAGMEG and Halobacteria within the Ligurian Sea sediments. Bacterial molecular diversity at both sites revealed mostly the presence of the classes Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria within Proteobacteria phylum, and also members of Bacteroidetes phylum. The second most abundant lineages were Actinobacteria and Firmicutes at the Gulf of Lion site and Chloroflexi at the Ligurian Sea site. Various substrates and cultivation conditions allowed us to isolate 75 strains belonging to four lineages: Alpha-, Gammaproteobacteria, Firmicutes and Actinobacteria. In molecular surveys, the Betaproteobacteria group was consistently detected in the Ligurian Sea sediments, characterized by a heterolithic facies with numerous turbidites from a deep-sea levee. Analysis of relative betaproteobacterial abundances and turbidite frequency suggested that the microbial diversity was a result of main climatic changes occurring during the last 20 ka. Statistical direct multivariate canonical correspondence

  12. Study of inter- and intra-individual variations in the salivary microbiota

    Directory of Open Access Journals (Sweden)

    François Patrice

    2010-09-01

    Full Text Available Abstract Background Oral bacterial communities contain species that promote health and others that have been implicated in oral and/or systemic diseases. Culture-independent approaches provide the best means to assess the diversity of oral bacteria because most of them remain uncultivable. Results The salivary microbiota from five adults was analyzed at three time-points by means of the 454 pyrosequencing technology. The V1-V3 region of the bacterial 16S rRNA genes was amplified by PCR using saliva lysates and broad-range primers. The bar-coded PCR products were pooled and sequenced unidirectionally to cover the V3 hypervariable region. Of 50,708 obtained sequences, 31,860 passed the quality control. Non-bacterial sequences (2.2% were removed leaving 31,170 reads. Samples were dominated by seven major phyla: members of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and candidate division TM7 were identified in all samples; Fusobacteria and Spirochaetes were identified in all individuals, but not at all time-points. The dataset was represented by 3,011 distinct sequences (100%-ID phylotypes of ~215 nucleotides and 583 phylotypes defined at ≥97% identity (97%-ID phylotypes. We compared saliva samples from different individuals in terms of the phylogeny of their microbial communities. Based on the presence and absence of phylotypes defined at 100% or 97% identity thresholds, samples from each subject formed separate clusters. Among individual taxa, phylum Bacteroidetes and order Clostridiales (Firmicutes were the best indicators of intraindividual similarity of the salivary flora over time. Fifteen out of 81 genera constituted 73 to 94% of the total sequences present in different samples. Of these, 8 were shared by all time points of all individuals, while 15-25 genera were present in all three time-points of different individuals. Representatives of the class Sphingobacteria, order Sphingobacteriales and family Clostridiaceae were

  13. Risks Involved in the Use of Enrofloxacin for Salmonella Enteritidis or Salmonella Heidelberg in Commercial Poultry

    Science.gov (United States)

    Morales-Barrera, Eduardo; Calhoun, Nicole; Lobato-Tapia, Jose L.; Lucca, Vivian; Prado-Rebolledo, Omar; Hernandez-Velasco, Xochitl; Merino-Guzman, Ruben; Petrone-García, Victor M.; Latorre, Juan D.; Mahaffey, Brittany D.; Teague, Kyle D.; Graham, Lucas E.; Wolfenden, Amanda D.; Baxter, Mikayla F. A.; Hargis, Billy M.; Tellez, Guillermo

    2016-01-01

    The objectives of the present study were to evaluate the risks involved in the use of Enrofloxacin for Salmonella Enteritidis (SE) or Salmonella Heidelberg (SH) in commercial poultry and determine the effects of a probiotic as an antibiotic alternative. Two experiments were conducted to evaluate the risks involved in the use of Enrofloxacin for SE or SH in commercial poultry. Experiment 1 consisted of two trials. In each trial, chickens were assigned to one of three groups; control + SE challenged; Enrofloxacin 25 mg/kg + SE; and Enrofloxacin 50 mg/kg + SE. Chickens received Enrofloxacin in the drinking water from days 1 to 5 of age. On day 6, all groups received fresh water without any treatment. All chickens were orally gavaged with 107 cfu/chick of SE at 7 days of age and euthanized on 8 days of age. In Experiment 2, turkey poults were assigned to one of the three groups; control + SH; probiotic + SH; and Enrofloxacin 50 mg/kg + SH. Poults received probiotic or Enrofloxacin in the drinking water from days 1 to 5 of age. On day 6, poults received fresh water without any treatment. Poults were orally gavaged with 107 cfu/poult of SH at 7 days of age. Poults were weighed and humanely killed 24 h post-SH challenge to evaluate serum concentration of fluorescein isothiocyanate-dextran to evaluate intestinal permeability, metagenomics, and SH infection. In both trials of Experiment 1, chickens treated with Enrofloxacin were more susceptible to SE organ invasion and intestinal colonization when compared with control non-treated chickens (P < 0.05). In Experiment 2, poults treated with 50 mg/kg of Enrofloxacin showed an increase in body weight, however, this group also showed an increase in SH susceptibility, intestinal permeability, and lower proportion of Firmicutes and Bacteroidetes, but with control group had the highest proportion of Proteobacteria. By contrast, poults that received the probiotic had the highest

  14. Pharmaceutically active compounds: Their removal during slow sand filtration and their impact on slow sand filtration bacterial removal.

    Science.gov (United States)

    D'Alessio, Matteo; Yoneyama, Bunnie; Kirs, Marek; Kisand, Veljo; Ray, Chittaranjan

    2015-08-15

    Slow sand filtration (SSF) has been widely used as a means of providing potable water due to its efficacy, low cost, and minimal maintenance. Advances in analytical instrumentation have revealed the occurrence of pharmaceutically active compounds (PhACs) in surface water as well as in groundwater. It is unclear if the presence of these compounds in the feed water can interfere with the performances of an SSF unit. The aim of this work was to examine i) the ability of two SSF units to remove six PhACs (caffeine, carbamazepine, 17-β estradiol [E2], estrone [E1], gemfibrozil, and phenazone), and ii) the impact of these PhACs on the removal of bacteria by two SSF units. The presence of PhACs in feed water for SSF can occur in surface waters impacted by wastewater or leakage from sewers and septic tanks, as well as in developing countries where unregulated use and improper disposal are prevalent. Two pilot-scale SSF units were used during the study. Unit B1 was fed with stream water with 1% of primary effluent added, while unit B2 was fed with stream water alone. Although limited removal (gemfibrozil, and phenazone occurred, the complete removal of caffeine, and the partial removal (11-92%) of E2 and E1 were observed in the two SSF units. The results of this study suggest that the occurrence of the selected PhACs, probably estrogens and caffeine, in the feed water at 50 μg L(-1) affected the ability of the schmutzdecke to remove total coliform and Escherichia coli. The bacterial removal achieved within the schmutzdecke dropped from 95% to less than 20% by the end of the study. This decrease in removal may be related to the change in the microbial community within the schmutzdecke. A diverse microbial community, including Bacteroidetes and several classes of Proteobacteria, was replaced by a microbial community in which Gammaproteobacteria was the predominant phylum (99%). Despite the low removal achieved within the schmutzdecke, removal of total coliform and E. coli

  15. Relationship between the rumen microbiome and residual feed intake-efficiency of Brahman bulls stocked on bermudagrass pastures.

    Directory of Open Access Journals (Sweden)

    Joshua C McCann

    Full Text Available Residual feed intake (RFI testing has increased selection pressure on biological efficiency in cattle. The objective of this study was to assess the association of the rumen microbiome in inefficient, positive RFI (p-RFI and efficient, negative RFI (n-RFI Brahman bulls grazing 'Coastal' bermudagrass [Cynodondactylon (L. Pers.]under two levels of forage allowance (high and low stocking intensity. Sixteen Brahman bulls were previously fed in confinement for 70 d to determine the RFI phenotype. Bulls were then allotted 60 d stocking on bermudagrass pastures to estimate RFI using the n-alkane technique. At the conclusion of the grazing period, rumen liquid samples were collected from each bull by stomach tube to evaluate the rumen microbiome. Extraction of DNA, amplification of the V4-V6 region of the 16S rRNA gene, and 454 pyrosequencing were performed on each sample. After denoising the sequences, chimera checking, and quality trimming, 4,573 ± 1,287 sequences were generated per sample. Sequences were then assigned taxonomy from the Greengenes database using the RDP classifier. Overall, 67.5 and 22.9% of sequences were classified as Bacteroidetes and Firmicutes, respectively. Within the phylum Bacteroidetes, Prevotella was the most predominant genus and was observed in greater relative abundance in p-RFI bulls compared with n-RFI bulls (P = 0.01. In contrast, an unidentified Bacteroidales family was greater in relative abundance for n-RFI bulls than p-RFI (26.7 vs. 19.1%; P = 0.03. Ruminococcaceae was the third most abundant family in our samples, but it was not affected by RFI phenotype. No effect of stocking intensity was observed for bacterial taxa, but there was a tendency for alpha diversity and operational taxonomic unit richness to increase with lower stocking intensity. Results suggested the rumen microbiome of p-RFI Brahman bulls has greater levels of Prevotella, but the bacterial community composition was unaffected by stocking

  16. The effect of selected synbiotics on microbial composition and short-chain fatty acid production in a model system of the human colon.

    Directory of Open Access Journals (Sweden)

    Gabriella C van Zanten

    Full Text Available BACKGROUND: Prebiotics, probiotics and synbiotics can be used to modulate both the composition and activity of the gut microbiota and thereby potentially affecting host health beneficially. The aim of this study was to investigate the effects of eight synbiotic combinations on the composition and activity of human fecal microbiota using a four-stage semicontinuous model system of the human colon. METHODS AND FINDINGS: Carbohydrates were selected by their ability to enhance growth of the probiotic bacteria Lactobacillus acidophilus NCFM (NCFM and Bifidobacterium animalis subsp. lactis Bl-04 (Bl-04 under laboratory conditions. The most effective carbohydrates for each probiotic were further investigated, using the colonic model, for the ability to support growth of the probiotic bacteria, influence the composition of the microbiota and stimulate formation of short-chain fatty acids (SCFA.The following combinations were studied: NCFM with isomaltulose, cellobiose, raffinose and an oat β-glucan hydrolysate (OBGH and Bl-04 with melibiose, xylobiose, raffinose and maltotriose. All carbohydrates showed capable of increasing levels of NCFM and Bl-04 during fermentations in the colonic model by 10(3-10(4 fold and 10-10(2 fold, respectively. Also the synbiotic combinations decreased the modified ratio of Bacteroidetes/Firmicutes (calculated using qPCR results for Bacteroides-Prevotella-Porphyromonas group, Clostridium perfringens cluster I, Clostridium coccoides - Eubacterium rectale group and Clostridial cluster XIV as well as significantly increasing SCFA levels, especially acetic and butyric acid, by three to eight fold, as compared to the controls. The decreases in the modified ratio of Bacteroidetes/Firmicutes were found to be correlated to increases in acetic and butyric acid (p=0.04 and p=0.03, respectively. CONCLUSIONS: The results of this study show that all synbiotic combinations investigated are able to shift the predominant bacteria and the

  17. Characterization of the Gut Microbial Community of Obese Patients Following a Weight-Loss Intervention Using Whole Metagenome Shotgun Sequencing

    Science.gov (United States)

    Damms-Machado, Antje; Huson, Daniel H.; Bischoff, Stephan C.

    2016-01-01

    Background/Objectives Cross-sectional studies suggested that obesity is promoted by the gut microbiota. However, longitudinal data on taxonomic and functional changes in the gut microbiota of obese patients are scarce. The aim of this work is to study microbiota changes in the course of weight loss therapy and the following year in obese individuals with or without co-morbidities, and to asses a possible predictive value of the gut microbiota with regard to weight loss maintenance. Subjects/Methods Sixteen adult patients, who followed a 52-week weight-loss program comprising low calorie diet, exercise and behavioral therapy, were selected according to their weight-loss course. Over two years, anthropometric and metabolic parameters were assessed and microbiota from stool samples was functionally and taxonomically analyzed using DNA shotgun sequencing. Results Overall the microbiota responded to the dietetic and lifestyle intervention but tended to return to the initial situation both at the taxonomical and functional level at the end of the intervention after one year, except for an increase in Akkermansia abundance which remained stable over two years (12.7x103 counts, 95%CI: 322–25100 at month 0; 141x103 counts, 95%CI: 49-233x103 at month 24; p = 0.005). The Firmicutes/Bacteroidetes ratio was higher in obese subjects with metabolic syndrome (0.64, 95%CI: 0.34–0.95) than in the “healthy obese” (0.27, 95%CI: 0.08–0.45, p = 0.04). Participants, who succeeded in losing their weight consistently over the two years, had at baseline a microbiota enriched in Alistipes, Pseudoflavonifractor and enzymes of the oxidative phosphorylation pathway compared to patients who were less successful in weight reduction. Conclusions Successful weight reduction in the obese is accompanied with increased Akkermansia numbers in feces. Metabolic co-morbidities are associated with a higher Firmicutes/Bacteroidetes ratio. Most interestingly, microbiota differences might allow

  18. Methane Inhibition Alters the Microbial Community, Hydrogen Flow, and Fermentation Response in the Rumen of Cattle.

    Science.gov (United States)

    Martinez-Fernandez, Gonzalo; Denman, Stuart E; Yang, Chunlei; Cheung, Jane; Mitsumori, Makoto; McSweeney, Christopher S

    2016-01-01

    Management of metabolic hydrogen ([H]) in the rumen has been identified as an important consideration when reducing ruminant CH4 emissions. However, little is known about hydrogen flux and microbial rumen population responses to CH4 inhibition when animals are fed with slowly degradable diets. The effects of the anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology, and H2/CH4 production were investigated in vivo. Eight rumen fistulated Brahman steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate diet (60:40) with increasing levels (low, mid, and high) of chloroform in a cyclodextrin matrix. The increasing levels of chloroform resulted in an increase in H2 expelled as CH4 production decreased with no effect on dry matter intakes. The amount of expelled H2 per mole of decreased methane, was lower for the hay diet suggesting a more efficient redirection of hydrogen into other microbial products compared with hay:concentrate diet. A shift in rumen fermentation toward propionate and branched-chain fatty acids was observed for both diets. Animals fed with the hay:concentrate diet had both higher formate concentration and H2 expelled than those fed only roughage hay. Metabolomic analyses revealed an increase in the concentration of amino acids, organic, and nucleic acids in the fluid phase for both diets when methanogenesis was inhibited. These changes in the rumen metabolism were accompanied by a shift in the microbiota with an increase in Bacteroidetes:Firmicutes ratio and a decrease in Archaea and Synergistetes for both diets. Within the Bacteroidetes family, some OTUs assigned to Prevotella were promoted under chloroform treatment. These bacteria may be partly responsible for the increase in amino acids and propionate in the rumen. No significant changes were observed for abundance of fibrolytic bacteria, protozoa, and fungi, which suggests that fiber degradation was not impaired. The observed 30% decrease in

  19. Potential use of bacterial community succession for estimating post-mortem interval as revealed by high-throughput sequencing.

    Science.gov (United States)

    Guo, Juanjuan; Fu, Xiaoliang; Liao, Huidan; Hu, Zhenyu; Long, Lingling; Yan, Weitao; Ding, Yanjun; Zha, Lagabaiyila; Guo, Yadong; Yan, Jie; Chang, Yunfeng; Cai, Jifeng

    2016-01-01

    Decomposition is a complex process involving the interaction of both biotic and abiotic factors. Microbes play a critical role in the process of carrion decomposition. In this study, we analysed bacterial communities from live rats and rat remains decomposed under natural conditions, or excluding sarcosaphagous insect interference, in China using Illumina MiSeq sequencing of 16S rRNA gene amplicons. A total of 1,394,842 high-quality sequences and 1,938 singleton operational taxonomic units were obtained. Bacterial communities showed notable variation in relative abundance and became more similar to each other across body sites during the decomposition process. As decomposition progressed, Proteobacteria (mostly Gammaproteobacteria) became the predominant phylum in both the buccal cavity and rectum, while Firmicutes and Bacteroidetes in the mouth and rectum, respectively, gradually decreased. In particular, the arrival and oviposition of sarcosaphagous insects had no obvious influence on bacterial taxa composition, but accelerated the loss of biomass. In contrast to the rectum, the microbial community structure in the buccal cavity of live rats differed considerably from that of rats immediately after death. Although this research indicates that bacterial communities can be used as a "microbial clock" for the estimation of post-mortem interval, further work is required to better understand this concept. PMID:27052375

  20. Six-week Diet Correction for Body Weight Reduction and Its Subsequent Changes of Gut Microbiota: A Case Report

    Science.gov (United States)

    2016-01-01

    Impact of intestinal microbes on obesity and health is a new topic recently started to get attention. Comparing to the global concern and research trends, there are few research on the association between intestinal bacteria and life style disease in Korean. One voluntary case (female) was reported to show the change in gut microbiota and weight by diet intervention. She was overweight (BMI 23.2 kg/m2) and has abnormal liver function, and the causes of overweight were frequent drinking and meat consumption at the late evening hours. For 47 days, she was administered an improved diet on breakfast and dinner with reduction of meat consumption frequency by 50%. Alcohol consumption was reduced to once a week. As a result, she lost 3 kilograms of body weight. Her fecal sample was collected before and after the intervention, and gut microbiota change was compared using a high-throughput sequencing technique. After diet correction, the shift of gut microbiota was clearly observed with decreased proportion of Firmicutes (from 75.7% to 47.3% in total microbiota) but increased proportion of Bacteroidetes upto 47.7%. After incorporating the diet intervention, it is meaningful to confirm the changes in dominant gut microbiota and weight loss. PMID:27152303

  1. Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants

    Science.gov (United States)

    Holman, Devin B.; Hao, Xiying; Topp, Edward; Yang, Hee Eun; Alexander, Trevor W.

    2016-01-01

    Agricultural operations generate large quantities of manure which must be eliminated in a manner that is consistent with public health guidelines. Meanwhile, construction and demolition waste makes up about 25% of total solid municipal waste. Co-composting of manure with construction and demolition waste offers a potential means to make manure safe for soil amendment and also divert construction and demolition waste from municipal landfills. Therefore, the archaeal, bacterial, and fungal microbiota of two different types of composted cattle manure and one co-composted with construction and demolition waste, were assessed over a 99-day composting period. The microbiota of the three compost mixtures did not differ, but significant changes over time and by sampling depth were observed. Bacillus and Halocella, however, were more relatively abundant in composted manure from cattle fed dried distillers’ grains and solubles. Proteobacteria and Bacteroidetes were enriched at day 0 and Firmicutes at day 99. The fungal genus Kernia was the most relatively abundant overall and was enriched at day 0. The concentration of 12 antimicrobial resistance determinants in the compost mixtures was also determined, and 10 of these determinants decreased significantly from days 0 to 99. The addition of construction and demolition waste did not affect the persistence of antimicrobial resistance genes or community structure of the compost microbiota and therefore co-composting construction and demolition waste with cattle manure offers a safe, viable way to divert this waste from landfills. PMID:27300323

  2. Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil

    Science.gov (United States)

    Ridl, Jakub; Kolar, Michal; Strejcek, Michal; Strnad, Hynek; Stursa, Petr; Paces, Jan; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas. PMID:27446035

  3. Characterising the microbiome of Corallina officinalis, a dominant calcified intertidal red alga.

    Science.gov (United States)

    Brodie, Juliet; Williamson, Christopher; Barker, Gary L; Walker, Rachel H; Briscoe, Andrew; Yallop, Marian

    2016-08-01

    The living prokaryotic microbiome of the calcified geniculate (articulated) red alga, Corallina officinalis from the intertidal seashore is characterised for the first time based on the V6 hypervariable region of 16S rRNA. Results revealed an extraordinary diversity of bacteria associated with the microbiome. Thirty-five prokaryotic phyla were recovered, of which Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Verrucomicrobia, Firmicutes and Chloroflexi made up the core microbiome. Unclassified sequences made up 25% of sequences, suggesting insufficient sampling of the world's oceans/macroalgae. The greatest diversity in the microbiome was on the upper shore, followed by the lower shore then the middle shore, although the microbiome community composition did not vary between shore levels. The C. officinalis core microbiome was broadly similar in composition to those reported in the literature for crustose coralline algae (CCAs) and free-living rhodoliths. Differences in relative abundance of the phyla between the different types of calcified macroalgal species may relate to the intertidal versus subtidal habit of the taxa and functionality of the microbiome components. The results indicate that much work is needed to identify prokaryotic taxa, and to determine the nature of the relationship of the bacteria with the calcified host spatially, temporally and functionally. PMID:27222222

  4. Exposure to soil, house dust and decaying plants increases gut microbial diversity and decreases serum immunoglobulin E levels in BALB/c mice.

    Science.gov (United States)

    Zhou, Dongrui; Zhang, Honglin; Bai, Zhimao; Zhang, Aidi; Bai, Futian; Luo, Xing; Hou, Yue; Ding, Xiao; Sun, Beili; Sun, Xiao; Ma, Ning; Wang, Cuifen; Dai, Xiaoniu; Lu, Zuhong

    2016-05-01

    To assess the impact of sanitation of a living environment on gut microbiota and development of the immune system, we raised BALB/c mice under three distinct environmental conditions: a specific pathogen-free animal room (SPF), a general animal room (XZ) and a farmhouse (JD). All other variables like diet, age, genetic background, physiological status and original gut microbiota were controlled for in the three groups. Using high-throughput sequencing of the 16S rRNA gene, we found that each mouse group had a specific structure of the gut microbial community. Groups JD and XZ harboured a significantly more diverse and richer gut microbiota than did group SPF. Bacteroidetes were significantly more abundant in groups XZ and JD than in group SPF, whereas Firmicutes showed the inverse pattern. Total serum immunoglobulin E (IgE) levels were significantly lower in groups XZ and JD than in group SPF. There were no significant differences in gut microbiota diversity and serum IgE concentration between groups JD and XZ, but we found higher abundance of dominant genera in the gut microflora of group JD. We conclude that exposure to soil, house dust and decaying plant material enhances gut microbial diversity and innate immunity. Our results seem to provide new evidence supporting the hygiene hypothesis. PMID:25958920

  5. Comparative molecular analysis of the prokaryotic diversity of two salt mine soils in southwest China.

    Science.gov (United States)

    Xiao, Wei; Wang, Zhi-Gang; Wang, Yong-Xia; Schneegurt, Mark A; Li, Zhi-Ying; Lai, Yong-Hong; Zhang, Shi-Ying; Wen, Meng-Liang; Cui, Xiao-Long

    2013-11-01

    While much is known about the microbial diversity in some hypersaline environments, little is known about those of salt mine tunnel soils. The objective of this study was to conduct a comprehensive phylogenetic comparison of the archaeal and bacterial communities present in Yipinglang salt mine (YPL) and Qiaohou salt mine (QH) tunnels differing in salinity and salt composition using 16S rRNA gene clone libraries. Two hundred twenty-eight sequences for QH and 182 sequences for YPL were analyzed by amplified ribosomal DNA-restriction analysis. Libraries revealed 44 bacterial and 57 archaeal different operational taxonomic units belonging to at least 8 bacterial and 3 archaeal divisions, but not all divisions were observed in both salt mines. The bacterial community affiliated with the Bacteroidetes was the most abundant (60% of clones) in QH, while the community in YPL was dominated by δ-Proteobacteria (45% of clones). All archaeal clones from QH were affiliated with Halobacteriaceae. In contrast, in the YPL library, 49% of clones belonged to Halobacteriaceae, 31% of clones related to unclassified archaea, and 21% of clones belonged to Crenarchaeota. Bioinformatic analysis and comparisons showed that the clone libraries were significantly different between two salt mines. PMID:23457089

  6. Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability.

    Science.gov (United States)

    Lewin, Gina R; Johnson, Amanda L; Soto, Rolando D Moreira; Perry, Kailene; Book, Adam J; Horn, Heidi A; Pinto-Tomás, Adrián A; Currie, Cameron R

    2016-01-01

    Deconstruction of the cellulose in plant cell walls is critical for carbon flow through ecosystems and for the production of sustainable cellulosic biofuels. Our understanding of cellulose deconstruction is largely limited to the study of microbes in isolation, but in nature, this process is driven by microbes within complex communities. In Neotropical forests, microbes in leaf-cutter ant refuse dumps are important for carbon turnover. These dumps consist of decaying plant material and a diverse bacterial community, as shown here by electron microscopy. To study the portion of the community capable of cellulose degradation, we performed enrichments on cellulose using material from five Atta colombica refuse dumps. The ability of enriched communities to degrade cellulose varied significantly across refuse dumps. 16S rRNA gene amplicon sequencing of enriched samples identified that the community structure correlated with refuse dump and with degradation ability. Overall, samples were dominated by Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. Half of abundant operational taxonomic units (OTUs) across samples were classified within genera containing known cellulose degraders, including Acidovorax, the most abundant OTU detected across samples, which was positively correlated with cellulolytic ability. A representative Acidovorax strain was isolated, but did not grow on cellulose alone. Phenotypic and compositional analyses of enrichment cultures, such as those presented here, help link community composition with cellulolytic ability and provide insight into the complexity of community-based cellulose degradation. PMID:26999749

  7. Towards high through-put biological treatment of municipal wastewater and enhanced phosphorus recovery using a hybrid microfiltration-forward osmosis membrane bioreactor with hydraulic retention time in sub-hour level.

    Science.gov (United States)

    Qiu, Guanglei; Zhang, Sui; Srinivasa Raghavan, Divya Shankari; Das, Subhabrata; Ting, Yen-Peng

    2016-11-01

    This work uncovers an important feature of the forward osmosis membrane bioreactor (FOMBR) process: the decoupling of contaminants retention time (CRT) and hydraulic retention time (HRT). Based on this concept, the capability of the hybrid microfiltration-forward osmosis membrane bioreactor (MF-FOMBR) in achieving high through-put treatment of municipal wastewater with enhanced phosphorus recovery was explored. High removal of TOC and NH4(+)-N (90% and 99%, respectively) was achieved with HRTs down to 47min, with the treatment capacity increased by an order of magnitude. Reduced HRT did not affect phosphorus removal and recovery. As a result, the phosphorus recovery capacity was also increased by the same order. Reduced HRT resulted in increased system loading rates and thus elevated concentrations of mixed liquor suspended solids and increased membrane fouling. 454-pyrosequecing suggested the thriving of Bacteroidetes and Proteobacteria (especially Sphingobacteriales Flavobacteriales and Thiothrix members), as well as the community succession and dynamics of ammonium oxidizing and nitrite oxidizing bacteria. PMID:27498011

  8. Castration influences intestinal microflora and induces abdominal obesity in high-fat diet-fed mice.

    Science.gov (United States)

    Harada, Naoki; Hanaoka, Ryo; Horiuchi, Hiroko; Kitakaze, Tomoya; Mitani, Takakazu; Inui, Hiroshi; Yamaji, Ryoichi

    2016-01-01

    Late-onset hypogonadism (i.e. androgen deficiency) raises the risk for abdominal obesity in men. The mechanism for this obesity is unclear. Here, we demonstrated that hypogonadism after castration caused abdominal obesity in high-fat diet (HFD)-fed, but not in standard diet (SD)-fed, C57BL/6J mice. Furthermore, the phenotype was not induced in mice treated with antibiotics that disrupt the intestinal microflora. In HFD-fed mice, castration increased feed efficiency and decreased fecal weight per food intake. Castration also induced in an increase of visceral fat mass only in the absence of antibiotics in HFD-fed mice, whereas subcutaneous fat mass was increased by castration irrespective of antibiotics. Castration reduced the expression in the mesenteric fat of both adipose triglyceride lipase and hormone-sensitive lipase in HFD-fed mice, which was not observed in the presence of antibiotics. Castration decreased thigh muscle (i.e. quadriceps and hamstrings) mass, elevated fasting blood glucose levels, and increased liver triglyceride levels in a HFD-dependent manner, whereas these changes were not observed in castrated mice treated with antibiotics. The Firmicutes/Bacteroidetes ratio and Lactobacillus species increased in the feces of HFD-fed castrated mice. These results show that androgen (e.g. testosterone) deficiency can alter the intestinal microbiome and induce abdominal obesity in a diet-dependent manner. PMID:26961573

  9. Microbial diversity and potential pathogens in ornamental fish aquarium water.

    Directory of Open Access Journals (Sweden)

    Katherine F Smith

    Full Text Available Ornamental fishes are among the most popular and fastest growing categories of pets in the United States (U.S.. The global scope and scale of the ornamental fish trade and growing popularity of pet fish in the U.S. are strong indicators of the myriad economic and social benefits the pet industry provides. Relatively little is known about the microbial communities associated with these ornamental fishes or the aquarium water in which they are transported and housed. Using conventional molecular approaches and next generation high-throughput amplicon sequencing of 16S ribosomal RNA gene hypervariable regions, we characterized the bacterial community of aquarium water containing common goldfish (Carassius auratus and Chinese algae eaters (Gyrinocheilus aymonieri purchased from seven pet/aquarium shops in Rhode Island and identified the presence of potential pathogens. Our survey identified a total of 30 phyla, the most common being Proteobacteria (52%, Bacteroidetes (18% and Planctomycetes (6%, with the top four phyla representing >80% of all sequences. Sequences from our water samples were most closely related to eleven bacterial species that have the potential to cause disease in fishes, humans and other species: Coxiella burnetii, Flavobacterium columnare, Legionella birminghamensis, L. pneumophila, Vibrio cholerae, V. mimicus. V. vulnificus, Aeromonas schubertii, A. veronii, A. hydrophila and Plesiomonas shigelloides. Our results, combined with evidence from the literature, suggest aquarium tank water harboring ornamental fish are an understudied source for novel microbial communities and pathogens that pose potential risks to the pet industry, fishes in trade, humans and other species.

  10. Composition of the Cockroach Gut Microbiome in the Presence of Parasitic Nematodes

    Science.gov (United States)

    Vicente, Cláudia S. L.; Ozawa, Sota; Hasegawa, Koichi

    2016-01-01

    Cockroaches are parasitized by thelastomatid nematodes, which live in an obligate manner in their hindgut and interact with the resident microbial community. In the present study, a composition analysis was performed on the gut microbiome of Periplaneta fuliginosa and P. americana to investigate natural and artificial infection by thelastomatid nematodes. Nine libraries of the 16S rRNA gene V3–V4 region were prepared for pyrosequencing. We examined the complete gut microbiome (fore-, mid-, and hindgut) of lab-reared P. fuliginosa naturally infected with the parasitic nematode Leidynema appendiculatum and those that were nematode-free, and complemented our study by characterizing the hindgut microbial communities of lab-reared P. americana naturally infected with Hammerschmidtiella diesingi and Thelastoma bulhoesi, artificially infected with L. appendiculatum, and those that were nematode-free. Our results revealed that the fore- and midgut of naturally infected and nematode-free P. fuliginosa have close microbial communities, which is in contrast with hindgut communities; the hindgut communities of both cockroaches exhibit higher microbial diversities in the presence of their natural parasites and marked differences were observed in the abundance of the most representative taxa, namely Firmicutes, Proteobacteria, and Bacteroidetes. Our results have provided basic information and encourage further studies on multitrophic interactions in the cockroach gut as well as the thelastomatid nematodes that play a role in this environment. PMID:27524304

  11. A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics

    Science.gov (United States)

    Sasaki, Daisuke; Fukuda, Itsuko; Tanaka, Kosei; Yoshida, Ken-ichi; Kondo, Akihiko; Osawa, Ro

    2016-01-01

    We devised a single-batch fermentation system to simulate human colonic microbiota from fecal samples, enabling the complex mixture of microorganisms to achieve densities of up to 1011 cells/mL in 24 h. 16S rRNA gene sequence analysis of bacteria grown in the system revealed that representatives of the major phyla, including Bacteroidetes, Firmicutes, and Actinobacteria, as well as overall species diversity, were consistent with those of the original feces. On the earlier stages of fermentation (up to 9 h), trace mixtures of acetate, lactate, and succinate were detectable; on the later stages (after 24 h), larger amounts of acetate accumulated along with some of propionate and butyrate. These patterns were similar to those observed in the original feces. Thus, this system could serve as a simple model to simulate the diversity as well as the metabolism of human colonic microbiota. Supplementation of the system with several prebiotic oligosaccharides (including fructo-, galacto-, isomalto-, and xylo-oligosaccharides; lactulose; and lactosucrose) resulted in an increased population in genus Bifidobacterium, concomitant with significant increases in acetate production. The results suggested that this fermentation system may be useful for in vitro, pre-clinical evaluation of the effects of prebiotics prior to testing in humans. PMID:27483470

  12. Illumina MiSeq sequencing reveals the key microorganisms involved in partial nitritation followed by simultaneous sludge fermentation, denitrification and anammox process.

    Science.gov (United States)

    Wang, Bo; Peng, Yongzhen; Guo, Yuanyuan; Zhao, Mengyue; Wang, Shuying

    2016-05-01

    A combined process including a partial nitritation SBR (PN-SBR) followed by a simultaneous sludge fermentation, denitrification and anammox reactor (SFDA) was established to treat low C/N domestic wastewater in this study. An average nitrite accumulation rate of 97.8% and total nitrogen of 9.4mg/L in the effluent was achieved during 140days' operation. The underlying mechanisms were investigated by using Illumina MiSeq sequencing to analyze the microbial community structures in the PN-SBR and SFDA. Results showed that the predominant bacterial phylum was Proteobacteria in the external waste activated sludge (WAS, added to the SFDA) and SFDA while Bacteroidetes in the PN-SBR. Further study indicated that in the PN-SBR, the dominant nitrobacteria, Nitrosomonas genus, facilitated nitritation and little nitrate was generated in the PN-SBR effluent. In the SFDA, the co-existence of functional microorganisms Thauera, Candidatus Anammoximicrobium and Pseudomonas were found to contribute to simultaneous sludge fermentation, denitrification and anammox. PMID:26874440

  13. Purification of high ammonia wastewater in a biofilm airlift loop bioreactor with microbial communities analysis.

    Science.gov (United States)

    Qiu, Chunsheng; Zhang, Dandan; Sun, Liping; Wen, Jianping

    2015-01-01

    A 70 m(3) gas-liquid-solid three-phase flow airlift loop bioreactor, in which biofilm attached on granular active carbon carriers, was used for purification of the high ammonia wastewater from bioethanol production. Under the optimum operating conditions, COD and NH4 (+)-N average removal rate of 89.0 and 98.6 % were obtained at hydraulic retention time of 10 h. Scanning electron microscopy was applied for observation of the biofilm formation. High contaminants removal efficiency was achieved by holding high biomass concentration in the reactor due to the attached biofilm over the carriers. The 16S rRNA gene clone library analysis indicated that 68.6 % of the clones were affiliated with the two phyla Bacteroidetes and Proteobacteria, and residual clones clustered with various sequences from uncultured bacteria. The presence of various anoxic/anaerobic bacteria indicated that the oxygen gradient inside the biofilm could provide appropriate micro-environment for nitrogen removal through simultaneous nitrification and denitrification. PMID:25344088

  14. Bacterial community composition of a wastewater treatment system reliant on N{sub 2} fixation

    Energy Technology Data Exchange (ETDEWEB)

    Reid, N.M.; Bowers, T.H.; Lloyd-Jones, G. [Scion, Rotorua (New Zealand)

    2008-05-15

    The temporal stability and change of the dominant phylogenetic groups of the domain bacteria were studied in a model plant-based industrial wastewater treatment system showing high levels of organic carbon removal supported by high levels of N{sub 2} fixation. Community profiles were obtained through terminal restriction fragment length polymorphism analysis and cloning of 16S rRNA amplicons followed by sequencing. Bacterial community profiles showed that ten common terminal restriction fragments made up approximately 50% of the measured bacterial community. As much as 42% of the measured bacterial community could be monitored by using quantitative PCR and primers that targeted three dominant operational taxonomic units. Despite changes in wastewater composition and dissolved oxygen levels, the bacterial community composition appeared stable and was dominated by {alpha}-Proteobacteria and {beta}-Proteobacteria, with a lesser amount of the highly diverse bacterial phylum Bacteroidetes. A short period of considerable change in the bacterial community composition did not appear to affect treatment performance indicating functional redundancy in this treatment system. (orig.)

  15. Microbial communities of urban stormwater sediments: the phylogenetic structure of bacterial communities varies with porosity.

    Science.gov (United States)

    Badin, Anne-Laure; Mustafa, Tarfa; Bertrand, Cédric; Monier, Armelle; Delolme, Cécile; Geremia, Roberto A; Bedell, Jean-Philippe

    2012-08-01

    This study focuses on the distribution of bacterial and fungal communities within the microstructure of a multi-contaminated sedimentary layer resulting from urban stormwater infiltration. Fractionation was performed on the basis of differential porosity and aggregate grain size, resulting in five fractions: leachable fitting macroporosity, 1000 μm. Amounts of both bacterial and fungal biomasses are greater in the < 10 μm and leachable fractions. The aggregates contain numerous bacteria but very low amounts of fungal biomass. Single-strand conformational polymorphism molecular profiles highlighted the differences between bacterial and fungal communities of the leachable fraction and those of the aggregates. Random Sanger sequencing of ssu clones revealed that these differences were mainly because of the presence of Epsilonproteobacteria and Firmicutes in the leachable fractions, while the aggregates contained more Cyanobacteria. The Cyanobacteria phylotypes in the aggregates were dominated by the sequences related to Microcoleus vaginatus while the leachable fractions presented the sequences of chloroplastic origin. Therefore, more than 50% of the phylotypes observed were related to Proteobacteria while 40% were related to Cyanobacteria and Bacteroidetes. Preferential distribution of clades in almost all the phyla or classes detected was observed. This study provides insight into the identities of dominant members of the bacterial communities of urban sediments. Microcoleus vaginatus appeared to predominate in pioneer soils. PMID:22404135

  16. Efficient electricity generation from sewage sludge using biocathode microbial fuel cell.

    Science.gov (United States)

    Zhang, Guodong; Zhao, Qingliang; Jiao, Yan; Wang, Kun; Lee, Duu-Jong; Ren, Nanqi

    2012-01-01

    Microbial fuel cells (MFCs) with abiotic cathodes require expensive catalyst (such as Pt) or catholyte (such as hexacynoferrate) to facilitate oxidation reactions. This study incorporated biocathodes into a three-chamber MFC to yield electricity from sewage sludge at maximum power output of 13.2 ± 1.7 W/m(3) during polarization, much higher than those previously reported. After 15 d operation, the total chemical oxygen demand (TCOD) removal and coulombic efficiency (CE) of cell reached 40.8 ± 9.0% and 19.4 ± 4.3%, respectively. The anolyte comprised principally acetate and propionate (minor) as metabolites. The use of biocathodes produced an internal resistance of 36-46 Ω, lower than those reported in literature works, hence yielding higher maximum power density from MFC. The massively parallel sequencing technology, 454 pyrosequencing technique, was adopted to probe microbial community on anode biofilm, with dominant phyla belonging to Proteobacteria (45% of total bacteria), Bacteroidetes (19%), Uncultured bacteria (9%), Actinobacteria (7%), Firmicutes (7%), Chloroflex (7%). At genera level, Rhodoferax, Ferruginibacter, Propionibacterium, Rhodopseudomonas, Ferribacterium, Clostridium, Chlorobaculum, Rhodobacter, Bradyrhizobium were the abundant taxa (relative abundances>2.0%). PMID:22078254

  17. Mediterranean diet and faecal microbiota: a transversal study.

    Science.gov (United States)

    Gutiérrez-Díaz, I; Fernández-Navarro, T; Sánchez, B; Margolles, A; González, S

    2016-05-18

    Despite the existing evidence on the impact of olive oil and red wine on the intestinal microbiota, the effect of the global Mediterranean Diet (MD) has not been sufficiently studied. We explored the association between the adherence to a Mediterranean dietary pattern, and its components, with faecal microbiota in a cohort of adults with non-declared pathology. This transversal study involved 31 adults without a previous diagnosis of cancer, autoimmune or digestive diseases. Based on the data obtained by means of an annual food frequency questionnaire (FFQ), and the information existing in the literature, a Mediterranean Diet Score (MDS) was calculated. Dietary fibre was obtained from Marlett et al. tables and Phenol-Explorer Database was used for phenolic compounds intake. Quantification of microbial groups was performed by Ion Torrent 16S rRNA gene-based analysis and quantification of short-chain fatty acids (SCFAs) was performed using gas chromatography-mass spectrometry (MS). MDS was associated with a higher abundance of Bacteroidetes (p = 0.001), Prevotellacea (p = 0.002) and Prevotella (p = 0.003) and a lower concentration of Firmicutes (p = 0.003) and Lachnospiraceae (p = 0.045). Also, in subjects with MDS ≥ 4, higher concentrations of faecal propionate (p = 0.034) and butyrate (p = 0.018) were detected. These results confirm the complexity of the diet-microbiota interrelationship. PMID:27137178

  18. Correlation between microbial community structure and biofouling as determined by analysis of microbial community dynamics.

    Science.gov (United States)

    Guo, Xuechao; Miao, Yu; Wu, Bing; Ye, Lin; Yu, Haiyan; Liu, Su; Zhang, Xu-Xiang

    2015-12-01

    Three lab-scale membrane bioreactors (MBRs) were continuously operated to treat saline wastewater under 0%, 0.75% and 1.5% NaCl stress. 0.75% and 1.5% NaCl reduced the COD and NH4(+)-N removal at the beginning, while the removal efficiencies could be recovered along with the operation of MBRs. Also, the polysaccharide in extracellular polymeric substances (EPS) and soluble microbial products (SMP) played an important role in the membrane fouling. Illumina sequencing of 16S rRNA gene showed that the increasing level of salinity reduced the diversity of the microbial community, and a higher salinity stimulated the growth of Bacteroidetes. At genus level, Flavobacterium, Aequorivita, Gelidibacter, Microbacterium, and Algoriphagus increased with the increase of salinity, which are shown to be highly salt tolerant. The strength of salinity or the duration of salinity could stimulate the microorganisms with similar functions, and the changes of polysaccharide in EPS and SMP were closely related to the membrane fouling rate as well as correlated with some saline-resistance genera. PMID:26318928

  19. Bacterial community analysis of contaminant soils from Chernobyl

    International Nuclear Information System (INIS)

    Complete text of publication follows: Shortly after the Chernobyl accident in 1986, vegetation, contaminated soil and other radioactive debris were buried in situ in trenches. The aims of this work are to analyse the structure of bacterial communities evolving in this environment since 20 years, and to evaluate the potential role of microorganisms in radionuclide migration in soils. Therefore, soil samples exhibiting contrasted radionuclides content were collected in and around the trench number 22. Bacterial communities were examined using a genetic fingerprinting method that allowed a comparative profiling of the samples (DGGE), with universal and group-specific PCR primers. Our results indicate that Chernobyl soil samples host a wide diversity of Bacteria, with stable patterns for Firmicutes and Actinobacteria and more variable for Proteobacteria. A collection of 650 aerobic and anaerobic culturable isolates was also constructed. A phylogenetic analysis of 250 heterotrophic aerobic isolates revealed that 5 phyla are represented: Beta-, Gamma-proteobacteria, Actinobacteria, Bacteroidetes and spore-forming Firmicutes, which is largely dominant. These collection will be screened for the presence of radionuclide-accumulating species in order to estimate the potential influence of microorganisms in radionuclides migration in soils

  20. Endo- and exoglucanase activities in bacteria from mangrove sediment.

    Science.gov (United States)

    Soares Júnior, Fábio Lino; Dias, Armando Cavalcante Franco; Fasanella, Cristiane Cipola; Taketani, Rodrigo Gouvêa; de Souza Lima, André Oliveira; Melo, Itamar Soares; Andreote, Fernando Dini

    2013-01-01

    The mangrove ecosystem is an unexplored source for biotechnological applications. In this unique environment, endemic bacteria have the ability to thrive in the harsh environmental conditions (salinity and anaerobiosis), and act in the degradation of organic matter, promoting nutrient cycles. Thus, this study aimed to assess the cellulolytic activities of bacterial groups present in the sediment from a mangrove located in Ilha do Cardoso (SP, Brazil). To optimize the isolation of cellulolytic bacteria, enrichments in two types of culture media (tryptone broth and minimum salt medium), both supplemented with 5% NaCl and 1% of cellulose, were performed. Tests conducted with the obtained colonies showed a higher occurrence of endoglycolytic activity (33 isolates) than exoglycolytic (19 isolates), and the degradation activity was shown to be modulated by the presence of NaCl. The isolated bacteria were clustered by BOX-PCR and further classified on the basis of partial 16S rRNA sequences as Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes or Bacteroidetes. Therefore, this study highlights the importance of studies focusing on the endemic species found in mangroves to exploit them as novel biotechnological tools for the degradation of cellulose. PMID:24516466

  1. Endo-and exoglucanase activities in bacteria from mangrove sediment

    Directory of Open Access Journals (Sweden)

    Fábio Lino Soares Júnior

    2013-09-01

    Full Text Available The mangrove ecosystem is an unexplored source for biotechnological applications. In this unique environment, endemic bacteria have the ability to thrive in the harsh environmental conditions (salinity and anaerobiosis, and act in the degradation of organic matter, promoting nutrient cycles. Thus, this study aimed to assess the cellulolytic activities of bacterial groups present in the sediment from a mangrove located in Ilha do Cardoso (SP, Brazil. To optimize the isolation of cellulolytic bacteria, enrichments in two types of culture media (tryptone broth and minimum salt medium, both supplemented with 5% NaCl and 1% of cellulose, were performed. Tests conducted with the obtained colonies showed a higher occurrence of endoglycolytic activity (33 isolates than exoglycolytic (19 isolates, and the degradation activity was shown to be modulated by the presence of NaCl. The isolated bacteria were clustered by BOX-PCR and further classified on the basis of partial 16S rRNA sequences as Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes or Bacteroidetes. Therefore, this study highlights the importance of studies focusing on the endemic species found in mangroves to exploit them as novel biotechnological tools for the degradation of cellulose.

  2. Isolation and Identification of Cellulolytic Bacteria from the Gut of Holotrichia parallela Larvae (Coleoptera: Scarabaeidae

    Directory of Open Access Journals (Sweden)

    Hongyu Zhang

    2012-02-01

    Full Text Available In this study, 207 strains of aerobic and facultatively anaerobic cellulolytic bacteria were isolated from the gut of Holotrichia parallela larvae. These bacterial isolates were assigned to 21 genotypes by amplified ribosomal DNA restriction analysis (ARDRA. A partial 16S rDNA sequence analysis and standard biochemical and physiological tests were used for the assignment of the 21 representative isolates. Our results show that the cellulolytic bacterial community is dominated by the Proteobacteria (70.05%, followed by the Actinobacteria (24.15%, the Firmicutes (4.35%, and the Bacteroidetes (1.45%. At the genus level, Gram-negative bacteria including Pseudomonas, Ochrobactrum, Rhizobium, Cellulosimicrobium, and Microbacterium were the predominant groups, but members of Bacillus, Dyadobacter, Siphonobacter, Paracoccus, Kaistia, Devosia, Labrys, Ensifer, Variovorax, Shinella, Citrobacter, and Stenotrophomonas were also found. Furthermore, our results suggest that a significant amount of bacterial diversity exists among the cellulolytic bacteria, and that Siphonobacter aquaeclarae, Cellulosimicrobium funkei, Paracoccus sulfuroxidans, Ochrobactrum cytisi, Ochrobactrum haematophilum, Kaistia adipata, Devosia riboflavina, Labrys neptuniae, Ensifer adhaerens, Shinella zoogloeoides, Citrobacter freundii, and Pseudomonas nitroreducens are reported to be cellulolytic for the first time in this study. Our results indicate that the scarab gut is an attractive source for the study of novel cellulolytic microorganisms and enzymes useful for cellulose degradation.

  3. Endo- and exoglucanase activities in bacteria from mangrove sediment

    Science.gov (United States)

    Júnior, Fábio Lino Soares; Dias, Armando Cavalcante Franco; Fasanella, Cristiane Cipola; Taketani, Rodrigo Gouvêa; de Souza Lima, André Oliveira; Melo, Itamar Soares; Andreote, Fernando Dini

    2013-01-01

    The mangrove ecosystem is an unexplored source for biotechnological applications. In this unique environment, endemic bacteria have the ability to thrive in the harsh environmental conditions (salinity and anaerobiosis), and act in the degradation of organic matter, promoting nutrient cycles. Thus, this study aimed to assess the cellulolytic activities of bacterial groups present in the sediment from a mangrove located in Ilha do Cardoso (SP, Brazil). To optimize the isolation of cellulolytic bacteria, enrichments in two types of culture media (tryptone broth and minimum salt medium), both supplemented with 5% NaCl and 1% of cellulose, were performed. Tests conducted with the obtained colonies showed a higher occurrence of endoglycolytic activity (33 isolates) than exoglycolytic (19 isolates), and the degradation activity was shown to be modulated by the presence of NaCl. The isolated bacteria were clustered by BOX-PCR and further classified on the basis of partial 16S rRNA sequences as Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes or Bacteroidetes. Therefore, this study highlights the importance of studies focusing on the endemic species found in mangroves to exploit them as novel biotechnological tools for the degradation of cellulose. PMID:24516466

  4. Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

    Science.gov (United States)

    Ridl, Jakub; Kolar, Michal; Strejcek, Michal; Strnad, Hynek; Stursa, Petr; Paces, Jan; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas. PMID:27446035

  5. Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke.

    Science.gov (United States)

    Yang, Hui; Hu, Jinxiang; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-01-01

    The interaction between roots and bacterial communities in halophytic species is poorly understood. Here, we used Jerusalem artichoke cultivar Nanyu 1 (NY-1) to characterise root distribution patterns and determine diversity and abundance of bacteria in the rhizosphere soil under variable salinity. Root growth was not inhibited within the salinity range 1.2 to 1.9 g salt/kg, but roots were mainly confined to 0-20 cm soil layer vertically and 0-30 cm horizontally from the plant centre. Root concentrations of K(+), Na(+), Mg(2+) and particularly Ca(2+) were relatively high under salinity stress. High salinity stress decreased soil invertase and catalase activity. Using a next-generation, Illumina-based sequencing approach, we determined higher diversity of bacteria in the rhizosphere soil at high than low salinity. More than 15,500 valid reads were obtained, and Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria predominated in all samples, accounting for >80% of the reads. On a genus level, 636 genera were common to the low and high salinity treatments at 0-5 cm and 5-10 cm depth. The abundance of Steroidobacter and Sphingomonas was significantly decreased by increasing salinity. Higher Shannon and Chao 1 indices with increasing severity of salt stress indicated that high salt stress increased diversity in the bacterial communities. PMID:26852800

  6. Pontibacter locisalis Sy30T sp. nov. isolated from soil collected from an abandoned saltern.

    Science.gov (United States)

    Zhou, Yan-Xia; Xie, Zhi-Hong; Zhao, Jin-Xin; Du, Zong-Jun; Chen, Guan-Jun

    2016-03-01

    A novel Gram-stain negative, red, rod-shaped, non-motile and aerobic bacterial strain, designated Sy30(T), was isolated from dry soils of an abandoned marine saltern at Weihai, China. 16S rRNA sequence analysis indicated that strain Sy30(T) belongs to the genus Pontibacter in the family Cytophagaceae, with sequence similarities ranging from 93.3 to 96.4 % with other type species of the genus Pontibacter. The predominant cellular fatty acids were iso-C15:0 and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B). The major menaquinone was MK-7. The major polyamine was sym-homospermidine. The DNA G+C content was 47.7 mol%. The major polar lipids consisted of phosphatidylethanolamine, phosphoaminolipid and two unidentified polar lipid. Based on phenotypic, chemotaxonomic and phylogenetic analysis, strain Sy30(T) represents a novel species of the genus Pontibacter in the family Cytophagaceae, phylum Bacteroidetes, for which the name Pontibacter locisalis sp. nov. is proposed. The type strain is Sy30(T) (=KCTC 42498(T) = CICC AB 2015060(T)). PMID:26833190

  7. Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters.

    Science.gov (United States)

    Gannoun, Hana; Omri, Ilhem; Chouari, Rakia; Khelifi, Eltaief; Keskes, Sajiaa; Godon, Jean-Jacques; Hamdi, Moktar; Sghir, Abdelghani; Bouallagui, Hassib

    2016-02-01

    The effect of increasing the organic loading rates (OLRs) on the performance of the anaerobic codigestion of olive mill (OMW) and abattoir wastewaters (AW) was investigated under mesophilic and thermophilic conditions. The structure of the microbial community was also monitored. Increasing OLR to 9g of chemical oxygen demand (COD) L(-1)d(-1) affected significantly the biogas yield and microbial diversity at 35°C. However, at 55°C digester remained stable until OLR of 12g of CODL(-1)d(-1) with higher COD removal (80%) and biogas yield (0.52Lg(-1) COD removed). Significant differences in the bacterial communities were detected between mesophilic and thermophilic conditions. The dominant phyla detected in the digester at both phases were the Firmicutes, Actinobacteria, Bacteroidetes, Synergistetes and Spirochaete. However, Verrucomicrobia, Proteobacteria and the candidate division BRC1 were only detected at thermophilic conditions. The Methanobacteriales and the Thermoplasmales were found as a high predominant archaeal member in the anaerobic sludge. PMID:26687494

  8. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Wuttichai Mhuantong

    Full Text Available The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

  9. Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans.

    Science.gov (United States)

    Ushida, Kazunari; Segawa, Takahiro; Tsuchida, Sayaka; Murata, Koichi

    2016-02-01

    Preservation of indigenous gastrointestinal microbiota is deemed to be critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we investigated cecal bacterial communities in wild Japanese rock ptarmigans (Lagopus muta japonica) and compared them with those in Svalbard rock ptarmigans (L. m. hyperborea) in captivity. Ultra-deep sequencing of 16S rRNA gene indicated that the community structure of cecal microbiota in wild rock ptarmigans was remarkably different from that in captive Svalbard rock ptarmigans. Fundamental differences between bacterial communities in the two groups of birds were detected at the phylum level. Firmicutes, Actinobacteria, Bacteroidetes and Synergistetes were the major phyla detected in wild Japanese rock ptarmigans, whereas Firmicutes alone occupied more than 80% of abundance in captive Svalbard rock ptarmigans. Furthermore, unclassified genera of Coriobacteriaceae, Synergistaceae, Bacteroidaceae, Actinomycetaceae, Veillonellaceae and Clostridiales were the major taxa detected in wild individuals, whereas in zoo-reared birds, major genera were Ruminococcus, Blautia, Faecalibacterium and Akkermansia. Zoo-reared birds seemed to lack almost all rock ptarmigan-specific bacteria in their intestine, which may explain the relatively high rate of pathogenic infections affecting them. We show evidence that preservation and reconstitution of indigenous cecal microflora are critical for successful ex situ conservation and future re-introduction plan for the Japanese rock ptarmigan. PMID:26468217

  10. Dynamics of Gut Microbiota According to the Delivery Mode in Healthy Korean Infants.

    Science.gov (United States)

    Lee, Eun; Kim, Byoung Ju; Kang, Mi Jin; Choi, Kil Yong; Cho, Hyun Ju; Kim, Yeongho; Yang, Song I; Jung, Young Ho; Kim, Hyung Young; Seo, Ju Hee; Kwon, Ji Won; Kim, Hyo Bin; Lee, So Yeon; Hong, Soo Jong

    2016-09-01

    Microbial colonization of the infant gut is unstable and shows a wide range of diversity between individuals. Gut microbiota play an important role in the development of the immune system, and an imbalance in these organisms can affect health, including an increased risk of allergic diseases. Microbial colonization of young infants is affected by the delivery mode at birth and the consequent alterations of gut microbiota in early life affect the development of allergic diseases. We investigated the effects of the delivery mode on the temporal dynamics of gut microbiota in healthy Korean infants. Fecal samples were collected at 1-3 days, 1 month, and 6 months after birth in six healthy infants. Microbiota were characterized by 16S rRNA shotgun sequencing. At the first and third days of life, infants born by vaginal delivery showed a higher richness and diversity of gut microbiota compared with those born by cesarean section. However, these differences disappeared with age. The Bacteroides genus and Bacteroidetes phylum were abundant in infants born by vaginal delivery, whereas Bacilli and Clostridium g4 were increased in infants born by cesarean section. The Firmicutes phylum and Bacteroides genus showed convergent dynamics with age. This study demonstrated the effect of delivery mode on the dynamics of gut microbiota profiles in healthy Korean infants. PMID:27334787

  11. A survey of bacterial diversity from successive life stages of black soldier fly (Diptera: Stratiomyidae) by using 16S rDNA pyrosequencing.

    Science.gov (United States)

    Zheng, Longyu; Crippen, Tawni L; Singh, Baneshwar; Tarone, Aaron M; Dowd, Scot; Yu, Ziniu; Wood, Thomas K; Tomberlin, Jeffery K

    2013-05-01

    Sustainable methods for managing waste associated with people and animals have been proposed in the past. Black soldier fly, Hermetia illucens (L.), larvae represent one of the more promising methods. Larvae reduce dry matter, bacteria, offensive odor, and house fly populations. Prepupae can be used as feedstuff for livestock. However, it is not known if such a method results in the proliferation of potential pathogens. Although some bacterial species have been cultured and identified from black soldier fly, a true appreciation of fly associated bacterial diversity is not known. Such information is needed to understand pathogen colonization on decomposing animal and plant waste in the presence of black soldier fly larvae as well as develop research strategies for maximizing the use of this fly to reduce waste without risking environmental harm. Using 454 sequencing, we surveyed bacterial diversity associated with successive life stages of the black soldier fly reared on plant material. Bacteria diversity classified (99.8%) across all life stages spanned six bacterial phyla with > or = 80% bootstrap support. Bacteroidetes and Proteobacteria were the most dominant phyla associated with the black soldier fly accounting for two-thirds of the fauna identified. Many of these bacteria would go undetected because of their inability to be cultured. PMID:23802462

  12. Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana.

    Science.gov (United States)

    Berlanga, Mercedes; Llorens, Carlos; Comas, Jaume; Guerrero, Ricardo

    2016-01-01

    Cryptocercus punctulatus and Parasphaeria boleiriana are two distantly related xylophagous and subsocial cockroaches. Cryptocercus is related to termites. Xylophagous cockroaches and termites are excellent model organisms for studying the symbiotic relationship between the insect and their microbiota. In this study, high-throughput 454 pyrosequencing of 16S rRNA was used to investigate the diversity of metagenomic gut communities of C. punctulatus and P. boleiriana, and thereby to identify possible shifts in symbiont allegiances during cockroaches evolution. Our results revealed that the hindgut prokaryotic communities of both xylophagous cockroaches are dominated by members of four Bacteria phyla: Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Other identified phyla were Spirochaetes, Planctomycetes, candidatus Saccharibacteria (formerly TM7), and Acidobacteria, each of which represented 1-2% of the total population detected. Community similarity based on phylogenetic relatedness by unweighted UniFrac analyses indicated that the composition of the bacterial community in the two species was significantly different (P termites and other cockroaches, but not with those from other animals or environments. These results suggest that, during their evolution, those cockroaches conserved several bacterial communities from the microbiota of a common ancestor. The ecological stability of those microbial communities may imply the important functional role for the survival of the host of providing nutrients in appropriate quantities and balance. PMID:27054320

  13. Molecular diversity of bacteria in commercially available "Spirulina" food supplements.

    Science.gov (United States)

    Vardaka, Elisabeth; Kormas, Konstantinos A; Katsiapi, Matina; Genitsaris, Savvas; Moustaka-Gouni, Maria

    2016-01-01

    The cyanobacterium Arthrospira is among the most well-known food supplements worldwide known as "Spirulina." While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of "Spirulina" supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of "Spirulina" dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) of Arthrospira platensis were the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9-157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e., Pseudomonas, Flavobacterium, Vibrio, Aeromonas, Clostridium, Bacillus, Fusobacterium, Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing of Arthrospira biomass for commercial purposes. PMID:26819852

  14. Altered Fecal Microbiota Correlates with Liver Biochemistry in Nonobese Patients with Non-alcoholic Fatty Liver Disease.

    Science.gov (United States)

    Wang, Baohong; Jiang, Xiangyang; Cao, Min; Ge, Jianping; Bao, Qiongling; Tang, Lingling; Chen, Yu; Li, Lanjuan

    2016-01-01

    Increasing evidence suggests a role of intestinal dysbiosis in obesity and non-alcoholic fatty liver disease (NAFLD). But it remains unknown in nonobese NAFLD. This prospective, cross-sectional study sought to characterize differences in fecal microbiota between nonobese adult individuals with and without NAFLD and their potential association with metabolic markers of disease progression. A total of 126 nonobese subjects were enrolled: 43 NAFLD and 83 healthy controls (HC). The microbial community was profiled by denaturing gradient gel electrophoresis and examined by 454 pyrosequencing of the 16S ribosomal RNA V3 region. Lower diversity and a phylum-level change in the fecal microbiome were found in NAFLD. Compared with HC, patients had 20% more phylum Bacteroidetes (p = 0.005) and 24% less Firmicutes (p = 0.002). Within Firmicutes, four families and their 8 genera, which were short-chain fatty acids-producing and 7α-dehydroxylating bacteria, were significantly decreased. Moreover, Gram-negative (G-) bacteria were prevalent in NAFLD (p = 0.008). Furthermore, a significant correlation with metabolic markers was revealed for disturbed microbiota in NAFLD. This novel study indicated that intestinal dysbiosis was associated with nonobese NAFLD and might increase the risk of NAFLD progression. PMID:27550547

  15. Characterization of microbiota composition and presence of selected antibiotic resistance genes in carriage water of ornamental fish.

    Directory of Open Access Journals (Sweden)

    Lenka Gerzova

    Full Text Available International trade with ornamental fish is gradually recognized as an important source of a wide range of different antibiotic resistant bacteria. In this study we therefore characterized the prevalence of selected antibiotic resistance genes in the microbiota found in the carriage water of ornamental fish originating from 3 different continents. Real-time PCR quantification showed that the sul1 gene was present in 11 out of 100 bacteria. tet(A was present in 6 out of 100 bacteria and strA, tet(G, sul2 and aadA were present in 1-2 copies per 100 bacteria. Class I integrons were quite common in carriage water microbiota, however, pyrosequencing showed that only 12 different antibiotic gene cassettes were present in class I integrons. The microbiota characterized by pyrosequencing of the V3/V4 variable region of 16S rRNA genes consisted of Proteobacteria (48%, Bacteroidetes (29.5%, Firmicutes (17.8%, Actinobacteria (2.1% and Fusobacteria (1.6%. Correlation analysis between antibiotic resistance gene prevalence and microbiota composition verified by bacterial culture showed that major reservoirs of sul1 sul2, tet(A, tet(B tet(G, cat, cml, bla, strA, aacA, aph and aadA could be found among Alpha-, Beta- and Gammaproteobacteria with representatives of Enterobacteriaceae, Pseudomonadaceae, Rhizobiaceae and Comamonadaceae being those most positively associated with the tested antibiotic resistance genes.

  16. Human symbionts inject and neutralize antibacterial toxins to persist in the gut.

    Science.gov (United States)

    Wexler, Aaron G; Bao, Yiqiao; Whitney, John C; Bobay, Louis-Marie; Xavier, Joao B; Schofield, Whitman B; Barry, Natasha A; Russell, Alistair B; Tran, Bao Q; Goo, Young Ah; Goodlett, David R; Ochman, Howard; Mougous, Joseph D; Goodman, Andrew L

    2016-03-29

    The human gut microbiome is a dynamic and densely populated microbial community that can provide important benefits to its host. Cooperation and competition for nutrients among its constituents only partially explain community composition and interpersonal variation. Notably, certain human-associated Bacteroidetes-one of two major phyla in the gut-also encode machinery for contact-dependent interbacterial antagonism, but its impact within gut microbial communities remains unknown. Here we report that prominent human gut symbionts persist in the gut through continuous attack on their immediate neighbors. Our analysis of just one of the hundreds of species in these communities reveals 12 candidate antibacterial effector loci that can exist in 32 combinations. Through the use of secretome studies, in vitro bacterial interaction assays and multiple mouse models, we uncover strain-specific effector/immunity repertoires that can predict interbacterial interactions in vitro and in vivo, and find that some of these strains avoid contact-dependent killing by accumulating immunity genes to effectors that they do not encode. Effector transmission rates in live animals can exceed 1 billion events per minute per gram of colonic contents, and multiphylum communities of human gut commensals can partially protect sensitive strains from these attacks. Together, these results suggest that gut microbes can determine their interactions through direct contact. An understanding of the strategies human gut symbionts have evolved to target other members of this community may provide new approaches for microbiome manipulation. PMID:26957597

  17. Bioaugmentation with an acetate-type fermentation bacterium Acetobacteroides hydrogenigenes improves methane production from corn straw.

    Science.gov (United States)

    Zhang, Jie; Guo, Rong-Bo; Qiu, Yan-Ling; Qiao, Jiang-Tao; Yuan, Xian-Zheng; Shi, Xiao-Shuang; Wang, Chuan-Shui

    2015-03-01

    The effect of bioaugmentation with an acetate-type fermentation bacterium in the phylum Bacteroidetes on the anaerobic digestion of corn straw was evaluated by batch experiments. Acetobacteroides hydrogenigenes is a promising strain for bioaugmentation with relatively high growth rate, hydrogen yields and acetate tolerance, which ferments a broad spectrum of pentoses, hexoses and polyoses mainly into acetate and hydrogen. During corn straw digestion, bioaugmentation with A. hydrogenigenes led to 19-23% increase of the methane yield, with maximum of 258.1 mL/g-corn straw achieved by 10% inoculation (control, 209.3 mL/g-corn straw). Analysis of lignocellulosic composition indicated that A. hydrogenigenes could increase removal rates of cellulose and hemicelluloses in corn straw residue by 12% and 5%, respectively. Further experiment verified that the addition of A. hydrogenigenes could improve the methane yields of methyl cellulose and xylan (models for cellulose and hemicelluloses, respectively) by 16.8% and 7.0%. PMID:25549904

  18. Impact of Chloramination on the Development of Laboratory-Grown Biofilms Fed with Filter-Pretreated Groundwater

    KAUST Repository

    Ling, Fangqiong

    2013-01-01

    This study evaluated the continuous impact of monochloramine disinfection on laboratory-grown biofilms through the characterization of biofilm architecture and microbial community structure. Biofilm development and disinfection were achieved using CDC (Centers for Disease Control and Prevention) biofilm reactor systems with polyvinyl chloride (PVC) coupons as the substratum and sand filter-pretreated groundwater as the source of microbial seeding and growth nutrient. After 2 weeks of growth, the biofilms were subjected to chloramination for 8 more weeks at concentrations of 7.5±1.4 to 9.1±0.4 mg Cl2 L-1. Control reactors received no disinfection during the development of biofilms. Confocal laser scanning microscopy and image analysis indicated that chloramination could lead to 81.4-83.5% and 86.3-95.6% reduction in biofilm biomass and thickness, respectively, but could not eliminate biofilm growth. 16S rRNA gene terminal restriction fragment length polymorphism analysis indicated that microbial community structures between chloraminated and non-chloraminated biofilms exhibited different successional trends. 16S rRNA gene pyrosequencing analysis further revealed that chloramination could select members of Actinobacteria and Acidobacteria as the dominant populations, whereas natural development leads to the selection of members of Nitrospira and Bacteroidetes as dominant biofilm populations. Overall, chloramination treatment could alter the growth of multi-species biofilms on the PVC surface, shape the biofilm architecture, and select a certain microbial community that can survive or proliferate under chloramination.

  19. Acylhomoserine lactone production and degradation by the fish pathogen Tenacibaculum maritimum, a member of the Cytophaga-Flavobacterium-Bacteroides (CFB) group.

    Science.gov (United States)

    Romero, Manuel; Avendaño-Herrera, Rubén; Magariños, Beatriz; Cámara, Miguel; Otero, Ana

    2010-03-01

    Tenacibaculum maritimum (formerly Flexibacter maritimus) is a filamentous, biofilm-forming member of the Cytophaga-Flavobacterium-Bacteroides group (or Bacteroidetes), which causes the widely distributed marine fish disease tenacibaculosis. A search for N-acylhomoserine lactones (AHLs) quorum-sensing (QS) signals in the culture media of nine representative strains of this species using different biosensor strains revealed the presence of short-type AHL activity in all of them. N-butyryl-L-homoserine lactone (C4-HSL) was identified in T. maritimum NCIMB2154(T) by LC-MS. A degradation activity for long-acyl AHLs (C10-HSL) was subsequently demonstrated in T. maritimum NCIMB2154(T). The acidification of the culture medium after degradation did not allow the recovery of C10-HSL, which indicates a possible acylase-type degradation activity. Even though the physiological processes under the control of AHL-mediated QS in T. maritimum need to be further characterized, this discovery extends the paradigm of AHL-mediated QS signalling beyond the Proteobacteria and reinforces its ecological significance. PMID:20377642

  20. Tenacibaculum dicentrarchi sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from European sea bass.

    Science.gov (United States)

    Piñeiro-Vidal, Maximino; Gijón, Daniel; Zarza, Carles; Santos, Ysabel

    2012-02-01

    A novel Gram-stain-negative rod-shaped gliding bacterial strain, designated 35/09(T), was isolated from diseased European sea bass (Dicentrarchus labrax L.) in Spain. Colonies were pale-yellow-pigmented with uneven edges and did not adhere to the agar. The DNA G+C content of the isolate was 31.3 mol%. 16S rRNA gene sequence analysis indicated affiliation to the genus Tenacibaculum (family Flavobacteriaceae, phylum 'Bacteroidetes'). Sequence similarities between the isolate and type strains of other members of the genus were 93.1-97.3 %. The major fatty acids (>5 % of the total fatty acids) were iso-C(15 : 0) (24.8 %), iso-C(15 : 0) 3-OH (18.0 %), anteiso-C(15 : 0) (8.1 %), C(15 : 1)ω6c (6.9 %) and iso-C(15 : 1) (6.2 %). Genotypic and phenotypic data indicate that strain 35/09(T) should be classified as a representative of a novel species in the genus Tenacibaculum, for which the name Tenacibaculum dicentrarchi sp. nov. is proposed; the type strain is 35/09(T) ( = CECT 7612(T) = NCIMB 14598(T)). PMID:21460137

  1. Spongiiferula fulva gen. nov., sp. nov., a Bacterium of the Family Flavobacteriaceae Isolated from a Marine Sponge.

    Science.gov (United States)

    Yoon, Jaewoo; Adachi, Kyoko; Kasai, Hiroaki

    2016-07-01

    A Gram stain-negative, strictly aerobic, brown-pigmented, non-motile, rod-shaped, chemoheterotrophic bacterial strain-designated A6F-119(T) was isolated from a marine sponge (Rhabdastrella sp.). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the new strain represented a member of the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (93 %) to Tenacibaculum maritimum NBRC 15946(T). The strain could be differentiated phenotypically from the recognized members of the family Flavobacteriaceae. The DNA G + C content of strain A6F-119(T) was determined to be 30.8 mol%; MK-6 was identified as the major menaquinone; and the presence of iso-C15:0, iso-C17:0 3-OH, and C16:1 ω7c and/or C16:1 ω6c as the major (>10 %) cellular fatty acids. A polar lipid profile was present consisting of phosphatidylethanolamine, an unidentified aminolipid, and three unidentified lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Spongiiferula fulva gen. nov., sp. nov. is proposed. The type strain of S. fulva is A6F-119(T) (= KCTC 42752(T) = NBRC 111402(T)). PMID:26960291

  2. Interactions between multiple helminths and the gut microbiota in wild rodents

    Science.gov (United States)

    Kreisinger, Jakub; Bastien, Géraldine; Hauffe, Heidi C; Marchesi, Julian; Perkins, Sarah E

    2015-01-01

    The gut microbiota is vital to host health and, as such, it is important to elucidate the mechanisms altering its composition and diversity. Intestinal helminths are host immunomodulators and have evolved both temporally and spatially in close association with the gut microbiota, resulting in potential mechanistic interplay. Host–helminth and host–microbiota interactions are comparatively well-examined, unlike microbiota–helminth relationships, which typically focus on experimental infection with a single helminth species in laboratory animals. Here, in addition to a review of the literature on helminth–microbiota interactions, we examined empirically the association between microbiota diversity and composition and natural infection of multiple helminth species in wild mice (Apodemus flavicollis), using 16S rRNA gene catalogues (metataxonomics). In general, helminth presence is linked with high microbiota diversity, which may confer health benefits to the host. Within our wild rodent system variation in the composition and abundance of gut microbial taxa associated with helminths was specific to each helminth species and occurred both up- and downstream of a given helminth's niche (gut position). The most pronounced helminth–microbiota association was between the presence of tapeworms in the small intestine and increased S24–7 (Bacteroidetes) family in the stomach. Helminths clearly have the potential to alter gut homeostasis. Free-living rodents with a diverse helminth community offer a useful model system that enables both correlative (this study) and manipulative inference to elucidate helminth–microbiota interactions. PMID:26150661

  3. Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana

    Science.gov (United States)

    Berlanga, Mercedes; Llorens, Carlos; Comas, Jaume; Guerrero, Ricardo

    2016-01-01

    Cryptocercus punctulatus and Parasphaeria boleiriana are two distantly related xylophagous and subsocial cockroaches. Cryptocercus is related to termites. Xylophagous cockroaches and termites are excellent model organisms for studying the symbiotic relationship between the insect and their microbiota. In this study, high-throughput 454 pyrosequencing of 16S rRNA was used to investigate the diversity of metagenomic gut communities of C. punctulatus and P. boleiriana, and thereby to identify possible shifts in symbiont allegiances during cockroaches evolution. Our results revealed that the hindgut prokaryotic communities of both xylophagous cockroaches are dominated by members of four Bacteria phyla: Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Other identified phyla were Spirochaetes, Planctomycetes, candidatus Saccharibacteria (formerly TM7), and Acidobacteria, each of which represented 1–2% of the total population detected. Community similarity based on phylogenetic relatedness by unweighted UniFrac analyses indicated that the composition of the bacterial community in the two species was significantly different (P host of providing nutrients in appropriate quantities and balance. PMID:27054320

  4. PGPR enhanced phytoremediation of petroleum contaminated soil and rhizosphere microbial community response.

    Science.gov (United States)

    Hou, Jinyu; Liu, Wuxing; Wang, Beibei; Wang, Qingling; Luo, Yongming; Franks, Ashley E

    2015-11-01

    The aim of this study was to investigate petroleum phytoremediation enhancement by plant growth promoting bacteria (PGPR), specifically the correlation between petroleum hydrocarbon fractions and bacterial community structure affected by remediation and PGPR inocula. Aged petroleum contaminated soil was remediated by tall fescue (Testuca arundinacea L.) inoculated with two PGPR strains. Hydrocarbon degradation was measured by GC-MS (Gas-chromatography Mass-spectrometer) based on carbon fraction numbers (C8-C34). Changes in bacterial community structure were analyzed by high-throughput pyrosequencing of 16s rRNA. PGPR inoculation increased tall fescue biomass and petroleum hydrocarbons were removed in all the treatments. Maximum hydrocarbon removal, particular high molecular weight (C21-C34) aliphatic hydrocarbons (AHs) and polycyclic aromatic hydrocarbons (PAHs), was observed in tall fescue inoculated with PGPR. The relative abundance of phyla γ-proteobacteria and Bacteroidetes increased after different treatments compared with controls. Moreover, a bacterial guild mainly comprising the genera Lysobacter, Pseudoxanthomonas, Planctomyces, Nocardioides, Hydrogenophaga, Ohtaekwangia was found to be positively correlated with C21-C34 petroleum hydrocarbons fractions removal by RDA analysis, implying that petroleum degradation was unrelated to bacterial community diversity but positively correlated with specific petroleum degraders and biosurfactant producers. PMID:26210024

  5. Six-week Diet Correction for Body Weight Reduction and Its Subsequent Changes of Gut Microbiota: A Case Report.

    Science.gov (United States)

    Oh, Bumjo; Kim, Jong Seung; Kweon, Meera; Kim, Bong-Soo; Huh, In Sil

    2016-04-01

    Impact of intestinal microbes on obesity and health is a new topic recently started to get attention. Comparing to the global concern and research trends, there are few research on the association between intestinal bacteria and life style disease in Korean. One voluntary case (female) was reported to show the change in gut microbiota and weight by diet intervention. She was overweight (BMI 23.2 kg/m(2)) and has abnormal liver function, and the causes of overweight were frequent drinking and meat consumption at the late evening hours. For 47 days, she was administered an improved diet on breakfast and dinner with reduction of meat consumption frequency by 50%. Alcohol consumption was reduced to once a week. As a result, she lost 3 kilograms of body weight. Her fecal sample was collected before and after the intervention, and gut microbiota change was compared using a high-throughput sequencing technique. After diet correction, the shift of gut microbiota was clearly observed with decreased proportion of Firmicutes (from 75.7% to 47.3% in total microbiota) but increased proportion of Bacteroidetes upto 47.7%. After incorporating the diet intervention, it is meaningful to confirm the changes in dominant gut microbiota and weight loss. PMID:27152303

  6. Changes in fecal microbiota and metabolomics in a child with juvenile idiopathic arthritis (JIA) responding to two treatment periods with exclusive enteral nutrition (EEN).

    Science.gov (United States)

    Berntson, Lillemor; Agback, Peter; Dicksved, Johan

    2016-06-01

    The microbiome and immune system of the digestive tract are highly important in both health and disease. Exclusive enteral nutrition (EEN) is a common anti-inflammatory treatment in children with Crohn's disease in the European countries, and the mechanism is most likely linked to changes in the intestinal microbiome. In the present study, EEN was given in two treatment periods several months apart to a patient with very severe, disabling juvenile idiopathic arthritis (JIA), with a remarkable clinical response as the result. The aim of the present study was to study how the EEN treatment influenced the microbiome and metabolome of this patient. Fecal samples from before, during, and between treatments with EEN were studied. The microbiome was analyzed by sequencing of 16S rRNA amplicons using Illumina MiSeq, and the metabolome was analyzed using nuclear magnetic resonance. The microbiome changed markedly from treatment with EEN, with a strong reduction of the Bacteroidetes phylum. Metabolic profiles showed clear differences before, during, and between treatment with EEN, where butyrate, propionate, and acetate followed a cyclic pattern with the lowest levels at the end of each treatment period. This patient with JIA showed remarkable clinical improvement after EEN treatment, and we found corresponding changes in both the fecal microbiome and the metabolome. Further studies are needed to explore the pathophysiological role of the intestinal canal in children with JIA. PMID:27021336

  7. Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a French river.

    Science.gov (United States)

    Bricheux, Geneviève; Morin, Loïc; Le Moal, Gwenaël; Coffe, Gérard; Balestrino, Damien; Charbonnel, Nicolas; Bohatier, Jacques; Forestier, Christiane

    2013-06-01

    Despite the recent and significant increase in the study of aquatic microbial communities, little is known about the microbial diversity of complex ecosystems such as running waters. This study investigated the biodiversity of biofilm communities formed in a river with 454 Sequencing™. This river has the particularity of integrating both organic and microbiological pollution, as receiver of agricultural pollution in its upstream catchment area and urban pollution through discharges of the wastewater treatment plant of the town of Billom. Different regions of the small subunit (SSU) ribosomal RNA gene were targeted using nine pairs of primers, either universal or specific for bacteria, eukarya, or archaea. Our aim was to characterize the widest range of rDNA sequences using different sets of polymerase chain reaction (PCR) primers. A first look at reads abundance revealed that a large majority (47-48%) were rare sequences (<5 copies). Prokaryotic phyla represented the species richness, and eukaryotic phyla accounted for a small part. Among the prokaryotic phyla, Proteobacteria (beta and alpha) predominated, followed by Bacteroidetes together with a large number of nonaffiliated bacterial sequences. Bacillariophyta plastids were abundant. The remaining bacterial phyla, Verrucomicrobia and Cyanobacteria, made up the rest of the bulk biodiversity. The most abundant eukaryotic phyla were annelid worms, followed by Diatoms, and Chlorophytes. These latter phyla attest to the abundance of plastids and the importance of photosynthetic activity for the biofilm. These findings highlight the existence and plasticity of multiple trophic levels within these complex biological systems. PMID:23520129

  8. Metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant.

    Directory of Open Access Journals (Sweden)

    Zhu Wang

    Full Text Available Antibiotics are often used to prevent sickness and improve production in animal agriculture, and the residues in animal bodies may enter tannery wastewater during leather production. This study aimed to use Illumina high-throughput sequencing to investigate the occurrence, diversity and abundance of antibiotic resistance genes (ARGs and mobile genetic elements (MGEs in aerobic and anaerobic sludge of a full-scale tannery wastewater treatment plant (WWTP. Metagenomic analysis showed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria dominated in the WWTP, but the relative abundance of archaea in anaerobic sludge was higher than in aerobic sludge. Sequencing reads from aerobic and anaerobic sludge revealed differences in the abundance of functional genes between both microbial communities. Genes coding for antibiotic resistance were identified in both communities. BLAST analysis against Antibiotic Resistance Genes Database (ARDB further revealed that aerobic and anaerobic sludge contained various ARGs with high abundance, among which sulfonamide resistance gene sul1 had the highest abundance, occupying over 20% of the total ARGs reads. Tetracycline resistance genes (tet were highly rich in the anaerobic sludge, among which tet33 had the highest abundance, but was absent in aerobic sludge. Over 70 types of insertion sequences were detected in each sludge sample, and class 1 integrase genes were prevalent in the WWTP. The results highlighted prevalence of ARGs and MGEs in tannery WWTPs, which may deserve more public health concerns.

  9. Prokaryotic Community Diversity Along an Increasing Salt Gradient in a Soda Ash Concentration Pond.

    Science.gov (United States)

    Simachew, Addis; Lanzén, Anders; Gessesse, Amare; Øvreås, Lise

    2016-02-01

    The effect of salinity on prokaryotic community diversity in Abijata-Shalla Soda Ash Concentration Pond system was investigated by using high-throughput 16S rRNA gene 454 pyrosequencing. Surface water and brine samples from five sites spanning a salinity range of 3.4 % (Lake Abijata) to 32 % (SP230F, crystallizer pond) were analyzed. Overall, 33 prokaryotic phyla were detected, and the dominant prokaryotic phyla accounted for more than 95 % of the reads consisting of Planctomycetes, Bacteroidetes, candidate division TM7, Deinococcus-Thermus, Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota. Diversity indices indicated that operational taxonomic unit (OTU) richness decreases drastically with increasing salinity in the pond system. A total of 471 OTUs were found at 3.4 % salinity whereas 49 OTUs were detected in pond SP211 (25 % salinity), and only 19 OTUs in the crystallization pond at 32 % salinity (SP230F). Along the salinity gradient, archaeal community gradually replaced bacterial community. Thus, archaeal community accounted for 0.4 % in Lake Abijata while 99.0 % in pond SP230F. This study demonstrates that salinity appears to be the key environmental parameter in structuring the prokaryotic communities of haloalkaline environments. Further, it confirmed that the prokaryotic diversity in Lake Abijata is high and it harbors taxa with low or no phylogenetic similarities to existing prokaryotic taxa and thus represents novel microorganisms. PMID:26408190

  10. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge.

    Science.gov (United States)

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

    2016-01-01

    Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents. PMID:27169490

  11. Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers

    Science.gov (United States)

    Niu, Yuhong; Meng, Qingxiang; Li, Shengli; Ren, Liping; Zhou, Bo; Schonewille, Thomas; Zhou, Zhenming

    2016-01-01

    This study investigated the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on the ruminal bacterial and archaeal community composition of finishing steers. Corn grain- and cotton meal-based concentrate was partially replaced with EML or SMFP. The diets had similar crude protein (CP), neutral detergent fiber (NDF), and metabolizable energy. Following the feeding trial, the steers were slaughtered and ruminal liquid samples were collected to study the ruminal microbiome. Extraction of DNA, amplification of the V4 region of the 16S rRNA gene, and Illumina MiSeq pyrosequencing were performed for each sample. Following sequence de-noising, chimera checking, and quality trimming, an average of 209,610 sequences were generated per sample. Quantitative real-time PCR was performed to examine the selected bacterial species in the rumen. Our results showed that the predominant phyla were Bacteroidetes (43.90%), Firmicutes (39.06%), Proteobacteria (4.31%), and Tenericutes (2.04%), and the predominant genera included Prevotella (13.82%), Ruminococcus (2.51%), Butyrivibrio (2.38%), and Succiniclasticum (2.26%). Compared to the control group, EML and SMFP groups had a higher abundance of total bacteria (p supplementation had no significant effects on the ruminal bacterial or archaeal community composition of finishing steers. PMID:27258373

  12. Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers.

    Science.gov (United States)

    Kõiv, Viia; Roosaare, Märt; Vedler, Eve; Kivistik, Paula Ann; Toppi, Kristel; Schryer, David W; Remm, Maido; Tenson, Tanel; Mäe, Andres

    2015-01-01

    Endophytes are microbes and fungi that live inside plant tissues without damaging the host. Herein we examine the dynamic changes in the endophytic bacterial community in potato (Solanum tuberosum) tuber in response to pathogenic infection by Pectobacterium atrosepticum, which causes soft rot in numerous economically important crops. We quantified community changes using both cultivation and next-generation sequencing of the 16S rRNA gene and found that, despite observing significant variability in both the mass of macerated tissue and structure of the endophytic community between individual potato tubers, P. atrosepticum is always taken over by the endophytes during maceration. 16S rDNA sequencing revealed bacteria from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, Verrucomicrobia, Acidobacteria, TM7, and Deinococcus-Thermus. Prior to infection, Propionibacterium acnes is frequently among the dominant taxa, yet is out competed by relatively few dominant taxa as the infection proceeds. Two days post-infection, the most abundant sequences in macerated potato tissue are Gammaproteobacteria. The most dominant genera are Enterobacter and Pseudomonas. Eight days post-infection, the number of anaerobic pectolytic Clostridia increases, probably due to oxygen depletion. These results demonstrate that the pathogenesis is strictly initiated by the pathogen (sensu stricto) and proceeds with a major contribution from the endophytic community. PMID:26118792

  13. Methane assimilation and trophic interactions with marine Methylomicrobium in deep-water coral reef sediment off the coast of Norway.

    Science.gov (United States)

    Jensen, Sigmund; Neufeld, Josh D; Birkeland, Nils-Kåre; Hovland, Martin; Murrell, John Colin

    2008-11-01

    Deep-water coral reefs are seafloor environments with diverse biological communities surrounded by cold permanent darkness. Sources of energy and carbon for the nourishment of these reefs are presently unclear. We investigated one aspect of the food web using DNA stable-isotope probing (DNA-SIP). Sediment from beneath a Lophelia pertusa reef off the coast of Norway was incubated until assimilation of 5 micromol 13CH4 g(-1) wet weight occurred. Extracted DNA was separated into 'light' and 'heavy' fractions for analysis of labelling. Bacterial community fingerprinting of PCR-amplified 16S rRNA gene fragments revealed two predominant 13C-specific bands. Sequencing of these bands indicated that carbon from 13CH4 had been assimilated by a Methylomicrobium and an uncultivated member of the Gammaproteobacteria. Cloning and sequencing of 16S rRNA genes from the heavy DNA, in addition to genes encoding particulate methane monooxygenase and methanol dehydrogenase, all linked Methylomicrobium with methane metabolism. Putative cross-feeders were affiliated with Methylophaga (Gammaproteobacteria), Hyphomicrobium (Alphaproteobacteria) and previously unrecognized methylotrophs of the Gammaproteobacteria, Alphaproteobacteria, Deferribacteres and Bacteroidetes. This first marine methane SIP study provides evidence for the presence of methylotrophs that participate in sediment food webs associated with deep-water coral reefs. PMID:18811651

  14. Snow surface microbiome on the High Antarctic Plateau (DOME C.

    Directory of Open Access Journals (Sweden)

    Luigi Michaud

    Full Text Available The cryosphere is an integral part of the global climate system and one of the major habitable ecosystems of Earth's biosphere. These permanently frozen environments harbor diverse, viable and metabolically active microbial populations that represent almost all the major phylogenetic groups. In this study, we investigated the microbial diversity in the surface snow surrounding the Concordia Research Station on the High Antarctic Plateau through a polyphasic approach, including direct prokaryotic quantification by flow cytometry and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH, and phylogenetic identification by 16S RNA gene clone library sequencing and 454 16S amplicon pyrosequencing. Although the microbial abundance was low (<10(3 cells/ml of snowmelt, concordant results were obtained with the different techniques. The microbial community was mainly composed of members of the Alpha-proteobacteria class (e.g. Kiloniellaceae and Rhodobacteraceae, which is one of the most well-represented bacterial groups in marine habitats, Bacteroidetes (e.g. Cryomorphaceae and Flavobacteriaceae and Cyanobacteria. Based on our results, polar microorganisms could not only be considered as deposited airborne particles, but as an active component of the snowpack ecology of the High Antarctic Plateau.

  15. Identification of household bacterial community and analysis of species shared with human microbiome.

    Science.gov (United States)

    Jeon, Yoon-Seong; Chun, Jongsik; Kim, Bong-Soo

    2013-11-01

    Microbial populations in indoor environments, where we live and eat, are important for public health. Various bacterial species reside in the kitchen, and refrigerators, the major means of food storage within kitchens, can be a direct source of food borne illness. Therefore, the monitoring of microbiota in the refrigerator is important for food safety. We investigated and compared bacterial communities that reside in the vegetable compartment of the refrigerator and on the seat of the toilet, which is recognized as highly colonized by microorganisms, in ten houses using high-throughput sequencing. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were predominant in refrigerator and toilet samples. However, Proteobacteria was more abundant in the refrigerator, and Firmicutes was more abundant in the toilet. These household bacterial communities were compared with those of human skin and gut to identify potential sources of household bacteria. Bacterial communities from refrigerators and toilets shared more species in common with human skin than gut. Opportunistic pathogens, including Propionibacterium acnes, Bacteroides vulgatus, and Staphylococcus epidermidis, were identified as species shared with human skin and gut microbiota. This approach can provide a general background of the household microbiota and a potential method of source-tracking for public health purposes. PMID:23743600

  16. A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection.

    Directory of Open Access Journals (Sweden)

    Brooke L Deatherage Kaiser

    Full Text Available The potential for commensal microorganisms indigenous to a host (the 'microbiome' or 'microbiota' to alter infection outcome by influencing host-pathogen interplay is largely unknown. We used a multi-omics "systems" approach, incorporating proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular interplay between the murine host, the pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium, and commensal gut microorganisms during intestinal infection with S. Typhimurium. We find proteomic evidence that S. Typhimurium thrives within the infected 129/SvJ mouse gut without antibiotic pre-treatment, inducing inflammation and disrupting the intestinal microbiome (e.g., suppressing Bacteroidetes and Firmicutes while promoting growth of Salmonella and Enterococcus. Alteration of the host microbiome population structure was highly correlated with gut environmental changes, including the accumulation of metabolites normally consumed by commensal microbiota. Finally, the less characterized phase of S. Typhimurium's lifecycle was investigated, and both proteomic and glycomic evidence suggests S. Typhimurium may take advantage of increased fucose moieties to metabolize fucose while growing in the gut. The application of multiple omics measurements to Salmonella-induced intestinal inflammation provides insights into complex molecular strategies employed during pathogenesis between host, pathogen, and the microbiome.

  17. Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea

    KAUST Repository

    Alzubaidy, Hanin

    2015-11-10

    Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide. In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in ‘metabolism of aromatic compounds’, ‘mobile genetic elements’, ‘potassium metabolism’ and ‘pathways that utilize osmolytes’ in the rhizosphere microbiomes. To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.

  18. Metagenomic Analysis of Antibiotic-Induced Changes in Gut Microbiota in a Pregnant Rat Model

    Science.gov (United States)

    Khan, Imran; Azhar, Esam I.; Abbas, Aymn T.; Kumosani, Taha; Barbour, Elie K.; Raoult, Didier; Yasir, Muhammad

    2016-01-01

    Food and Drug Administration (FDA, USA)-approved category B antibiotics are commonly prescribed to treat infections during pregnancy. The aim of this study was to investigate antibiotic-induced changes in gut microbiota (GM) that occur during pregnancy. The 16S rRNA amplicon deep-sequencing method was used to analyze the effect of category B antibiotics (azithromycin, amoxicillin and cefaclor) on GM during pregnancy using a rat model. The GM composition was substantially modulated by pregnancy and antibiotics administration. Firmicutes, Bacteroidetes, Proteobacteria, Chlamydiae, Actinobacteria, and Cyanobacteria were the dominant phyla. Antibiotic treatment during pregnancy increased the relative abundance of Proteobacteria and reduced Firmicutes. The genera Shigella, Streptococcus, Candidatus Arthromitus, and Helicobacter were significantly (p < 0.05) more abundant during pregnancy. Antibiotics significantly (p < 0.05) reduced the relative abundance of Lactobacillus but increased that of Enterobacter. There was a significant (p < 0.05) decrease in Lactobacillus sp., Lactobacillus gallinarum and Lactobacillus crispatus during pregnancy. Antibiotic treatment reduced bacterial diversity; the lowest number of operational taxonomic units (OTUs) were detected in the cefaclor-treated groups. Antibiotics significantly (p < 0.05) promoted weight gain during pregnancy, and increased relative abundance of Shigella sonnei, Enterococcus hormaechei, and Acinetobacter sp. GM perturbations were accompanied by increases in Proteobacteria abundance and weight gain in pregnancy following antibiotic treatment. PMID:27199748

  19. Abundance of broad bacterial taxa in the sargasso sea explained by environmental conditions but not water mass.

    Science.gov (United States)

    Sjöstedt, Johanna; Martiny, Jennifer B H; Munk, Peter; Riemann, Lasse

    2014-05-01

    To explore the potential linkage between distribution of marine bacterioplankton groups, environmental conditions, and water mass, we investigated the factors determining the abundance of bacterial taxa across the hydrographically complex Subtropical Convergence Zone in the Sargasso Sea. Based on information from 16S rRNA gene clone libraries from various locations and two depths, abundances of the predominant taxa (eubacteria, Archaea, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and the Roseobacter, SAR11, and SAR86 clades) were quantified by real-time PCR. In addition, the abundances of Synechococcus, Prochlorococcus, and picoalgae were determined by flow cytometry. Linear multiple-regression models determining the relative effects of eight environmental variables and of water mass explained 35 to 86% of the variation in abundance of the quantified taxa, even though only one to three variables were significantly related to any particular taxon's abundance. Most of the variation in abundance was explained by depth and chlorophyll a. The predominant phototrophs, Prochlorococcus and picoalgae, were negatively correlated with phosphate, whereas eubacteria, heterotrophic bacteria, and SAR86 were negatively correlated with nitrite. Water mass showed limited importance for explaining the abundance of the taxonomical groups (significant only for Roseobacter, explaining 14% of the variation). The results suggest the potential for predicting the abundance of broad bacterioplankton groups throughout the Sargasso Sea using only a few environmental parameters. PMID:24561593

  20. Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome

    Science.gov (United States)

    Nolla-Ardèvol, Vímac; Strous, Marc; Tegetmeyer, Halina E.

    2015-01-01

    A haloalkaline anaerobic microbial community obtained from soda lake sediments was used to inoculate anaerobic reactors for the production of methane rich biogas. The microalga Spirulina was successfully digested by the haloalkaline microbial consortium at alkaline conditions (pH 10, 2.0 M Na+). Continuous biogas production was observed and the obtained biogas was rich in methane, up to 96%. Alkaline medium acted as a CO2 scrubber which resulted in low amounts of CO2 and no traces of H2S in the produced biogas. A hydraulic retention time (HRT) of 15 days and 0.25 g Spirulina L−1 day−1 organic loading rate (OLR) were identified as the optimal operational parameters. Metagenomic and metatranscriptomic analysis showed that the hydrolysis of the supplied substrate was mainly carried out by Bacteroidetes of the “ML635J-40 aquatic group” while the hydrogenotrophic pathway was the main producer of methane in a methanogenic community dominated by Methanocalculus. PMID:26157422

  1. Interspecific variations in the faecal microbiota of Procellariiform seabirds.

    Science.gov (United States)

    Dewar, Meagan L; Arnould, John P Y; Krause, Lutz; Dann, Peter; Smith, Stuart C

    2014-07-01

    Despite the enormous amount of data available on the importance of gut microbiota in vertebrates (especially mammals), there is no information available on the microbiota of seabirds. Procellariiformes are long-lived seabirds that consume a diet high in lipids and are characterised by their ability to produce and store large amount of stomach oils through the partial digestion of prey (with the exception of the Pelecanoididae). Examining the faecal microbiota of three Procellariiform species (short-tailed shearwater, common diving petrel and fairy prion) provided a unique opportunity to not only characterise the gastrointestinal (GI) microbial composition of seabirds but to also examine the influence of stomach oils on the microbial community. The results indicated that Procellariiform seabirds host a highly diverse community of faecal microorganisms, dominated by three phyla (Firmicutes, Proteobacteria and Bacteroidetes) and that each species has its own species-specific GI microbiota. In addition, significant differences were observed in the microbial communities of oil-producing and non-oil-producing seabirds. This study is the first whole-community examination and classification of the faecal microbiota of Procellariiform seabirds. PMID:24684257

  2. A Meta-Analysis of the Bacterial and Archaeal Diversity Observed in Wetland Soils

    Directory of Open Access Journals (Sweden)

    Xiaofei Lv

    2014-01-01

    Full Text Available This study examined the bacterial and archaeal diversity from a worldwide range of wetlands soils and sediments using a meta-analysis approach. All available 16S rRNA gene sequences recovered from wetlands in public databases were retrieved. In November 2012, a total of 12677 bacterial and 1747 archaeal sequences were collected in GenBank. All the bacterial sequences were assigned into 6383 operational taxonomic units (OTUs 0.03, representing 31 known bacterial phyla, predominant with Proteobacteria (2791 OTUs, Bacteroidetes (868 OTUs, Acidobacteria (731 OTUs, Firmicutes (540 OTUs, and Actinobacteria (418 OTUs. The genus Flavobacterium (11.6% of bacterial sequences was the dominate bacteria in wetlands, followed by Gp1, Nitrosospira, and Nitrosomonas. Archaeal sequences were assigned to 521 OTUs from phyla Euryarchaeota and Crenarchaeota. The dominating archaeal genera were Fervidicoccus and Methanosaeta. Rarefaction analysis indicated that approximately 40% of bacterial and 83% of archaeal diversity in wetland soils and sediments have been presented. Our results should be significant for well-understanding the microbial diversity involved in worldwide wetlands.

  3. Halotolerant aerobic heterotrophic bacteria from the Great Salt Plains of Oklahoma.

    Science.gov (United States)

    Caton, T M; Witte, L R; Ngyuen, H D; Buchheim, J A; Buchheim, M A; Schneegurt, M A

    2004-11-01

    The Salt Plains National Wildlife Refuge (SPNWR) near Cherokee, Oklahoma, contains a barren salt flat where Permian brine rises to the surface and evaporates under dry conditions to leave a crust of white salt. Rainfall events dissolve the salt crust and create ephemeral streams and ponds. The rapidly changing salinity and high surface temperatures, salinity, and UV exposure make this an extreme environment. The Salt Plains Microbial Observatory (SPMO) examined the soil microbial community of this habitat using classic enrichment and isolation techniques and phylogenetic rDNA studies. Rich growth media have been emphasized that differ in total salt concentration and composition. Aerobic heterotrophic enrichments were performed under a variety of conditions. Heterotrophic enrichments and dilution plates have generated 105 bacterial isolates, representing 46 phylotypes. The bacterial isolates have been characterized phenotypically and subjected to rDNA sequencing and phylogenetic analyses. Fast-growing isolates obtained from enrichments with 10% salt are predominantly from the gamma subgroup of the Proteobacteria and from the low GC Gram-positive cluster. Several different areas on the salt flats have yielded a variety of isolates from the Gram-negative genera Halomonas, Idiomarina, Salinivibrio, and Bacteroidetes. Gram-positive bacteria are well represented in the culture collection including members of the Bacillus, Salibacillus, Oceanobacillus, and Halobacillus. PMID:15696379

  4. Start-up of an anaerobic dynamic membrane digester for waste activated sludge digestion: temporal variations in microbial communities.

    Directory of Open Access Journals (Sweden)

    Hongguang Yu

    Full Text Available An anaerobic dynamic membrane digester (ADMD was developed to digest waste sludge, and pyrosequencing was used to analyze the variations of the bacterial and archaeal communities during the start-up. Results showed that bacterial community richness decreased and then increased over time, while bacterial diversity remained almost the same during the start-up. Proteobacteria and Bacteroidetes were the major phyla. At the class level, Betaproteobacteria was the most abundant at the end of start-up, followed by Sphingobacteria. In the archaeal community, richness and diversity peaked at the end of the start-up stage. Principle component and cluster analyses demonstrated that archaeal consortia experienced a distinct shift and became stable after day 38. Methanomicrobiales and Methanosarcinales were the two predominant orders. Further investigations indicated that Methanolinea and Methanosaeta were responsible for methane production in the ADMD system. Hydrogenotrophic pathways might prevail over acetoclastic means for methanogenesis during the start-up, supported by specific methanogenic activity tests.

  5. Intrinsic rates of petroleum hydrocarbon biodegradation in Gulf of Mexico intertidal sandy sediments and its enhancement by organic substrates

    International Nuclear Information System (INIS)

    The rates of crude oil degradation by the extant microorganisms in intertidal sediments from a northern Gulf of Mexico beach were determined. The enhancement in crude oil degradation by amending the microbial communities with marine organic matter was also examined. Replicate mesocosm treatments consisted of: (i) controls (intertidal sand), (ii) sand contaminated with crude oil, (iii) sand plus organic matter, and (iv) sand plus crude oil and organic matter. Carbon dioxide (CO2) production was measured daily for 42 days and the carbon isotopic ratio of CO2 (δ13CO2) was used to determine the fraction of CO2 derived from microbial respiration of crude oil. Bacterial 16S rRNA clone library analyses indicated members of Actinobacteria, Bacteroidetes, and Chloroflexi occurred exclusively in control sediments whereas Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Firmicutes occurred in both control and oil contaminated sediments. Members of the hydrocarbon-degrading genera Hydrocarboniphaga, Pseudomonas, and Pseudoxanthomonas were found primarily in oil contaminated treatments. Hydrocarbon mineralization was 76% higher in the crude oil amended with organic matter treatment compared to the rate in the crude oil only treatment indicating that biodegradation of crude oil in the intertidal zone by an extant microbial community is enhanced by input of organic matter

  6. Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem.

    Directory of Open Access Journals (Sweden)

    Guo-Chun Ding

    Full Text Available Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results in losses of characteristic flora and fauna, and may also affect microbial diversity. In the present study, the long-term effect (50 years of such a transition on soil bacterial communities was explored at two sites typical of semi-arid deserts. Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods based on 16S rRNA gene fragments amplified from total community DNA. Denaturing gradient gel electrophoresis (DGGE analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. Redundancy analysis suggested that the community composition of phyla responding to agricultural use (except for Spirochaetes correlated with soil parameters that were significantly different between the agricultural and scrubland soil. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. The variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses, suggesting reduced beta diversity due to agricultural practices. The long-term use for agriculture resulted in profound changes in the bacterial community and physicochemical characteristics of former scrublands, which may irreversibly affect the natural soil ecosystem.

  7. High diversity of microplankton surrounds deep-water coral reef in the Norwegian Sea.

    Science.gov (United States)

    Jensen, Sigmund; Bourne, David G; Hovland, Martin; Murrell, J Colin

    2012-10-01

    Coral reefs that exist in the depths of the oceans are surrounded by Eukarya, Archaea and bacterial communities that may play an important role in the nutrition and health of the reef. The first interdomain community structure of planktonic organisms in seawater from a deep-water coral reef is described. Community profiling and analysis of ribosomal RNA gene sequences from a coral reef system at 350 m depth in the Norwegian Sea revealed a rich diversity of Eukarya and Bacteria and a moderate diversity of Archaea. Most sequences affiliated with marine microplankton from deep-sea to cold-surface regions, with many sequences being similar to those described in studies of mesopelagic and oxygen minimum zones. Dominant phylotypes belonged to the Alveolata (group I, II, dinoflagellates), Stramenopiles (silicoflagellates), Alphaproteobacteria (Pelagibacter ubique), Gammaproteobacteria (ARCTIC96BD-19), Bacteroidetes (Flavobacteria) and mesophilic Crenarchaeota (Nitrosopumilus maritimus). Several rare and novel members of the community fell into distinct phylogenetic groups. The inferred function of dominant community members suggested autotrophs that utilise light, ammonium or sulphide, and lifestyles based on host associations. The high diversity reflected a microplankton community structure, which is significantly different from that of microplankton collected at the same depth at a pelagic station away from reefs. PMID:22571287

  8. Dietary Polyphenols Promote Growth of the Gut Bacterium Akkermansia muciniphila and Attenuate High-Fat Diet-Induced Metabolic Syndrome.

    Science.gov (United States)

    Roopchand, Diana E; Carmody, Rachel N; Kuhn, Peter; Moskal, Kristin; Rojas-Silva, Patricio; Turnbaugh, Peter J; Raskin, Ilya

    2015-08-01

    Dietary polyphenols protect against metabolic syndrome, despite limited absorption and digestion, raising questions about their mechanism of action. We hypothesized that one mechanism may involve the gut microbiota. To test this hypothesis, C57BL/6J mice were fed a high-fat diet (HFD) containing 1% Concord grape polyphenols (GP). Relative to vehicle controls, GP attenuated several effects of HFD feeding, including weight gain, adiposity, serum inflammatory markers (tumor necrosis factor [TNF]α, interleukin [IL]-6, and lipopolysaccharide), and glucose intolerance. GP lowered intestinal expression of inflammatory markers (TNFα, IL-6, inducible nitric oxide synthase) and a gene for glucose absorption (Glut2). GP increased intestinal expression of genes involved in barrier function (occludin) and limiting triglyceride storage (fasting-induced adipocyte factor). GP also increased intestinal gene expression of proglucagon, a precursor of proteins that promote insulin production and gut barrier integrity. 16S rRNA gene sequencing and quantitative PCR of cecal and fecal samples demonstrated that GP dramatically increased the growth of Akkermansia muciniphila and decreased the proportion of Firmicutes to Bacteroidetes, consistent with prior reports that similar changes in microbial community structure can protect from diet-induced obesity and metabolic disease. These data suggest that GP act in the intestine to modify gut microbial community structure, resulting in lower intestinal and systemic inflammation and improved metabolic outcomes. The gut microbiota may thus provide the missing link in the mechanism of action of poorly absorbed dietary polyphenols. PMID:25845659

  9. Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds.

    Directory of Open Access Journals (Sweden)

    Bo Xu

    Full Text Available The animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host. An analysis of 78,619 pyrosequencing reads generated from pygmy loris fecal DNA extracts was performed to help better understand the microbial diversity and functional capacity of the pygmy loris gut microbiome. The taxonomic analysis of the metagenomic reads indicated that pygmy loris fecal microbiomes were dominated by Bacteroidetes and Proteobacteria phyla. The hierarchical clustering of several gastrointestinal metagenomes demonstrated the similarities of the microbial community structures of pygmy loris and mouse gut systems despite their differences in functional capacity. The comparative analysis of function classification revealed that the metagenome of the pygmy loris was characterized by an overrepresentation of those sequences involved in aromatic compound metabolism compared with humans and other animals. The key enzymes related to the benzoate degradation pathway were identified based on the Kyoto Encyclopedia of Genes and Genomes pathway assignment. These results would contribute to the limited body of primate metagenome studies and provide a framework for comparative metagenomic analysis between human and non-human primates, as well as a comparative understanding of the evolution of humans and their microbiome. However, future studies on the metagenome sequencing of pygmy loris and other prosimians regarding the effects of age, genetics, and environment on the composition and activity of the metagenomes are required.

  10. Bacterial Diversity of Gut Content in Sea Cucumber (Apostichopus japonicus) and Its Habitat Surface Sediment

    Institute of Scientific and Technical Information of China (English)

    GAO Fei; TAN Jie; SUN Huiling; YAN Jingping

    2014-01-01

    This study investigated the bacterial diversity of gut content of sea cucumber (Apostichopus japonicus) and its habitat surface sediment in a bottom enhancement area using PCR-based denaturing gradient gel electrophoresis (DGGE) technique. Bacte-rial diversity evaluation showed that the value of the Shannon-Wiener index of gut content in different intestinal segments of A. ja-ponicus varied between 2.88 and 3.00, lower than that of the surrounding sediment (3.23). Phylogenetic analysis showed that bacte-rial phylotypes in gut content and the surrounding sediment of A. japonicus were closely related to Proteobacteria includingγ-,α-,δ-andε-proteobacteria, Bacteroidetes, Firmicute, and Actinobacteria, of whichγ-proteobacteria were predominant. These results sug-gested that the sea cucumber A. japonicus was capable of feeding selectively, and PCR-DGGE was applicable for characterizing the bacterial community composition in gut content and the surrounding sediment of sea cucumber. Further investigation targeting longer 16S rDNA gene fragments and/or functional genes was recommended for obtaining more information of the diversity and function of bacterial community in the gut content of sea cucumber.

  11. Impairment of cellulose- and cellobiose-degrading soil Bacteria by two acidic herbicides.

    Science.gov (United States)

    Schellenberger, Stefanie; Drake, Harold L; Kolb, Steffen

    2012-02-01

    Herbicides have the potential to impair the metabolism of soil microorganisms. The current study addressed the toxic effect of bentazon and 4-chloro-2-methylphenoxyacetic acid on aerobic and anaerobic Bacteria that are involved in cellulose and cellobiose degradation in an agricultural soil. Aerobic saccharide degradation was reduced at concentrations of herbicides above environmental values. Microbial processes (e.g. fermentations, ferric iron reduction) that were linked to anaerobic cellulose and cellobiose degradation were reduced in the presence of both herbicides at concentrations above and at those that occur in crop field soil. 16S rRNA gene transcript numbers of total Bacteria, and selected bacterial taxa (Clostridia [Group I], Planctomycetaceae, and two uncultivated taxa of Bacteroidetes) decreased more in anoxic than in oxic cellulose-supplemented soil microcosms in the presence of both herbicides. Collectively, the results suggested that the metabolism of anaerobic cellulose-degrading Bacteria was impaired by typical in situ herbicide concentrations, whereas in situ concentrations did not impair metabolism of aerobic cellulose- and cellobiose-degrading soil Bacteria. PMID:22098368

  12. Functionally redundant cellobiose-degrading soil bacteria respond differentially to oxygen.

    Science.gov (United States)

    Schellenberger, Stefanie; Drake, Harold L; Kolb, Steffen

    2011-09-01

    The availability of oxygen (O(2)) in aerated (i.e., water-unsaturated) soils affects the metabolic activities of aerobic and anaerobic soil prokaryotes that degrade plant-derived saccharides. Fluctuating availabilities of O(2) were imposed on agricultural soil slurries supplemented with cellobiose. Slurries were subjected to oxic conditions (48 h), followed by an anoxic period (120 h) and a final oxic period (24 h). Redox potential was stable at 500 mV during oxic periods but decreased rapidly (within 10 h) under anoxic conditions to -330 mV. The consumption of cellobiose occurred without apparent delay at all redox potentials. The metabolic activities of seven previously identified saccharolytic family-level taxa of the investigated soil were measured with newly designed quantitative PCR assays targeting the 16S rRNA. Four taxa responded to the experimental conditions. The amounts of rRNAs of Micrococcaceae and Cellulomonadaceae (Actinobacteria) increased under oxic conditions. In contrast, the RNA contents of Clostridiaceae (cluster I, Firmicutes) and two uncultured family-level-taxa, i.e., "Cellu" and "Sphingo" (both Bacteroidetes) increased under anoxic conditions. That the degradation of cellobiose was independent of the availability of O(2) and that redox potentials decreased in response to anaerobic activities indicated that the degradation of cellobiose was linked to functionally redundant cellobiose-degrading taxa capable of altering redox conditions. PMID:21742909

  13. Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants.

    Directory of Open Access Journals (Sweden)

    Devin B Holman

    Full Text Available Agricultural operations generate large quantities of manure which must be eliminated in a manner that is consistent with public health guidelines. Meanwhile, construction and demolition waste makes up about 25% of total solid municipal waste. Co-composting of manure with construction and demolition waste offers a potential means to make manure safe for soil amendment and also divert construction and demolition waste from municipal landfills. Therefore, the archaeal, bacterial, and fungal microbiota of two different types of composted cattle manure and one co-composted with construction and demolition waste, were assessed over a 99-day composting period. The microbiota of the three compost mixtures did not differ, but significant changes over time and by sampling depth were observed. Bacillus and Halocella, however, were more relatively abundant in composted manure from cattle fed dried distillers' grains and solubles. Proteobacteria and Bacteroidetes were enriched at day 0 and Firmicutes at day 99. The fungal genus Kernia was the most relatively abundant overall and was enriched at day 0. The concentration of 12 antimicrobial resistance determinants in the compost mixtures was also determined, and 10 of these determinants decreased significantly from days 0 to 99. The addition of construction and demolition waste did not affect the persistence of antimicrobial resistance genes or community structure of the compost microbiota and therefore co-composting construction and demolition waste with cattle manure offers a safe, viable way to divert this waste from landfills.

  14. Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks.

    Science.gov (United States)

    Reis, Mariana P; Dias, Marcela F; Costa, Patrícia S; Ávila, Marcelo P; Leite, Laura R; de Araújo, Flávio M G; Salim, Anna C M; Bucciarelli-Rodriguez, Mônica; Oliveira, Guilherme; Chartone-Souza, Edmar; Nascimento, Andréa M A

    2016-10-01

    Bacteria from aquatic ecosystems significantly contribute to biogeochemical cycles, but details of their community structure in tropical mining-impacted environments remain unexplored. In this study, we analyzed a bacterial community from circumneutral-pH tropical stream sediment by 16S rRNA and shotgun deep sequencing. Carrapatos stream sediment, which has been exposed to metal stress due to gold and iron mining (21 [g Fe]/kg), revealed a diverse community, with predominance of Proteobacteria (39.4%), Bacteroidetes (12.2%), and Parcubacteria (11.4%). Among Proteobacteria, the most abundant reads were assigned to neutrophilic iron-oxidizing taxa, such as Gallionella, Sideroxydans, and Mariprofundus, which are involved in Fe cycling and harbor several metal resistance genes. Functional analysis revealed a large number of genes participating in nitrogen and methane metabolic pathways despite the low concentrations of inorganic nitrogen in the Carrapatos stream. Our findings provide important insights into bacterial community interactions in a mining-impacted environment. PMID:27441985

  15. Pyrosequencing-based assessment of bacterial community structure in mine soils affected by mining subsidence

    Institute of Scientific and Technical Information of China (English)

    Li Yuanyuan a; Chen Longqian a; ⇑; Wen Hongyu b; Zhou Tianjian a; Zhang Ting a

    2014-01-01

    Based on the 454 pyrosequencing approach, this research evaluated the influence of coal mining subsi-dence on soil bacterial diversity and community structure in Chinese mining area. In order to characterize the bacterial community comparatively, this study selected a field experiment site with coal-excavated subsidence soils and an adjacent site with non-disturbed agricultural soils, respectively. The dataset com-prises 24512 sequences that are affiliated to the 7 phylogenetic groups: proteobacteria, actinobacteria, bacteroidetes, gemmatimonadetes, chloroflexi, nitrospirae and unclassified phylum. Proteobacteria is the largest bacterial phylum in all samples, with a marked shift of the proportions of alpha-, beta-, and gammaproteobacteria. The results show that undisturbed soils are relatively more diverse and rich than subsided soils, and differences in abundances of dominant taxonomic groups between the two soil groups are visible. Compared with the control, soil nutrient contents decline achieves significant level in subsided soils. Correlational analysis showed bacterial diversity indices have significantly positive corre-lation with soil organic matter, total N, total P, and available K, but in negative relation with soil salinity. Ground subsidence noticeably affects the diversity and composition of soil microbial community. Degen-eration of soil fertility and soil salinization inhibits the sole-carbon-source metabolic ability of microbial community, leading to the simplification of advantage species and uneven distribution of microbial spe-cies. This work demonstrates the great potential of pyrosequencing technique in revealing microbial diversity and presents background information of microbial communities of mine subsidence land.

  16. Bacterial Diversity in Microbial Mats and Sediments from the Atacama Desert.

    Science.gov (United States)

    Rasuk, Maria Cecilia; Fernández, Ana Beatriz; Kurth, Daniel; Contreras, Manuel; Novoa, Fernando; Poiré, Daniel; Farías, María Eugenia

    2016-01-01

    The Atacama Desert has extreme environmental conditions that allow the development of unique microbial communities. The present paper reports the bacterial diversity of microbial mats and sediments and its mineralogical components. Some physicochemical conditions of the water surrounding these ecosystems have also been studied trying to determine their influence on the diversity of these communities. In that way, mats and sediments distributed among different hypersaline lakes located in salt flats of the Atacama Desert were subjected to massive parallel sequencing of the V4 region of the 16S rRNA genes of Bacteria. A higher diversity in sediment than in mat samples have been found. Lakes that harbor microbial mats have higher salinity than lakes where mats are absent. Proteobacteria and/or Bacteroidetes are the major phyla represented in all samples. An interesting item is the finding of a low proportion or absence of Cyanobacteria sequences in the ecosystems studied, suggesting the possibility that other groups may be playing an essential role as primary producers in these extreme environments. Additionally, the large proportion of 16S rRNA gene sequences that could not be classified at the level of phylum indicates potential new phyla present in these ecosystems. PMID:26224164

  17. Altered Fecal Microbiota Correlates with Liver Biochemistry in Nonobese Patients with Non-alcoholic Fatty Liver Disease

    Science.gov (United States)

    Wang, Baohong; Jiang, Xiangyang; Cao, Min; Ge, Jianping; Bao, Qiongling; Tang, Lingling; Chen, Yu; Li, Lanjuan

    2016-01-01

    Increasing evidence suggests a role of intestinal dysbiosis in obesity and non-alcoholic fatty liver disease (NAFLD). But it remains unknown in nonobese NAFLD. This prospective, cross-sectional study sought to characterize differences in fecal microbiota between nonobese adult individuals with and without NAFLD and their potential association with metabolic markers of disease progression. A total of 126 nonobese subjects were enrolled: 43 NAFLD and 83 healthy controls (HC). The microbial community was profiled by denaturing gradient gel electrophoresis and examined by 454 pyrosequencing of the 16S ribosomal RNA V3 region. Lower diversity and a phylum-level change in the fecal microbiome were found in NAFLD. Compared with HC, patients had 20% more phylum Bacteroidetes (p = 0.005) and 24% less Firmicutes (p = 0.002). Within Firmicutes, four families and their 8 genera, which were short-chain fatty acids-producing and 7α-dehydroxylating bacteria, were significantly decreased. Moreover, Gram-negative (G−) bacteria were prevalent in NAFLD (p = 0.008). Furthermore, a significant correlation with metabolic markers was revealed for disturbed microbiota in NAFLD. This novel study indicated that intestinal dysbiosis was associated with nonobese NAFLD and might increase the risk of NAFLD progression. PMID:27550547

  18. Cloacal Microbiome Structure in a Long-Distance Migratory Bird Assessed Using Deep 16sRNA Pyrosequencing

    Science.gov (United States)

    Kreisinger, Jakub; Čížková, Dagmar; Kropáčková, Lucie; Albrecht, Tomáš

    2015-01-01

    Effects of vertebrate-associated microbiota on physiology and health are of significant interest in current biological research. Most previous studies have focused on host-microbiota interactions in captive-bred mammalian models. These interactions and their outcomes are still relatively understudied, however, in wild populations and non-mammalian taxa. Using deep pyrosequencing, we described the cloacal microbiome (CM) composition in free living barn swallows Hirundo rustica, a long-distance migratory passerine bird. Barn swallow CM was dominated by bacteria of the Actinobacteria, Proteobacteria and Firmicutes phyla. Bacteroidetes, which represent an important proportion of the digestive tract microbiome in many vertebrate species, was relatively rare in barn swallow CM (< 5%). CM composition did not differ between males and females. A significant correlation of CM within breeding pair members is consistent with the hypothesis that cloacal contact during within-pair copulation may promote transfer of bacterial assemblages. This effect on CM composition had a relatively low effect size, however, possibly due to the species’ high level of sexual promiscuity. PMID:26360776

  19. [Analysis of Prokaryotic Community Structure in River Waters of the Ningbo Sanjiang Mouth].

    Science.gov (United States)

    Hu, An-yi; Li, Jiang-wei; Yang, Xiao-yong; Wang, Hong-jie; Yu, Chang-ping

    2015-07-01

    The prokaryotic community structure in river waters of the Ningbo Sanjiang Mouth was analyzed for the first time using 16S rRNA gene based-Illumina Miseq high-throughput sequencing. A total of 215 504 high-quality sequences were obtained, and the results of alpha-diversity analysis revealed that Yongjiang River Watershed (YRW) harbored high diversity and richness of prokaryotic communities. Taxonomic assignment analysis indicated that β-Proteobacterium, Actinobacteria and Bacteroidetes dominated in the river water of YRW, and accounted for 78. 88% of the total prokaryotic communities. Hydrological condition may play an important role in influencing the composition and structure of YRW prokaryotic community. In addition, several kinds of sewer- and fecal-pollution indicator bacterial groups were observed in this area with the highest abundance of pollution indicator bacteria occurring in the water sample of Yuyao River, implying that the Yuyao River might have a high potential risk of sewer- and fecal-pollution. Moreover, a total of 76 species and 18 subspecies of potential pathogenic bacteria, which accounted for 2. 19% and 0. 40% of total sequences respectively, were identified using BLASTN analysis with a local pathogenic bacteria database. Overall, this study provided an important basic data for shedding light on the structure and ecological function of YRW prokaryotic community. PMID:26489316

  20. Diversity of extremophilic bacteria in the sediment of high-altitude lakes located in the mountain desert of Ojos del Salado volcano, Dry-Andes.

    Science.gov (United States)

    Aszalós, Júlia Margit; Krett, Gergely; Anda, Dóra; Márialigeti, Károly; Nagy, Balázs; Borsodi, Andrea K

    2016-09-01

    Ojos del Salado, the highest volcano on Earth is surrounded by a special mountain desert with extreme aridity, great daily temperature range, intense solar radiation, and permafrost from 5000 meters above sea level. Several saline lakes and permafrost derived high-altitude lakes can be found in this area, often surrounded by fumaroles and hot springs. The aim of this study was to gain information about the bacterial communities inhabiting the sediment of high-altitude lakes of the Ojos del Salado region located between 3770 and 6500 m. Altogether 11 sediment samples from 4 different altitudes were examined with 16S rRNA gene based denaturing gradient gel electrophoresis and clone libraries. Members of 17 phyla or candidate divisions were detected with the dominance of Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. The bacterial community composition was determined mainly by the altitude of the sampling sites; nevertheless, the extreme aridity and the active volcanism had a strong influence on it. Most of the sequences showed the highest relation to bacterial species or uncultured clones from similar extreme environments. PMID:27315168

  1. Analysis and characterization of cultivable heavy metal-resistant bacterial endophytes isolated from Cd-hyperaccumulator Solanum nigrum L. and their potential use for phytoremediation.

    Science.gov (United States)

    Luo, Sheng-lian; Chen, Liang; Chen, Jue-liang; Xiao, Xiao; Xu, Tao-ying; Wan, Yong; Rao, Chan; Liu, Cheng-bin; Liu, Yu-tang; Lai, Cui; Zeng, Guang-ming

    2011-11-01

    This study investigates the heavy metal-resistant bacterial endophytes of Cd-hyperaccumulator Solanum nigrum L. grown on a mine tailing by using cultivation-dependent technique. Thirty Cd-tolerant bacterial endophytes were isolated from roots, stems, and leaves of S. nigrum L. and classified by amplified ribosomal DNA-restriction analysis into 18 different types. Phylogenetic analysis based on 16S rDNA sequences showed that these isolates belonged to four groups: Actinobacteria (43%), Proteobacteria (23%), Bacteroidetes (27%) and Firmicutes (7%). All the isolates were then characterized for their plant growth promoting traits as well as their resistances to different heavy metals; and the actual plant growth promotion and colonization ability were also assessed. Four isolates were re-introduced into S. nigrum L. under Cd stress and resulted in Cd phytotoxicity decrease, as dry weights of roots increased from 55% to 143% and dry weights of above-ground from 64% to 100% compared to the uninoculated ones. The total Cd accumulation of inoculated plants increased from 66% to 135% (roots) and from 22% to 64% (above-ground) compared to the uninoculated ones. Our research suggests that bacterial endophytes are a most promising resource and may be the excellent candidates of bio-inoculants for enhancing the phytoremediation efficiency. PMID:21868057

  2. Microbiome and Biocatalytic Bacteria in Monkey Cup (Nepenthes Pitcher) Digestive Fluid.

    Science.gov (United States)

    Chan, Xin-Yue; Hong, Kar-Wai; Yin, Wai-Fong; Chan, Kok-Gan

    2016-01-01

    Tropical carnivorous plant, Nepenthes, locally known as "monkey cup", utilises its pitcher as a passive trap to capture insects. It then secretes enzymes into the pitcher fluid to digest the insects for nutrients acquisition. However, little is known about the microbiota and their activity in its pitcher fluid. Eighteen bacteria phyla were detected from the metagenome study in the Nepenthes pitcher fluid. Proteobacteria, Bacteroidetes and Actinobacteria are the dominant phyla in the Nepenthes pitcher fluid. We also performed culturomics approach by isolating 18 bacteria from the Nepenthes pitcher fluid. Most of the bacterial isolates possess chitinolytic, proteolytic, amylolytic, and cellulolytic and xylanolytic activities. Fifteen putative chitinase genes were identified from the whole genome analysis on the genomes of the 18 bacteria isolated from Nepenthes pitcher fluid and expressed for chitinase assay. Of these, six clones possessed chitinase activity. In conclusion, our metagenome result shows that the Nepenthes pitcher fluid contains vast bacterial diversity and the culturomic studies confirmed the presence of biocatalytic bacteria within the Nepenthes pitcher juice which may act in symbiosis for the turn over of insects trapped in the Nepenthes pitcher fluid. PMID:26817720

  3. Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality.

    Science.gov (United States)

    Jordaan, K; Bezuidenhout, C C

    2016-03-01

    The aim of this study was to determine the impacts of anthropogenic disturbances on bacterial community composition in an urban river (Mooi River). Physico-chemical analysis, bacterial enumeration and 454-pyrosequencing were conducted on the Mooi River system upstream and downstream of an urban settlement in the North West Province, South Africa. Pyrosequencing and multivariate analysis showed that nutrient inputs and faecal pollution strongly impacted the physico-chemical and microbiological quality at the downstream sites. Also, bacterial communities showed higher richness and evenness at the downstream sites. Multivariate analysis suggested that the abundances of Betaproteobacteria, Epsilonproteobacteria, Acidobacteria, Bacteroidetes and Verrucomicrobia are related to temperature, pH, dissolved oxygen (DO), sulphate and chlorophyll-a levels. These results suggest that urbanisation caused the overall water quality of this river to deteriorate, which in turn affected the bacterial community composition. In addition, our work identified potential indicator groups that may be used to track faecal and organic pollution in freshwater systems. PMID:26593724

  4. Intrinsic rates of petroleum hydrocarbon biodegradation in Gulf of Mexico intertidal sandy sediments and its enhancement by organic substrates

    Energy Technology Data Exchange (ETDEWEB)

    Mortazavi, Behzad, E-mail: bmortazavi@ua.edu [University of Alabama, Department of Biological Sciences, Box 870344, University of Alabama, Tuscaloosa, AL 35487 (United States); Dauphin Island Sea Lab, 101 Bienville Boulevard, Dauphin Island, AL, 36528 (United States); Horel, Agota [University of Alabama, Department of Biological Sciences, Box 870344, University of Alabama, Tuscaloosa, AL 35487 (United States); Dauphin Island Sea Lab, 101 Bienville Boulevard, Dauphin Island, AL, 36528 (United States); Beazley, Melanie J.; Sobecky, Patricia A. [University of Alabama, Department of Biological Sciences, Box 870344, University of Alabama, Tuscaloosa, AL 35487 (United States)

    2013-01-15

    The rates of crude oil degradation by the extant microorganisms in intertidal sediments from a northern Gulf of Mexico beach were determined. The enhancement in crude oil degradation by amending the microbial communities with marine organic matter was also examined. Replicate mesocosm treatments consisted of: (i) controls (intertidal sand), (ii) sand contaminated with crude oil, (iii) sand plus organic matter, and (iv) sand plus crude oil and organic matter. Carbon dioxide (CO{sub 2}) production was measured daily for 42 days and the carbon isotopic ratio of CO{sub 2} (δ{sup 13}CO{sub 2}) was used to determine the fraction of CO{sub 2} derived from microbial respiration of crude oil. Bacterial 16S rRNA clone library analyses indicated members of Actinobacteria, Bacteroidetes, and Chloroflexi occurred exclusively in control sediments whereas Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Firmicutes occurred in both control and oil contaminated sediments. Members of the hydrocarbon-degrading genera Hydrocarboniphaga, Pseudomonas, and Pseudoxanthomonas were found primarily in oil contaminated treatments. Hydrocarbon mineralization was 76% higher in the crude oil amended with organic matter treatment compared to the rate in the crude oil only treatment indicating that biodegradation of crude oil in the intertidal zone by an extant microbial community is enhanced by input of organic matter.

  5. Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

    Science.gov (United States)

    Pepe-Ranney, Charles; Campbell, Ashley N.; Koechli, Chantal N.; Berthrong, Sean; Buckley, Daniel H.

    2016-01-01

    We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes. PMID:27242725

  6. Dust Rains Deliver Diverse Assemblages of Microorganisms to the Eastern Mediterranean

    Science.gov (United States)

    Itani, Ghida Nouhad; Smith, Colin Andrew

    2016-03-01

    Dust rains may be particularly effective at delivering microorganisms, yet their biodiversities have been seldom examined. During 2011 and 2012 in Beirut, Lebanon, 16 of 21 collected rainfalls appeared dusty. Trajectory modelling of air mass origins was consistent with North African sources and at least one Southwest Asian source. As much as ~4 g particulate matter, ~20 μg DNA, and 50 million colony forming units were found deposited per square meter during rainfalls each lasting less than one day. Sequencing of 93 bacteria and 25 fungi cultured from rain samples revealed diverse bacterial phyla, both Gram positive and negative, and Ascomycota fungi. Denaturing Gradient Gel Electrophoresis of amplified 16S rDNA of 13 rains revealed distinct and diverse assemblages of bacteria. Dust rain 16S libraries yielded 131 sequences matching, in decreasing order of abundance, Betaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria, Epsilonproteobacteria, Gammaproteobacteria, and Deltaproteobacteria. Clean rain 16S libraries yielded 33 sequences matching only Betaproteobacteria family Oxalobacteraceae. Microbial composition varied between dust rains, and more diverse and different microbes were found in dust rains than clean rains. These results show that dust rains deliver diverse communities of microorganisms that may be complex products of revived desert soil species and fertilized cloud species.

  7. A metagenomic snapshot of taxonomic and functional diversity in an alpine glacier cryoconite ecosystem

    International Nuclear Information System (INIS)

    Cryoconite is a microbe–mineral aggregate which darkens the ice surface of glaciers. Microbial process and marker gene PCR-dependent measurements reveal active and diverse cryoconite microbial communities on polar glaciers. Here, we provide the first report of a cryoconite metagenome and culture-independent study of alpine cryoconite microbial diversity. We assembled 1.2 Gbp of metagenomic DNA sequenced using an Illumina HiScanSQ from cryoconite holes across the ablation zone of Rotmoosferner in the Austrian Alps. The metagenome revealed a bacterially-dominated community, with Proteobacteria (62% of bacterial-assigned contigs) and Bacteroidetes (14%) considerably more abundant than Cyanobacteria (2.5%). Streptophyte DNA dominated the eukaryotic metagenome. Functional genes linked to N, Fe, S and P cycling illustrated an acquisitive trend and a nitrogen cycle based upon efficient ammonia recycling. A comparison of 32 metagenome datasets revealed a similarity in functional profiles between the cryoconite and metagenomes characterized from other cold microbe–mineral aggregates. Overall, the metagenomic snapshot reveals the cryoconite ecosystem of this alpine glacier as dependent on scavenging carbon and nutrients from allochthonous sources, in particular mosses transported by wind from ice-marginal habitats, consistent with net heterotrophy indicated by productivity measurements. A transition from singular snapshots of cryoconite metagenomes to comparative analyses is advocated. (letter)

  8. Seasonal dynamics of the microbiome of chernozems of the long-term agrochemical experiment in Kamennaya Steppe

    Science.gov (United States)

    Chernov, T. I.; Tkhakakhova, A. K.; Ivanova, E. A.; Kutovaya, O. V.; Turusov, V. I.

    2015-12-01

    The seasonal variability (spring-summer-autumn) of the taxonomic structure of prokaryotic microbiomes in chernozems of Kamennaya Steppe was studied using sequencing of the 16S rRNA gene. The samples were collected from the topsoil (0-20 cm) horizons of a long-term fallow and croplands differing in the rates of application of mineral fertilizers (NPK). The seasonal dynamics of the prokaryotic community in the soils of the fallow and croplands were similar: the summer samples significantly differed from the spring ones; in autumn, the microbiome structure approached that in spring; these changes were probably related to corresponding changes in the temperature and moisture conditions of the growing season. For all the plots, significant seasonal changes in the proportions of Thaumarchaeota (Cranarchaeota), Acidobacteria, Bacteroidetes, Firmicutes, and V errucomicrobia phylogenetic groups were observed. The significant changes in the structure of the microbiomes (especially in the number of representatives of the Firmicutes, Cemmatiomonadetes, and Verrucomicrobia phyla) were revealed in the arable and fallow soils irrespectively of the season. The phylogenetic diversity estimated by the Shannon index, the number of the operating taxonomic units found, and the Chao1 index differed little in the soils of the studies plots. The long-term application of mineral fertilizers at different rates had little effect on the taxonomic structure and diversity of prokaryotic communities in the agrochernozems.

  9. The microbiome of North Sea copepods

    Science.gov (United States)

    Gerdts, G.; Brandt, P.; Kreisel, K.; Boersma, M.; Schoo, K. L.; Wichels, A.

    2013-12-01

    Copepods can be associated with different kinds and different numbers of bacteria. This was already shown in the past with culture-dependent microbial methods or microscopy and more recently by using molecular tools. In our present study, we investigated the bacterial community of four frequently occurring copepod species, Acartia sp., Temora longicornis, Centropages sp. and Calanus helgolandicus from Helgoland Roads (North Sea) over a period of 2 years using DGGE (denaturing gradient gel electrophoresis) and subsequent sequencing of 16S-rDNA fragments. To complement the PCR-DGGE analyses, clone libraries of copepod samples from June 2007 to 208 were generated. Based on the DGGE banding patterns of the two years survey, we found no significant differences between the communities of distinct copepod species, nor did we find any seasonality. Overall, we identified 67 phylotypes (>97 % similarity) falling into the bacterial phyla of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The most abundant phylotypes were affiliated to the Alphaproteobacteria. In comparison with PCR-DGGE and clone libraries, phylotypes of the Gammaproteobacteria dominated the clone libraries, whereas Alphaproteobacteria were most abundant in the PCR-DGGE analyses.

  10. Perturbation dynamics of the rumen microbiota in response to exogenous butyrate.

    Directory of Open Access Journals (Sweden)

    Robert W Li

    Full Text Available The capacity of the rumen microbiota to produce volatile fatty acids (VFAs has important implications in animal well-being and production. We investigated temporal changes of the rumen microbiota in response to butyrate infusion using pyrosequencing of the 16S rRNA gene. Twenty one phyla were identified in the rumen microbiota of dairy cows. The rumen microbiota harbored 54.5±6.1 genera (mean ± SD and 127.3±4.4 operational taxonomic units (OTUs, respectively. However, the core microbiome comprised of 26 genera and 82 OTUs. Butyrate infusion altered molar percentages of 3 major VFAs. Butyrate perturbation had a profound impact on the rumen microbial composition. A 72 h-infusion led to a significant change in the numbers of sequence reads derived from 4 phyla, including 2 most abundant phyla, Bacteroidetes and Firmicutes. As many as 19 genera and 43 OTUs were significantly impacted by butyrate infusion. Elevated butyrate levels in the rumen seemingly had a stimulating effect on butyrate-producing bacteria populations. The resilience of the rumen microbial ecosystem was evident as the abundance of the microorganisms returned to their pre-disturbed status after infusion withdrawal. Our findings provide insight into perturbation dynamics of the rumen microbial ecosystem and should guide efforts in formulating optimal uses of probiotic bacteria treating human diseases.

  11. Revealing the combined effects of lactulose and probiotic enterococci on the swine faecal microbiota using 454 pyrosequencing.

    Science.gov (United States)

    Chae, Jong Pyo; Pajarillo, Edward Alain B; Oh, Ju Kyoung; Kim, Heebal; Kang, Dae-Kyung

    2016-07-01

    Demand for the development of non-antibiotic growth promoters in animal production has increased in recent years. This report compared the faecal microbiota of weaned piglets under the administration of a basal diet (CON) or that containing prebiotic lactulose (LAC), probiotic Enterococcus faecium NCIMB 11181 (PRO) or their synbiotic combination (SYN). At the phylum level, the Firmicutes to Bacteroidetes ratio increased in the treatment groups compared with the CON group, and the lowest proportion of Proteobacteria was observed in the LAC group. At the family level, Enterobacteriaceae decreased in all treatments; more than a 10-fold reduction was observed in the LAC (0.99%) group compared with the CON group. At the genus level, the highest Oscillibacter proportion was detected in PRO, the highest Clostridium in LAC and the highest Lactobacillus in SYN; the abundance of Escherichia was lowest in the LAC group. Clustering in the discriminant analysis of principal components revealed distinct separation of the feeding groups (CON, LAC, PRO and SYN), showing different microbial compositions according to different feed additives or their combination. These results suggest that individual materials and their combination have unique actions and independent mechanisms for changes in the distal gut microbiota. PMID:27305897

  12. Influence of bacterial communities based on 454-pyrosequencing on the survival of Escherichia coli O157:H7 in soils.

    Science.gov (United States)

    Ma, Jincai; Ibekwe, Abasiofiok M; Yang, Ching-Hong; Crowley, David E

    2013-06-01

    Shiga toxin-producing Escherichia coli O157:H7 has been implicated in many foodborne illnesses. In this study, survival of E. coli O157:H7 in 32 soils from California (CA) and Arizona (AZ) was investigated. Our goal was to correlate the survival time of E. coli O157:H7 in soils with 16S rRNA pyrosequencing based bacterial community composition. Kohonen self-organizing map of survival and associated soil chemical, physical and biological variables using artificial neural network analysis showed that survival of E. coli O157:H7 in soils was negatively correlated with salinity (EC), but positively correlated with total nitrogen (TN) and water soluble organic carbon (WSOC). Bacterial diversity as determined by the Shannon diversity index had no significant (P = 0.635) effect on ttd, but individual bacterial phyla had different effects. The survival of E. coli O157:H7 was positively correlated with the abundances of Actinobacteria (P < 0.001) and Acidobacteria (P < 0.05), and negatively correlated with those of Proteobacteria and Bacteroidetes (P < 0.05). Our data showed that specific groups of bacteria correlate with the persistence of E. coli O157:H7 in soils thus opening new ways to study the influence of certain bacterial phyla on persistence of this pathogen and other related pathogens in complex environments. PMID:23360569

  13. The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles.

    Science.gov (United States)

    Hakim, Joseph A; Koo, Hyunmin; Kumar, Ranjit; Lefkowitz, Elliot J; Morrow, Casey D; Powell, Mickie L; Watts, Stephen A; Bej, Asim K

    2016-09-01

    In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. The gut digesta and egested fecal pellets exhibited a microbial profile comprised of Gammaproteobacteria, mainly Vibrio, and Bacteroidetes. Both the seagrass and surrounding sea water revealed Alpha- and Betaproteobacteria. Bray-Curtis distances of microbial communities indicated a clustering profile with low intrasample variation. Predictive metagenomics performed on the microbial communities revealed that the gut tissue had high relative abundances of metabolisms assigned to the KEGG-Level-2 designation of energy metabolisms compared to the gut digesta, which had higher carbohydrate, amino acid and lipid metabolisms. Overall, the results of this study elaborate the spatial distribution of microbial communities in the gut ecosystem of L. variegatus, and specifically a selective attribute for Campylobacteraceae in the gut tissue. Also, the predictive functional significance of bacterial communities in uniquely compartmentalized gut ecosystems of L. variegatus has been described. PMID:27368709

  14. Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease

    Directory of Open Access Journals (Sweden)

    Nylund Lotta

    2013-01-01

    Full Text Available Abstract Background Deviations in composition and diversity of intestinal microbiota in infancy have been associated with both the development and recurrence of atopic eczema. Thus, we decided to use a deep and global microarray-based method to characterize the diversity and temporal changes of the intestinal microbiota in infancy and to define specific bacterial signatures associated with eczema. Faecal microbiota at 6 and 18 months of age were analysed from 34 infants (15 with eczema and 19 healthy controls selected from a prospective follow-up study based on the availability of faecal samples. The infants were originally randomized to receive either Lactobacillus rhamnosus GG or placebo. Results Children with eczema harboured a more diverse total microbiota than control subjects as assessed by the Simpson’s reciprocal diversity index of the microarray profiles. Composition of the microbiota did not differ between study groups at age of 6 months, but was significantly different at age of 18 months as assessed by MCPP (p=0.01. At this age healthy children harboured 3 -fold greater amount of members of the Bacteroidetes (p=0.01. Microbiota of children suffering from eczema had increased abundance of the Clostridium clusters IV and XIVa, which are typically abundant in adults. Probiotic Lactobacillus rhamnosus GG supplementation in early infancy was observed to have minor long-term effects on the microbiota composition. Conclusion A diverse and adult-type microbiota in early childhood is associated with eczema and it may contribute to the perpetuation of eczema.

  15. Phylogenetic diversity and community structure of sponge-associated bacteria from mangroves of the Caribbean Sea

    KAUST Repository

    Yang, Jiangke

    2011-02-08

    To gain insight into the species richness and phylogeny of the microbial communities associated with sponges in mangroves, we performed an extensive phylogenetic analysis, based on terminal restriction fragment length polymorphism profiling and 16S ribosomal RNA gene sequences, of the 4 sponge species Aplysina fulva, Haliclona hogarthi, Tedania ignis and Ircinia strobilina as well as of ambient seawater. The sponge-associated bacterial communities contained 13 phyla, including Poribacteria and an unclassified group not found in the ambient seawater community, 98% of which comprised Proteobacteria, Cyanobacteria and Bacteroidetes. Although the sponges themselves were phylogenetically distant and bacterial community variation within the host species was observed, microbial phyla such as Proteobacteria, Acidobacteria, Chloroflexi and the unclassified group were consistently observed as the dominant populations within the communities. The sponge-associated bacterial communities resident in the Caribbean Sea mangroves are phylogenetically similar but significantly distinct from communities found in other biogeographical sites such as the deep-water environments of the Caribbean Sea, the South China Sea and Australia. The interspecific variation within the host species and the distinct biogeographical characteristics that the sponge-associated bacteria exhibited indicate that the acquisition, establishment and formation of functional sponge-associated bacterial communities may initially be the product of both vertical and horizontal transmission, and is then shaped by the internal environment created by the sponge species and certain external environmental factors. © Inter-Research 2011.

  16. Soil bacterial diversity changes in response to agricultural land use in semi-arid soils

    Science.gov (United States)

    Ding, Guo-Chun; Piceno, Yvette M.; Heuer, Holger; Weinert, Nicole; Dohrmann, Anja B.; Carrillo, Angel; Andersen, Gary L.; Castellanos, Thelma; Tebbe, Christoph C.; Smalla, Kornelia

    2013-04-01

    Natural scrublands in semi-arid deserts are increasingly being converted into agricultural lands. The long-term effect of such a transition in land use on soil bacterial communities was explored at two sites typical of semi-arid deserts in Mexico (Baja California). Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods - denaturing gradient gel electrophoresis (DGGE) and PhyloChip hybridization -employed to analyze 16S rRNA gene fragments amplified from total community DNA. DGGE analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. Soil parameters that differed between land uses were highly correlated with the community composition of taxa responding to land use. Variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses. The long term use for agriculture resulted in profound changes in the bacterial community composition and physicochemical characteristics of former scrublands, which may affect various soil ecosystem functions.

  17. Microbial hitchhikers on intercontinental dust: catching a lift in Chad.

    Science.gov (United States)

    Favet, Jocelyne; Lapanje, Ales; Giongo, Adriana; Kennedy, Suzanne; Aung, Yin-Yin; Cattaneo, Arlette; Davis-Richardson, Austin G; Brown, Christopher T; Kort, Renate; Brumsack, Hans-Jürgen; Schnetger, Bernhard; Chappell, Adrian; Kroijenga, Jaap; Beck, Andreas; Schwibbert, Karin; Mohamed, Ahmed H; Kirchner, Timothy; de Quadros, Patricia Dorr; Triplett, Eric W; Broughton, William J; Gorbushina, Anna A

    2013-04-01

    Ancient mariners knew that dust whipped up from deserts by strong winds travelled long distances, including over oceans. Satellite remote sensing revealed major dust sources across the Sahara. Indeed, the Bodélé Depression in the Republic of Chad has been called the dustiest place on earth. We analysed desert sand from various locations in Chad and dust that had blown to the Cape Verde Islands. High throughput sequencing techniques combined with classical microbiological methods showed that the samples contained a large variety of microbes well adapted to the harsh desert conditions. The most abundant bacterial groupings in four different phyla included: (a) Firmicutes-Bacillaceae, (b) Actinobacteria-Geodermatophilaceae, Nocardiodaceae and Solirubrobacteraceae, (c) Proteobacteria-Oxalobacteraceae, Rhizobiales and Sphingomonadaceae, and (d) Bacteroidetes-Cytophagaceae. Ascomycota was the overwhelmingly dominant fungal group followed by Basidiomycota and traces of Chytridiomycota, Microsporidia and Glomeromycota. Two freshwater algae (Trebouxiophyceae) were isolated. Most predominant taxa are widely distributed land inhabitants that are common in soil and on the surfaces of plants. Examples include Bradyrhizobium spp. that nodulate and fix nitrogen in Acacia species, the predominant trees of the Sahara as well as Herbaspirillum (Oxalobacteraceae), a group of chemoorganotrophic free-living soil inhabitants that fix nitrogen in association with Gramineae roots. Few pathogenic strains were found, suggesting that African dust is not a large threat to public health. PMID:23254516

  18. Use of the second-generation antipsychotic, risperidone, and secondary weight gain are associated with an altered gut microbiota in children

    Science.gov (United States)

    Bahr, S M; Tyler, B C; Wooldridge, N; Butcher, B D; Burns, T L; Teesch, L M; Oltman, C L; Azcarate-Peril, M A; Kirby, J R; Calarge, C A

    2015-01-01

    The atypical antipsychotic risperidone (RSP) is often associated with weight gain and cardiometabolic side effects. The mechanisms for these adverse events are poorly understood and, undoubtedly, multifactorial in etiology. In light of growing evidence implicating the gut microbiome in the host's energy regulation and in xenobiotic metabolism, we hypothesized that RSP treatment would be associated with changes in the gut microbiome in children and adolescents. Thus, the impact of chronic (>12 months) and short-term use of RSP on the gut microbiome of pediatric psychiatrically ill male participants was examined in a cross-sectional and prospective (up to 10 months) design, respectively. Chronic treatment with RSP was associated with an increase in body mass index (BMI) and a significantly lower ratio of Bacteroidetes:Firmicutes as compared with antipsychotic-naïve psychiatric controls (ratio=0.15 vs 1.24, respectively; Pgut microbiota dominating the RSP-treated participants are enriched for pathways that have been implicated in weight gain, such as short-chain fatty acid production. PMID:26440540

  19. Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica.

    Science.gov (United States)

    Shi, Ying-wu; Lou, Kai; Li, Chun; Wang, Lei; Zhao, Zhen-yong; Zhao, Shuai; Tian, Chang-yan

    2015-10-01

    We used Illumina-based 16S rRNA V3 amplicon pyrosequencing to investigate the community structure of soil bacteria from the rhizosphere surrounding Salicornia europaea, and endophytic bacteria living in Salicornia europaea plants and Sueada aralocaspica seeds growing at the Fukang Desert Ecosystem Observation and Experimental Station (FDEOES) in Xinjiang Province, China, using an Illumina genome analyzer. A total of 89.23 M effective sequences of the 16S rRNA gene V3 region were obtained from the two halophyte species. These sequences revealed a number of operational taxonomic units (OTUs) in the halophytes. There were between 22-2,206 OTUs in the halophyte plant sample, at the 3% cutoff level, and a sequencing depth of 30,000 sequences. We identified 25 different phyla, 39 classes and 141 genera from the resulting 134,435 sequences. The most dominant phylum in all the samples was Proteobacteria (41.61%-99.26%; average, 43.30%). The other large phyla were Firmicutes (0%- 7.19%; average, 1.15%), Bacteroidetes (0%-1.64%; average, 0.44%) and Actinobacteria (0%-0.46%; average, 0.24%). This result suggested that the diversity of bacteria is abundant in the rhizosphere soil, while the diversity of bacteria was poor within Salicornia europaea plant samples. To the extent of our knowledge, this study is the first to characterize and compare the endophytic bacteria found within different halophytic plant species roots using PCR-based Illumina pyrosequencing method. PMID:26428918

  20. Picoplankton seasonal variation and community structure in the northeast Adriatic coastal zone.

    Science.gov (United States)

    Silović, Tina; Balagué, Vanessa; Orlić, Sandi; Pedrós-Alió, Carlos

    2012-12-01

    The bacterial community in coastal waters of northeastern Adriatic Sea was dominated by SAR11 and Sulfitobacter taxa throughout the year. The seasonal distribution of bacterioplankton taxa showed continual differences between surface (0 m) and bottom (27 m) layers. The surface assemblage was represented by Actinobacteria, Cyanobacteria, Alphaproteobacteria, and Gammaproteobacteria, while the bottom assemblage was made up of Bacteroidetes, Cyanobacteria and Alphaproteobacteria. As SAR11 was more dominant in the bottom layer, its appearance may be linked to northward transport of oligotrophic waters of higher salinity from the south. Gammaproteobacteria appeared only in the surface layer during summer, influenced by higher amounts of nutrients, brought in by the Po River. Synechococcus was the most abundant taxon at the genus level. Dominance of Synechococcus during the whole season agrees with its dominance in terms of abundance determined by flow cytometry, and confirms its utmost importance in the picoplankton community of this area. We found two different types of Synechococcus: one type with high similarity to Synechococcus CC9902, present in the surface and bottom layers, and another one similar to Synechococcus WH7803, present only in the surface layer. Oligotrophic conditions together with complex hydrological features of this area were reflected in diversification and dynamic shifts of surface and bottom assemblages. PMID:22748097

  1. Effects of large river dam regulation on bacterioplankton community structure.

    Science.gov (United States)

    Ruiz-González, Clara; Proia, Lorenzo; Ferrera, Isabel; Gasol, Josep M; Sabater, Sergi

    2013-05-01

    Large rivers are commonly regulated by damming, yet the effects of such disruption on prokaryotic communities have seldom been studied. We describe the effects of the three large reservoirs of the Ebro River (NE Iberian Peninsula) on bacterioplankton assemblages by comparing several sites located before and after the impoundments on three occasions. We monitored the abundances of several bacterial phylotypes identified by rRNA gene probing, and those of two functional groups (picocyanobacteria and aerobic anoxygenic phototrophic bacteria-AAPs). Much greater numbers of particles colonized by bacteria were found in upstream waters than downstream sites. Picocyanobacteria were found in negligible numbers at most sites, whereas AAPs constituted up to 14% of total prokaryotes, but there was no clear effect of reservoirs on the spatial dynamics of these two groups. Instead, damming caused a pronounced decline in Betaproteobacteria, Gammaproteobacteria and Bacteroidetes from upstream to downstream sites, whereas Alphaproteobacteria and Actinobacteria significantly increased after the reservoirs. Redundancy analysis revealed that conductivity, temperature and dissolved inorganic nitrogen were the environmental predictors that best explained the observed variability in bacterial community composition. Our data show that impoundments exerted significant impacts on bacterial riverine assemblages and call attention to the unforeseen ecological consequences of river regulation. PMID:23278359

  2. Biogeography of bacterioplankton in the tropical seawaters of Singapore.

    Science.gov (United States)

    Lau, Stanley C K; Zhang, Rui; Brodie, Eoin L; Piceno, Yvette M; Andersen, Gary; Liu, Wen-Tso

    2013-05-01

    Knowledge about the biogeography of marine bacterioplankton on the global scale in general and in Southeast Asia in particular has been scarce. This study investigated the biogeography of bacterioplankton community in Singapore seawaters. Twelve stations around Singapore island were sampled on different schedules over 1 year. Using PCR-DNA fingerprinting, DNA cloning and sequencing, and microarray hybridization of the 16S rRNA genes, we observed clear spatial variations of bacterioplankton diversity within the small area of the Singapore seas. Water samples collected from the Singapore Strait (south) throughout the year were dominated by DNA sequences affiliated with Cyanobacteria and Alphaproteobacteria that were believed to be associated with the influx of water from the open seas in Southeast Asia. On the contrary, water in the relatively polluted Johor Strait (north) were dominated by Betaproteobacteria, Gammaproteobacteria, and Bacteroidetes and that were presumably associated with river discharge and the relatively eutrophic conditions of the waterway. Bacterioplankton diversity was temporally stable, except for the episodic surge of Pseudoalteromonas, associated with algal blooms. Overall, these results provide valuable insights into the diversity of bacterioplankton communities in Singapore seas and the possible influences of hydrological conditions and anthropogenic activities on the dynamics of the communities. PMID:23237658

  3. Catchment-scale biogeography of riverine bacterioplankton.

    Science.gov (United States)

    Read, Daniel S; Gweon, Hyun S; Bowes, Michael J; Newbold, Lindsay K; Field, Dawn; Bailey, Mark J; Griffiths, Robert I

    2015-02-01

    Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared with macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water samples collected across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel were characterised using 16S rRNA gene pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from a community dominated by Bacteroidetes in the headwaters to Actinobacteria-dominated downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid bacteria relative to high nucleic acid bacteria were found to correspond with these downstream changes in community structure, suggesting corresponding functional changes. Our findings show that bacterial communities across the Thames basin exhibit an ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physico-chemical status of the river. PMID:25238398

  4. Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time.

    Science.gov (United States)

    Crump, Byron C; Hopkinson, Charles S; Sogin, Mitchell L; Hobbie, John E

    2004-03-01

    Shifts in bacterioplankton community composition along the salinity gradient of the Parker River estuary and Plum Island Sound, in northeastern Massachusetts, were related to residence time and bacterial community doubling time in spring, summer, and fall seasons. Bacterial community composition was characterized with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA. Average community doubling time was calculated from bacterial production ([(14)C]leucine incorporation) and bacterial abundance (direct counts). Freshwater and marine populations advected into the estuary represented a large fraction of the bacterioplankton community in all seasons. However, a unique estuarine community formed at intermediate salinities in summer and fall, when average doubling time was much shorter than water residence time, but not in spring, when doubling time was similar to residence time. Sequencing of DNA in DGGE bands demonstrated that most bands represented single phylotypes and that matching bands from different samples represented identical phylotypes. Most river and coastal ocean bacterioplankton were members of common freshwater and marine phylogenetic clusters within the phyla Proteobacteria, Bacteroidetes, and ACTINOBACTERIA: Estuarine bacterioplankton also belonged to these phyla but were related to clones and isolates from several different environments, including marine water columns, freshwater sediments, and soil. PMID:15006771

  5. Characterization of anaerobic consortia coupled lignin depolymerization with biomethane generation.

    Science.gov (United States)

    Wu, Yi-Rui; He, Jianzhong

    2013-07-01

    Two sediment-free microbial consortia (LI3 and LP3) were established to depolymerize lignin under anaerobic conditions. During depolymerizing high molecular weight lignin to low molecular weight molecules, the two cultures produced biomethane up to 151.7 and 113.0 mL g(-1) total lignin. Furthermore, LI3 and LP3 could also utilize the biomass - oil palm empty fruit bunch fiber (OPEFB) to produce 190.6 and 195.6 mL methaneg(-1) total lignin in OPEFB, and at the same time improve the bioavailability of lignocellulosic matters for further enzymatic hydrolysis. The microbial community analysis by denature gradient gel electrophoresis (DGGE) and the high-density 16S rDNA gene microarray (PhyloChip) exhibited that Methanomethylovorans sp. (LI3) and Methanoculleus sp. (LP3) were the main methanogens present, and phylum Firmicutes and Bacteroidetes were mainly involved in the lignin depolymerization. The established microbial consortia with both lignin depolymerization and biomethane production provide profound application on the environmental friendly pretreatment of lignocellulosic materials. PMID:23639408

  6. Using in situ bacterial communities to monitor contaminants in river sediments.

    Science.gov (United States)

    Xie, Yuwei; Wang, Jizhong; Wu, Yaketon; Ren, Chen; Song, Chao; Yang, Jianghua; Yu, Hongxia; Giesy, John P; Zhang, Xiaowei

    2016-05-01

    Bacterial communities in sediments of human-impacted rivers are exposed to multiple anthropogenic contaminants and eventually lead to biodiversity lost and ecological functions disable. Nanfei River of Anhui province has been contaminated by pollutants from industrial and/or agricultural sources. This study was conducted to investigate the structure of in situ sediment bacterial communities in Nanfei River and to examine the correlation between the different taxonomic components and contaminant concentrations. The bacterial communities were dominated by Proteobacteria, Bacteroidetes and Chloroflexi. Both the profiles of environmental predictors and the composition of microbial communities differed among agriculture, industrial and confluence regions. There were significant associations between bacterial community phylogenies and the measured contaminants in the sediments. Nutrients (TN and TP) and two metals (Cd and Zn) were negatively correlated with the essential "core" of the bacterial interaction network (Betaproteobacteria and Deltaproteobacteria). Metals (Fe, Ni and Zn) and nutrients (TN and TP) had higher impact on bacterial community compositions than PAHs, OPs and PRTs according to the correlation and network analyses. Furthermore, several sensitive candidate genera were identified as potential bioindicators to monitor key contaminants by species contaminant correlation analysis. Overall, in situ bacterial communities could provide a useful tool for monitoring and assessing ecological stressors in freshwater sediments. PMID:26866572

  7. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Natacha Bodenhausen

    Full Text Available Diverse communities of bacteria inhabit plant leaves and roots and those bacteria play a crucial role for plant health and growth. Arabidopsis thaliana is an important model to study plant pathogen interactions, but little is known about its associated bacterial community under natural conditions. We used 454 pyrosequencing to characterize the bacterial communities associated with the roots and the leaves of wild A. thaliana collected at 4 sites; we further compared communities on the outside of the plants with communities in the endophytic compartments. We found that the most heavily sequenced bacteria in A. thaliana associated community are related to culturable species. Proteobacteria, Actinobacteria, and Bacteroidetes are the most abundant phyla in both leaf and root samples. At the genus level, sequences of Massilia and Flavobacterium are prevalent in both samples. Organ (leaf vs root and habitat (epiphytes vs endophytes structure the community. In the roots, richness is higher in the epiphytic communities compared to the endophytic compartment (P = 0.024, while the reverse is true for the leaves (P = 0.032. Interestingly, leaf and root endophytic compartments do not differ in richness, diversity and evenness, while they differ in community composition (P = 0.001. The results show that although the communities associated with leaves and roots share many bacterial species, the associated communities differ in structure.

  8. Predominance of Roseobacter, Sulfitobacter, Glaciecola and Psychrobacter in seawater collected off Ushuaia, Argentina, Sub-Antarctica.

    Science.gov (United States)

    Prabagaran, Solai Ramatchandirane; Manorama, Ruth; Delille, Daniel; Shivaji, Sisinthy

    2007-02-01

    Bacterial diversity in sub-Antarctic seawater, collected off Ushuaia, Argentina, was examined using a culture independent approach. The composition of the 16S rRNA gene libraries from seawater and seawater contaminated with the water soluble fraction of crude oil was statistically different (P value 0.001). In both libraries, clones representing the Alphaproteobacteria, Gammaproteobacteria, the Cytophaga-Flavobacterium-Bacteroidetes group and unculturable bacteria were dominant. Clones associated with the genera Roseobacter, Sulfitobacter, Staleya, Glaciecola, Colwellia, Marinomonas, Cytophaga and Cellulophaga were common to both the libraries. However, clones associated with Psychrobacter, Arcobacter, Formosa algae, Polaribacter, Ulvibacter and Tenacibaculum were found only in seawater contaminated with hydrocarbons (Table 1). Further, the percentage of clones of Roseobacter, Sulfitobacter and Glaceicola was high in seawater (43%, 90% and 12% respectively) compared to seawater contaminated with hydrocarbons (35%, 4% and 9% respectively). One of the clones F2C63 showed 100% similarity with Marinomonas ushuaiensis a bacterium identified by us from the same site. PMID:17026513

  9. Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata.

    Directory of Open Access Journals (Sweden)

    Dustin W Kemp

    Full Text Available Coral surface mucus layer (SML microbiota are critical components of the coral holobiont and play important roles in nutrient cycling and defense against pathogens. We sequenced 16S rRNA amplicons to examine the structure of the SML microbiome within and between colonies of the threatened Caribbean reef-building coral Acropora palmata in the Florida Keys. Samples were taken from three spatially distinct colony regions--uppermost (high irradiance, underside (low irradiance, and the colony base--representing microhabitats that vary in irradiance and water flow. Phylogenetic diversity (PD values of coral SML bacteria communities were greater than surrounding seawater and lower than adjacent sediment. Bacterial diversity and community composition was consistent among the three microhabitats. Cyanobacteria, Bacteroidetes, Alphaproteobacteria, and Proteobacteria, respectively were the most abundant phyla represented in the samples. This is the first time spatial variability of the surface mucus layer of A. palmata has been studied. Homogeneity in the microbiome of A. palmata contrasts with SML heterogeneity found in other Caribbean corals. These findings suggest that, during non-stressful conditions, host regulation of SML microbiota may override diverse physiochemical influences induced by the topographical complexity of A. palmata. Documenting the spatial distribution of SML microbes is essential to understanding the functional roles these microorganisms play in coral health and adaptability to environmental perturbations.

  10. Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata.

    Science.gov (United States)

    Kemp, Dustin W; Rivers, Adam R; Kemp, Keri M; Lipp, Erin K; Porter, James W; Wares, John P

    2015-01-01

    Coral surface mucus layer (SML) microbiota are critical components of the coral holobiont and play important roles in nutrient cycling and defense against pathogens. We sequenced 16S rRNA amplicons to examine the structure of the SML microbiome within and between colonies of the threatened Caribbean reef-building coral Acropora palmata in the Florida Keys. Samples were taken from three spatially distinct colony regions--uppermost (high irradiance), underside (low irradiance), and the colony base--representing microhabitats that vary in irradiance and water flow. Phylogenetic diversity (PD) values of coral SML bacteria communities were greater than surrounding seawater and lower than adjacent sediment. Bacterial diversity and community composition was consistent among the three microhabitats. Cyanobacteria, Bacteroidetes, Alphaproteobacteria, and Proteobacteria, respectively were the most abundant phyla represented in the samples. This is the first time spatial variability of the surface mucus layer of A. palmata has been studied. Homogeneity in the microbiome of A. palmata contrasts with SML heterogeneity found in other Caribbean corals. These findings suggest that, during non-stressful conditions, host regulation of SML microbiota may override diverse physiochemical influences induced by the topographical complexity of A. palmata. Documenting the spatial distribution of SML microbes is essential to understanding the functional roles these microorganisms play in coral health and adaptability to environmental perturbations. PMID:26659364

  11. Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Hollister, Emily B.; Gentry, Terry J. [Texas A and M Univ., College Station, TX (United States). Dept. of Soil and Crop Sciences; Forrest, Andrea K.; Holtzapple, Mark T. [Texas A and M Univ., College Station, TX (United States). Dept. of Chemical Engineering; Wilkinson, Heather H.; Ebbole, Daniel J. [Texas A and M Univ., College Station, TX (United States). Dept. of Plant Pathology and Microbiology; Malfatti, Stephanie A.; Tringe, Susannah G. [DOE Joint Genome Institute, Walnut Creek, CA (United States)

    2010-09-15

    The carboxylate platform utilizes a mixed microbial community to convert lignocellulosic biomass into chemicals and fuels. While much of the platform is well understood, little is known about its microbiology. Mesophilic (40 C) and thermophilic (55 C) fermentations employing a sorghum feedstock and marine sediment inoculum were profiled using 16S rRNA tag-pyrosequencing over the course of a 30-day incubation. The contrasting fermentation temperatures converted similar amounts of biomass, but the mesophilic community was significantly more productive, and the two temperatures differed significantly with respect to propionic and butyric acid production. Pyrotag sequencing revealed the presence of dynamic communities that responded rapidly to temperature and changed substantially over time. Both temperatures were dominated by bacteria resembling Clostridia, but they shared few taxa in common. The species-rich mesophilic community harbored a variety of Bacteroidetes, Actinobacteria, and {gamma}-Proteobacteria, whereas the thermophilic community was composed mainly of Clostridia and Bacilli. Despite differences in composition and productivity, similar patterns of functional class dynamics were observed. Over time, organisms resembling known cellulose degraders decreased in abundance, while organisms resembling known xylose degraders increased. Improved understanding of the carboxylate platform's microbiology will help refine platform performance and contribute to our growing knowledge regarding biomass conversion and biofuel production processes. (orig.)

  12. Characterization and in-vivo evaluation of potential probiotics of the bacterial flora within the water column of a healthy shrimp larviculture system

    Science.gov (United States)

    Xue, Ming; Liang, Huafang; He, Yaoyao; Wen, Chongqing

    2016-05-01

    A thorough understanding of the normal bacterial flora associated with shrimp larviculture systems contributes to probiotic screening and disease control. The bacterial community of the water column over a commercial Litopenaeus vannamei larval rearing run was characterized with both culture-dependent and culture-independent methods. A total of 27 phylotypes at the species level were isolated and identified based on 16S rDNA sequence analysis. Denaturing gradient gel electrophoresis (DGGE) analysis of the V3-V5 region of 16S rRNA genes showed a dynamic bacterial community with major changes occurred from stages zoea to mysis during the rearing run. The sequences retrieved were affiliated to four phyla, Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, with the family Rhodobacteraceae being the most frequently recovered one. Subsequently, 13 representative strains conferred higher larval survival than the control when evaluated in the in-vivo experiments; in particular, three candidates, assigned to Phaeobacter sp., Arthrobacter sp., and Microbacterium sp., significantly improved larval survival ( P < 0.05). Therefore, the healthy shrimp larviculture system harbored a diverse and favorable bacterial flora, which contribute to larval development and are of great importance in exploiting novel probiotics.

  13. Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application

    Science.gov (United States)

    Ventorino, Valeria; Aliberti, Alberto; Faraco, Vincenza; Robertiello, Alessandro; Giacobbe, Simona; Ercolini, Danilo; Amore, Antonella; Fagnano, Massimo; Pepe, Olimpia

    2015-02-01

    The aims of this study were to evaluate the microbial diversity of different lignocellulosic biomasses during degradation under natural conditions and to isolate, select, characterise new well-adapted bacterial strains to detect potentially improved enzyme-producing bacteria. The microbiota of biomass piles of Arundo donax, Eucalyptus camaldulensis and Populus nigra were evaluated by high-throughput sequencing. A highly complex bacterial community was found, composed of ubiquitous bacteria, with the highest representation by the Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes phyla. The abundances of the major and minor taxa retrieved during the process were determined by the selective pressure produced by the lignocellulosic plant species and degradation conditions. Moreover, cellulolytic bacteria were isolated using differential substrates and screened for cellulase, cellobiase, xylanase, pectinase and ligninase activities. Forty strains that showed multienzymatic activity were selected and identified. The highest endo-cellulase activity was seen in Promicromonospora sukumoe CE86 and Isoptericola variabilis CA84, which were able to degrade cellulose, cellobiose and xylan. Sixty-two percent of bacterial strains tested exhibited high extracellular endo-1,4-ß-glucanase activity in liquid media. These approaches show that the microbiota of lignocellulosic biomasses can be considered an important source of bacterial strains to upgrade the feasibility of lignocellulose conversion for the `greener' technology of second-generation biofuels.

  14. First microbiota assessments of children's paddling pool waters evaluated using 16S rRNA gene-based metagenome analysis.

    Science.gov (United States)

    Sawabe, Toko; Suda, Wataru; Ohshima, Kenshiro; Hattori, Masahira; Sawabe, Tomoo

    2016-01-01

    Insufficient chloric sterilization of children's paddling pool waters increases the risk of diarrheal illness. Therefore, we investigated the microbiota changes after children use pools. First, we applied 16S rRNA gene-based metagenome analysis to understand the dynamics of microbiota in pool water, especially with respect to the bio-contamination by potential pathogens. Proteobacteria were major taxa detected in every pool water sample after children spent time in the pool. In more detail, Gammaproteobacteria comprised the dominant class, which was followed by Betaproteobacteria. Five phyla, Bacteroidetes, Firmicutes, Actinobacteria and Deinococcus-Thermus phyla were minor groups. The pool water microbiota are likely to be a consortium of intestinal and skin microbiota from humans. Interestingly, the ratio of Gammaproteobacteria and Betaproteobacteria differed according to the age of the children who used the pool, which means the pool water was additionally contaminated by soil microbiota as a result of the children's behavior. Furthermore, potential pathogens, such as Campylobacter spp., Comamonas testosteroni and Burkholderia pseudomallei, were also found. Considering the standard plate counts, the abundances of these human pathogens are unlikely to be a sufficiently infectious dose. We suggest the importance of sanitary measures in paddling pool waters to reduce bio-contamination from both humans and the environment. PMID:26671497

  15. Molecular characterization of the stomach microbiota in patients with gastric cancer and controls

    Energy Technology Data Exchange (ETDEWEB)

    Dicksved, J.; Lindberg, M.; Rosenquist, M.; Enroth, H.; Jansson, J.K.; Engstrand, L.

    2009-01-15

    Persistent infection of the gastric mucosa by Helicobacter pylori, can initiate an inflammatory cascade that progresses into atrophic gastritis, a condition associated with reduced capacity for secretion of gastric acid and an increased risk in developing gastric cancer. The role of H. pylori as an initiator of inflammation is evident but the mechanism for development into gastric cancer has not yet been proven. A reduced capacity for gastric acid secretion allows survival and proliferation of other microbes that normally are killed by the acidic environment. It has been postulated that some of these species may be involved in the development of gastric cancer, however their identities are poorly defined. In this study, the gastric microbiota from ten patients with gastric cancer was characterized and compared with five dyspeptic controls using the molecular profiling approach, terminal-restriction fragment length polymorphism (T-RFLP), in combination with 16S rRNA gene cloning and sequencing. T-RFLP analysis revealed a complex bacterial community in the cancer patients that was not significantly different from the controls. Sequencing of 140 clones revealed 102 phylotypes, with representatives from five bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria). The data revealed a relatively low abundance of H. pylori and showed that the gastric cancer microbiota was instead dominated by different species of the genera Streptococcus, Lactobacillus, Veillonella and Prevotella. The respective role of these species in development of gastric cancer remains to be determined.

  16. Enrichment and isolation of Flavobacterium strains with tolerance to high concentrations of cesium ion.

    Science.gov (United States)

    Kato, Souichiro; Goya, Eri; Tanaka, Michiko; Kitagawa, Wataru; Kikuchi, Yoshitomo; Asano, Kozo; Kamagata, Yoichi

    2016-01-01

    Interest in the interaction of microorganisms with cesium ions (Cs(+)) has arisen, especially in terms of their potent ability for radiocesium bioaccumulation and their important roles in biogeochemical cycling. Although high concentrations of Cs(+) display toxic effects on microorganisms, there have been only limited reports for Cs(+)-tolerant microorganisms. Here we report enrichment and isolation of Cs(+)-tolerant microorganisms from soil microbiota. Microbial community analysis revealed that bacteria within the phylum Bacteroidetes, especially Flavobacterium spp., dominated in enrichment cultures in the medium supplemented with 50 or 200 mM Cs(+), while Gammaproteobacteria was dominant in the control enrichment cultures (in the presence of 50 and 200 mM K(+) instead of Cs(+)). The dominant Flavobacterium sp. was successfully isolated from the enrichment culture and was closely related to Flavobacterium chungbukense with 99.5% identity. Growth experiments clearly demonstrated that the isolate has significantly higher tolerance to Cs(+) compared to its close relatives, suggesting the Cs(+)-tolerance is a specific trait of this strain, but not a universal trait in the genus Flavobacterium. Measurement of intracellular K(+) and Cs(+) concentrations of the Cs(+)-tolerant isolate and its close relatives suggested that the ability to maintain low intracellular Cs(+) concentration confers the tolerance against high concentrations of external Cs(+). PMID:26883718

  17. Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants.

    Science.gov (United States)

    Holman, Devin B; Hao, Xiying; Topp, Edward; Yang, Hee Eun; Alexander, Trevor W

    2016-01-01

    Agricultural operations generate large quantities of manure which must be eliminated in a manner that is consistent with public health guidelines. Meanwhile, construction and demolition waste makes up about 25% of total solid municipal waste. Co-composting of manure with construction and demolition waste offers a potential means to make manure safe for soil amendment and also divert construction and demolition waste from municipal landfills. Therefore, the archaeal, bacterial, and fungal microbiota of two different types of composted cattle manure and one co-composted with construction and demolition waste, were assessed over a 99-day composting period. The microbiota of the three compost mixtures did not differ, but significant changes over time and by sampling depth were observed. Bacillus and Halocella, however, were more relatively abundant in composted manure from cattle fed dried distillers' grains and solubles. Proteobacteria and Bacteroidetes were enriched at day 0 and Firmicutes at day 99. The fungal genus Kernia was the most relatively abundant overall and was enriched at day 0. The concentration of 12 antimicrobial resistance determinants in the compost mixtures was also determined, and 10 of these determinants decreased significantly from days 0 to 99. The addition of construction and demolition waste did not affect the persistence of antimicrobial resistance genes or community structure of the compost microbiota and therefore co-composting construction and demolition waste with cattle manure offers a safe, viable way to divert this waste from landfills. PMID:27300323

  18. The impact of environmental heterogeneity and life stage on the hindgut microbiota of Holotrichia parallela larvae (Coleoptera: Scarabaeidae.

    Directory of Open Access Journals (Sweden)

    Shengwei Huang

    Full Text Available Gut microbiota has diverse ecological and evolutionary effects on its hosts. However, the ways in which it responds to environmental heterogeneity and host physiology remain poorly understood. To this end, we surveyed intestinal microbiota of Holotrichia parallela larvae at different instars and from different geographic regions. Bacterial 16S rRNA gene clone libraries were constructed and clones were subsequently screened by DGGE and sequenced. Firmicutes and Proteobacteria were the major phyla, and bacteria belonging to Ruminococcaceae, Lachnospiraceae, Enterobacteriaceae, Desulfovibrionaceae and Rhodocyclaceae families were commonly found in all natural populations. However, bacterial diversity (Chao1 and Shannon indices and community structure varied across host populations, and the observed variation can be explained by soil pH, organic carbon and total nitrogen, and the climate factors (e.g., mean annual temperature of the locations where the populations were sampled. Furthermore, increases in the species richness and diversity of gut microbiota were observed during larval growth. Bacteroidetes comprised the dominant group in the first instar; however, Firmicutes composed the majority of the hindgut microbiota during the second and third instars. Our results suggest that the gut's bacterial community changes in response to environmental heterogeneity and host's physiology, possibly to meet the host's ecological needs or physiological demands.

  19. Optimizing the performance of microbial fuel cells fed a combination of different synthetic organic fractions in municipal solid waste.

    Science.gov (United States)

    Pendyala, Brahmaiah; Chaganti, Subba Rao; Lalman, Jerald A; Heath, Daniel D

    2016-03-01

    The objective of this study was to establish the impact of different steam exploded organic fractions in municipal solid waste (MSW) on electricity production using microbial fuel cells (MFCs). In particular, the influence of individual steam exploded liquefied waste components (food waste (FW), paper-cardboard waste (PCW) and garden waste (GW)) and their blends on chemical oxygen demand (COD) removal, columbic efficiency (CE) and microbial diversity was examined using a mixture design. Maximum power densities from 0.56 to 0.83Wm(-2) were observed for MFCs fed with different feedstocks. The maximum COD removed and minimum CE were observed for a GW feed. However, a reverse trend (minimum COD removed and maximum CE) was observed for the FW feed. A maximum COD removal (78%) accompanied with a maximum CE (24%) was observed for a combined feed of FW, PCW plus GW in a 1:1:1 ratio. Lactate, the major byproduct detected, was unutilized by the anodic biofilm community. The organic fraction of municipal solid waste (OFMSW) could serve as a potential feedstock for electricity generation in MFCs; however, elevated protein levels will lead to reduced COD removal. The microbial communities in cultures fed FW and PCW was highly diversified; however, the communities in cultures fed FW or a feed mixture containing high FW levels were similar and dominated by Bacteroidetes and β-proteobacteria. PMID:26777306

  20. Application of Molecular Techniques to Elucidate the Influence of Cellulosic Waste on the Bacterial Community Structure at a Simulated Low-Level-Radioactive-Waste Site

    International Nuclear Information System (INIS)

    Low-level radioactive waste sites, including those at various U.S. Department of Energy (DOE) sites, frequently contain cellulosic waste in the form of paper towels, cardboard boxes, or wood contaminated with heavy metals and radionuclides such as chromium and uranium. To understand how the soil microbial community is influenced by the presence of cellulosic waste products, multiple soil samples were obtained from a non-radioactive model low-level waste test pit at the Idaho National Laboratory. Samples were analyzed using 16S rDNA clone libraries and 16S rRNA gene microarray (PhyloChip) analyses. Both the clone library and PhyloChip results revealed changes in the bacterial community structure with depth. In all samples, the PhyloChip detected significantly more unique Operational Taxonomic Units (OTUs), and therefore more relative diversity, than the clone libraries. Calculated diversity indices suggest that diversity is lowest in the Fill (F) and Fill Waste (FW) layers and greater in the Wood Waste (WW) and Waste Clay (WC) layers. Principal coordinates analysis and lineage specific analysis determined that Bacteroidetes and Actinobacteria phyla account for most of the significant differences observed between the layers. The decreased diversity in the FW layer and increased members of families containing known cellulose degrading microorganisms suggests the FW layer is an enrichment environment for cellulose degradation. Overall, these results suggest that the presence of the cellulosic material significantly influences the bacterial community structure in a stratified soil system.

  1. Role of the Gut Microbiome in Obesity and Diabetes Mellitus.

    Science.gov (United States)

    Barlow, Gillian M; Yu, Allen; Mathur, Ruchi

    2015-12-01

    Type 2 diabetes mellitus (T2DM) and obesity represent two of the biggest global health challenges of this century and are associated with significant comorbidities and healthcare costs. Although multiple factors undoubtedly contribute to the development and progression of DM and obesity, research over the last decade has demonstrated that the microbes that colonize the human gut may play key contributory roles. Gut microbes are now known to codevelop with the human host and are strongly influenced by mode of birth and early diet and nutrition, as well as environmental and other factors including antibiotic exposure. Gut microbes contribute to human health through roles in polysaccharide breakdown, nutrient absorption, inflammatory responses, gut permeability, and bile acid modification. Numerous studies have suggested that disruptions in the relative proportions of gut microbial populations may contribute to weight gain and insulin resistance, including alterations in Gammaproteobacteria and Verrucomicrobia and the ratios of Firmicutes to Bacteroidetes in weight gain and possible alterations in butyrate-producing bacteria such as Faecalibacterium prausnitzii in DM. In addition, it has been shown that the methanogenic Archaea may contribute to altered metabolism and weight gain in the host. However, the majority of studies are performed with stool or colonic samples and may not be representative of the metabolically active small intestine. Studies predominantly in rodent models are beginning to elucidate the mechanisms by which gut microbes contribute to DM and obesity, but much remains to be learned before we can begin to approach targeted treatments. PMID:26452391

  2. Effects of a ciliate protozoa predator on microbial communities in pitcher plant (Sarracenia purpurea leaves.

    Directory of Open Access Journals (Sweden)

    Taylor K Paisie

    Full Text Available The aquatic communities found within the water filled leaves of the pitcher plant, Sarracenia purpurea, have a simple trophic structure providing an ideal system to study microscale interactions between protozoan predators and their bacterial prey. In this study, replicate communities were maintained with and without the presence of the bactivorous protozoan, Colpoda steinii, to determine the effects of grazing on microbial communities. Changes in microbial (Archaea and Bacteria community structure were assessed using iTag sequencing of 16S rRNA genes. The microbial communities were similar with and without the protozoan predator, with>1000 species. Of these species, Archaea were negligible, with Bacteria comprising 99.99% of the microbial community. The Proteobacteria and Bacteroidetes were the most dominant phyla. The addition of a protozoan predator did not have a significant effect on microbial evenness nor richness. However, the presence of the protozoan did cause a significant shift in the relative abundances of a number of bacterial species. This suggested that bactivorous protozoan may target specific bacterial species and/or that certain bacterial species have innate mechanisms by which they evade predators. These findings help to elucidate the effect that trophic structure perturbations have on predator prey interactions in microbial systems.

  3. Molecular Techniques Revealed Highly Diverse Microbial Communities in Natural Marine Biofilms on Polystyrene Dishes for Invertebrate Larval Settlement

    KAUST Repository

    Lee, On On

    2014-01-09

    Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups. © 2014 Springer Science+Business Media New York.

  4. Understanding diversity patterns in bacterioplankton communities from a sub-Antarctic peatland.

    Science.gov (United States)

    Quiroga, María Victoria; Valverde, Angel; Mataloni, Gabriela; Cowan, Don

    2015-06-01

    Bacterioplankton communities inhabiting peatlands have the potential to influence local ecosystem functions. However, most microbial ecology research in such wetlands has been done in ecosystems (mostly peat soils) of the Northern Hemisphere, and very little is known of the factors that drive bacterial community assembly in other regions of the world. In this study, we used high-throughput sequencing to analyse the structure of the bacterial communities in five pools located in a sub-Antarctic peat bog (Tierra del Fuego, Argentina), and tested for relationships between bacterial communities and environmental conditions. Bacterioplankton communities in peat bog pools were diverse and dominated by members of the Proteobacteria, Actinobacteria, Bacteroidetes and Verrucomicrobia. Community structure was largely explained by differences in hydrological connectivity, pH and nutrient status (ombrotrophic versus minerotrophic pools). Bacterioplankton communities in ombrotrophic pools showed phylogenetic clustering, suggesting a dominant role of deterministic processes in shaping these assemblages. These correlations between habitat characteristics and bacterial diversity patterns provide new insights into the factors regulating microbial populations in peatland ecosystems. PMID:25727763

  5. Effects of growth stage and fulvic acid on the diversity and dynamics of endophytic bacterial community in Stevia rebaudiana Bertoni leaves

    Directory of Open Access Journals (Sweden)

    Xuejian eYu

    2015-08-01

    Full Text Available The aim of this study was to learn the interactions among the endophytic bacteria, the plant growth, the foliar spray of fulvic acid, and the accumulation of steviol glycosides in the leaves of Stevia rebaudiana. Metagenomic DNA was extracted from the Stevia leaves at different growth stages with or without the fulvic acid treatment; and the diversity of endophytic bacteria in Stevia leaves was estimated by pyrosequencing of 16S rRNA genes. As results, Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were found to be the dominant phyla despite the growth stages and fulvic acid application. Stevia growth stages strongly regulated composition of endophytic community. The genera Agrobacterium (12.3 % and Erwinia (7.2 % dominated in seedling stage were apparently declined in the vegetable and initial flowering stages, while Sphingomonas and Methylobacterium increased in mature leaves at harvest time, which showed that the mature leaves of Stevia preferred to accumulate some certain endophytic bacteria. Sphingomonas and Methylobacterium constituted an important part of the core endophytic community and were positively correlated with the stevioside content and UGT74G1 gene expression, respectively; while Erwinia, Agrobacterium and Bacillus were negatively correlated with the stevioside accumulation. Fulvic acid treatment accelerated the variation of endophytes along the growth stages.

  6. Effect of separator and inoculum type on electricity generation and microbial community in single-chamber microbial fuel cells.

    Science.gov (United States)

    Yu, Jaecheul; Park, Younghyun; Lee, Taeho

    2014-04-01

    Single-chamber microbial fuel cell (SMFC)-I consisted of 4 separator-electrode assemblies (SEAs) with two types of cation exchange membrane (CEM: Nafion and CMI 7000) and an anion exchange membrane (AEM: AMI 7001). SMFC-II consisted of 4 SEAs with Nafion and three types of nonwoven fabric. SMFC-I and -II were inoculated with anaerobic digested and activated sludge, respectively, and operated under fed-batch mode. In SMFC I, AEM-SEA showed a maximum power density (PDmax). Nafion-SEA showed a PDmax in SMFC II, which was similar to that of Nafion-SEA of SMFC I. Although different bacteria were developed in SMFC-I (Deltaproteobacteria and Firmicutes) and SMFC-II (Gammaproteobacteria, Betaproteobacteria and Bacteroidetes), the inoculum type little affects electricity generation. Variations of pH and oxygen in biofilm have influenced microbial community structure and electricity generation according to the electrode and separator material. Although the electricity generation of non-woven fabric-SEA was less than that of Nafion-SEA, the use of non-woven fabrics is expected to reduce the construction and operating costs of MFCs. PMID:24009019

  7. A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus and humans (Homo sapiens

    Directory of Open Access Journals (Sweden)

    Hildebrand Falk

    2012-09-01

    Full Text Available Abstract Background Guinea pig (Cavia porcellus is an important model for human intestinal research. We have characterized the faecal microbiota of 60 guinea pigs using Illumina shotgun metagenomics, and used this data to compile a gene catalogue of its prevalent microbiota. Subsequently, we compared the guinea pig microbiome to existing human gut metagenome data from the MetaHIT project. Results We found that the bacterial richness obtained for human samples was lower than for guinea pig samples. The intestinal microbiotas of both species were dominated by the two phyla Bacteroidetes and Firmicutes, but at genus level, the majority of identified genera (320 of 376 were differently abundant in the two hosts. For example, the guinea pig contained considerably more of the mucin-degrading Akkermansia, as well as of the methanogenic archaea Methanobrevibacter than found in humans. Most microbiome functional categories were less abundant in guinea pigs than in humans. Exceptions included functional categories possibly reflecting dehydration/rehydration stress in the guinea pig intestine. Finally, we showed that microbiological databases have serious anthropocentric biases, which impacts model organism research. Conclusions The results lay the foundation for future gastrointestinal research applying guinea pigs as models for humans.

  8. A comprehensive repertoire of prokaryotic species identified in human beings.

    Science.gov (United States)

    Hugon, Perrine; Dufour, Jean-Charles; Colson, Philippe; Fournier, Pierre-Edouard; Sallah, Kankoe; Raoult, Didier

    2015-10-01

    The compilation of the complete prokaryotic repertoire associated with human beings as commensals or pathogens is a major goal for the scientific and medical community. The use of bacterial culture techniques remains a crucial step to describe new prokaryotic species. The large number of officially acknowledged bacterial species described since 1980 and the recent increase in the number of recognised pathogenic species have highlighted the absence of an exhaustive compilation of species isolated in human beings. By means of a thorough investigation of several large culture databases and a search of the scientific literature, we built an online database containing all human-associated prokaryotic species described, whether or not they had been validated and have standing in nomenclature. We list 2172 species that have been isolated in human beings. They were classified in 12 different phyla, mostly in the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. Our online database is useful for both clinicians and microbiologists and forms part of the Human Microbiome Project, which aims to characterise the whole human microbiota and help improve our understanding of the human predisposition and susceptibility to infectious agents. PMID:26311042

  9. Bacterial Rhizosphere Biodiversity from Several Pioneer Desert Sand Plants Near Jizan, Saudi Arabia

    KAUST Repository

    Osman, Jorge R.

    2016-04-08

    Life in arid regions and, in particular, hot deserts is often limited due to their harsh environmental conditions, such as large temperature fluctuations and low amounts of water. These extreme environments can influence the microbial community present on the surface sands and any rhizosphere members surrounding desert plant roots. The Jizan desert area, located in Saudi Arabia, supports particular vegetation that grows in the large sandy flat terrain. We examined five different samples, four from the rhizosphere of pioneer plants plus a surface sand sample, and used pyrosequencing of PCR-amplified V1-V3 regions of 16S rDNA genes from total extracted DNA to reveal and compare the bacterial population diversity of the samples. The results showed a total of 3,530 OTUs in the five samples, calculated using ≥ 97% sequence similarity levels. The Chao1 estimation of the bacterial diversity fluctuated from 637 to 2,026 OTUs for a given sample. The most abundant members found in the samples belong to the Bacteroidetes, Firmicutes and Proteobacteria phyla. This work shows that the Jizan desert area of Saudi Arabia can contain a diverse bacterial community on the sand and surrounding the roots of pioneer desert plants. It also shows that desert sand microbiomes can vary depending on conditions, with broad implications for sandstone monument bacterial communities

  10. Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora

    KAUST Repository

    Gao, Zhao-Ming

    2015-06-11

    Sponge diseases have been widely reported, yet the causal factors and major pathogenic microbes remain elusive. In this study, two individuals of the sponge Crella cyathophora in total that showed similar disease-like characteristics were collected from two different locations along the Red Sea coast separated by more than 30 kilometers. The disease-like parts of the two individuals were both covered by green surfaces, and the body size was much smaller compared with adjacent healthy regions. Here, using high-throughput pyrosequencing technology, we investigated the prokaryotic communities in healthy and disease-like sponge tissues as well as adjacent seawater. Microbes in healthy tissues belonged mainly to the Proteobacteria, Cyanobacteria and Bacteroidetes, and were much more diverse at the phylum level than reported previously. Interestingly, the disease-like tissues from the two sponge individuals underwent shifts of prokaryotic communities and were both enriched with a novel clade affiliated with the phylum Verrucomicrobia, implying its intimate connection with the disease-like Red Sea sponge C. cyathophora. Enrichment of the phylum Verrucomicrobia was also considered to be correlated with the presence of algae assemblages forming the green surface of the disease-like sponge tissues. This finding represents an interesting case of sponge disease and is valuable for further study.

  11. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Wrighton, Kelly C.; Castelle, Cindy; Wilkins, Michael J.; Hug, Laura A.; Sharon, I.; Thomas, Brian C.; Handley, Kim M.; Mullin, Sean W.; Nicora, Carrie D.; Singh, Andrea; Lipton, Mary S.; Long, Philip E.; Williams, Kenneth H.; Banfield, Jillian F.

    2014-07-08

    Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge, and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, Colorado, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via two acetate-based biostimulation treatments. Samples were collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include genomes from a new phylum (ACD20), phylogenetically novel members of the Chloroflexi and Bacteroidetes, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER, and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate, and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen currency in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate, and iron reduction. Thus, fermentation carried out by previously unstudied members of sediment microbial communities may be an important driver of diverse subsurface biogeochemical cycles.

  12. Reconciling Phylogeny and Function During Plant Litter Decomposition by High-Throughput Functional Metagenomics

    Science.gov (United States)

    Nyyssonen, M.; Weihe, C.; Goulden, M.; Treseder, K. K.; Martiny, J.; Martiny, A.; Allison, S. D.; Brodie, E. L.

    2012-12-01

    Integrating information on microbial diversity and functionality with ecosystem processes may be critical to predicting how ecosystems respond to environmental change. While theoretical models can be used to link microbial processes to environmental responses and rates, accurate predictions of ecosystem functioning would benefit from detailed information on microbial community composition and function. In this study, our aim was to identify functional traits involved in plant litter decomposition, a model process for carbon cycling, from decomposing plant litter. The overall goal is then to link these traits with individual microbial taxa and use this information to build predictive trait-based models of ecosystem responses to global change. In order to identify activities involved in plant litter decomposition we used automated high-throughput assays for functional screening of metagenomic fosmid libraries prepared from decomposing plant litter. Litter was collected over 15 month period from a global change field experiment undergoing rainfall and nitrogen manipulations. We identified over 600 cellulose, hemicellulose, chitin and starch hydrolyzing clones following screening of over 300,000 clones. The frequency of positive clones was ten times lower during dry season but no significant differences in hit rates were observed between different treatments. The positive clones were shotgun sequenced on the Illumina sequencing platform and the identified hydrolytic genes were shown to represent variety bacterial taxonomic groups including Proteobacteria and Bacteroidetes.

  13. Taxonomic and Functional Metagenomic Signature of Turfs in the Abrolhos Reef System (Brazil).

    Science.gov (United States)

    Walter, Juline M; Tschoeke, Diogo A; Meirelles, Pedro M; de Oliveira, Louisi; Leomil, Luciana; Tenório, Márcio; Valle, Rogério; Salomon, Paulo S; Thompson, Cristiane C; Thompson, Fabiano L

    2016-01-01

    Turfs are widespread assemblages (consisting of microbes and algae) that inhabit reef systems. They are the most abundant benthic component in the Abrolhos reef system (Brazil), representing greater than half the coverage of the entire benthic community. Their presence is associated with a reduction in three-dimensional coral reef complexity and decreases the habitats available for reef biodiversity. Despite their importance, the taxonomic and functional diversity of turfs remain unclear. We performed a metagenomics and pigments profile characterization of turfs from the Abrolhos reefs. Turf microbiome primarily encompassed Proteobacteria (mean 40.57% ± s.d. 10.36, N = 1.548,192), Cyanobacteria (mean 35.04% ± s.d. 15.5, N = 1.337,196), and Bacteroidetes (mean 11.12% ± s.d. 4.25, N = 424,185). Oxygenic and anoxygenic phototrophs, chemolithotrophs, and aerobic anoxygenic phototrophic (AANP) bacteria showed a conserved functional trait of the turf microbiomes. Genes associated with oxygenic photosynthesis, AANP, sulfur cycle (S oxidation, and DMSP consumption), and nitrogen metabolism (N2 fixation, ammonia assimilation, dissimilatory nitrate and nitrite ammonification) were found in the turf microbiomes. Principal component analyses of the most abundant taxa and functions showed that turf microbiomes differ from the other major Abrolhos benthic microbiomes (i.e., corals and rhodoliths) and seawater. Taken together, these features suggest that turfs have a homogeneous functional core across the Abrolhos Bank, which holds diverse microbial guilds when comparing with other benthic organisms. PMID:27548380

  14. A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection

    Energy Technology Data Exchange (ETDEWEB)

    Kaiser, Brooke LD; Li, Jie; Sanford, James A.; Kim, Young-Mo; Kronewitter, Scott R.; Jones, Marcus B.; Peterson, Christine; Peterson, Scott N.; Frank, Bryan C.; Purvine, Samuel O.; Brown, Joseph N.; Metz, Thomas O.; Smith, Richard D.; Heffron, Fred; Adkins, Joshua N.

    2013-06-26

    The potential for commensal microorganisms indigenous to a host (the ‘microbiome’ or ‘microbiota’) to alter infection outcome by influencing host-pathogen interplay is largely unknown. We used a multi-omics “systems” approach, incorporating proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular interplay between the murine host, the pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium), and commensal gut microorganisms during intestinal infection with S. Typhimurium. We find proteomic evidence that S. Typhimurium thrives within the infected 129/SvJ mouse gut without antibiotic pre-treatment, inducing inflammation and disrupting the intestinal microbiome (e.g., suppressing Bacteroidetes and Firmicutes while promoting growth of Salmonella and Enterococcus). Alteration of the host microbiome population structure was highly correlated with gut environmental changes, including the accumulation of metabolites normally consumed by commensal microbiota. Finally, the less characterized phase of S. Typhimurium’s lifecycle was investigated, and both proteomic and glycomic evidence suggests S. Typhimurium may take advantage of increased fucose moieties to metabolize fucose while growing in the gut. The application of multiple omics measurements to Salmonella-induced intestinal inflammation provides insights into complex molecular strategies employed during pathogenesis between host, pathogen, and the microbiome.

  15. Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach

    Directory of Open Access Journals (Sweden)

    Ana Beatriz eFernández

    2014-05-01

    Full Text Available We analyzed the prokaryotic community structure of a saltern pond with 21 % total salts located in Isla Cristina, Huelva, Southwest Spain, close to the Atlantic ocean coast. For this purpose, we constructed a metagenome (designated as IC21 obtained by pyrosequencing consisting of 486 Mb with an average read length of 397 bp and compared it with other metagenomic datasets obtained from ponds with 19, 33 and 37 % total salts acquired from Santa Pola marine saltern, located in Alicante, East Spain, on the Mediterranean coast. Although the salinity in IC21 is closer to the pond with 19 % total salts from Santa Pola saltern (designated as SS19, IC21 is more similar at higher taxonomic levels to the pond with 33 % total salts from Santa Pola saltern (designated as SS33, since both are predominated by the phylum Euryarchaeota. However, there are significant differences at lower taxonomic levels where most sequences were related to the genus Halorubrum in IC21 and to Haloquadratum in SS33. Within the Bacteroidetes, the genus Psychroflexus is the most abundant in IC21 while Salinibacter dominates in SS33. Sequences related to bacteriorhodopsins and halorhodopsins correlate with the abundance of Haloquadratum in Santa Pola SS19 to SS33 and of Halorubrum in Isla Cristina IC21 dataset, respectively. Differences in composition might be attributed to local ecological conditions since IC21 showed a decrease in the number of sequences related to the synthesis of compatible solutes and in the utilization of phosphonate.

  16. Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts.

    Science.gov (United States)

    Le, Phuong Thi; Makhalanyane, Thulani P; Guerrero, Leandro D; Vikram, Surendra; Van de Peer, Yves; Cowan, Don A

    2016-01-01

    Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes. PMID:27503299

  17. Taxonomic and functional metagenomic analysis of anodic communities in two pilot-scale microbial fuel cells treating different industrial wastewaters.

    Science.gov (United States)

    Kiseleva, Larisa; Garushyants, Sofya K; Ma, Hongwu; Simpson, David J W; Fedorovich, Viatcheslav; Cohen, Michael F; Goryanin, Igor

    2015-01-01

    The combined processes of microbial biodegradation accompanied by extracellular electron transfer make microbial fuel cells (MFCs) a promising new technology for cost-effective and sustainable wastewater treatment. Although a number of microbial species that build biofilms on the anode surfaces of operating MFCs have been identified, studies on the metagenomics of entire electrogenic communities are limited. Here we present the results of whole-genome metagenomic analysis of electrochemically active robust anodic microbial communities, and their anaerobic digester (AD) sludge inocula, from two pilot-scale MFC bioreactors fed with different distillery wastewaters operated under ambient conditions in distinct climatic zones. Taxonomic analysis showed that Proteobacteria, Bacteroidetes and Firmicutes were abundant in AD sludge from distinct climatic zones, and constituted the dominant core of the MFC microbiomes. Functional analysis revealed species involved in degradation of organic compounds commonly present in food industry wastewaters. Also, accumulation of methanogenic Archaea was observed in the electrogenic biofilms, suggesting a possibility for simultaneous electricity and biogas recovery from one integrated wastewater treatment system. Finally, we found a range of species within the anode communities possessing the capacity for extracellular electron transfer, both via direct contact and electron shuttles, and show differential distribution of bacterial groups on the carbon cloth and activated carbon granules of the anode surface. Overall, this study provides insights into structural shifts that occur in the transition from an AD sludge to an MFC microbial community and the metabolic potential of electrochemically active microbial populations with wastewater-treating MFCs. PMID:26673789

  18. Responses in ileal and cecal bacteria to low and high amylose/amylopectin ratio diets in growing pigs.

    Science.gov (United States)

    Luo, Yu-Heng; Yang, Can; Wright, André-Denis G; He, Jun; Chen, Dai-Wen

    2015-12-01

    Dietary starch that escapes digestion in the small intestine may serve as a carbon source for bacterial fermentation in the distal intestine. This study aimed to compare the bacterial community in the ileal and cecal digesta of growing pigs fed diets with low (0.14, LR pigs) and high (0.43, HR pigs) amylose/amylopectin ratio. Pyrosequencing based on MiSeq 2000 platform showed that in ileum digesta, Bacteroidetes of LR pigs was markedly higher than that in HR pigs (P Halomonas pacifica, Escherichia fergusonii, and Actinobacillus minor which belong to class Gammaproteobacteria were significantly lower (P < 0.01) in HR pigs with a significant increase (P < 0.01) of Lactobacillus acetotolerans-like bacteria. Therefore, the changed bacterial community may lead to a transformation of microbial function, such as the alteration of fermentation mode which is showed on the change of microbial metabolites like the concentration of short-chain fatty acids (SCFAs), to a response to the switch of dietary composition, and in turn, to help host absorb and utilize nutrients efficiently. The increase of dietary amylose induced the reduction of conditioned pathogens which may probably be due to the increase of some probiotics such as Lactobacillus, thus reducing the risk of intestinal disease. PMID:26318448

  19. Bacterial Diversity in Çamalti Saltern, Turkey.

    Science.gov (United States)

    Mutlu, Mehmet Burçin; Güven, Kiymet

    2015-01-01

    A combination of culture-dependent and culture-independent approaches was employed to identify the bacterial diversity of Çamalti solar saltern in Turkey. The bacterial communities of Çamalti Saltern were analyzed by molecular techniques that included denaturing gradient gel electrophoresis of 16S rRNA gene fragments PCR amplified from DNA extracted from the water samples of the saltern and 16S rRNA gene library analysis. A total of 42 isolates were identified at the genus/species level and 17 of them were found to belong to the Bacteria domain. All bacterial isolates were phylogenetically related to Halobacillus, Virgibacillus and Halomonas genus. A total of 50 clones from 16S rRNA gene library were analyzed by ARDRA. 16S rRNA sequence analysisof these clones revealed that most (85%) of the bacterial clones were related to Salinibacter genus members of the Bacteroidetes. The sequences of DGGE bands were related to the uncultured Salinibacter, uncultured halophilic bacterium and Halomonas sp. This work highlights the halophilic bacterial diversity of Çamalti marine solar saltern. PMID:26094314

  20. High-Throughput Sequencing Analysis of the Endophytic Bacterial Diversity and Dynamics in Roots of the Halophyte Salicornia europaea.

    Science.gov (United States)

    Zhao, Shuai; Zhou, Na; Zhao, Zheng-Yong; Zhang, Ke; Tian, Chang-Yan

    2016-05-01

    Endophytic bacterial communities of halophyte Salicornia europaea roots were analyzed by 16S rRNA gene pyrosequencing. A total of 20,151 partial 16S rRNA gene sequences were obtained. These sequences revealed huge amounts of operational taxonomic units (OTUs), that is, 747-1405 OTUs in a root sample, at 3 % cut-off level. Root endophytes mainly comprised four phyla, among which Proteobacteria was the most represented, followed by Bacteroidetes, Actinobacteria, and Firmicutes. Gammaproteobacteria was the most abundant class of Proteobacteria, followed by Betaproteobacteria and Alphaproteobacteria. Genera Pantoea, Halomonas, Azomonas, Serpens, and Pseudomonas were shared by all growth periods. A marked difference in endophytic bacterial communities was evident in roots from different host life-history stages. Gammaproteobacteria increased during the five periods, while Betaproteobacteria decreased. The richest endophytic bacteria diversity was detected in the seedling stage. Endophytic bacteria diversity was reduced during the flowering stage and fruiting stage. The five libraries contained 2321 different OTUs with 41 OTUs in common. As a whole, this study first surveys communities of endophytic bacteria by tracing crucial stages in the process of halophyte growth using high-throughput sequencing methods. PMID:26787546

  1. Diversity and ecological tolerance of bacteria isolated from the rhizosphere of halophyton plants living nearby Kiskunság soda ponds, Hungary.

    Science.gov (United States)

    Borsodi, Andrea K; Bárány, Ágnes; Krett, Gergely; Márialigeti, Károly; Szili-Kovács, Tibor

    2015-06-01

    Many halophytes and halophilic microorganisms are capable to adapt to the extremities of saline habitats. This study reveals the taxonomic diversity and ecological tolerance of bacteria isolated from the rhizosphere of three different halophytes (Bolboschoenus maritimus, Puccinellia limosa and Aster tripolium) living in the vicinity of Kiskunság soda ponds. Following a sampling in September 2013, altogether 76 bacterial strains were isolated using two different media. The strains were identified on the basis of 16S rRNA gene sequencing following ARDRA grouping. Salt and pH tolerance of the strains were examined by measuring their growth in broths containing 0-15% NaCl (w/V) and characterized with pH 7-12 values. Among the strains genera of Anaerobacillus, Bacillus and Exiguobacterium (Firmicutes), Agromyces, Isoptericola, Microbacterium, Micrococcus, Nocardiopsis, Nesterenkonia and Streptomyces (Actinobacteria), Halomonas and Idiomarina (Proteobacteria) and Anditalea (Bacteroidetes) were identified. The Bolboschoenus and Puccinellia samples characterized with the highest pH and electric conductivity values were dominated by Bacillus, Halomonas and Nesterenkonia, respectively. The salt tolerance of the bacterial strains was strongly dependent on the sampling location and plant species. In contrast, growth of bacterial strains in broths with alkaline pH values was more balanced. The strains from the Puccinellia sample showed the widest salt and pH tolerance. PMID:26132838

  2. Lactobacillus fermentum CRL1446 Ameliorates Oxidative and Metabolic Parameters by Increasing Intestinal Feruloyl Esterase Activity and Modulating Microbiota in Caloric-Restricted Mice.

    Science.gov (United States)

    Russo, Matias; Fabersani, Emanuel; Abeijón-Mukdsi, María C; Ross, Romina; Fontana, Cecilia; Benítez-Páez, Alfonso; Gauffin-Cano, Paola; Medina, Roxana B

    2016-01-01

    The purpose of this study was to determine whether the administration of the feruloyl esterase (FE)-producing strain Lactobacillus fermentum CRL1446 enhances metabolic and oxidative parameters in caloric-restricted (CR) mice. Balb/c male mice were divided into ad libitum fed Group (ALF Group), CR diet Group (CR Group) and CR diet plus L. fermentum Group (CR-Lf Group). CR diet was administered during 45 days and CRL1446 strain was given in the dose of 10⁸ cells/mL/day/mouse. FE activity was determined in intestinal mucosa and content at Day 1, 20 and 45. Triglyceride, total cholesterol, glucose, thiobarbituric acid reactive substances (TBARS) levels and glutathione reductase activity were determined in plasma. Gut microbiota was evaluated by high-throughput sequencing of 16S rRNA gene amplicons. At Day 45, total intestinal FE activity in CR-Lf Group was higher (p = 0.020) than in CR and ALF groups and an improvement in both metabolic (reductions in triglyceride (p = 0.0025), total cholesterol (p = 0.005) and glucose (p < 0.0001) levels) and oxidative (decrease of TBARS levels and increase of plasmatic glutathione reductase activity (p = 0.006)) parameters was observed, compared to ALF Group. CR diet increased abundance of Bacteroidetes and CRL1446 administration increased abundance of Bifidobacterium and Lactobacillus genus. L. fermentun CRL1446 exerted a bifidogenic effect under CR conditions. PMID:27399766

  3. The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities

    Science.gov (United States)

    Zhang, Zilian; Chen, Yi; Wang, Rui; Cai, Ruanhong; Fu, Yingnan; Jiao, Nianzhi

    2015-01-01

    Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that bacterial EPS rich in uronic acid is resistant to mineralization by microbes and thus has a long residence time in global oceans. To confirm this hypothesis, bacterial EPS rich in galacturonic acid was isolated from Alteromonas sp. JL2810. The EPS was used to amend natural seawater to investigate the bioavailability of this EPS by native populations, in the presence and absence of ammonium and phosphate amendment. The data indicated that the bacterial EPS could not be completely consumed during the cultivation period and that the bioavailability of EPS was not only determined by its intrinsic properties, but was also determined by other factors such as the availability of inorganic nutrients. During the experiment, the humic-like component of fluorescent dissolved organic matter (FDOM) was freshly produced. Bacterial community structure analysis indicated that the class Flavobacteria of the phylum Bacteroidetes was the major contributor for the utilization of EPS. This report is the first to indicate that Flavobacteria are a major contributor to bacterial EPS degradation. The fraction of EPS that could not be completely utilized and the FDOM (e.g., humic acid-like substances) produced de novo may be refractory and may contribute to the carbon storage in the oceans. PMID:26571122

  4. Comprehensive insights into microcystin-LR effects on hepatic lipid metabolism using cross-omics technologies.

    Science.gov (United States)

    Zhang, Zongyao; Zhang, Xu-Xiang; Wu, Bing; Yin, Jinbao; Yu, Yunjiang; Yang, Liuyan

    2016-09-01

    Microcystin-LR (MC-LR) can induce hepatic tissue damages and molecular toxicities, but its effects on lipid metabolism remain unknown. This study investigated the effects of MC-LR exposure on mice lipid metabolism and uncovered the underlying mechanism through metabonomic, transcriptomic and metagenomic analyses after administration of mice with MC-LR by gavage for 28 d. Increased liver weight and abdominal fat weight, and evident hepatic lipid vacuoles accumulation were observed in the mice fed with 0.2mg/kg/d MC-LR. Serum nuclear magnetic resonance analysis showed that MC-LR treatment altered the levels of serum metabolites including triglyceride, unsaturated fatty acid (UFA) and very low density lipoprotein. Digital Gene Expression technology was used to reveal differential expression of hepatic transcriptomes, demonstrating that MC-LR treatment disturbed hepatic UFA biosynthesis and activated peroxisome proliferator-activated receptor (PPAR) signaling pathways via Pparγ, Fabp1 and Fabp2 over-expression. Metagenomic analyses of gut microbiota revealed that MC-LR exposure also increased abundant ratio of Firmicutes vs. Bacteroidetes in gut and altered biosynthetic pathways of various microbial metabolic and pro-inflammatory molecules. In conclusion, oral MC-LR exposure can induce hepatic lipid metabolism disorder mediated by UFA biosynthesis and PPAR activation, and gut microbial community shift may play an important role in the metabolic disturbance. PMID:27208774

  5. Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage.

    Science.gov (United States)

    Korehi, Hananeh; Blöthe, Marco; Schippers, Axel

    2014-11-01

    In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values <3 at which acidophilic iron- and sulfur-oxidizing prokaryotes prevail and accelerate the oxidation processes, well described for several mine waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2-6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at

  6. Microbial profiles of liquid and solid fraction associated biomaterial in buffalo rumen fed green and dry roughage diets by tagged 16S rRNA gene pyrosequencing.

    Science.gov (United States)

    Singh, K M; Jisha, T K; Reddy, Bhaskar; Parmar, Nidhi; Patel, Anand; Patel, A K; Joshi, C G

    2015-01-01

    The microbiome of buffalo rumen plays an important role in animal health and productivity. The rumen bacterial composition of both liquid and solid fraction was surveyed using pyrosequencing of the 16S rRNA gene. Sequences were analyzed using taxonomy-dependent clustering methods and revealed that the dominant ruminal bacteria shared by samples belonged to phyla Bacteroidetes, Firmicutes, Fibrobacteres and Proteobacteria. The core rumen microbiome of the rumen consisted of 10 phyla, 19 classes, 22 orders and 25 families. However, the relative abundance of these bacterial groups was markedly affected by diet composition as well as in type of biomaterial. In animals fed with a green and dry roughage diet, the cellulolytic bacteria, Ruminococcaceae, and Fibrobacteraceae was found in highest abundance in all biomaterials which reflected the need for enhanced fiber-digesting capacity in buffalo. The polysaccharide-degrading Prevotellaceae bacteria were most abundant in buffalo rumen. In taxonomic comparison of rumen bacteria, about 26 genera were differentially abundant among liquid and solid fraction of ruminal fluid. These results highlight the buffalo ruminal microbiome's ability to adapt to feed with different composition. PMID:25249226

  7. Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men.

    Science.gov (United States)

    Salonen, Anne; Lahti, Leo; Salojärvi, Jarkko; Holtrop, Grietje; Korpela, Katri; Duncan, Sylvia H; Date, Priya; Farquharson, Freda; Johnstone, Alexandra M; Lobley, Gerald E; Louis, Petra; Flint, Harry J; de Vos, Willem M

    2014-11-01

    There is growing interest in understanding how diet affects the intestinal microbiota, including its possible associations with systemic diseases such as metabolic syndrome. Here we report a comprehensive and deep microbiota analysis of 14 obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSPs) and a weight-loss (WL) diet. We analyzed the composition, diversity and dynamics of the fecal microbiota on each dietary regime by phylogenetic microarray and quantitative PCR (qPCR) analysis. In addition, we analyzed fecal short chain fatty acids (SCFAs) as a proxy of colonic fermentation, and indices of insulin sensitivity from blood samples. The diet explained around 10% of the total variance in microbiota composition, which was substantially less than the inter-individual variance. Yet, each of the study diets induced clear and distinct changes in the microbiota. Multiple Ruminococcaceae phylotypes increased on the RS diet, whereas mostly Lachnospiraceae phylotypes increased on the NSP diet. Bifidobacteria decreased significantly on the WL diet. The RS diet decreased the diversity of the microbiota significantly. The total 16S ribosomal RNA gene signal estimated by qPCR correlated positively with the three major SCFAs, while the amount of propionate specifically correlated with the Bacteroidetes. The dietary responsiveness of the individual's microbiota varied substantially and associated inversely with its diversity, suggesting that individuals can be stratified into responders and non-responders based on the features of their intestinal microbiota. PMID:24763370

  8. Temperature impacts differentially on the methanogenic food web of cellulose-supplemented peatland soil.

    Science.gov (United States)

    Schmidt, Oliver; Horn, Marcus A; Kolb, Steffen; Drake, Harold L

    2015-03-01

    The impact of temperature on the largely unresolved intermediary ecosystem metabolism and associated unknown microbiota that link cellulose degradation and methane production in soils of a moderately acidic (pH 4.5) fen was investigated. Supplemental [(13) C]cellulose stimulated the accumulation of propionate, acetate and carbon dioxide as well as initial methane production in anoxic peat soil slurries at 15°C and 5°C. Accumulation of organic acids at 15°C was twice as fast as that at 5°C. 16S rRNA [(13) C]cellulose stable isotope probing identified novel unclassified Bacteria (79% identity to the next cultured relative Fibrobacter succinogenes), unclassified Bacteroidetes (89% identity to Prolixibacter bellariivorans), Porphyromonadaceae, Acidobacteriaceae and Ruminococcaceae as main anaerobic degraders of cellulose-derived carbon at both 15°C and 5°C. Holophagaceae and Spirochaetaceae were more abundant at 15°C. Clostridiaceae dominated the degradation of cellulose-derived carbon only at 5°C. Methanosarcina was the dominant methanogenic taxa at both 15°C and 5°C. Relative abundance of Methanocella increased at 15°C whereas that of Methanoregula and Methanosaeta increased at 5°C. Thaumarchaeota closely related to Nitrosotalea (presently not known to grow anaerobically) were abundant at 5°C but absent at 15°C indicating that Nitrosotalea sp. might be capable of anaerobic growth at low temperatures in peat. PMID:24813682

  9. Determination of the archaeal and bacterial communities in two-phase and single-stage anaerobic systems by 454 pyrosequencing.

    Science.gov (United States)

    Maspolim, Yogananda; Zhou, Yan; Guo, Chenghong; Xiao, Keke; Ng, Wun Jern

    2015-10-01

    2-Phase anaerobic digestion (AD), where the acidogenic phase was operated at 2day hydraulic retention time (HRT) and the methanogenic phase at 10days HRT, had been evaluated to determine if it could provide higher organic reduction and methane production than the conventional single-stage AD (also operated at 12days HRT). 454 pyrosequencing was performed to determine and compare the microbial communities. The acidogenic reactor of the 2-phase system yielded a unique bacterial community of the lowest richness and diversity, while bacterial profiles of the methanogenic reactor closely followed the single-stage reactor. All reactors were predominated by hydrogenotrophic methanogens, mainly Methanolinea. Unusually, the acidogenic reactor contributed up to 24% of total methane production in the 2-phase system. This could be explained by the presence of Methanosarcina and Methanobrevibacter, and their activities could also help regulate reactor alkalinity during high loading conditions through carbon dioxide production. The enrichment of hydrolytic and acidogenic Porphyromonadaceae, Prevotellaceae, Ruminococcaceae and unclassified Bacteroidetes in the acidogenic reactor would have contributed to the improved sludge volatile solids degradation, and ultimately the overall 2-phase system's performance. Syntrophic acetogenic microorganisms were absent in the acidogenic reactor but present in the downstream methanogenic reactor, indicating the retention of various metabolic pathways also found in a single-stage system. The determination of key microorganisms further expands our understanding of the complex biological functions in AD process. PMID:26456614

  10. Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Lisa-Maree Gulino

    Full Text Available Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering. Thirty-two OTUs were identified as 'shared' OTUS (i.e. present in all samples belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales. These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.

  11. Characterization of the faecal bacterial community of wild young South American (Arctocephalus australis) and Subantarctic fur seals (Arctocephalus tropicalis).

    Science.gov (United States)

    Medeiros, Aline Weber; Giongo, Adriana; Valdez, Fernanda P; Blaese de Amorin, Derek; Tavares, Maurício; d'Azevedo, Pedro A; Franco, Ana Claudia; Frazzon, Jeverson; Frazzon, Ana P G

    2016-03-01

    The microbiota of wild marine mammals is poorly understood, perhaps due to the migratory habits of some species and the difficulty in obtaining samples. Using high-throughput sequencing, the present study examines the faecal bacterial community of wild young South American (Arctocephalus australis) and Subantarctic fur seals (A. tropicalis). Faecal samples from South American (n = 6) and Subantarctic fur seals (n = 4) found dead along the south coast of Brazil were collected. Sequences were assigned to taxa using the Ribosomal Database Project-Bayesian classifier. Diversity of the microbiota was assessed by categorization of sequence reads into operational taxonomic units. Results indicate that Firmicutes (88.556%-84.016%) was the predominant phylum in South American and Subantarctic fur seals. The distribution of Actinobacteria and Proteobacteria varied according to the fur seal species. Fusobacteria and Bacteroidetes represented less than 1% of the sequences. The most abundant order in both fur seals was Clostridiales (88.64% and 87.49%). Individual variable incidences were observed in the composition of family among the fur seals, though the families Lachnospiraceae, Peptostreptococcaceae, Ruminococcaceae and Coriobacteriaceae were more prevalent. This study provides insight into the faecal bacterial community of wild young South American and Subantarctic fur seals. PMID:26880785

  12. Effects of microcystin-LR on gut microflora in different gut regions of mice.

    Science.gov (United States)

    Chen, Jing; Xie, Ping; Lin, Juan; He, Jun; Zeng, Cheng; Chen, Jun

    2015-08-01

    To reveal the toxicological effects of the hepatotoxic microcystin-leucine arginine (MC-LR) on gut microbial community composition in different gut regions, we conducted a subchronic exposure of BALB/c mice to MC-LR via intragastric administration. Denaturing gradient gel electrophoresis (DGGE) was employed to profile the shifts of microbes after MC-LR treatment in the jejuno-ileum, caecum and colon. DGGE profiles analysis showed that MC-LR increased the microbial species richness (number of microbial bands) in the caecum and colon as well as microbial diversity (Shannon-Wiener index) in the caecum. The cluster analysis of DGGE profiles indicated that the microbial structures in the caecum and colon shifted significantly after MC-LR treatment, while that in the jejuno-ileum did not. All the relatively decreased gut microbes belonged to Clostridia in the Firmicutes phylum, and most of them were Lachnospiraceae. The increased ones derived from a variety of microbes including species from Porphyromonadaceae and Prevotellaceae in the Bacteroidetes phylum, as well as Lachnospiraceae and Ruminococcaceae in the Firmicutes phylum, and among which, the increase of Barnesiella in Porphyromonadaceae was most remarkable. In conclusion, subchronic exposure to MC-LR could disturb the balance of gut microbes in mice, and its toxicological effects varied between the jejuno-ileum and the other two gut regions. PMID:26165645

  13. Early-life establishment of the swine gut microbiome and impact on host phenotypes.

    Science.gov (United States)

    Mach, Núria; Berri, Mustapha; Estellé, Jordi; Levenez, Florence; Lemonnier, Gaëtan; Denis, Catherine; Leplat, Jean-Jacques; Chevaleyre, Claire; Billon, Yvon; Doré, Joël; Rogel-Gaillard, Claire; Lepage, Patricia

    2015-06-01

    Early bacterial colonization and succession within the gastrointestinal tract has been suggested to be crucial in the establishment of specific microbiota composition and the shaping of host phenotype. Here, the composition and dynamics of faecal microbiomes were studied for 31 healthy piglets across five age strata (days 14, 36, 48, 60 and 70 after birth) together with their mothers. Faecal microbiome composition was assessed by 16S rRNA gene 454-pyrosequencing. Bacteroidetes and Firmicutes were the predominant phyla present at each age. For all piglets, luminal secretory IgA concentration was measured at day 70, and body weight was recorded until day 70. The microbiota of suckling piglets was mainly represented by Bacteroides, Oscillibacter, Escherichia/Shigella, Lactobacillus and unclassified Ruminococcaceae genera. This pattern contrasted with that of Acetivibrio, Dialister, Oribacterium, Succinivibrio and Prevotella genera, which appeared increased after weaning. Lactobacillus fermentum might be vertically transferred via breast milk or faeces. The microbiota composition coevolved with their hosts towards two different clusters after weaning, primarily distinguished by unclassified Ruminococcaceae and Prevotella abundances. Prevotella was positively correlated with luminal secretory IgA concentrations, and body weight. Our study opens up new possibilities for health and feed efficiency manipulation via genetic selection and nutrition in the agricultural domain. PMID:25727666

  14. Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors?

    Science.gov (United States)

    Siles, José A; Margesin, Rosa

    2016-07-01

    Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site. PMID:26961712

  15. Pathogenic shifts in endogenous microbiota impede tissue regeneration via distinct activation of TAK1/MKK/p38

    Science.gov (United States)

    Arnold, Christopher P; Merryman, M Shane; Harris-Arnold, Aleishia; McKinney, Sean A; Seidel, Chris W; Loethen, Sydney; Proctor, Kylie N; Guo, Longhua; Sánchez Alvarado, Alejandro

    2016-01-01

    The interrelationship between endogenous microbiota, the immune system, and tissue regeneration is an area of intense research due to its potential therapeutic applications. We investigated this relationship in Schmidtea mediterranea, a model organism capable of regenerating any and all of its adult tissues. Microbiome characterization revealed a high Bacteroidetes to Proteobacteria ratio in healthy animals. Perturbations eliciting an expansion of Proteobacteria coincided with ectopic lesions and tissue degeneration. The culture of these bacteria yielded a strain of Pseudomonas capable of inducing progressive tissue degeneration. RNAi screening uncovered a TAK1 innate immune signaling module underlying compromised tissue homeostasis and regeneration during infection. TAK1/MKK/p38 signaling mediated opposing regulation of apoptosis during infection versus normal tissue regeneration. Given the complex role of inflammation in either hindering or supporting reparative wound healing and regeneration, this invertebrate model provides a basis for dissecting the duality of evolutionarily conserved inflammatory signaling in complex, multi-organ adult tissue regeneration. DOI: http://dx.doi.org/10.7554/eLife.16793.001 PMID:27441386

  16. Bamboo shoot fiber prevents obesity in mice by modulating the gut microbiota.

    Science.gov (United States)

    Li, Xiufen; Guo, Juan; Ji, Kailong; Zhang, Ping

    2016-01-01

    Dietary fiber has been shown to prevent high-fat diet induced obesity through modulating the gut microbiota; however, quality difference in fiber type is largely unknown. We performed a 6 week study on C57BL/6J mice fed a macronutrient matched high-fat diet with different fiber types including cellulose (HFC), bamboo shoot fiber (HFBS) and several other commonly consumed fibers. Our results showed that the HFBS group exhibited the lowest weight gain among all diet groups and had improved lipid profiles and glycemic control compared with the HFC group. As revealed by 16S rRNA gene sequencing, loss of diversity in the gut microbiota induced by the HFC diet was largely prevented by the HFBS diet. Moreover, compared with the HFC diet, the HFBS diet resulted in markedly increased relative abundance of Bacteroidetes and strong inhibition of Verrucomicrobia, two divisions strongly correlated with body weight. In conclusion, the present study provides evidence of a quality difference among different types of dietary fibers and shows that bamboo shoot fiber is the most effective in suppressing high-fat diet induced obesity. Our findings indicate that bamboo shoot fiber is a potential prebiotic fiber which modulates the gut microbiota and improves host metabolism. PMID:27599699

  17. Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability

    Science.gov (United States)

    Lewin, Gina R.; Johnson, Amanda L.; Soto, Rolando D. Moreira; Perry, Kailene; Book, Adam J.; Horn, Heidi A.; Pinto-Tomás, Adrián A.; Currie, Cameron R.

    2016-01-01

    Deconstruction of the cellulose in plant cell walls is critical for carbon flow through ecosystems and for the production of sustainable cellulosic biofuels. Our understanding of cellulose deconstruction is largely limited to the study of microbes in isolation, but in nature, this process is driven by microbes within complex communities. In Neotropical forests, microbes in leaf-cutter ant refuse dumps are important for carbon turnover. These dumps consist of decaying plant material and a diverse bacterial community, as shown here by electron microscopy. To study the portion of the community capable of cellulose degradation, we performed enrichments on cellulose using material from five Atta colombica refuse dumps. The ability of enriched communities to degrade cellulose varied significantly across refuse dumps. 16S rRNA gene amplicon sequencing of enriched samples identified that the community structure correlated with refuse dump and with degradation ability. Overall, samples were dominated by Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. Half of abundant operational taxonomic units (OTUs) across samples were classified within genera containing known cellulose degraders, including Acidovorax, the most abundant OTU detected across samples, which was positively correlated with cellulolytic ability. A representative Acidovorax strain was isolated, but did not grow on cellulose alone. Phenotypic and compositional analyses of enrichment cultures, such as those presented here, help link community composition with cellulolytic ability and provide insight into the complexity of community-based cellulose degradation. PMID:26999749

  18. Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation.

    Science.gov (United States)

    Browne, Hilary P; Forster, Samuel C; Anonye, Blessing O; Kumar, Nitin; Neville, B Anne; Stares, Mark D; Goulding, David; Lawley, Trevor D

    2016-05-26

    Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and wellbeing. Intestinal colonization begins at birth and climaxes with the acquisition of two dominant groups of strict anaerobic bacteria belonging to the Firmicutes and Bacteroidetes phyla. Culture-independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases. However, owing to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown. Here we describe a novel workflow based on targeted phenotypic culturing linked to large-scale whole-genome sequencing, phylogenetic analysis and computational modelling that demonstrates that a substantial proportion of the intestinal bacteria are culturable. Applying this approach to healthy individuals, we isolated 137 bacterial species from characterized and candidate novel families, genera and species that were archived as pure cultures. Whole-genome and metagenomic sequencing, combined with computational and phenotypic analysis, suggests that at least 50-60% of the bacterial genera from the intestinal microbiota of a healthy individual produce resilient spores, specialized for host-to-host transmission. Our approach unlocks the human intestinal microbiota for phenotypic analysis and reveals how a marked proportion of oxygen-sensitive intestinal bacteria can be transmitted between individuals, affecting microbiota heritability. PMID:27144353

  19. No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls.

    Science.gov (United States)

    Dlugosz, Aldona; Winckler, Björn; Lundin, Elin; Zakikhany, Katherina; Sandström, Gunnar; Ye, Weimin; Engstrand, Lars; Lindberg, Greger

    2015-01-01

    Several studies have indicated that colonic microbiota may exhibit important differences between patients with irritable bowel syndrome (IBS) and healthy controls. Less is known about the microbiota of the small bowel. We used massive parallel sequencing to explore the composition of small bowel mucosa-associated microbiota in patients with IBS and healthy controls. We analysed capsule biopsies from the jejunum of 35 patients (26 females) with IBS aged 18-(36)-57 years and 16 healthy volunteers (11 females) aged 20-(32)-48 years. Sequences were analysed based on taxonomic classification. The phyla with the highest total abundance across all samples were: Firmicutes (43%), Proteobacteria (23%), Bacteroidetes (15%), Actinobacteria (9.3%) and Fusobacteria (7.0%). The most abundant genera were: Streptococcus (19%), Veillonella (13%), Prevotella (12%), Rothia (6.4%), Haemophilus (5.7%), Actinobacillus (5.5%), Escherichia (4.6%) and Fusobacterium (4.3%). We found no difference among major phyla or genera between patients with IBS and controls. We identified a cluster of samples in the small bowel microbiota dominated by Prevotella, which may represent a common enterotype of the upper small intestine. The remaining samples formed a gradient, dominated by Streptococcus at one end and Escherichia at the other. PMID:25687743

  20. Impact of two different colistin dosing strategies on healthy piglet fecal microbiota.

    Science.gov (United States)

    Fleury, M A; Jouy, E; Eono, F; Cariolet, R; Couet, W; Gobin, P; Le Goff, O; Blanquet-Diot, S; Alric, M; Kempf, I

    2016-08-01

    Colistin is often used in piglets but underdosing and overdosing are frequent. The impact of such administrations on fecal microbiota was studied. Piglets were given either underdoses of colistin by oral gavage for five days or overdoses by in-feed medication for 14days. The composition of fecal microbiota was studied by quantitative PCR, 16S rRNA sequencing, culture of Enterobacteriaceae, and quantification of short-chain fatty acids (SCFAs). The mean colistin concentrations during the treatment for underdosed and overdosed groups were 14.4μg/g and 64.9μg/g of feces respectively. Whatever the piglet and the sampling day, the two main phyla were Firmicutes and Bacteroidetes, The main families were Lactobacillaceae, Clostridiales, Lachnospiraceae and Ruminococcaceae. The main perturbation was the significant but transitory decrease in the Escherichia coli population during treatment, yet all the E. coli isolates were susceptible to colistin. Moreover, colistin did not affect the production of SCFAs. These results show that under- or overdoses of colistin do not result in any major disturbance of piglet fecal microbiota and rarely select for chromosomal resistance in the dominant E. coli population. PMID:27473989

  1. Characterization of bromate-reducing bacterial isolates and their potential for drinking water treatment.

    Science.gov (United States)

    Davidson, Andrew N; Chee-Sanford, Joanne; Lai, Hoi Yi Mandy; Ho, Chi-hua; Klenzendorf, J Brandon; Kirisits, Mary Jo

    2011-11-15

    The objective of the current study was to isolate and characterize several bromate-reducing bacteria and to examine their potential for bioaugmentation to a drinking water treatment process. Fifteen bromate-reducing bacteria were isolated from three sources. According to 16S rRNA gene sequencing, the bromate-reducing bacteria are phylogenetically diverse, representing the Actinobacteria, Bacteroidetes, Firmicutes, and α-, β-, and γ-Proteobacteria. The broad diversity of bromate-reducing bacteria suggests the widespread capability for microbial bromate reduction. While the cometabolism of bromate via nitrate reductase and (per)chlorate reductase has been postulated, five of our bromate-reducing isolates were unable to reduce nitrate or perchlorate. This suggests that a bromate-specific reduction pathway might exist in some microorganisms. Bioaugmentation of activated carbon filters with eight of the bromate-reducing isolates did not significantly decrease start-up time or increase bromate removal as compared to control filters. To optimize bromate reduction in a biological drinking water treatment process, the predominant mechanism of bromate reduction (i.e., cometabolic or respiratory) needs to be assessed so that appropriate measures can be taken to improve bromate removal. PMID:21943884

  2. Molecular analysis of gut microbiota in obesity among Indian individuals

    Indian Academy of Sciences (India)

    Deepak P Patil; Dhiraj P Dhotre; Sachin G Chavan; Armiya Sultan; Dhawal S Jain; Vikram B Lanjekar; Jayshree Gangawani; Poonam S Shah; Jayshree S Todkar; Shashank Shah; Dilip R Ranade; Milind S Patole; Yogesh S Shouche

    2012-09-01

    Obesity is a consequence of a complex interplay between the host genome and the prevalent obesogenic factors among the modern communities. The role of gut microbiota in the pathogenesis of the disorder was recently discovered; however, 16S-rRNA-based surveys revealed compelling but community-specific data. Considering this, despite unique diets, dietary habits and an uprising trend in obesity, the Indian counterparts are poorly studied. Here, we report a comparative analysis and quantification of dominant gut microbiota of lean, normal, obese and surgically treated obese individuals of Indian origin. Representative gut microbial diversity was assessed by sequencing fecal 16S rRNA libraries for each group (n=5) with a total of over 3000 sequences. We detected no evident trend in the distribution of the predominant bacterial phyla, Bacteroidetes and Firmicutes. At the genus level, the bacteria of genus Bacteroides were prominent among the obese individuals, which was further confirmed by qPCR ( > 0.05). In addition, a remarkably high archaeal density with elevated fecal SCFA levels was also noted in the obese group. On the contrary, the treated-obese individuals exhibited comparatively reduced Bacteroides and archaeal counts along with reduced fecal SCFAs. In conclusion, the study successfully identified a representative microbial diversity in the Indian subjects and demonstrated the prominence of certain bacterial groups in obese individuals; nevertheless, further studies are essential to understand their role in obesity.

  3. Genomic and Transcriptomic Resolution of Organic Matter Utilization Among Deep-Sea Bacteria in Guaymas Basin Hydrothermal Plumes

    Science.gov (United States)

    Li, Meng; Jain, Sunit; Dick, Gregory J.

    2016-01-01

    Microbial chemosynthesis within deep-sea hydrothermal vent plumes is a regionally important source of organic carbon to the deep ocean. Although chemolithoautotrophs within hydrothermal plumes have attracted much attention, a gap remains in understanding the fate of organic carbon produced via chemosynthesis. In the present study, we conducted shotgun metagenomic and metatranscriptomic sequencing on samples from deep-sea hydrothermal vent plumes and surrounding background seawaters at Guaymas Basin (GB) in the Gulf of California. De novo assembly of metagenomic reads and binning by tetranucleotide signatures using emergent self-organizing maps (ESOM) revealed 66 partial and nearly complete bacterial genomes. These bacterial genomes belong to 10 different phyla: Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria, Verrucomicrobia. Although several major transcriptionally active bacterial groups (Methylococcaceae, Methylomicrobium, SUP05, and SAR324) displayed methanotrophic and chemolithoautotrophic metabolisms, most other bacterial groups contain genes encoding extracellular peptidases and carbohydrate metabolizing enzymes with significantly higher transcripts in the plume than in background, indicating they are involved in degrading organic carbon derived from hydrothermal chemosynthesis. Among the most abundant and active heterotrophic bacteria in deep-sea hydrothermal plumes are Planctomycetes, which accounted for seven genomes with distinct functional and transcriptional activities. The Gemmatimonadetes and Verrucomicrobia also had abundant transcripts involved in organic carbon utilization. These results extend our knowledge of heterotrophic metabolism of bacterial communities in deep-sea hydrothermal plumes. PMID:27512389

  4. Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic ▿ †

    Science.gov (United States)

    Perreault, Nancy N.; Greer, Charles W.; Andersen, Dale T.; Tille, Stefanie; Lacrampe-Couloume, Georges; Lollar, Barbara Sherwood; Whyte, Lyle G.

    2008-01-01

    The saline springs of Gypsum Hill in the Canadian high Arctic are a rare example of cold springs originating from deep groundwater and rising to the surface through thick permafrost. The heterotrophic bacteria and autotrophic sulfur-oxidizing bacteria (up to 40% of the total microbial community) isolated from the spring waters and sediments were classified into four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) based on 16S rRNA gene analysis; heterotrophic isolates were primarily psychrotolerant, salt-tolerant, facultative anaerobes. Some of the isolates contained genes for thiosulfate oxidation (soxB) and anoxygenic photosynthesis (pufM), possibly enabling the strains to better compete in these sulfur-rich environments subject to long periods of illumination in the Arctic summer. Although leucine uptake by the spring water microbial community was low, CO2 uptake was relatively high under dark incubation, reinforcing the idea that primary production by chemoautotrophs is an important process in the springs. The small amounts of hydrocarbons in gases exsolving from the springs (0.38 to 0.51% CH4) were compositionally and isotopically consistent with microbial methanogenesis and possible methanotrophy. Anaerobic heterotrophic sulfur oxidation and aerobic autotrophic sulfur oxidation activities were demonstrated in sediment slurries. Overall, our results describe an active microbial community capable of sustainability in an extreme environment that experiences prolonged periods of continuous light or darkness, low temperatures, and moderate salinity, where life seems to rely on chemolithoautotrophy. PMID:18805995

  5. Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host's metabolism.

    Science.gov (United States)

    Zheng, P; Zeng, B; Zhou, C; Liu, M; Fang, Z; Xu, X; Zeng, L; Chen, J; Fan, S; Du, X; Zhang, X; Yang, D; Yang, Y; Meng, H; Li, W; Melgiri, N D; Licinio, J; Wei, H; Xie, P

    2016-06-01

    Major depressive disorder (MDD) is the result of complex gene-environment interactions. According to the World Health Organization, MDD is the leading cause of disability worldwide, and it is a major contributor to the overall global burden of disease. However, the definitive environmental mechanisms underlying the pathophysiology of MDD remain elusive. The gut microbiome is an increasingly recognized environmental factor that can shape the brain through the microbiota-gut-brain axis. We show here that the absence of gut microbiota in germ-free (GF) mice resulted in decreased immobility time in the forced swimming test relative to conventionally raised healthy control mice. Moreover, from clinical sampling, the gut microbiotic compositions of MDD patients and healthy controls were significantly different with MDD patients characterized by significant changes in the relative abundance of Firmicutes, Actinobacteria and Bacteroidetes. Fecal microbiota transplantation of GF mice with 'depression microbiota' derived from MDD patients resulted in depression-like behaviors compared with colonization with 'healthy microbiota' derived from healthy control individuals. Mice harboring 'depression microbiota' primarily exhibited disturbances of microbial genes and host metabolites involved in carbohydrate and amino acid metabolism. This study demonstrates that dysbiosis of the gut microbiome may have a causal role in the development of depressive-like behaviors, in a pathway that is mediated through the host's metabolism. PMID:27067014

  6. Characterization of the fecal microbiota of pigs before and after inoculation with "Brachyspira hampsonii".

    Directory of Open Access Journals (Sweden)

    Matheus O Costa

    Full Text Available "Brachyspira hampsonii" causes disease indistinguishable from swine dysentery, and the structure of the intestinal microbiome likely plays a role in determining susceptibility of individual pigs to infection and development of clinical disease. The objectives of the current study were to determine if the pre-inoculation fecal microbiota differed between inoculated pigs that did (INOC MH or did not (INOC non-MH develop mucohaemorrhagic diarrhea following challenge with "B. hampsonii", and to quantify changes in the structure of the microbiome following development of clinical disease. Fecal microbiota profiles were generated based on amplification and sequencing of the cpn60 universal target sequence from 89 samples from 18 pigs collected at -8, -5, -3 and 0 days post-inoculation, and at termination. No significant differences in richness, diversity or taxonomic composition distinguished the pre-inoculation microbiomes of INOC MH and INOC non-MH pigs. However, the development of bloody diarrhea in inoculated pigs was associated with perturbation of the microbiota relative to INOC non-MH or sham-inoculated control pigs. Specifically, the fecal microbiota of INOC MH pigs was less dense (fewer total 16S rRNA copies per gram of feces, and had a lower Bacteroidetes:Firmicutes ratio. Further investigation of the potential long-term effects of Brachyspira disease on intestinal health and performance is warranted.

  7. Profiling of Sediment Microbial Community in Dongting Lake before and after Impoundment of the Three Gorges Dam

    Directory of Open Access Journals (Sweden)

    Wei Huang

    2016-06-01

    Full Text Available The sediment microbial community in downstream-linked lakes can be affected by the operation of large-scale water conservancy projects. The present study determined Illumina reads (16S rRNA gene amplicons to analyze and compare the bacterial communities from sediments in Dongting Lake (China before and after impoundment of the Three Gorges Dam (TGD, the largest hydroelectric project in the world. Bacterial communities in sediment samples in Dongting Lake before impoundment of the TGD (the high water period had a higher diversity than after impoundment of the TGD (the low water period. The most abundant phylum in the sediment samples was Proteobacteria (36.4%–51.5%, and this result was due to the significant abundance of Betaproteobacteria and Deltaproteobacteria in the sediment samples before impoundment of the TGD and the abundance of Gammaproteobacteria in the sediment samples after impoundment of the TGD. In addition, bacterial sequences of the sediment samples are also affiliated with Acidobacteria (11.0% on average, Chloroflexi (10.9% on average, Bacteroidetes (6.7% on average, and Nitrospirae (5.1% on average. Variations in the composition of the bacterial community within some sediment samples from the river estuary into Dongting Lake were related to the pH values. The bacterial community in the samples from the three lake districts of Dongting Lake before and after impoundment of the TGD was linked to the nutrient concentration.

  8. Differential utilization patterns of dissolved organic phosphorus compounds by heterotrophic bacteria in two mountain lakes.

    Science.gov (United States)

    Rofner, Carina; Sommaruga, Ruben; Pérez, María Teresa

    2016-09-01

    Although phosphorus limitation is common in freshwaters and bacteria are known to use dissolved organic phosphorus (DOP), little is known about how efficiently DOP compounds are taken up by individual bacterial taxa. Here, we assessed bacterial uptake of three model DOP substrates in two mountain lakes and examined whether DOP uptake followed concentration-dependent patterns. We determined bulk uptake rates by the bacterioplankton and examined bacterial taxon-specific substrate uptake patterns using microautoradiography combined with catalyzed reporter deposition-fluorescence in situ hybridization. Our results show that in the oligotrophic alpine lake, bacteria took up ATP, glucose-6-phosphate and glycerol-3-phosphate to similar extents (mean 29.7 ± 4.3% Bacteria), whereas in the subalpine mesotrophic lake, ca. 40% of bacteria took up glucose-6-phosphate, but only ∼20% took up ATP or glycerol-3-phosphate. In both lakes, the R-BT cluster of Betaproteobacteria (lineage of genus Limnohabitans) was over-represented in glucose-6-phosphate and glycerol-3-phosphate uptake, whereas AcI Actinobacteria were under-represented in the uptake of those substrates. Alphaproteobacteria and Bacteroidetes contributed to DOP uptake proportionally to their in situ abundance. Our results demonstrate that R-BT Betaproteobacteria are the most active bacteria in DOP acquisition, whereas the abundant AcI Actinobacteria may either lack high affinity DOP uptake systems or have reduced phosphorus requirements. PMID:27312963

  9. High Performance Bioanode Development for Fermentable Substrates via Controlled Electroactive Biofilm Growth

    Energy Technology Data Exchange (ETDEWEB)

    Ichihashi, Osamu [ORNL; Vishnivetskaya, Tatiana A [ORNL; Borole, Abhijeet P [ORNL

    2014-11-11

    A bioanode was optimized to generate current densities reaching 38.4 4.9 A m-2, which brings bioelectrochemical systems closer to commercial consideration. Glucose and lactate were fed together in a continuous or fed-batch mode. The current density increased from 2.3 A m-2 to 38.4 A m-2 over a 33 day period and remained stable thereafter. The coulombic efficiency ranged from 50% to 80%. A change in substrate concentration from 200 mg L-1 to 5 mg L-1 decreased maximum current density from 38.4 A m-2 to 12.3 A m-2. The anode consortia included Firmicutes (55.0%), Proteobacteria (41.8%) and Bacteroidetes (2.1%) constituting two potential electrogenic genera: Geobacter (6.8%) and Aeromonas (31.9%). The current production was found to be limited by kinetics during the growth period (33 days), and mass transfer, thereafter. The results indicate the necessity of removing spent biomass for efficient long term operation and treatment of wastewater streams.

  10. [Physicochemical and ecological characteristics of the granular sludge during start-up of Anammox reactor].

    Science.gov (United States)

    Song, Yuxia; Xiong, Lei; Chai, Liyuan; Liao, Qi; Tang, Chongjian; Min, Xiaobo; Yang, Zhihui

    2014-12-01

    The anaerobic granular sludge from an Internal Circulation (IC) reactor of a paper mill wastewater treatment plant were seeded in an Anammox upflow anaerobic sludge blanket reactor. After 185 days operation, the reactor was finally started up by increasing the influent ammonium and nitrite concentrations to 224 mg/L and 255 mg/L, respectively, with volumetric nitrogen removal rate increasing to 3.76 kg/(m3·d). The physicochemical characteristics of the cultivated Anammox granules were observed by scanning electron microscope, transmission electron microscope and Fourier Transform infrared spectroscopy (FTIR). Results suggested that during the start-up course, the granular sludge initially disintegrated and then re-aggregated. FTIR spectra results revealed that the Anammox granular sludge contained abundant functional groups, indicating that it may also possess good adsorption properties. The ecological structure of the granular sludge, analyzed by the metagenomic sequencing methods, suggested that the relative abundance of the dominant bacterial community in the seeding sludge, i.e., Proteobacteria, Firmicutes, Bacteroidetes, significantly reduced, while Planctomycetes which contains anaerobic ammonium oxidation bacteria remarkably increased from 1.59% to 23.24% in the Anammox granules. PMID:26016375

  11. The microbial community of a passive biochemical reactor treating arsenic, zinc, and sulfate-rich seepage.

    Science.gov (United States)

    Baldwin, Susan Anne; Khoshnoodi, Maryam; Rezadehbashi, Maryam; Taupp, Marcus; Hallam, Steven; Mattes, Al; Sanei, Hamed

    2015-01-01

    Sulfidogenic biochemical reactors (BCRs) for metal removal that use complex organic carbon have been shown to be effective in laboratory studies, but their performance in the field is highly variable. Successful operation depends on the types of microorganisms supported by the organic matrix, and factors affecting the community composition are unknown. A molecular survey of a field-based BCR that had been removing zinc and arsenic for over 6 years revealed that the microbial community was dominated by methanogens related to Methanocorpusculum sp. and Methanosarcina sp., which co-occurred with Bacteroidetes environmental groups, such as Vadin HA17, in places where the organic matter was more degraded. The metabolic potential for organic matter decomposition by Ruminococcaceae was prevalent in samples with more pyrolyzable carbon. Rhodobium- and Hyphomicrobium-related genera within the Rhizobiales order that have the metabolic potential for dark hydrogen fermentation and methylotrophy, and unclassified Comamonadaceae were the dominant Proteobacteria. The unclassified environmental group Sh765B-TzT-29 was an important Delta-Proteobacteria group in this BCR that co-occurred with the dominant Rhizobiales operational taxonomic units. Organic matter degradation is one driver for shifting the microbial community composition and therefore possibly the performance of these bioreactors over time. PMID:25798439

  12. Effects of Cocoa Husk Feeding on the Composition of Swine Intestinal Microbiota.

    Science.gov (United States)

    Magistrelli, Damiano; Zanchi, Raffaella; Malagutti, Luca; Galassi, Gianluca; Canzi, Enrica; Rosi, Fabia

    2016-03-16

    A two-diet/two-period change over experiment was performed to investigate the effects of cocoa husks, as a source of dietary fiber and polyphenols, on pig intestinal microbial composition. Six pigs were fed a conventional cereal-based diet or a diet obtained by substitution of 7.5% of the conventional diet with cocoa husks for 3 weeks. Experimental diets were isoproteic and isoenergetic. At the end of each 3 week testing period, samples of fresh feces were collected and analyzed for microbial composition by fluorescence in situ hybridization. Cocoa husks did not affect feed intake, weight gain, and feed efficiency. Analysis of fecal microbial populations, grouped by phyla, showed a decrease of Firmicutes and an increase of Bacteroidetes in cocoa husk-fed pigs. Particularly, cocoa husks reduced fecal populations of the Lactobacillus-Enterococcus group and Clostridium histolyticum and increased the Bacteroides-Prevotella group and Faecalibacterium prausnitzii, suggesting a potential for cocoa husks in the improvement of intestinal microbial balance. PMID:26877143

  13. Enhanced waste activated sludge digestion using a submerged anaerobic dynamic membrane bioreactor: performance, sludge characteristics and microbial community

    Science.gov (United States)

    Yu, Hongguang; Wang, Zhiwei; Wu, Zhichao; Zhu, Chaowei

    2016-02-01

    Anaerobic digestion (AD) plays an important role in waste activated sludge (WAS) treatment; however, conventional AD (CAD) process needs substantial improvements, especially for the treatment of WAS with low solids content and poor anaerobic biodegradability. Herein, we propose a submerged anaerobic dynamic membrane bioreactor (AnDMBR) for simultaneous WAS thickening and digestion without any pretreatment. During the long-term operation, the AnDMBR exhibited an enhanced sludge reduction and improved methane production over CAD process. Moreover, the biogas generated in the AnDMBR contained higher methane content than CAD process. Stable carbon isotopic signatures elucidated the occurrence of combined methanogenic pathways in the AnDMBR process, in which hydrogenotrophic methanogenic pathway made a larger contribution to the total methane production. It was also found that organic matter degradation was enhanced in the AnDMBR, thus providing more favorable substrates for microorganisms. Pyrosequencing revealed that Proteobacteria and Bacteroidetes were abundant in bacterial communities and Methanosarcina and Methanosaeta in archaeal communities, which played an important role in the AnDMBR system. This study shed light on the enhanced digestion of WAS using AnDMBR technology.

  14. Bacterial symbionts of the leafhopper Evacanthus interruptus (Linnaeus, 1758) (Insecta, Hemiptera, Cicadellidae: Evacanthinae).

    Science.gov (United States)

    Szklarzewicz, Teresa; Grzywacz, Beata; Szwedo, Jacek; Michalik, Anna

    2016-03-01

    Plant sap-feeding hemipterans harbor obligate symbiotic microorganisms which are responsible for the synthesis of amino acids missing in their diet. In this study, we characterized the obligate symbionts hosted in the body of the xylem-feeding leafhopper Evacanthus interruptus (Cicadellidae: Evacanthinae: Evacanthini) by means of histological, ultrastructural and molecular methods. We observed that E. interruptus is associated with two types of symbiotic microorganisms: bacterium 'Candidatus Sulcia muelleri' (Bacteroidetes) and betaproteobacterium that is closely related to symbionts which reside in two other Cicadellidae representatives: Pagaronia tredecimpunctata (Evacanthinae: Pagaronini) and Hylaius oregonensis (Bathysmatophorinae: Bathysmatophorini). Both symbionts are harbored in their own bacteriocytes which are localized between the body wall and ovaries. In E. interruptus, both Sulcia and betaproteobacterial symbionts are transovarially transmitted from one generation to the next. In the mature female, symbionts leave the bacteriocytes and gather around the posterior pole of the terminal oocytes. Then, they gradually pass through the cytoplasm of follicular cells surrounding the posterior pole of the oocyte and enter the space between them and the oocyte. The bacteria accumulate in the deep depression of the oolemma and form a characteristic 'symbiont ball'. In the light of the results obtained, the phylogenetic relationships within modern Cicadomorpha and some Cicadellidae subfamilies are discussed. PMID:25900723

  15. Role of the normal gut microbiota.

    Science.gov (United States)

    Jandhyala, Sai Manasa; Talukdar, Rupjyoti; Subramanyam, Chivkula; Vuyyuru, Harish; Sasikala, Mitnala; Nageshwar Reddy, D

    2015-08-01

    Relation between the gut microbiota and human health is being increasingly recognised. It is now well established that a healthy gut flora is largely responsible for overall health of the host. The normal human gut microbiota comprises of two major phyla, namely Bacteroidetes and Firmicutes. Though the gut microbiota in an infant appears haphazard, it starts resembling the adult flora by the age of 3 years. Nevertheless, there exist temporal and spatial variations in the microbial distribution from esophagus to the rectum all along the individual's life span. Developments in genome sequencing technologies and bioinformatics have now enabled scientists to study these microorganisms and their function and microbe-host interactions in an elaborate manner both in health and disease. The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens. Several factors play a role in shaping the normal gut microbiota. They include (1) the mode of delivery (vaginal or caesarean); (2) diet during infancy (breast milk or formula feeds) and adulthood (vegan based or meat based); and (3) use of antibiotics or antibiotic like molecules that are derived from the environment or the gut commensal community. A major concern of antibiotic use is the long-term alteration of the normal healthy gut microbiota and horizontal transfer of resistance genes that could result in reservoir of organisms with a multidrug resistant gene pool. PMID:26269668

  16. Effects and mode of action of chitosan and ivy fruit saponins on the microbiome, fermentation and methanogenesis in the rumen simulation technique.

    Science.gov (United States)

    Belanche, Alejandro; Pinloche, Eric; Preskett, David; Newbold, C Jamie

    2016-01-01

    This study investigates the effects of supplementing a control diet (CON) with chitosan (CHI) or ivy fruit saponins (IVY) as natural feed additives. Both additives had similar abilities to decrease rumen methanogenesis (-42% and -40%, respectively) using different mechanisms: due to its antimicrobial and nutritional properties CHI promoted a shift in the fermentation pattern towards propionate production which explained about two thirds of the decrease in methanogenesis. This shift was achieved by a simplification of the structure in the bacterial community and a substitution of fibrolytic (Firmicutes and Fibrobacteres) by amylolytic bacteria (Bacteroidetes and Proteobacteria) which led to greater amylase activity, lactate and microbial protein yield with no detrimental effect on feed digestibility. Contrarily, IVY had negligible nutritional properties promoting minor changes in the fermentation pattern and on the bacterial community. Instead, IVY modified the structure of the methanogen community and decreased its diversity. This specific antimicrobial effect of IVY against methanogens was considered its main antimethanogenic mechanism. IVY had however a negative impact on microbial protein synthesis. Therefore, CHI and IVY should be further investigated in vivo to determine the optimum doses which maintain low methanogenesis but prevent negative effects on the rumen fermentation and animal metabolism. PMID:26676056

  17. Large cryoconite aggregates on a Svalbard glacier support a diverse microbial community including ammonia-oxidizing archaea

    Science.gov (United States)

    Zarsky, Jakub D.; Stibal, Marek; Hodson, Andy; Sattler, Birgit; Schostag, Morten; Hansen, Lars H.; Jacobsen, Carsten S.; Psenner, Roland

    2013-09-01

    The aggregation of surface debris particles on melting glaciers into larger units (cryoconite) provides microenvironments for various microorganisms and metabolic processes. Here we investigate the microbial community on the surface of Aldegondabreen, a valley glacier in Svalbard which is supplied with carbon and nutrients from different sources across its surface, including colonies of seabirds. We used a combination of geochemical analysis (of surface debris, ice and meltwater), quantitative polymerase chain reactions (targeting the 16S ribosomal ribonucleic acid and amoA genes), pyrosequencing and multivariate statistical analysis to suggest possible factors driving the ecology of prokaryotic microbes on the surface of Aldegondabreen and their potential role in nitrogen cycling. The combination of high nutrient input with subsidy from the bird colonies, supraglacial meltwater flow and the presence of fine, clay-like particles supports the formation of centimetre-scale cryoconite aggregates in some areas of the glacier surface. We show that a diverse microbial community is present, dominated by the cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria, that are well-known in supraglacial environments. Importantly, ammonia-oxidizing archaea were detected in the aggregates for the first time on an Arctic glacier.

  18. Bacterial communities in the sediments of Dianchi Lake, a partitioned eutrophic waterbody in China.

    Directory of Open Access Journals (Sweden)

    Yaohui Bai

    Full Text Available Bacteria play an important role in the decomposition and cycling of a variety of compounds in freshwater aquatic environments, particularly nutrient-rich eutrophic lakes. A unique Chinese eutrophic lake--Dianchi--was selected for study because it has two separate and distinct basins, Caohai with higher organic carbon levels and Waihai with lower organic carbon levels. Sediment bacterial communities were studied in the two basins using samples collected in each season from June 2010 to March 2011. Barcoded pyrosequencing based on the 16 S rRNA gene found that certain common phyla, Proteobacteria, Bacteroidetes, Firmicutes and Chloroflexi, were dominant in the sediments from both basins. However, from the class to genus level, the dominant bacterial groups found in the sediments were distinct between the two basins. Correlation analysis revealed that, among the environmental parameters examined, total organic carbon (TOC accounted for the greatest proportion of variability in bacterial community. Interestingly, study results suggest that increasing allochthonous organic carbon could enhance bacterial diversity and biomass in the sediment. In addition, analysis of function genes (amoA and nosZ demonstrated that ammonia-oxidizing bacteria (AOB were dominant in sediments, with 99% belonging to Nitrosomonas. Denitrifying bacteria were comparatively diverse and were associated with some cultivatable bacteria.

  19. Microbial structures and community functions of anaerobic sludge in six full-scale wastewater treatment plants as revealed by 454 high-throughput pyrosequencing.

    Science.gov (United States)

    Shu, Duntao; He, Yanling; Yue, Hong; Wang, Qingyi

    2015-06-01

    The microbial communities and abundance in anaerobic sludge from 4 industrial and 2 municipal wastewater treatment plants were investigated using 454 pyrosequencing technology in this study. A total of 5482-8692 high-quality reads of 16S rRNA V3-V5 regions were obtained. Taxonomic analysis using QIIME and RDP classifier found that Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes were the most abundant phyla in these samples. Furthermore, real-time PCR was used to validate the absolute abundance of these 16S rRNAs and some functional genes, including total bacteria, anammox bacteria, NOB (Nitrobacter, Nitrospira), AOA amoA, AOB amoA, nosZ, nirS, nirK, narG, napA, nrfA, mcrA and dsrA. Multivariate linear regression analysis indicated that AOA might be mixotrophic. Finally, redundancy analysis was used to reveal the relationships between operation parameters and microbial communities. Results showed that the coexistence of anammox, denitrification and DNRA could be useful for the simultaneous removal of nitrogen and organic matter. PMID:25817026

  20. The dissemination of C10 cysteine protease genes in Bacteroides fragilis by mobile genetic elements

    Directory of Open Access Journals (Sweden)

    Kagawa Todd F

    2010-04-01

    Full Text Available Abstract Background The C10 family of cysteine proteases includes enzymes that contribute to the virulence of bacterial pathogens, such as SpeB in Streptococcus pyogenes. The presence of homologues of cysteine protease genes in human commensal organisms has not been examined. Bacteroides fragilis is a member of the dominant Bacteroidetes phylum of the human intestinal microbiota, and is a significant opportunistic pathogen. Results Four homologues of the streptococcal virulence factor SpeB were identified in the B. fragilis genome. These four protease genes, two were directly contiguous to open reading frames predicted to encode staphostatin-like inhibitors, with which the protease genes were co-transcribed. Two of these protease genes are unique to B. fragilis 638R and are associated with two large genomic insertions. Gene annotation indicated that one of these insertions was a conjugative Tn-like element and the other was a prophage-like element, which was shown to be capable of excision. Homologues of the B. fragilis C10 protease genes were present in a panel of clinical isolates, and in DNA extracted from normal human faecal microbiota. Conclusions This study suggests a mechanism for the evolution and dissemination of an important class of protease in major members of the normal human microbiota.

  1. Influence of oligomeric herbicidal ionic liquids with MCPA and Dicamba anions on the community structure of autochthonic bacteria present in agricultural soil.

    Science.gov (United States)

    Ławniczak, Ł; Syguda, A; Borkowski, A; Cyplik, P; Marcinkowska, K; Wolko, Ł; Praczyk, T; Chrzanowski, Ł; Pernak, J

    2016-09-01

    The aim of this study was to evaluate the impact of selected herbicidal ionic liquids (HILs), which exhibit high efficacy in terms of weed control and low toxicity, but may be persistent due to limited biodegradability, on the community structure of autochthonic bacteria present in agricultural soil. Four different oligomeric HILs (with two types of cations and different ratio of herbicidal anions) were synthesized and characterized by employing (1)H and (13)C NMR. The results of biodegradation assay indicated that none of the tested HILs could be classified as readily biodegradable (biodegradation rate ranged from 0 to 7%). The conducted field studies confirmed that the herbicidal efficacy of the HILs was higher compared to the reference herbicide mixture by 10 to 30%, depending on the dose and weed species. After termination of field studies, the soil treated with the tested HILs was subjected to next generation sequencing in order to investigate the potential changes in the bacterial community structure. Proteobacteria was the dominant phylum in all studied samples. Treatment with the studied HILs resulted in an increase of Actinobacteria compared to the reference herbicidal mixture. Differenced among the studied HILs were generally associated with a significantly higher abundance of Bacteroidetes in case of 1-HIL-Dicamba 1/3 and Firmicutes in case of 2-HIL-Dicamba 1/3. PMID:27135587

  2. Antimicrobial activities of novel cultivable bacteria isolated from marine sponge Tedania anhelans

    Institute of Scientific and Technical Information of China (English)

    ZENG Zhen; ZHAO Jing; KE Caihuan; WANG Dexiang

    2013-01-01

    Marine sponge Tedania anhelans distributes throughout the intertidal zone of Fujian,southeastern China,and is a potential source of natural bioactive products.The sponge harbors a large number of bacterial groups that have been identified using various techniques,including fluorescent in situ hybridization (FISH).Fractionation of dissociated sponge allowed isolation of 25 bacterial species.Based on 16S rRNA gene sequencing,phylogenetic analysis attributed most of these eubacteria to a-Proteobacteria,γ-Proteobacteria,Cytophaga/Flavobacterium/Bacteroidetes (CFB group),and the family Bacillaceae of Gram-positive bacteria.In sequence similarity,five putatively novel species were identified with less than 98% similarity to other strains in the NCBI database.Tests for antimicrobial activities were performed against Gram-positive bacteria,Gram-negative bacteria,fungi,antitumor indicators Escherichia coli 343/591 (with DNA repair deficiency),regular E.coli 343/636 (with different DNA repair capacity),and 10 bacterial isolates exhibited inhibitory bioactivities.Among these strains,three isolates were detected involving function gene NRPS-A domains,which were most closely related to the amino acid sequences of linear gramicidin synthetase and pyoverdine synthetase.These results contribute to our knowledge of the microbes associated with marine sponges and further reveal novel bacterial resources for the screening of bioactive marine natural products.

  3. Strict vegetarian diet improves the risk factors associated with metabolic diseases by modulating gut microbiota and reducing intestinal inflammation.

    Science.gov (United States)

    Kim, Min-Soo; Hwang, Seong-Soo; Park, Eun-Jin; Bae, Jin-Woo

    2013-10-01

    Low-grade inflammation of the intestine results in metabolic dysfunction, in which dysbiosis of the gut microbiota is intimately involved. Dietary fibre induces prebiotic effects that may restore imbalances in the gut microbiota; however, no clinical trials have been reported in patients with metabolic diseases. Here, six obese subjects with type 2 diabetes and/or hypertension were assigned to a strict vegetarian diet (SVD) for 1 month, and blood biomarkers of glucose and lipid metabolisms, faecal microbiota using 454-pyrosequencing of 16S ribosomal RNA genes, faecal lipocalin-2 and short-chain fatty acids were monitored. An SVD reduced body weight and the concentrations of triglycerides, total cholesterol, low-density lipoprotein cholesterol and haemoglobin A1c, and improved fasting glucose and postprandial glucose levels. An SVD reduced the Firmicutes-to-Bacteroidetes ratio in the gut microbiota, but did not alter enterotypes. An SVD led to a decrease in the pathobionts such as the Enterobacteriaceae and an increase in commensal microbes such as Bacteroides fragilis and Clostridium species belonging to clusters XIVa and IV, resulting in reduced intestinal lipocalin-2 and short-chain fatty acids levels. This study underscores the benefits of dietary fibre for improving the risk factors of metabolic diseases and shows that increased fibre intake reduces gut inflammation by changing the gut microbiota. PMID:24115628

  4. Prey selectivity of bacterivorous protists in different size fractions of reservoir water amended with nutrients.

    Science.gov (United States)

    Jezbera, Jan; Hornák, Karel; Simek, Karel

    2006-08-01

    An experiment designed to examine food preferences of heterotrophic nanoflagellates (HNF) grazing on bacterioplankton was performed in the freshwater Rímov reservoir (Czech Republic). Water samples were size-fractionated to obtain preferences by analysing bacterial prey in HNF food vacuoles compared with available bacteria. Actinobacteria (the HGC69a probe) were avoided by HNF in all treatments. Cytophaga-Flavobacterium-Bacteroidetes bacteria (the CF319a probe) were positively selected mainly in treatments in which bacteria were heavily grazed, the < 5 microm treatments, but this trend was less pronounced towards the end of the study. The members of a small subcluster of Betaproteobacteria (the R-BT065 probe) were mostly positively selected. The nutrient amendments differentially affected bacterioplankton dynamics in almost all treatments, and together with the size fractionation, altered HNF overall bacterivory as well as prey selection. Analyses of bacterivores in unfiltered treatments allowed to detect the effect of different protists on shifts in HNF selectivity observed in < 5 microm compared with unfiltered treatments. PMID:16872397

  5. Seasonal patterns of bacterial communities in the coastal brackish sediments of the Gulf of Finland, Baltic Sea

    Science.gov (United States)

    Vetterli, Adrien; Hyytiäinen, Kirsi; Ahjos, Minttu; Auvinen, Petri; Paulin, Lars; Hietanen, Susanna; Leskinen, Elina

    2015-11-01

    Coastal areas are critical in mitigating the impact of nutrient runoffs and downstream eutrophication of aquatic ecosystems. In the Gulf of Finland, the easternmost sub-basin of the Baltic Sea, seasonal and long-term oxygen depletion at the surface of the sediment feeds back the eutrophication loop by promoting the release of nutrients locked in the sediment matrix. In order to understand how the bacterial community responds to the seasonal variations, we sequenced ribosomal gene fragments from the top sediment layer at two coastal sites in southern Finland in spring, summer and late autumn during two consecutive years. Analysis of the samples collected at a shallow (11 m) and deep site (33 m) revealed that the overall community composition was rather constant over time with an extensive collection of shared operational taxonomic units (OTU) between sites. The dominant taxa were related to organoheterotrophs and sulfate reducers and the variation in community structure was linked to the availability of organic matter in the surface sediment. Proteobacteria formed the most abundant and diverse group. The taxa characteristic of spring samples belonged primarily to Actinobacteria, possibly of fresh water origin and linked to humic carbon. Summer communities were characterized by an increase in the number of reads associated with heterotrophic bacteria such as Bacteroidetes which feed on labile organic matter from spring bloom. Taxa typical of autumn samples were linked to Cyanobacteria and other bloom-forming bacteria from the overlying water and to bacteria feeding on organic matter drifting from the phytal zone.

  6. A review of microbial diversity in polar terrestrial environments

    Directory of Open Access Journals (Sweden)

    Weidong Kong

    2013-07-01

    Full Text Available Polar regions refer to the areas at high latitudes and altitudes, that are characterized by low temperature and limited nutrients, and are very vulnerable and sensitive to global climate change. They include the Antarctic, the Arctic and the Tibetan Plateau, which is recognized as “the third pole”. The harsh polar environments are inhabited by abundant microbes that shape and maintain ecosystems by driving biogeochemical cycles. This article herein reviews microbial diversity in these polar terrestrial environments, including soils, lakes and glaciers in the Antarctic, the Arctic and the Tibetan Plateau. In the three poles, five major groups of microbes have been detected, e.g. Acidobacteria, Actinobacteria, Bacteroidetes, Cynobacteria, and Firmicutes. These microbes are salt- and cold-tolerant. Research in polar microbial ecology in China is currently lagging behind developed countries. Priorities should be given to long-term observations on theTibetan Plateau, which is easily approached. This will facilitate microbial ecology research and expand our understanding of microbial processes and their ecological roles in extreme environments.

  7. Different substrates and starter inocula govern microbial community structures in biogas reactors.

    Science.gov (United States)

    Satpathy, Preseela; Steinigeweg, Sven; Cypionka, Heribert; Engelen, Bert

    2016-06-01

    The influence of different starter inocula on the microbial communities in biogas batch reactors fed with fresh maize and maize silage as substrates was investigated. Molecular biological analysis by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rRNA gene fragments showed that each inoculum bore specific microbial communities with varying predominant phylotypes. Both, bacterial and archaeal DGGE profiles displayed three distinct communities that developed depending on the type of inoculum. Although maize and silage are similar substrates, different communities dominated the lactate-rich silage compared to lactate-free fresh maize. Cluster analysis of DGGE gels showed the communities of the same substrates to be stable with their respective inoculum. Bacteria-specific DGGE analysis revealed a rich diversity with Firmicutes being predominant. The other abundant phylotypes were Bacteroidetes and Synergistetes. Archaea-specific DGGE analysis displayed less diverse community structures, identifying members of the Methanosarcinales as the dominant methanogens present in all the three biogas digesters. In general, the source of inoculum played a significant role in shaping microbial communities. Adaptability of the inoculum to the substrates fed also influenced community compositions which further impacted the rates of biogas production. PMID:26585859

  8. Improving Power Production in Acetate-Fed Microbial Fuel Cells via Enrichment of Exoelectrogenic Organisms in Flow-Through Systems

    International Nuclear Information System (INIS)

    An exoelectrogenic, biofilm-forming microbial consortium was enriched in an acetate-fed microbial fuel cell (MFC) using a flow-through anode coupled to an air-cathode. Multiple parameters known to improve MFC performance were integrated in one design including electrode spacing, specific electrode surface area, flow-through design, minimization of dead volume within anode chamber, and control of external resistance. In addition, continuous feeding of carbon source was employed and the MFC was operated at intermittent high flows to enable removal of non-biofilm forming organisms over a period of six months. The consortium enriched using the modified design and operating conditions resulted in a power density of 345 W m-3 of net anode volume (3650 mW m-2), when coupled to a ferricyanide cathode. The enriched consortium included -, -, -Proteobacteria, Bacteroidetes and Firmicutes. Members of the order Rhodocyclaceae and Burkholderiaceae (Azospira spp. (49%), Acidovorax spp. (11%) and Comamonas spp. (7%)), dominated the microbial consortium. Denaturing gradient gel electrophoresis (DGGE) analysis based on primers selective for Archaea suggested a very low abundance of methanogens. Limiting the delivery of the carbon source via continuous feeding corresponding to the maximum cathodic oxidation rates permitted in the flow-through, air-cathode MFC resulted in coulombic efficiencies reaching 88 5.7%.

  9. The salivary microbiome for differentiating individuals: proof of principle.

    Science.gov (United States)

    Leake, Sarah L; Pagni, Marco; Falquet, Laurent; Taroni, Franco; Greub, Gilbert

    2016-06-01

    Human identification has played a prominent role in forensic science for the past two decades. Identification based on unique genetic traits is driving the field. However, this may have limitations, for instance, for twins. Moreover, high-throughput sequencing techniques are now available and may provide a high amount of data likely useful in forensic science. This study investigates the potential for bacteria found in the salivary microbiome to be used to differentiate individuals. Two different targets (16S rRNA and rpoB) were chosen to maximise coverage of the salivary microbiome and when combined, they increase the power of differentiation (identification). Paired-end Illumina high-throughput sequencing was used to analyse the bacterial composition of saliva from two different people at four different time points (t = 0 and t = 28 days and then one year later at t = 0 and t = 28 days). Five major phyla dominate the samples: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Streptococcus, a Firmicutes, is one of the most abundant aerobic genera found in saliva and targeting Streptococcus rpoB has enabled a deeper characterisation of the different streptococci species, which cannot be differentiated using 16S rRNA alone. We have observed that samples from the same person group together regardless of time of sampling. The results indicate that it is possible to distinguish two people using the bacterial microbiota present in their saliva. PMID:27063111

  10. Isolation and characterization of culturable seed-associated bacterial endophytes from gnotobiotically grown Marama bean seedlings.

    Science.gov (United States)

    Chimwamurombe, Percy Maruwa; Grönemeyer, Jann Lasse; Reinhold-Hurek, Barbara

    2016-06-01

    Marama bean (Tylosema esculentum) is an indigenous non-nodulating legume to the arid agro-ecological parts of Southern Africa. It is a staple food for the Khoisan and Bantu people from these areas. It is intriguing how it is able to synthesize the high-protein content in the seeds since its natural habitat is nitrogen deficient. The aim of the study was to determine the presence of seed transmittable bacterial endophytes that may have growth promoting effects, which may be particularly important for the harsh conditions. Marama bean seeds were surface sterilized and gnotobiotically grown to 2 weeks old seedlings. From surface-sterilized shoots and roots, 123 distinct bacterial isolates were cultured using three media, and identified by BOX-PCR fingerprinting and sequence analyses of the 16S rRNA and nifH genes. Phylogenetic analyses of 73 putative endophytes assigned them to bacterial species from 14 genera including Proteobacteria (Rhizobium, Massilia, Kosakonia, Pseudorhodoferax, Caulobacter, Pantoea, Sphingomonas, Burkholderia, Methylobacterium), Firmicutes (Bacillus), Actinobacteria (Curtobacterium, Microbacterium) and Bacteroidetes (Mucilaginibacter, Chitinophaga). Screening for plant growth-promoting activities revealed that the isolates showed production of IAA, ACC deaminase, siderophores, endoglucanase, protease, AHLs and capacities to solubilize phosphate and fix nitrogen. This is the first report that marama bean seeds may harbor endophytes that can be cultivated from seedlings; in this community of bacteria, physiological characteristics that are potentially plant growth promoting are widespread. PMID:27118727

  11. Microbial abundance and community in subsurface flow constructed wetland microcosms: role of plant presence.

    Science.gov (United States)

    Wang, Qian; Xie, Huijun; Ngo, Huu Hao; Guo, Wenshan; Zhang, Jian; Liu, Cui; Liang, Shuang; Hu, Zhen; Yang, Zhongchen; Zhao, Congcong

    2016-03-01

    In this research, the role of plants in improving microorganism growth conditions in subsurface flow constructed wetland (CW) microcosms was determined. In particular, microbial abundance and community were investigated during summer and winter in Phragmites australis-planted CW microcosms (PA) and unplanted CW microcosms (control, CT). Results revealed that the removal efficiencies of pollutants and microbial community structure varied in winter with variable microbial abundance. During summer, PA comprised more dominant phyla (e.g., Proteobacteria, Actinobacteria, and Bacteroidetes), whereas CT contained more Cyanobacteria and photosynthetic bacteria. During winter, the abundance of Proteobacteria was >40 % in PA but dramatically decreased in CT. Moreover, Cyanobacteria and photosynthetic bacterial dominance in CT decreased. In both seasons, bacteria were more abundant in root surfaces than in sand. Plant presence positively affected microbial abundance and community. The potential removal ability of CT, in which Cyanobacteria and photosynthetic bacteria were abundant during summer, was more significantly affected by temperature reduction than that of PA with plant presence. PMID:25772872

  12. Archaeal abundance in post-mortem ruminal digesta may help predict methane emissions from beef cattle

    Science.gov (United States)

    Wallace, R. John; Rooke, John A.; Duthie, Carol-Anne; Hyslop, Jimmy J.; Ross, David W.; McKain, Nest; de Souza, Shirley Motta; Snelling, Timothy J.; Waterhouse, Anthony; Roehe, Rainer

    2014-07-01

    Methane produced from 35 Aberdeen-Angus and 33 Limousin cross steers was measured in respiration chambers. Each group was split to receive either a medium- or high-concentrate diet. Ruminal digesta samples were subsequently removed to investigate correlations between methane emissions and the rumen microbial community, as measured by qPCR of 16S or 18S rRNA genes. Diet had the greatest influence on methane emissions. The high-concentrate diet resulted in lower methane emissions (P < 0.001) than the medium-concentrate diet. Methane was correlated, irrespective of breed, with the abundance of archaea (R = 0.39), bacteria (-0.47), protozoa (0.45), Bacteroidetes (-0.37) and Clostridium Cluster XIVa (-0.35). The archaea:bacteria ratio provided a stronger correlation (0.49). A similar correlation was found with digesta samples taken 2-3 weeks later at slaughter. This finding could help enable greenhouse gas emissions of large animal cohorts to be predicted from samples taken conveniently in the abattoir.

  13. Feruloylated Oligosaccharides from Maize Bran Modulated the Gut Microbiota in Rats.

    Science.gov (United States)

    Ou, Juan-Ying; Huang, Jun-Qing; Song, Yuan; Yao, Sheng-Wen; Peng, Xi-Chun; Wang, Ming-Fu; Ou, Shi-Yi

    2016-06-01

    Corn bran is a byproduct produced from corn milling; it is rich in ferulic acid and hemicellulose. In this research, the effects of feruloylated oligosaccharides (FOs) from maize bran on the microbial diversity and profiles in rat feces were investigated through 16S rRNA sequencing. FOs significantly increased bacterial richness and diversity compared with the control and xylooligosaccharides (XOS) alone. In comparison with the control group and the group administrated with XOS, FOs orally administered at 300 mg/kg increased OTU in feces by 57.0 and 24.8 %, and Chao value by 93.4 and 37.6 %, respectively. FOs also influenced obesity- and diabetes-associated bacteria. Oral administration of FOs at 300 mg/kg decreased the ratio of Firmicutes to Bacteroidetes from 477.7:1 to 55.1:1; greatly increased the reads of bacteria that were previously found resistant against diabetes in rats, such as Actinobacteria, Bacteroides, and Lactobacillus; whereas decreased diabetes-prone bacteria, such as Clostridium and Firmicutes. PMID:27165128

  14. Bacterial communities associated with the rhizosphere of pioneer plants (Bahia xylopoda and Viguiera linearis) growing on heavy metals-contaminated soils.

    Science.gov (United States)

    Navarro-Noya, Yendi E; Jan-Roblero, Janet; González-Chávez, Maria del Carmen; Hernández-Gama, Regina; Hernández-Rodríguez, César

    2010-05-01

    In this study, the bacterial communities associated with the rhizospheres of pioneer plants Bahia xylopoda and Viguiera linearis were explored. These plants grow on silver mine tailings with high concentration of heavy metals in Zacatecas, Mexico. Metagenomic DNAs from rhizosphere and bulk soil were extracted to perform a denaturing gradient gel electrophoresis analysis (DGGE) and to construct 16S rRNA gene libraries. A moderate bacterial diversity and twelve major phylogenetic groups including Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Firmicutes, Verrucomicrobia, Nitrospirae and Actinobacteria phyla, and divisions TM7, OP10 and OD1 were recognized in the rhizospheres. Only 25.5% from the phylotypes were common in the rhizosphere libraries and the most abundant groups were members of the phyla Acidobacteria and Betaproteobacteria (Thiobacillus spp., Nitrosomonadaceae). The most abundant groups in bulk soil library were Acidobacteria and Actinobacteria, and no common phylotypes were shared with the rhizosphere libraries. Many of the clones detected were related with chemolithotrophic and sulfur-oxidizing bacteria, characteristic of an environment with a high concentration of heavy metal-sulfur complexes, and lacking carbon and organic energy sources. PMID:20084459

  15. Metagenomic analysis of the rhizosphere soil microbiome with respect to phytic acid utilization.

    Science.gov (United States)

    Unno, Yusuke; Shinano, Takuro

    2013-01-01

    While phytic acid is a major form of organic phosphate in many soils, plant utilization of phytic acid is normally limited; however, culture trials of Lotus japonicus using experimental field soil that had been managed without phosphate fertilizer for over 90 years showed significant usage of phytic acid applied to soil for growth and flowering and differences in the degree of growth, even in the same culture pot. To understand the key metabolic processes involved in soil phytic acid utilization, we analyzed rhizosphere soil microbial communities using molecular ecological approaches. Although molecular fingerprint analysis revealed changes in the rhizosphere soil microbial communities from bulk soil microbial community, no clear relationship between the microbiome composition and flowering status that might be related to phytic acid utilization of L. japonicus could be determined. However, metagenomic analysis revealed changes in the relative abundance of the classes Bacteroidetes, Betaproteobacteria, Chlorobi, Dehalococcoidetes and Methanobacteria, which include strains that potentially promote plant growth and phytic acid utilization, and some gene clusters relating to phytic acid utilization, such as alkaline phosphatase and citrate synthase, with the phytic acid utilization status of the plant. This study highlights phylogenetic and metabolic features of the microbial community of the L. japonicus rhizosphere and provides a basic understanding of how rhizosphere microbial communities affect the phytic acid status in soil. PMID:23257911

  16. Genetic and functional diversities of bacterial communities in the rhizosphere of Arachis hypogaea.

    Science.gov (United States)

    Haldar, Shyamalina; Choudhury, Susanta Roy; Sengupta, Sanghamitra

    2011-06-01

    Bioinoculants are environmentally friendly, energy efficient and economically viable resources in sustainable agriculture. Knowledge of the structure and activities of microbial population in the rhizosphere of a plant is essential to formulate an effective bioinoculant. In this study, the bacterial community present in the rhizosphere of an important oilseed legume, Arachis hypogaea (L.) was described with respect to adjoining bulk soil as a baseline control using a 16S rDNA based metagenomic approach. Significantly higher abundance of Gamma-proteobacteria, a prevalence of Bacillus and the Cytophaga-Flavobacteria group of Bacteroidetes and absence of the Rhizobiaceae family of Alpha-proteobacteria were the major features observed in the matured Arachis-rhizosphere. The functional characterization of the rhizosphere-competent bacteria was performed using culture-dependent determination of phenotypes. Most bacterial isolates from the groundnut-rhizosphere exhibited multiple biochemical activities associated with plant growth and disease control. Validation of the beneficial traits in candidate bioinoculants in pot-cultures and field trials is necessary before their targeted application in the groundnut production system. PMID:21380504

  17. Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea.

    Science.gov (United States)

    Alzubaidy, Hanin; Essack, Magbubah; Malas, Tareq B; Bokhari, Ameerah; Motwalli, Olaa; Kamanu, Frederick Kinyua; Jamhor, Suhaiza Ahmad; Mokhtar, Noor Azlin; Antunes, André; Simões, Marta Filipa; Alam, Intikhab; Bougouffa, Salim; Lafi, Feras F; Bajic, Vladimir B; Archer, John A C

    2016-02-01

    Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide. In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in 'metabolism of aromatic compounds', 'mobile genetic elements', 'potassium metabolism' and 'pathways that utilize osmolytes' in the rhizosphere microbiomes. To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea. PMID:26475934

  18. Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils

    Energy Technology Data Exchange (ETDEWEB)

    Lipson, David A.; Raab, Theodore K.; Parker , Melanie; Kelley , Scott T.; Brislawn, Colin J.; Jansson, Janet K.

    2015-07-21

    This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska, and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth and were most oxidized in shallow regions of polygon rims. Organic matter and pH also changed with depth and topography, but were less effective predictors of the microbial community structure and relative abundance of specific taxa. Of all other measured variables, lactic acid concentration was the best, in combination with redox, for describing the microbial community. We conclude that redox conditions are the dominant force in shaping microbial communities in this landscape. Oxygen and other electron acceptors allowed for the greatest diversity of microbes: at depth the community was reduced to a simpler core of anaerobes, dominated by fermenters (Bacteroidetes and Firmicutes).

  19. The dissemination of C10 cysteine protease genes in Bacteroides fragilis by mobile genetic elements

    LENUS (Irish Health Repository)

    Thornton, Roibeard F

    2010-04-23

    Abstract Background The C10 family of cysteine proteases includes enzymes that contribute to the virulence of bacterial pathogens, such as SpeB in Streptococcus pyogenes. The presence of homologues of cysteine protease genes in human commensal organisms has not been examined. Bacteroides fragilis is a member of the dominant Bacteroidetes phylum of the human intestinal microbiota, and is a significant opportunistic pathogen. Results Four homologues of the streptococcal virulence factor SpeB were identified in the B. fragilis genome. These four protease genes, two were directly contiguous to open reading frames predicted to encode staphostatin-like inhibitors, with which the protease genes were co-transcribed. Two of these protease genes are unique to B. fragilis 638R and are associated with two large genomic insertions. Gene annotation indicated that one of these insertions was a conjugative Tn-like element and the other was a prophage-like element, which was shown to be capable of excision. Homologues of the B. fragilis C10 protease genes were present in a panel of clinical isolates, and in DNA extracted from normal human faecal microbiota. Conclusions This study suggests a mechanism for the evolution and dissemination of an important class of protease in major members of the normal human microbiota.

  20. Pyrosequencing Reveals the Microbial Communities in the Red Sea Sponge Carteriospongia foliascens and Their Impressive Shifts in Abnormal Tissues

    KAUST Repository

    Gao, Zhaoming

    2014-04-24

    Abnormality and disease in sponges have been widely reported, yet how sponge-associated microbes respond correspondingly remains inconclusive. Here, individuals of the sponge Carteriospongia foliascens under abnormal status were collected from the Rabigh Bay along the Red Sea coast. Microbial communities in both healthy and abnormal sponge tissues and adjacent seawater were compared to check the influences of these abnormalities on sponge-associated microbes. In healthy tissues, we revealed low microbial diversity with less than 100 operational taxonomic units (OTUs) per sample. Cyanobacteria, affiliated mainly with the sponge-specific species “Candidatus Synechococcus spongiarum,” were the dominant bacteria, followed by Bacteroidetes and Proteobacteria. Intraspecies dynamics of microbial communities in healthy tissues were observed among sponge individuals, and potential anoxygenic phototrophic bacteria were found. In comparison with healthy tissues and the adjacent seawater, abnormal tissues showed dramatic increase in microbial diversity and decrease in the abundance of sponge-specific microbial clusters. The dominated cyanobacterial species Candidatus Synechococcus spongiarum decreased and shifted to unspecific cyanobacterial clades. OTUs that showed high similarity to sequences derived from diseased corals, such as Leptolyngbya sp., were found to be abundant in abnormal tissues. Heterotrophic Planctomycetes were also specifically enriched in abnormal tissues. Overall, we revealed the microbial communities of the cyanobacteria-rich sponge, C. foliascens, and their impressive shifts under abnormality.

  1. Microbial community analysis of a coastal salt marsh affected by the Deepwater Horizon oil spill.

    Directory of Open Access Journals (Sweden)

    Melanie J Beazley

    Full Text Available Coastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf of Mexico coastal salt marsh during and after the influx of petroleum hydrocarbons following the Deepwater Horizon oil spill. Total hydrocarbon concentrations in salt marsh sediments were highest in June and July 2010 and decreased in September 2010. Coupled PhyloChip and GeoChip microarray analyses demonstrated that the microbial community structure and function of the extant salt marsh hydrocarbon-degrading microbial populations changed significantly during the study. The relative richness and abundance of phyla containing previously described hydrocarbon-degrading bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria increased in hydrocarbon-contaminated sediments and then decreased once hydrocarbons were below detection. Firmicutes, however, continued to increase in relative richness and abundance after hydrocarbon concentrations were below detection. Functional genes involved in hydrocarbon degradation were enriched in hydrocarbon-contaminated sediments then declined significantly (p<0.05 once hydrocarbon concentrations decreased. A greater decrease in hydrocarbon concentrations among marsh grass sediments compared to inlet sediments (lacking marsh grass suggests that the marsh rhizosphere microbial communities could also be contributing to hydrocarbon degradation. The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems.

  2. Profile of bacterial communities in South African mine-water samples using Illumina next-generation sequencing platform.

    Science.gov (United States)

    Keshri, Jitendra; Mankazana, Boitumelo B J; Momba, Maggy N B

    2015-04-01

    Mine water is an example of an extreme environment that contains a large number of diverse and specific bacteria. It is imperative to gain an understanding of these bacterial communities in order to develop effective strategies for the bioremediation of polluted aquatic systems. In this study, the high-throughput sequencing approach was used to characterize the bacterial communities in two different mine waters of South Africa: vanadium and gold mine water. Over 2629 operational taxonomic units (OTUs) were recovered from 15,802 reads of the 16S ribosomal RNA (rRNA) gene. They represented 8 phyla, 43 orders, 84 families and 105 genera. Proteobacteria and unclassified bacterial sequences were the most dominant. Apart from these, Firmicutes, Bacteroidetes, Actinobacteria, Candidate phylum OD1, Cyanobacteria, Verrucomicrobia and Deinococcus-Thermus were the recovered phyla, although their relative abundance differed between both the mine-water samples. Yet, diversity indices suggested that the bacterial communities inhabiting the vanadium mine water were more diverse than those in gold mine water. Interestingly, substantial percentages of the reads from either sample (58 % in vanadium and 17 % in gold mine water) could not be assigned to any phylum and remained unclassified, suggesting hitherto unidentified populations, and vast untapped microbial diversity. Overall, the results of this study exhibited bacterial community structures with high diversity in mine water, which can be explored further for their role in bioremediation and environmental management. PMID:25416590

  3. Plants rather than mineral fertilization shape microbial community structure and functional potential in legacy contaminated soil

    Directory of Open Access Journals (Sweden)

    Jakub eRidl

    2016-06-01

    Full Text Available Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microbial guilds which are adapted to ephemeral carbon inputs are enriched in the vegetated soil.. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism, differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

  4. Microbiome and immunological interactions.

    Science.gov (United States)

    Kelly, Denise; Mulder, Imke E

    2012-08-01

    The healthy human gut supports a complex and diverse microbiota, dominated by bacterial phylotypes belonging to Bacteroidetes and Firmicutes. In the inflamed gut, overall diversity decreases, coincident with a greater representation of Proteobacteria. There is growing evidence supporting an important role for human gut bacteria in mucosal immunity; interactions at the level of both intestinal and colonic epithelial cells, dendritic cells, and T and B immune cells have been documented. These interactions influence gut barrier and defense mechanisms that include antimicrobial peptide and secretory IgA synthesis. The functional effects of commensal bacteria on T helper cell differentiation have led to the emerging concept that microbiota composition determines T effector- and T regulatory-cell balance, immune responsiveness, and homeostasis. The importance of this biology in relation to immune homeostasis, inflammatory bowel disease, and the rising incidence of autoimmune diseases will be discussed. The detailed description of the human gut microbiota, integrated with evidence-based mechanisms of immune modulation, provides an exciting platform for the identification of next-generation probiotics and related pharmaceutical products. PMID:22861803

  5. Microbial Corrosion in Linepipe Steel Under the Influence of a Sulfate-Reducing Consortium Isolated from an Oil Field

    Science.gov (United States)

    AlAbbas, Faisal M.; Williamson, Charles; Bhola, Shaily M.; Spear, John R.; Olson, David L.; Mishra, Brajendra; Kakpovbia, Anthony E.

    2013-11-01

    This work investigates microbiologically influenced corrosion of API 5L X52 linepipe steel by a sulfate-reducing bacteria (SRB) consortium. The SRB consortium used in this study was cultivated from a sour oil well in Louisiana, USA. 16S rRNA gene sequence analysis indicated that the mixed bacterial consortium contained three phylotypes: members of Proteobacteria ( Desulfomicrobium sp.), Firmicutes ( Clostridium sp.), and Bacteroidetes ( Anaerophaga sp.). The biofilm and the pits that developed with time were characterized using field emission scanning electron microscopy (FE-SEM). In addition, electrochemical impedance spectroscopy (EIS), linear polarization resistance (LPR) and open circuit potential (OCP) were used to analyze the corrosion behavior. Through circuit modeling, EIS results were used to interpret the physicoelectric interactions between the electrode, biofilm and solution interfaces. The results confirmed that extensive localized corrosion activity of SRB is due to a formed biofilm in conjunction with a porous iron sulfide layer on the metal surface. X-ray diffraction (XRD) revealed semiconductive corrosion products predominantly composed of a mixture of siderite (FeCO3), iron sulfide (Fe x S y ), and iron (III) oxide-hydroxide (FeOOH) constituents in the corrosion products for the system exposed to the SRB consortium.

  6. Freshwater ice as habitat: partitioning of phytoplankton and bacteria between ice and water in central European reservoirs.

    Science.gov (United States)

    McKay, Robert M L; Prášil, Ondrej; Pechar, Libor; Lawrenz, Evelyn; Rozmarynowycz, Mark J; Bullerjahn, George S

    2015-12-01

    Abundant phytoplankton and bacteria were identified by high-throughput 16S rRNA tag Illumina sequencing of samples from water and ice phases collected during winter at commercial fish ponds and a sand pit lake within the UNESCO Třeboň Basin Biosphere Reserve, Czech Republic. Bacterial reads were dominated by Proteobacteria and Bacteroidetes. Despite dominance by members of just two phyla, UniFrac principal coordinates analysis of the bacterial community separated the water community of Klec fish pond, as well as the ice-associated community of Klec-Sand Pit from other samples. Both phytoplankton and cyanobacteria were represented with hundreds of sequence reads per sample, a finding corroborated by microscopy. In particular, ice from Klec-Sand Pit contained high contributions from photoautotrophs accounting for 25% of total reads with reads dominated by single operational taxonomic units (OTUs) of the cyanobacterium Planktothrix sp. and two filamentous diatoms. Dominant OTUs recovered from ice were largely absent (supporting ice as viable habitat for phytoplankton in freshwater lakes and reservoirs. PMID:26224255

  7. Microbial source markers assessment in the Bogotá River basin (Colombia).

    Science.gov (United States)

    Venegas, Camilo; Diez, Hugo; Blanch, Anicet R; Jofre, Juan; Campos, Claudia

    2015-09-01

    The microbiological indicators traditionally used to assess fecal contamination are insufficient to identify the source. The aim of this study was to detect microbial markers to identify the source of fecal pollution in the Bogotá River (Colombia). For this, we determined non-discriminating indicators such as Escherichia coli, somatic coliphages and phages infecting strain RYC2056 of Bacteroides, and potential source tracking markers as phages infecting strains GA17, HB13, and CA8 of Bacteroides, sorbitol-fermenting bifidobacteria, and molecular markers of Bifidobacterium adolescentis, Bifiodobacterium dentium, and Bacteroidetes in raw municipal wastewaters, slaughterhouse wastewaters, and the Bogotá River. Bacteriophages infecting Bacteroides strain GA17 and the molecular markers identified the wastewater sources. In contrast, sorbitol-fermenting bifidobacteria failed regarding specificity. In the Bogotá River, phages infecting strain GA17 were detected in all samples downstream of Bogotá, whereas they should be concentrated from 1 l samples in upstream samples containing less than 10(3) E. coli/100 ml to be detected. In the river water, the fraction of positive detections of molecular markers was lower than that of phages infecting strain GA17. The ratio SOMCPH/GA17PH was shown also to be a good marker. These results provide information that will allow focusing measures for sanitation of the Bogotá River. PMID:26322765

  8. Standard filtration practices may significantly distort planktonic microbial diversity estimates

    Directory of Open Access Journals (Sweden)

    Cory Cruz Padilla

    2015-06-01

    Full Text Available Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40-60% of prefilter datasets at low volumes (0.05-0.5 L to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold. Taxon richness (97% similarity clusters also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.

  9. Uterine Microbiota Progression from Calving until Establishment of Metritis in Dairy Cows

    Science.gov (United States)

    Jeon, Soo Jin; Vieira-Neto, Achilles; Gobikrushanth, Mohanathas; Daetz, Rodolfo; Mingoti, Rodolfo D.; Parize, Ana Carolina Brigolin; de Freitas, Sabrina Lucas; da Costa, Antonio Nelson Lima; Bicalho, Rodrigo C.; Lima, Svetlana; Jeong, K. Casey

    2015-01-01

    The objective of this study was to evaluate the progression of the uterine microbiota from calving until establishment of metritis. Uterine swabs (n = 72) collected at 0, 2, and 6 ± 2 days postpartum (dpp) from 12 metritic and 12 healthy cows were used for metagenomic sequencing of the 16S rRNA gene on the Illumina MiSeq platform. A heat map showed that uterine microbiota was established at calving. The microbiota changed rapidly from 0 to 6 ± 2 dpp, with a decrease in the abundance of Proteobacteria and an increase in the abundance of Bacteroidetes and Fusobacteria, which were dominant in metritic cows. Uterine microbiota composition was shared; however, metritic and healthy cows could be discriminated using relative abundance of bacterial genera at 0, 2, and 6 ± 2 dpp. Bacteroides was the main genus associated with metritis because it was the only genus that showed significantly greater abundance in cows with metritis. As the abundance of Bacteroides organisms increased, the uterine discharge score, a measure of uterine health, worsened. Fusobacterium was also an important genus associated with metritis because Fusobacterium abundance increased as Bacteroides abundance increased and the uterine discharge score worsened as the abundance increased. The correlation with uterine discharge score and the correlation with Bacteroides or Fusobacterium showed that other bacteria, such as Helcoccocus, Filifactor, and Porphyromonas, were also associated with metritis. There were also bacteria associated with uterine health, such as “Candidatus Blochmannia,” Escherichia, Sneathia, and Pedobacter. PMID:26150453

  10. Identification and Phylogeny of the First T Cell Epitope Identified from a Human Gut Bacteroides Species.

    Directory of Open Access Journals (Sweden)

    Maria Elisa Perez-Muñoz

    Full Text Available Host T cell reactivity toward gut bacterial epitopes has been recognized as part of disease pathogenesis. However, the specificity of T cells that recognize this vast number of epitopes has not yet been well described. After colonizing a C57BL/6J germ-free mouse with the human gut symbiotic bacteria Bacteroides thetaiotaomicron, we isolated a T cell that recognized these bacteria in vitro. Using this T cell, we mapped the first known non-carbohydrate T cell epitope within the phylum Bacteroidetes. The T cell also reacted to two other additional Bacteroides species. We identified the peptide that stimulated the T cell by using a genetic approach. Genomic data from the epitope-positive and epitope-negative bacteria explain the cross-reactivity of the T cell to multiple species. This epitope degeneracy should shape our understanding of the T cell repertoire stimulated by the complex microbiome residing in the gastrointestinal tract in both healthy and disease states.

  11. Long-term performance of rapid oxidation of arsenite in simulated groundwater using a population of arsenite-oxidizing microorganisms in a bioreactor.

    Science.gov (United States)

    Li, Hao; Zeng, Xian-Chun; He, Zhong; Chen, Xiaoming; E, Guoji; Han, Yiyang; Wang, Yanxin

    2016-09-15

    A population of arsenite-oxidizing microorganisms enriched from the tailing of the Shimen realgar mine was used to generate biofilms on the surfaces of perlites. This bioreactor is able to completely oxidize 1100 μg/L As(III) dissolved in simulated groundwater into As(V) within 10 min; after 140 days of operation, approximately 20 min were required to completely oxidize the same concentration of As(III). Analysis for the 16S rRNA genes of the microbial community showed that Bacteroidetes and Proteobacteria are dominant in the reactor. Six different bacterial strains were randomly isolated from the reactor. Function and gene analysis indicated that all the isolates possess arsenite-oxidizing activity, and five of them are chemoautotrophic. Further analysis showed that a large diversity of AioAs and two types of RuBisCOs are present in the microbial community. This suggests that many chemoautotrophic arsenite-oxidizing microorganisms were responsible for quick oxidation of arsenite in the reactor. We also found that the reactor is easily regenerated and its number is readily expanded. To the best of our knowledge, the arsenite-oxidizing efficiency, which was expressed as the minimum time for complete oxidization of a certain concentration of As(III) under a single operation, of this bioreactor is the highest among the described bioreactors; it is also the most stable, economic and environment-friendly. PMID:27288673

  12. Antibiotic resistance among aquatic bacteria in natural freshwater environments of Korea.

    Science.gov (United States)

    Kim, Tae Woon; Joung, Yochan; Han, Ji-Hye; Jung, Wonwha; Kim, Seung Bum

    2015-12-01

    The taxonomic diversity and antibiotic resistance among freshwater bacterial communities in the major water bodies of Korea was examined using 437 penicillin-resistant, and 110 tetracycline-resistant bacterial isolates. Based on 16S rRNA gene sequence analysis, most isolates were assigned to Proteobacteria, which was then followed by Bacteroidetes. Strains of Aeromonas were found as the most abundant penicillin-resistant populations, whereas those affiliated to diverse species including enteric groups were found as the most abundant tetracycline-resistant populations. Most strains exhibited multiple antibiotic resistance, and all tested strains were resistant to penicillin and hygromycin. High levels of resistance were observed for antibiotics acting on cell wall synthesis, whereas low levels were for those acting on DNA replication or transcription in general. It is apparent from this study that penicillin resistance is widespread among environmental bacteria, although the antibiotic has been generally non-detectable in the environment. It is also likely from the taxonomic composition of the resistant communities that various sources including terrestrial animals and humans may contribute to antibiotic resistance in the freshwater environment. PMID:26608770

  13. Profiling of Sediment Microbial Community in Dongting Lake before and after Impoundment of the Three Gorges Dam

    Science.gov (United States)

    Huang, Wei; Jiang, Xia

    2016-01-01

    The sediment microbial community in downstream-linked lakes can be affected by the operation of large-scale water conservancy projects. The present study determined Illumina reads (16S rRNA gene amplicons) to analyze and compare the bacterial communities from sediments in Dongting Lake (China) before and after impoundment of the Three Gorges Dam (TGD), the largest hydroelectric project in the world. Bacterial communities in sediment samples in Dongting Lake before impoundment of the TGD (the high water period) had a higher diversity than after impoundment of the TGD (the low water period). The most abundant phylum in the sediment samples was Proteobacteria (36.4%–51.5%), and this result was due to the significant abundance of Betaproteobacteria and Deltaproteobacteria in the sediment samples before impoundment of the TGD and the abundance of Gammaproteobacteria in the sediment samples after impoundment of the TGD. In addition, bacterial sequences of the sediment samples are also affiliated with Acidobacteria (11.0% on average), Chloroflexi (10.9% on average), Bacteroidetes (6.7% on average), and Nitrospirae (5.1% on average). Variations in the composition of the bacterial community within some sediment samples from the river estuary into Dongting Lake were related to the pH values. The bacterial community in the samples from the three lake districts of Dongting Lake before and after impoundment of the TGD was linked to the nutrient concentration. PMID:27338434

  14. The amphibian skin-associated microbiome across species, space and life history stages.

    Science.gov (United States)

    Kueneman, Jordan G; Parfrey, Laura Wegener; Woodhams, Douglas C; Archer, Holly M; Knight, Rob; McKenzie, Valerie J

    2014-03-01

    Skin-associated bacteria of amphibians are increasingly recognized for their role in defence against pathogens, yet we have little understanding of their basic ecology. Here, we use high-throughput 16S rRNA gene sequencing to examine the host and environmental influences on the skin microbiota of the cohabiting amphibian species Anaxyrus boreas, Pseudacris regilla, Taricha torosa and Lithobates catesbeianus from the Central Valley in California. We also studied populations of Rana cascadae over a large geographic range in the Klamath Mountain range of Northern California, and across developmental stages within a single site. Dominant bacterial phylotypes on amphibian skin included taxa from Bacteroidetes, Gammaproteobacteria, Alphaproteobacteria, Firmicutes, Sphingobacteria and Actinobacteria. Amphibian species identity was the strongest predictor of microbial community composition. Secondarily, within a given amphibian species, wetland site explained significant variation. Amphibian-associated microbiota differed systematically from microbial assemblages in their environments. Rana cascadae tadpoles have skin bacterial communities distinct from postmetamorphic conspecifics, indicating a strong developmental shift in the skin microbes following metamorphosis. Establishing patterns observed in the skin microbiota of wild amphibians and environmental factors that underlie them is necessary to understand skin symbiont community assembly, and ultimately, the role skin microbiota play in the extended host phenotype including disease resistance. PMID:24171949

  15. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

    Directory of Open Access Journals (Sweden)

    Seung Hak Yang

    2015-09-01

    Full Text Available The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1–2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site.

  16. Bacterial community composition and abundance in leachate of semi-aerobic and anaerobic landfills

    Institute of Scientific and Technical Information of China (English)

    Wei Zhang; Bo Yue; Qi Wang; Zechun Huang; Qifei Huang; Zengqiang Zhang

    2011-01-01

    The abundance and phylogenetic composition of bacterial community in leachate of semi-aerobic and anaerobic landfill were compared through real-time polymerase chain reaction and denaturing gradient gel electrophoresis.In semi-aerobic landfill scenario,the bacterial 16S rRNA copy numbers in leachate had no significant reduction from initial stage to stable period.In the scenario of anaerobic landfill,the largest bacterial 16S rRNA gene copy number was found in leachate at initial stage,but it reduced significantly at stable period.Moreover,methane-oxidizing bacteria population in stable period was lower than that in initial period in both two landfill processes.However,semi-aerobic landfill leachate had more methanotrophic bacteria populations than that in the anaerobic one.Furthermore,according to the sequences and phylogenetic analysis,obvious difference could be detected in bacterial community composition in different scenarios.Proteobacteria and bacteroidetes took up a dominantly higher proportion in semi-aerobic landfill leachate.To summarize up,different landfill methods and its landfill ages had crucial impacts on bacterial abundance and composition in leachate of semi-aerobic and anaerobic landfills.

  17. Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats

    Science.gov (United States)

    Wong, Hon Lun; Smith, Daniela-Lee; Visscher, Pieter T.; Burns, Brendan P.

    2015-10-01

    Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism.

  18. Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures.

    Science.gov (United States)

    Aira, Manuel; Bybee, Seth; Pérez-Losada, Marcos; Domínguez, Jorge

    2015-11-01

    Earthworms play a key role in nutrient cycling by interacting with microorganisms thus accelerating organic matter turnover in soil systems. As detritivores, some earthworm types ingest and digest a mixture of dead organic matter and microorganisms, like animal manures (i.e. animal gut microbiomes). Here we described the earthworm cast microbiome and the role ingested bacteria play on its composition. We fed Eisenia andrei with cow, horse and pig manures and determined the taxonomic and phylogenetic composition of the these manures before and after passage through the earthworm gut. Earthworm cast microbiomes showed a smaller diversity than the manure they fed on. Manures strongly differed in their taxonomic and phylogenetic composition, but these differences were markedly reduced once transformed into earthworm cast microbiomes after passage through the earthworm gut. The core earthworm cast microbiome comprised 30 OTUs (2.6% of OTUs from cast samples), of which 10 are possibly native to the earthworm gut. Most of the core cast microbiome OTUs belonged to phyla Actinobacteria and Proteobacteria, as opposed to already described animal core gut microbiomes, which are composed mainly of Firmicutes and Bacteroidetes. Our results suggest that earthworms build up their cast microbiome by selecting from the pool of ingested bacteria. PMID:26432803

  19. The microbial community of a passive biochemical reactor treating arsenic, zinc and sulfate-rich seepage

    Directory of Open Access Journals (Sweden)

    Susan Anne Baldwin

    2015-03-01

    Full Text Available Sulfidogenic biochemical reactors for metal removal that use complex organic carbon have been shown to be effective in laboratory studies, but their performance in the field is highly variable. Successful operation depends on the types of microorganisms supported by the organic matrix, and factors affecting the community composition are unknown. A molecular survey of a field-based biochemical reactor that had been removing zinc and arsenic for over six years revealed that the microbial community was dominated by methanogens related to Methanocorpusculum sp. and Methanosarcina sp., which co-occurred with Bacteroidetes environmental groups, such as Vadin HA17, in places where the organic matter was more degraded. The metabolic potential for organic matter decomposition by Ruminococcaceae was prevalent in samples with more pyrolysable carbon. Rhodobium- and Hyphomicrobium-related genera within the Rhizobiales Order that have the metabolic potential for dark hydrogen fermentation and methylotrophy, and unclassified Comamonadaceae were the dominant Proteobacteria. The unclassified environmental group Sh765B-TzT-29 was an important Delta-Proteobacteria group in this BCR, that co-occurred with the dominant Rhizobiales OTUs. Organic matter degradation is one driver for shifting the microbial community composition and therefore possibly the performance of these bioreactors over time.

  20. 'Core species' in three sources of indoor air belonging to the human micro-environment to the exclusion of outdoor air.

    Science.gov (United States)

    Gaüzère, Carole; Godon, Jean-Jacques; Blanquart, Hélène; Ferreira, Stéphanie; Moularat, Stéphane; Robine, Enric; Moletta-Denat, Marina

    2014-07-01

    Although we spend the majority of our lives indoors, the airborne microbial content of enclosed spaces still remains inadequately described. The objective of this study was to characterize the bacterial diversity of indoor air in three different enclosed spaces with three levels of occupancy, and, in particular, to highlight the 'core' species, the opportunistic pathogens and their origins. Our findings provide an overall description of bacterial diversity in these indoor environments. Data gathered from the three enclosed spaces revealed the presence of a common indoor signature (60% of total sequences in common). This work will provide a clearer understanding of the dominant groups of bacteria encountered in enclosed spaces: Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes. Thus, certain evidence revealed a connection between 'core' species and the human micro-environment (20% of phylotypes and 12% of sequences of human origin). Overall PCA analysis showed that the indoor environment is influenced mainly by the microbial diversity from nose and skin. Among the 'core species' found during this study, a large number (72% of all pathogen-related sequences were concentrated in 'core species') of genera and species are known to be responsible for opportunistic or nosocomial diseases or to include human commensal bacteria such as Mycobacterium sp., Acinetobacter baumanii, Aerococcus viridians, Thermoactinomyces vulgaris or Clostridium perfringens. PMID:24747243

  1. Cultivable bacterial microbiota of northern bobwhite (Colinus virginianus: a new reservoir of antimicrobial resistance?

    Directory of Open Access Journals (Sweden)

    Hongwen Su

    Full Text Available The northern bobwhite (Colinus virginianus is an ecologically and economically important avian species. At the present time, little is known about the microbial communities associated with these birds. As the first step to create a quail microbiology knowledge base, the current study conducted an inventory of cultivable quail tracheal, crop, cecal, and cloacal microbiota and associated antimicrobial resistance using a combined bacteriology and DNA sequencing approach. A total of 414 morphologically unique bacterial colonies were selected from nonselective aerobic and anaerobic cultures, as well as selective and enrichment cultures. Analysis of the first 500-bp 16S rRNA gene sequences in conjunction with biochemical identifications revealed 190 non-redundant species-level taxonomic units, representing 160 known bacterial species and 30 novel species. The bacterial species were classified into 4 phyla, 14 orders, 37 families, and 59 or more genera. Firmicutes was the most commonly encountered phylum (57% followed by Actinobacteria (24%, Proteobacteria (17% and Bacteroidetes (0.02%. Extensive diversity in the species composition of quail microbiota was observed among individual birds and anatomical locations. Quail microbiota harbored several opportunistic pathogens, such as E. coli and Ps. aeruginosa, as well as human commensal organisms, including Neisseria species. Phenotypic characterization of selected bacterial species demonstrated a high prevalence of resistance to the following classes of antimicrobials: phenicol, macrolide, lincosamide, quinolone, and sulphate. Data from the current investigation warrant further investigation on the source, transmission, pathology, and control of antimicrobial resistance in wild quail populations.

  2. Effects of bitter melon (Momordica charantia L.) on the gut microbiota in high fat diet and low dose streptozocin-induced rats.

    Science.gov (United States)

    Zhu, Ying; Bai, Juan; Zhang, Yi; Xiao, Xiang; Dong, Ying

    2016-09-01

    The effects on gut microbiota of type 2 diabetic rats fed a bitter melon formulation (BLSP, a lyophilized superfine powder) were investigated. BLSP treatment significantly reduced fasting blood glucose levels (p < 0.05) and serum insulin levels (p < 0.05) of the diabetic rats. The gut microbiota of treated and control rats were profiled by PCR amplification and pyrosequencing of 16S rRNA genes (V3-V9 region). BLSP significantly reduced the ratio of Firmicutes to Bacteroidetes in diabetic rats, while the relative abundances of Ruminococcaceae, Bacteroides and Ruminococcus were significantly lowered in BLSP-treated rats compared to diabetic rats. Additionally, BLSP significantly suppressed the activation of MAPK (JNK and p38). The results indicate that BLSP can significantly modify the proportions of particular gut microbiota in diabetic rats without disturbing the normal population diversity. By suppressing the activation of MAPK signaling pathway, a BLSP containing diet may ameliorate type 2 diabetes. PMID:27352776

  3. Bacterial and eukaryotic biodiversity patterns in terrestrial and aquatic habitats in the Sør Rondane Mountains, Dronning Maud Land, East Antarctica.

    Science.gov (United States)

    Obbels, Dagmar; Verleyen, Elie; Mano, Marie-José; Namsaraev, Zorigto; Sweetlove, Maxime; Tytgat, Bjorn; Fernandez-Carazo, Rafael; De Wever, Aaike; D'hondt, Sofie; Ertz, Damien; Elster, Josef; Sabbe, Koen; Willems, Anne; Wilmotte, Annick; Vyverman, Wim

    2016-06-01

    The bacterial and microeukaryotic biodiversity were studied using pyrosequencing analysis on a 454 GS FLX+ platform of partial SSU rRNA genes in terrestrial and aquatic habitats of the Sør Rondane Mountains, including soils, on mosses, endolithic communities, cryoconite holes and supraglacial and subglacial meltwater lenses. This inventory was complemented with Denaturing Gradient Gel Electrophoresis targeting Chlorophyta and Cyanobacteria. OTUs belonging to the Rotifera, Chlorophyta, Tardigrada, Ciliophora, Cercozoa, Fungi, Bryophyta, Bacillariophyta, Collembola and Nematoda were present with a relative abundance of at least 0.1% in the eukaryotic communities. Cyanobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, FBP and Actinobacteria were the most abundant bacterial phyla. Multivariate analyses of the pyrosequencing data revealed a general lack of differentiation of both eukaryotes and prokaryotes according to habitat type. However, the bacterial community structure in the aquatic habitats was dominated by the filamentous cyanobacteria Leptolyngbya and appeared to be significantly different compared with those in dry soils, on mosses, and in endolithic habitats. A striking feature in all datasets was the detection of a relatively large amount of sequences new to science, which underscores the need for additional biodiversity assessments in Antarctic inland locations. PMID:26936447

  4. Nutrient treatments alter microbial mat colonization in two glacial meltwater streams from the McMurdo Dry Valleys, Antarctica.

    Science.gov (United States)

    Kohler, Tyler J; Van Horn, David J; Darling, Joshua P; Takacs-Vesbach, Cristina D; McKnight, Diane M

    2016-04-01

    Microbial mats are abundant in many alpine and polar aquatic ecosystems. With warmer temperatures, new hydrologic pathways are developing in these regions and increasing dissolved nutrient fluxes. In the McMurdo Dry Valleys, thermokarsting may release both nutrients and sediment, and has the potential to influence mats in glacial meltwater streams. To test the role of nutrient inputs on community structure, we created nutrient diffusing substrata (NDS) with agar enriched in N, P and N + P, with controls, and deployed them into two Dry Valley streams. We found N amendments (N and N + P) to have greater chlorophyll-a concentrations, total algal biovolume, more fine filamentous cyanobacteria and a higher proportion of live diatoms than other treatments. Furthermore, N treatments were substantially elevated in Bacteroidetes and the small diatom, Fistulifera pelliculosa. On the other hand, species richness was almost double in P and N + P treatments over others, and coccoid green algae and Proteobacteria were more abundant in both streams. Collectively, these data suggest that nutrients have the potential to stimulate growth and alter community structure in glacial meltwater stream microbial mats, and the recent erosion of permafrost and accelerated glacial melt will likely impact resident biota in polar lotic systems here and elsewhere. PMID:26940086

  5. Bacterial succession in Antarctic soils of two glacier forefields on Larsemann Hills, East Antarctica.

    Science.gov (United States)

    Bajerski, Felizitas; Wagner, Dirk

    2013-07-01

    Antarctic glacier forefields are extreme environments and pioneer sites for ecological succession. Increasing temperatures due to global warming lead to enhanced deglaciation processes in cold-affected habitats, and new terrain is becoming exposed to soil formation and microbial colonization. However, only little is known about the impact of environmental changes on microbial communities and how they develop in connection to shifting habitat characteristics. In this study, using a combination of molecular and geochemical analysis, we determine the structure and development of bacterial communities depending on soil parameters in two different glacier forefields on Larsemann Hills, East Antarctica. Our results demonstrate that deglaciation-dependent habitat formation, resulting in a gradient in soil moisture, pH and conductivity, leads to an orderly bacterial succession for some groups, for example Cyanobacteria, Bacteroidetes and Deltaproteobacteria in a transect representing 'classical' glacier forefields. A variable bacterial distribution and different composed communities were revealed according to soil heterogeneity in a slightly 'matured' glacier forefield transect, where Gemmatimonadetes, Flavobacteria, Gamma- and Deltaproteobacteria occur depending on water availability and soil depth. Actinobacteria are dominant in both sites with dominance connected to certain trace elements in the glacier forefields. PMID:23480659

  6. Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota

    Directory of Open Access Journals (Sweden)

    Jessica Ann Thompson

    2015-03-01

    Full Text Available The mammalian gut microbiota harbors a diverse ecosystem where hundreds of bacterial species interact with each other and their host. Given that bacteria use signals to communicate and regulate group behaviors (quorum sensing, we asked whether such communication between different commensal species can influence the interactions occurring in this environment. We engineered the enteric bacterium, Escherichia coli, to manipulate the levels of the interspecies quorum sensing signal, autoinducer-2 (AI-2, in the mouse intestine and investigated the effect upon antibiotic-induced gut microbiota dysbiosis. E. coli that increased intestinal AI-2 levels altered the composition of the antibiotic-treated gut microbiota, favoring the expansion of the Firmicutes phylum. This significantly increased the Firmicutes/Bacteroidetes ratio, to oppose the strong effect of the antibiotic, which had almost cleared the Firmicutes. This demonstrates that AI-2 levels influence the abundance of the major phyla of the gut microbiota, the balance of which is known to influence human health.

  7. The bacterial community associated with the leech Myzobdella lugubris Leidy 1851 (Hirudinea: Piscicolidae) from Lake Erie, Michigan, USA.

    Science.gov (United States)

    Schulz, C; Faisal, M

    2010-06-01

    Leeches are widespread in the Great Lakes Basin, yet their potential to harbor disease-causing agents has not been investigated. The purpose of this study was to identify the bacterial community of the commonly occurring leech, Myzobdella lugubris, within the Lake Erie Watershed. Leech samples were collected from the pectoral fins of channel catfish, Ictalurus punctatus, and freshwater drum, Aplodinotus grunniens, from Lake Erie in commercial trap nets and pooled into two samples based on host attachment. Bacteria from within the viscera of M. lugubris were identified by sequencing their 16S rRNA (rDNA) gene of amplified community bacterial DNA extracted from pooled leech homogenate samples and were checked for similarity in two public databases: the Ribosomal Database Project and BLAST. Bacteria belonging to the phylum Bacteroidetes, beta-proteobacteria, Verrucomicrobia, and unclassified Bacteria were present in the leech samples. A large number of bacteria found within leeches attached to channel catfish consisted of sequences that could not be classified beyond the Domain Bacteria. However, many of these sequences were homologous (Cold Water Disease. While the occurrence of genera varies, bacteria associated with the two fish species were similar. PMID:20597437

  8. Genetic diversity of bacterial communities and gene transfer agents in northern South China Sea.

    Directory of Open Access Journals (Sweden)

    Fu-Lin Sun

    Full Text Available Pyrosequencing of the 16S ribosomal RNA gene (rDNA amplicons was performed to investigate the unique distribution of bacterial communities in northern South China Sea (nSCS and evaluate community structure and spatial differences of bacterial diversity. Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes constitute the majority of bacteria. The taxonomic description of bacterial communities revealed that more Chroococcales, SAR11 clade, Acidimicrobiales, Rhodobacterales, and Flavobacteriales are present in the nSCS waters than other bacterial groups. Rhodobacterales were less abundant in tropical water (nSCS than in temperate and cold waters. Furthermore, the diversity of Rhodobacterales based on the gene transfer agent (GTA major capsid gene (g5 was investigated. Four g5 gene clone libraries were constructed from samples representing different regions and yielded diverse sequences. Fourteen g5 clusters could be identified among 197 nSCS clones. These clusters were also related to known g5 sequences derived from genome-sequenced Rhodobacterales. The composition of g5 sequences in surface water varied with the g5 sequences in the sampling sites; this result indicated that the Rhodobacterales population could be highly diverse in nSCS. Phylogenetic tree analysis result indicated distinguishable diversity patterns among tropical (nSCS, temperate, and cold waters, thereby supporting the niche adaptation of specific Rhodobacterales members in unique environments.

  9. Got worms? Perinatal exposure to helminths prevents persistent immune sensitization and cognitive dysfunction induced by early-life infection.

    Science.gov (United States)

    Williamson, Lauren L; McKenney, Erin A; Holzknecht, Zoie E; Belliveau, Christine; Rawls, John F; Poulton, Susan; Parker, William; Bilbo, Staci D

    2016-01-01

    The incidence of autoimmune and inflammatory diseases has risen dramatically in post-industrial societies. "Biome depletion" - loss of commensal microbial and multicellular organisms such as helminths (intestinal worms) that profoundly modulate the immune system - may contribute to these increases. Hyperimmune-associated disorders also affect the brain, especially neurodevelopment, and increasing evidence links early-life infection to cognitive and neurodevelopmental disorders. We have demonstrated previously that rats infected with bacteria as newborns display life-long vulnerabilities to cognitive dysfunction, a vulnerability that is specifically linked to long-term hypersensitivity of microglial cell function, the resident immune cells of the brain. Here, we demonstrate that helminth colonization of pregnant dams attenuated the exaggerated brain cytokine response of their offspring to bacterial infection, and that combined with post-weaning colonization of offspring with helminths (consistent with their mothers treatment) completely prevented enduring microglial sensitization and cognitive dysfunction in adulthood. Importantly, helminths had no overt impact on adaptive immune cell subsets, whereas exaggerated innate inflammatory responses in splenic macrophages were prevented. Finally, helminths altered the effect of neonatal infection on the gut microbiome; neonatal infection with Escherichia coli caused a shift from genera within the Actinobacteria and Tenericutes phyla to genera in the Bacteroidetes phylum in rats not colonized with helminths, but helminths attenuated this effect. In sum, these data point toward an inter-relatedness of various components of the biome, and suggest potential mechanisms by which this helminth might exert therapeutic benefits in the treatment of neuroinflammatory and cognitive disorders. PMID:26162711

  10. Antimicrobial activity observed among cultured marine epiphytic bacteria reflects their potential as a source of new drugs.

    Science.gov (United States)

    Penesyan, Anahit; Marshall-Jones, Zoe; Holmstrom, Carola; Kjelleberg, Staffan; Egan, Suhelen

    2009-07-01

    The surfaces of marine eukaryotes provide a unique habitat for colonizing microorganisms where competition between members of these communities and chemically mediated interactions with their host are thought to influence both microbial diversity and function. For example, it is believed that marine eukaryotes may use their surface-associated bacteria to produce bioactive compounds in defence against competition and to protect the host against further colonization. With the increasing need for novel drug discovery, marine epibiotic bacteria may thus represent a largely underexplored source of new antimicrobial compounds. In the current study, 325 bacterial isolates were obtained from the surfaces of marine algae Delisea pulchra and Ulva australis. Thirty-nine showed to have antimicrobial activity and were identified via 16S rRNA gene sequencing. The majority of those isolates belonged to Alpha- and Gammaproteobacteria. Interestingly, the most commonly isolated bacterial strain, Microbulbifer sp., from the surface of D. pulchra has previously been described as an ecologically significant epibiont of different marine eukaryotes. Other antimicrobial isolates obtained in this study belonged to the phyla Actinobacteria, Firmicutes and Bacteroidetes. Phylogenetically, little overlap was observed among the bacteria obtained from surfaces of D. pulchra and U. australis. The high abundance of cultured isolates that produce antimicrobials suggest that culturing remains a powerful resource for exploring novel bioactives of bacterial origin. PMID:19453738

  11. A Metaproteomic Analysis of the Response of a Freshwater Microbial Community under Nutrient Enrichment.

    Science.gov (United States)

    Russo, David A; Couto, Narciso; Beckerman, Andrew P; Pandhal, Jagroop

    2016-01-01

    Eutrophication can lead to an uncontrollable increase in algal biomass, which has repercussions for the entire microbial and pelagic community. Studies have shown how nutrient enrichment affects microbial species succession, however details regarding the impact on community functionality are rare. Here, we applied a metaproteomic approach to investigate the functional changes to algal and bacterial communities, over time, in oligotrophic and eutrophic conditions, in freshwater microcosms. Samples were taken early during algal and cyanobacterial dominance and later under bacterial dominance. 1048 proteins, from the two treatments and two timepoints, were identified and quantified by their exponentially modified protein abundance index. In oligotrophic conditions, Bacteroidetes express extracellular hydrolases and Ton-B dependent receptors to degrade and transport high molecular weight compounds captured while attached to the phycosphere. Alpha- and Beta-proteobacteria were found to capture different substrates from algal exudate (carbohydrates and amino acids, respectively) suggesting resource partitioning to avoid direct competition. In eutrophic conditions, environmental adaptation proteins from cyanobacteria suggested better resilience compared to algae in a low carbon nutrient enriched environment. This study provides insight into differences in functional microbial processes between oligo- and eutrophic conditions at different timepoints and highlights how primary producers control bacterial resources in freshwater environments. The data have been deposited to the ProteomeXchange with identifier PXD004592. PMID:27536273

  12. Diversity of chemotactic heterotrophic bacteria associated with arctic cyanobacteria.

    Science.gov (United States)

    Prasad, Sathish; Pratibha, Mambatta Shankaranarayanan; Manasa, Poorna; Buddhi, Sailaja; Begum, Zareena; Shivaji, Sisinthy

    2013-01-01

    The abundance and diversity of chemotactic heterotrophic bacteria associated with Arctic cyanobacteria was determined. The viable numbers ranged between 10(4) and 10(6) cell g(-1) cyanobacterial biomass. A total of 112 morphotypes, representing 22 phylotypes based on their 16S rRNA sequence similarity were isolated from the samples. All the phylotypes were Gram-negative with affiliation to the proteobacterial and bacteroidetes divisions. Among the 22 phylotypes, 14 were chemotactic to glucose. Majority of the phylotypes were psychrotolerant showing growth up to 30 °C. Representatives of Alphaproteobacteria, the genus Flavobacterium and the gammaproteobacterial Alcanivorax sp, were psychrophilic with growth at or below 18 °C. A significant percentage of phylotypes were pigmented (~68 %), rich in unsaturated membrane fatty acids and tolerated pH values and NaCl concentrations between 5.0-8.0 and 0.15-1.0 M, respectively. The percentages of phylotypes producing extracellular cold-active enzymes at 4 °C were amylase (18.18 %), lipase and urease (45.45 %), caseinase (59.09 %) and gelatinase (31.8 %). PMID:23053490

  13. The role of the intestinal microbiota in type 1 diabetes mellitus.

    Science.gov (United States)

    Knip, Mikael; Siljander, Heli

    2016-03-01

    Type 1 diabetes mellitus (T1DM) is a chronic immune-mediated disease with a subclinical prodromal period, characterized by selective loss of insulin-producing-β cells in the pancreatic islets of genetically susceptible individuals. The incidence of T1DM has increased several fold in most developed countries since World War II, in conjunction with other immune-mediated diseases. Rapid environmental changes and modern lifestyles are probably the driving factors that underlie this increase. These effects might be mediated by changes in the human microbiota, particularly the intestinal microbiota. Research on the gut microbiome of individuals at risk of developing T1DM and in patients with established disease is still in its infancy, but initial findings indicate that the intestinal microbiome of individuals with prediabetes or diabetes mellitus is different to that of healthy individuals. The gut microbiota in individuals with preclinical T1DM is characterized by Bacteroidetes dominating at the phylum level, a dearth of butyrate-producing bacteria, reduced bacterial and functional diversity and low community stability. However, these changes seem to emerge after the appearance of autoantibodies that are predictive of T1DM, which suggests that the intestinal microbiota might be involved in the progression from β-cell autoimmunity to clinical disease rather than in the initiation of the disease process. PMID:26729037

  14. An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia.

    Science.gov (United States)

    Dillon, S M; Lee, E J; Kotter, C V; Austin, G L; Dong, Z; Hecht, D K; Gianella, S; Siewe, B; Smith, D M; Landay, A L; Robertson, C E; Frank, D N; Wilson, C C

    2014-07-01

    Human immunodeficiency virus-1 (HIV-1) infection disrupts the intestinal immune system, leading to microbial translocation and systemic immune activation. We investigated the impact of HIV-1 infection on the intestinal microbiome and its association with mucosal T-cell and dendritic cell (DC) frequency and activation, as well as with levels of systemic T-cell activation, inflammation, and microbial translocation. Bacterial 16S ribosomal DNA sequencing was performed on colon biopsies and fecal samples from subjects with chronic, untreated HIV-1 infection and uninfected control subjects. Colon biopsies of HIV-1-infected subjects had increased abundances of Proteobacteria and decreased abundances of Firmicutes compared with uninfected donors. Furthermore at the genus level, a significant increase in Prevotella and decrease in Bacteroides was observed in HIV-1-infected subjects, indicating a disruption in the Bacteroidetes bacterial community structure. This HIV-1-associated increase in Prevotella abundance was associated with increased numbers of activated colonic T cells and myeloid DCs. Principal coordinates analysis demonstrated an HIV-1-related change in the microbiome that was associated with increased mucosal cellular immune activation, microbial translocation, and blood T-cell activation. These observations suggest that an important relationship exists between altered mucosal bacterial communities and intestinal inflammation during chronic HIV-1 infection. PMID:24399150

  15. Diversity and Composition of Bacterial Community in Soils and Lake Sediments from an Arctic Lake Area

    Science.gov (United States)

    Wang, Neng Fei; Zhang, Tao; Yang, Xiao; Wang, Shuang; Yu, Yong; Dong, Long Long; Guo, Yu Dong; Ma, Yong Xing; Zang, Jia Ye

    2016-01-01

    This study assessed the diversity and composition of bacterial communities within soils and lake sediments from an Arctic lake area (London Island, Svalbard). A total of 2,987 operational taxonomic units were identified by high-throughput sequencing, targeting bacterial 16S rRNA gene. The samples from four sites (three samples in each site) were significantly different in geochemical properties and bacterial community composition. Proteobacteria and Acidobacteria were abundant phyla in the nine soil samples, whereas Proteobacteria and Bacteroidetes were abundant phyla in the three sediment samples. Furthermore, Actinobacteria, Chlorobi, Chloroflexi, Elusimicrobia, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria significantly varied in their abundance among the four sampling sites. Additionally, members of the dominant genera, such as Clostridium, Luteolibacter, Methylibium, Rhodococcus, and Rhodoplanes, were significantly different in their abundance among the four sampling sites. Besides, distance-based redundancy analysis revealed that pH (p soils and sediments from a lake area in the Arctic harbor a high diversity of bacterial communities, which are influenced by many geochemical factors of Arctic environments.

  16. Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis.

    Directory of Open Access Journals (Sweden)

    Amaro E Trindade-Silva

    Full Text Available The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (∼150 Mb. Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome.

  17. Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil

    Directory of Open Access Journals (Sweden)

    Charles ePepe-Ranney

    2016-05-01

    Full Text Available We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP. Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs, respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi and Planctomycetes.

  18. Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil.

    Science.gov (United States)

    Pepe-Ranney, Charles; Campbell, Ashley N; Koechli, Chantal N; Berthrong, Sean; Buckley, Daniel H

    2016-01-01

    We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either (13)C-xylose or (13)C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for (13)C-incorporation into DNA from (13)C-xylose and (13)C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated (13)C in the (13)C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These (13)C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes. PMID:27242725

  19. Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition

    Directory of Open Access Journals (Sweden)

    An eYang

    2015-08-01

    Full Text Available We evaluated effects of 9-year simulation of simulated nitrogen (N deposition on microbial composition and diversity in the rhizosphere of two dominant temperate grassland species: grass Stipa krylovii and forb Artemisia frigida. Microbiomes in S. krylovii and A.frigida rhizosphere differed, but changed consistently along the N gradient. These changes were correlated to N-induced shifts to plant community. Hence, as plant biomass changed, so did bacterial rhizosphere communities, a result consistent with the role that N fertilizer has been shown to play in altering plant-microbial mutualisms. A total of 23 bacterial phyla were detected in the two rhizospheric soils by pyrosequencing, with Proteobacteria, Acidobacteria and Bacteroidetes dominating the sequences of all samples. Bacterioidetes and Proteobacteria tended to increase, while Acidobacteria declined with increase in N addition rates. TM7 increased >5-fold in the high N addition rates, especially in S. krylovii rhizosphere. Nitrogen addition also decreased diversity of OTUs (operational taxonomic units, Shannon and Chao1 indices of rhizospheric microbes regardless of plant species. These results suggest that there were both similar but also specific changes in microbial communities of temperate steppes due to N deposition.

  20. Ribosome reinitiation at leader peptides increases translation of bacterial proteins.

    Science.gov (United States)

    Korolev, Semen A; Zverkov, Oleg A; Seliverstov, Alexandr V; Lyubetsky, Vassily A

    2016-01-01

    Short leader genes usually do not encode stable proteins, although their importance in expression control of bacterial genomes is widely accepted. Such genes are often involved in the control of attenuation regulation. However, the abundance of leader genes suggests that their role in bacteria is not limited to regulation. Specifically, we hypothesize that leader genes increase the expression of protein-coding (structural) genes via ribosome reinitiation at the leader peptide in the case of a short distance between the stop codon of the leader gene and the start codon of the structural gene. For instance, in Actinobacteria, the frequency of leader genes at a distance of 10-11 bp is about 70 % higher than the mean frequency within the 1 to 65 bp range; and it gradually decreases as the range grows longer. A pronounced peak of this frequency-distance relationship is also observed in Proteobacteria, Bacteroidetes, Spirochaetales, Acidobacteria, the Deinococcus-Thermus group, and Planctomycetes. In contrast, this peak falls to the distance of 15-16 bp and is not very pronounced in Firmicutes; and no such peak is observed in cyanobacteria and tenericutes. Generally, this peak is typical for many bacteria. Some leader genes located close to a structural gene probably play a regulatory role as well. PMID:27084079

  1. Dynamic variation of the microbial community structure during the long-time mono-fermentation of maize and sugar beet silage.

    Science.gov (United States)

    Klang, Johanna; Theuerl, Susanne; Szewzyk, Ulrich; Huth, Markus; Tölle, Rainer; Klocke, Michael

    2015-09-01

    This study investigated the development of the microbial community during a long-term (337 days) anaerobic digestion of maize and sugar beet silage, two feedstocks that significantly differ in their chemical composition. For the characterization of the microbial dynamics, the community profiling method terminal restriction fragment length polymorphism (TRFLP) in combination with a cloning-sequencing approach was applied. Our results revealed a specific adaptation of the microbial community to the supplied feedstocks. Based on the high amount of complex compounds, the anaerobic conversion rate of maize silage was slightly lower compared with the sugar beet silage. It was demonstrated that members from the phylum Bacteroidetes are mainly involved in the degradation of low molecular weight substances such as sugar, ethanol and acetate, the main compounds of the sugar beet silage. It was further shown that species of the genus Methanosaeta are highly sensitive against sudden stress situations such as a strong decrease in the ammonium nitrogen (NH₄(+)-N) concentration or a drop of the pH value. In both cases, a functional compensation by members of the genera Methanoculleus and/or Methanosarcina was detected. However, the overall biomass conversion of both feedstocks proceeded efficiently as a steady state between acid production and consumption was recorded, which further resulted in an equal biogas yield. PMID:25712194

  2. Variation in the hindgut microbial communities of the Florida manatee, Trichechus manatus latirostris over winter in Crystal River, Florida.

    Science.gov (United States)

    Merson, Samuel D; Ouwerkerk, Diane; Gulino, Lisa-Maree; Klieve, Athol; Bonde, Robert K; Burgess, Elizabeth A; Lanyon, Janet M

    2014-03-01

    The Florida manatee, Trichechus manatus latirostris, is a hindgut-fermenting herbivore. In winter, manatees migrate to warm water overwintering sites where they undergo dietary shifts and may suffer from cold-induced stress. Given these seasonally induced changes in diet, the present study aimed to examine variation in the hindgut bacterial communities of wild manatees overwintering at Crystal River, west Florida. Faeces were sampled from 36 manatees of known sex and body size in early winter when manatees were newly arrived and then in mid-winter and late winter when diet had probably changed and environmental stress may have increased. Concentrations of faecal cortisol metabolite, an indicator of a stress response, were measured by enzyme immunoassay. Using 454-pyrosequencing, 2027 bacterial operational taxonomic units were identified in manatee faeces following amplicon pyrosequencing of the 16S rRNA gene V3/V4 region. Classified sequences were assigned to eight previously described bacterial phyla; only 0.36% of sequences could not be classified to phylum level. Five core phyla were identified in all samples. The majority (96.8%) of sequences were classified as Firmicutes (77.3 ± 11.1% of total sequences) or Bacteroidetes (19.5 ± 10.6%). Alpha-diversity measures trended towards higher diversity of hindgut microbiota in manatees in mid-winter compared to early and late winter. Beta-diversity measures, analysed through PERMANOVA, also indicated significant differences in bacterial communities based on the season. PMID:24215517

  3. A metagenomic snapshot of taxonomic and functional diversity in an alpine glacier cryoconite ecosystem

    Science.gov (United States)

    Edwards, Arwyn; Pachebat, Justin A.; Swain, Martin; Hegarty, Matt; Hodson, Andrew J.; Irvine-Fynn, Tristram D. L.; Rassner, Sara M. E.; Sattler, Birgit

    2013-09-01

    Cryoconite is a microbe-mineral aggregate which darkens the ice surface of glaciers. Microbial process and marker gene PCR-dependent measurements reveal active and diverse cryoconite microbial communities on polar glaciers. Here, we provide the first report of a cryoconite metagenome and culture-independent study of alpine cryoconite microbial diversity. We assembled 1.2 Gbp of metagenomic DNA sequenced using an Illumina HiScanSQ from cryoconite holes across the ablation zone of Rotmoosferner in the Austrian Alps. The metagenome revealed a bacterially-dominated community, with Proteobacteria (62% of bacterial-assigned contigs) and Bacteroidetes (14%) considerably more abundant than Cyanobacteria (2.5%). Streptophyte DNA dominated the eukaryotic metagenome. Functional genes linked to N, Fe, S and P cycling illustrated an acquisitive trend and a nitrogen cycle based upon efficient ammonia recycling. A comparison of 32 metagenome datasets revealed a similarity in functional profiles between the cryoconite and metagenomes characterized from other cold microbe-mineral aggregates. Overall, the metagenomic snapshot reveals the cryoconite ecosystem of this alpine glacier as dependent on scavenging carbon and nutrients from allochthonous sources, in particular mosses transported by wind from ice-marginal habitats, consistent with net heterotrophy indicated by productivity measurements. A transition from singular snapshots of cryoconite metagenomes to comparative analyses is advocated.

  4. Aureisphaera galaxeae gen. nov., sp. nov., a marine member of the family Flavobacteriaceae isolated from the hard coral Galaxea fascicularis.

    Science.gov (United States)

    Yoon, Jaewoo; Yasumoto-Hirose, Mina; Kasai, Hiroaki

    2015-06-01

    A novel Gram-stain negative, spherical, non-motile, strictly aerobic, heterotrophic, yellow pigmented bacterium, designated strain 04OKA003-7(T) was isolated from the hard coral Galaxea fascicularis L. collected at Akajima, Okinawa, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (92.9 %) to Vitellibacter aestuarii JC2436(T) and Aureitalea marina S1-66(T). The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain 04OKA003-7(T) were identified as iso-C15:0 and iso-C17:0 3-OH as defined by the MIDI system. The DNA G+C content was determined to be 41 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Aureisphaera galaxeae gen. nov., sp. nov. is proposed. The type strain of A. galaxeae is 04OKA003-7(T) (=KCTC 32993(T) = NBRC 110018(T)). PMID:25795444

  5. Identification of Bacterial Community Composition in Freshwater Aquaculture System Farming of Litopenaeus vannamei Reveals Distinct Temperature-Driven Patterns

    Directory of Open Access Journals (Sweden)

    Yuyi Tang

    2014-08-01

    Full Text Available Change in temperature is often a major environmental factor in triggering waterborne disease outbreaks. Previous research has revealed temporal and spatial patterns of bacterial population in several aquatic ecosystems. To date, very little information is available on aquaculture environment. Here, we assessed environmental temperature effects on bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei (FASFL. Water samples were collected over a one-year period, and aquatic bacteria were characterized by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE and 16S rDNA pyrosequencing. Resulting DGGE fingerprints revealed a specific and dynamic bacterial population structure with considerable variation over the seasonal change, suggesting that environmental temperature was a key driver of bacterial population in the FASFL. Pyrosequencing data further demonstrated substantial difference in bacterial community composition between the water at higher (WHT and at lower (WLT temperatures in the FASFL. Actinobacteria, Proteobacteria and Bacteroidetes were the highest abundant phyla in the FASFL, however, a large number of unclassified bacteria contributed the most to the observed variation in phylogenetic diversity. The WHT harbored remarkably higher diversity and richness in bacterial composition at genus and species levels when compared to the WLT. Some potential pathogenenic species were identified in both WHT and WLT, providing data in support of aquatic animal health management in the aquaculture industry.

  6. Biogeographic Patterns Between Bacterial Phyllosphere Communities of the Southern Magnolia (Magnolia grandiflora) in a Small Forest.

    Science.gov (United States)

    Stone, Bram W G; Jackson, Colin R

    2016-05-01

    The phyllosphere presents a unique system of discrete and easily replicable surfaces colonized primarily by bacteria. However, the biogeography of bacteria in the phyllosphere is little understood, especially at small to intermediate scales. Bacterial communities on the leaves of 91 southern magnolia (Magnolia grandiflora) trees 1-452 m apart in a small forest plot were analyzed and fragments of the 16S ribosomal RNA (rRNA) gene sequenced using the Illumina platform. Assemblages were dominated by members of the Alphaproteobacteria, Bacteroidetes, and Acidobacteria. Patterns in community composition were measured by both relative abundance (theta) and presence-absence (Jaccard) dissimilarity metrics. Distance-based Moran's eigenvector map analyses of the distance-decay relationship found a significant, positive relationship between each dissimilarity metric and significant eigenfunctions derived from geographic distance between trees, indicating trees that were closer together had more similar bacterial phyllosphere communities. Indirect gradient analyses revealed that several environmental parameters (canopy cover, tree elevation, and the slope and aspect of the ground beneath trees) were significantly related to multivariate ordination scores based on relative bacterial sequence abundances; however, these relationships were not significant when looking at the incidence of bacterial taxa. This suggests that bacterial growth and abundance in the phyllosphere is shaped by different assembly mechanisms than bacterial presence or absence. More broadly, this study demonstrates that the distance-decay relationship applies to phyllosphere communities at local scales, and that environmental parameters as well as neutral forces may both influence spatial patterns in the phyllosphere. PMID:26883131

  7. Partial Enteral Nutrition Preserves Elements of Gut Barrier Function, Including Innate Immunity, Intestinal Alkaline Phosphatase (IAP Level, and Intestinal Microbiota in Mice

    Directory of Open Access Journals (Sweden)

    Xiao Wan

    2015-08-01

    Full Text Available Lack of enteral nutrition (EN during parenteral nutrition (PN leads to higher incidence of infection because of gut barrier dysfunction. However, the effects of partial EN on intestina linnate immunity, intestinal alkaline phosphatase (IAP and microbiota remain unclear. The mice were randomized into six groups to receive either standard chow or isocaloric and isonitrogenous nutritional support with variable partial EN to PN ratios. Five days later, the mice were sacrificed and tissue samples were collected. Bacterial translocation, the levels of lysozyme, mucin 2 (MUC2, and IAP were analyzed. The composition of intestinal microbiota was analyzed by 16S rRNA pyrosequencing. Compared with chow, total parenteral nutrition (TPN resulted in a dysfunctional mucosal barrier, as evidenced by increased bacterial translocation (p < 0.05, loss of lysozyme, MUC2, and IAP, and changes in the gut microbiota (p < 0.001. Administration of 20% EN supplemented with PN significantly increased the concentrations of lysozyme, MUC2, IAP, and the mRNA levels of lysozyme and MUC2 (p < 0.001. The percentages of Bacteroidetes and Tenericutes were significantly lower in the 20% EN group than in the TPN group (p < 0.001. These changes were accompanied by maintained barrier function in bacterial culture (p < 0.05. Supplementation of PN with 20% EN preserves gut barrier function, by way of maintaining innate immunity, IAP and intestinal microbiota.

  8. Humpback whales harbour a combination of specific and variable skin bacteria.

    Science.gov (United States)

    Apprill, Amy; Mooney, T Aran; Lyman, Edward; Stimpert, Alison K; Rappé, Michael S

    2011-04-01

    Investigations of marine mammal skin-associated microbiota are limited to cultivation-based studies of lesioned individuals, resulting in a lack of understanding about the composition of 'normal' skin-associated microbial communities, their variation among individuals, and whether or not the microbial communities change with host health or environmental exposures. In this study, bacterial communities associated with the skin of 19 North Pacific humpback whales (Megaptera novaeangliae), including skin from three health-compromised individuals, were examined using small subunit ribosomal RNA gene-based culture-independent techniques. These analyses revealed that the skin-associated bacteria were significantly different from free-living bacterial communities in the surrounding seawater. Two novel groups within the Flavobacteriaceae family of the Bacteroidetes phylum were found to be associated with multiple whales, including a species within the Tenacibaculum genus that associated with 95% of the individuals. Statistical analyses revealed that a group of eight 'healthy' whales harboured similar microbial communities, while the health-compromised and other 'healthy' animals harboured communities that were unique to the specific animal. These results describe two components of the whale skin bacterial community: a specific and potentially co-evolved fraction, and a more variable microbial community fraction that may offer a diagnostic-type tool for investigating the health and life-related events of these endangered animals. PMID:23761254

  9. Bacterial communities in an ultrapure water containing storage tank of a power plant.

    Science.gov (United States)

    Bohus, Veronika; Kéki, Zsuzsa; Márialigeti, Károly; Baranyi, Krisztián; Patek, Gábor; Schunk, János; Tóth, Erika M

    2011-12-01

    Ultrapure waters (UPWs) containing low levels of organic and inorganic compounds provide extreme environment. On contrary to that microbes occur in such waters and form biofilms on surfaces, thus may induce corrosion processes in many industrial applications. In our study, refined saltless water (UPW) produced for the boiler of a Hungarian power plant was examined before and after storage (sampling the inlet [TKE] and outlet [TKU] waters of a storage tank) with cultivation and culture independent methods. Our results showed increased CFU and direct cell counts after the storage. Cultivation results showed the dominance of aerobic, chemoorganotrophic α-Proteobacteria in both samples. In case of TKU sample, a more complex bacterial community structure could be detected. The applied molecular method (T-RFLP) indicated the presence of a complex microbial community structure with changes in the taxon composition: while in the inlet water sample (TKE) α-Proteobacteria (Sphingomonas sp., Novosphingobium hassiacum) dominated, in the outlet water sample (TKU) the bacterial community shifted towards the dominance of α-Proteobacteria (Rhodoferax sp., Polynucleobacter sp., Sterolibacter sp.), CFB (Bacteroidetes, formerly Cytophaga-Flavobacterium-Bacteroides group) and Firmicutes. This shift to the direction of fermentative communities suggests that storage could help the development of communities with an increased tendency toward corrosion. PMID:22207294

  10. Two New Xylanases with Different Substrate Specificities from the Human Gut Bacterium Bacteroides intestinalis DSM 17393

    KAUST Repository

    Hong, Pei-Ying

    2014-01-24

    Xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium Bacteroides intestinalis DSM 17393 revealed the presence of two putative GH8 xylanases. In the current study, we demonstrate that the two genes encode enzymes that differ in activity. The xyn8A gene encodes an endoxylanase (Xyn8A), and rex8A encodes a reducing-end xylose-releasing exo-oligoxylanase (Rex8A). Xyn8A hydrolyzed both xylopentaose (X5) and xylohexaose (X6) to a mixture of xylobiose (X2) and xylotriose (X3), while Rex8A hydrolyzed X3 through X6 to a mixture of xylose (X1) and X2. Moreover, rex8A is located downstream of a GH3 gene (xyl3A) that was demonstrated to exhibit β-xylosidase activity and would be able to further hydrolyze X2 to X1. Mutational analyses of putative active site residues of both Xyn8A and Rex8A confirm their importance in catalysis by these enzymes. Recent genome sequences of gut bacteria reveal an increase in GH8 Rex enzymes, especially among the Bacteroidetes, indicating that these genes contribute to xylan utilization in the human gut.

  11. Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica

    Directory of Open Access Journals (Sweden)

    Neus eGarcias-Bonet

    2012-09-01

    Full Text Available Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known about the presence and importance of bacterial endophytes of marine plants. We conducted a survey of the endophytic bacterial community of the long-living Mediterranean marine angiosperm Posidonia oceanica in surface-sterilized tissues (roots, rhizomes and leaves by DGGE. A total of 26 Posidonia oceanica meadows around the Balearic Islands were sampled, and the band patterns obtained for each meadow were compared for the three sampled tissues. Endophytic bacterial sequences were detected in most of the samples analyzed. A total of 34 OTUs (Operational Taxonomic Units were detected. The main OTUs of endophytic bacteria present in P. oceanica tissues belonged primarily to Proteobacteria (α, γ and δ subclasses and Bacteroidetes. The OTUs found in roots significantly differed from those of rhizomes and leaves. Moreover, some OTUs were found to be associated to each type of tissue. Bipartite network analysis revealed differences in the bacterial endophyte communities present on different islands. The results of this study provide a pioneering step toward the characterization of the endophytic bacterial community associated with tissues of a marine angiosperm and reveal the presence of bacterial endophytes that differed among locations and tissue types.

  12. Spatiotemporal development of the bacterial community in a tubular longitudinal microbial fuel cell

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jung Rae; Premier, Giuliano C. [Glamorgan Univ., Pontypridd (United Kingdom). Faculty of Advnaced Technology; Beecroft, Nelli J.; Avignone-Rossa, Claudio [Surrey Univ., Guildford (United Kingdom). Microbial Sciences; Varcoe, John R.; Slade, Robert C.T. [Surrey Univ., Guildford (United Kingdom). Chemical Sciences; Dinsdale, Richard M.; Guwy, Alan J. [Glamorgan Univ., Pontypridd (United Kingdom). Faculty of Health, Sport and Science; Thumser, Alfred [Surrey Univ., Guildford (United Kingdom). Biochemical Sciences

    2011-05-15

    The spatiotemporal development of a bacterial community in an exoelectrogenic biofilm was investigated in sucrose-fed longitudinal tubular microbial fuel cell reactors, consisting of two serially connected modules. The proportional changes in the microbial community composition were assessed by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) and DNA sequencing in order to relate them to the performance and stability of the bioelectrochemical system. The reproducibility of duplicated reactors, evaluated by cluster analysis and Jaccard's coefficient, shows 80-90% similarity in species composition. Biofilm development through fed-batch start-up and subsequent stable continuous operation results in a population shift from {gamma}-Proteobacteria- and Bacteroidetes- to Firmicutes-dominated communities, with other diverse species present at much lower relative proportions. DGGE patterns were analysed by range-weighted richness (Rr) and Pareto-Lorenz evenness distribution curves to investigate the evolution of the bacterial community. The first modules shifted from dominance by species closely related to Bacteroides graminisolvens, Raoultella ornithinolytica and Klebsiella sp. BM21 at the start of continuous-mode operation to a community dominated by Paludibacter propionicigenes-, Lactococcus sp.-, Pantoea agglomerans- and Klebsiella oxytoca-related species with stable power generation (6.0 W/m{sup 3}) at day 97. Operational strategies that consider the dynamics of the population will provide useful parameters for evaluating system performance in the practical application of microbial fuel cells. (orig.)

  13. HORSE SPECIES SYMPOSIUM: Canine intestinal microbiology and metagenomics: From phylogeny to function.

    Science.gov (United States)

    Guard, B C; Suchodolski, J S

    2016-06-01

    Recent molecular studies have revealed a complex microbiota in the dog intestine. Convincing evidence has been reported linking changes in microbial communities to acute and chronic gastrointestinal inflammation, especially in canine inflammatory bowel disease (IBD). The most common microbial changes observed in intestinal inflammation are decreases in the bacterial phyla Firmicutes (i.e., Lachnospiraceae, Ruminococcaceae, and ) and Bacteroidetes, with concurrent increases in Proteobacteria (i.e., ). Due to the important role of microbial-derived metabolites for host health, it is important to elucidate the metabolic consequences of gastrointestinal dysbiosis and physiological pathways implicated in specific disease phenotypes. Metagenomic studies have used shotgun sequencing of DNA as well as phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) to characterize functional changes in the bacterial metagenome in gastrointestinal disease. Furthermore, wide-scale and untargeted measurements of metabolic products derived by the host and the microbiota in intestinal samples allow a better understanding of the functional alterations that occur in gastrointestinal disease. For example, changes in bile acid metabolism and tryptophan catabolism recently have been reported in humans and dogs. Also, metabolites associated with the pentose phosphate pathway were significantly altered in chronic gastrointestinal inflammation and indicate the presence of oxidative stress in dogs with IBD. This review focuses on the advancements made in canine metagenomics and metabolomics and their implications in understanding gastrointestinal disease as well as the development of better treatment approaches. PMID:27285902

  14. The outer-membrane export signal of Porphyromonas gingivalis type IX secretion system (T9SS) is a conserved C-terminal β-sandwich domain.

    Science.gov (United States)

    de Diego, Iñaki; Ksiazek, Miroslaw; Mizgalska, Danuta; Koneru, Lahari; Golik, Przemyslaw; Szmigielski, Borys; Nowak, Magdalena; Nowakowska, Zuzanna; Potempa, Barbara; Houston, John A; Enghild, Jan J; Thøgersen, Ida B; Gao, Jinlong; Kwan, Ann H; Trewhella, Jill; Dubin, Grzegorz; Gomis-Rüth, F Xavier; Nguyen, Ky-Anh; Potempa, Jan

    2016-01-01

    In the recently characterized Type IX Secretion System (T9SS), the conserved C-terminal domain (CTD) in secreted proteins functions as an outer membrane translocation signal for export of virulence factors to the cell surface in the Gram-negative Bacteroidetes phylum. In the periodontal pathogen Porphyromonas gingivalis, the CTD is cleaved off by PorU sortase in a sequence-independent manner, and anionic lipopolysaccharide (A-LPS) is attached to many translocated proteins, thus anchoring them to the bacterial surface. Here, we solved the atomic structure of the CTD of gingipain B (RgpB) from P. gingivalis, alone and together with a preceding immunoglobulin-superfamily domain (IgSF). The CTD was found to possess a typical Ig-like fold encompassing seven antiparallel β-strands organized in two β-sheets, packed into a β-sandwich structure that can spontaneously dimerise through C-terminal strand swapping. Small angle X-ray scattering (SAXS) revealed no fixed orientation of the CTD with respect to the IgSF. By introducing insertion or substitution of residues within the inter-domain linker in the native protein, we were able to show that despite the region being unstructured, it nevertheless is resistant to general proteolysis. These data suggest structural motifs located in the two adjacent Ig-like domains dictate the processing of CTDs by the T9SS secretion pathway. PMID:27005013

  15. Microbial community structure and nitrogenase gene diversity of sediment from a deep-sea hydrothermal vent field on the Southwest Indian Ridge

    Institute of Scientific and Technical Information of China (English)

    WU Yuehong; CAO Yi; WANG Chunsheng; WU Min; AHARON Oren; XU Xuewei

    2014-01-01

    A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase chain reaction (PCR) amplification of the 16S rRNA and nifH genes. Within the Archaea, the dominant clones were from marine benthic group E (MBGE) and marine group I (MGI) belonging to the phyla Euryarchaeota and Thaumarchaeota, respectively. More than half of the bacterial clones belonged to the Proteobacteria, and most fell within the Gammaproteobacteria. No epsilonproteobacterial sequence was observed. Additional phyla were detected including the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3 and TM6, confirming their existence in hydrothermal vent environments. The detection of nifH gene suggests that biological nitrogen fixation may occur in the hydrothermal vent field of the South-west Indian Ridge. Phylogenetic analysis indicated that only Clusters I and III NifH were present. This is consistent with the phylogenetic analysis of the microbial 16S rRNA genes, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.

  16. Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge.

    Science.gov (United States)

    Forget, Nathalie L; Kim Juniper, S

    2013-04-01

    We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobacteria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus-Thermus. Statistically significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, available energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities. PMID:23401293

  17. Comparative analysis of bacterial community and antibiotic-resistant strains in different developmental stages of the housefly (Musca domestica).

    Science.gov (United States)

    Wei, Ting; Hu, Jun; Miyanaga, Kazuhiko; Tanji, Yasunori

    2013-02-01

    The housefly (Musca domestica) is an important host for a variety of bacteria, including some pathogenic and antibiotic-resistant strains. To further investigate the relationship between the housefly and the bacteria it harbors, it is necessary to understand the fate of microorganisms during the larval metamorphosis. The major bacterial communities in three developmental stages of the housefly (maggot, pupa, and adult fly) were investigated by a culture-independent method, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of 16S rRNA genes. The bacteria that were identified using DGGE analysis spanned phyla Proteobacteria, Firmicutes, and Bacteroidetes. Changes in the predominant genera were observed during the housefly development. Bacteroides, Koukoulia, and Schineria were detected in maggots, Neisseria in pupae, and Macrococcus, Lactococcus, and Kurthia in adult flies. Antibiotic-resistant bacteria were screened using a selective medium and tested for antibiotic susceptibility. Most resistant isolates from maggots and pupae were classified as Proteus spp., while those from adult flies were much more diverse and spanned 12 genera. Among 20 tested strains across the three stages, 18 were resistant to at least two antibiotics. Overall, we demonstrated that there are changes in the major bacterial communities and antibiotic-resistant strains as the housefly develops. PMID:22526786

  18. Phenylketonuria and Gut Microbiota: A Controlled Study Based on Next-Generation Sequencing

    Science.gov (United States)

    Pinheiro de Oliveira, Felipe; Mendes, Roberta Hack; Dobbler, Priscila Thiago; Mai, Volker; Pylro, Victor Salter; Waugh, Sheldon G; Vairo, Filippo; Refosco, Lilia Farret; Schwartz, Ida Vanessa Doederlein

    2016-01-01

    Phenylketonuria (PKU) is an inborn error of metabolism associated with high blood levels of phenylalanine (Phe). A Phe-restricted diet supplemented with L-amino acids is the main treatment strategy for this disease; if started early, most neurological abnormalities can be prevented. The healthy human gut contains trillions of commensal bacteria, often referred to as the gut microbiota. The composition of the gut microbiota is known to be modulated by environmental factors, including diet. In this study, we compared the gut microbiota of 8 PKU patients on Phe-restricted dietary treatment with that of 10 healthy individuals. The microbiota were characterized by 16S rRNA sequencing using the Ion Torrent™ platform. The most dominant phyla detected in both groups were Bacteroidetes and Firmicutes. PKU patients showed reduced abundance of the Clostridiaceae, Erysipelotrichaceae, and Lachnospiraceae families, Clostridiales class, Coprococcus, Dorea, Lachnospira, Odoribacter, Ruminococcus and Veillonella genera, and enrichment of Prevotella, Akkermansia, and Peptostreptococcaceae. Microbial function prediction suggested significant differences in starch/glucose and amino acid metabolism between PKU patients and controls. Together, our results suggest the presence of distinct taxonomic groups within the gut microbiome of PKU patients, which may be modulated by their plasma Phe concentration. Whether our findings represent an effect of the disease itself, or a consequence of the modified diet is unclear. PMID:27336782

  19. Cellulose degrading bacteria isolated from industrial samples and the gut of native insects from Northwest of Argentina.

    Science.gov (United States)

    Manfredi, Adriana P; Perotti, Nora I; Martínez, María A

    2015-12-01

    The raw materials used to produce bioethanol mostly are food crops, which has led to conflicts on food security. It is, therefore, recommended the gradual replacement for second generation substrates such as lignocellulosic materials. Herein, cellulolytic bacteria were isolated from the gut content of native larvae from Lepidoptera, Coleoptera, and adults of Isoptera. Few environmental samples from the pulp and paper feedstock were also assessed. A total of 233 isolates were obtained using enrichment cultures and classic criteria. Interestingly, several halo-forming colonies were found to be bacterial consortia that presented difficulties to take apart the microbial members. Those pure isolates which hydrolyzed cellulose in larger extend (45 strains) were selected and identified by means of 16S rRNA sequence analysis. Firmicutes was the prevalent phylum (62.2%) being Bacillus spp. the most frequent genus, while Paenibacillus, Brevibacillus, Cohnella, and Staphylococcus species were less frequent. The phylum Actinobacteria (6.7%) was represented by isolates related to Agromyces spp. and Microbacterium spp. Regarding Gram-negative bacteria (31.1%), the more depicted genus was Pseudomonas spp., and members of Achromobacter spp., Enterobacter spp., and Bacteroidetes phylum were also selected. These native bacterial strains are expected to enlarge the cellulolytic toolbox for efficient biomass deconstruction. PMID:26370071

  20. Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau

    Science.gov (United States)

    Zhang, Kaoping; Shi, Yu; Jing, Xin; He, Jin-Sheng; Sun, Ruibo; Yang, Yunfeng; Shade, Ashley; Chu, Haiyan

    2016-01-01

    Soil microbial communities are influenced by climate change drivers such as warming and altered precipitation. These changes create abiotic stresses, including desiccation and nutrient limitation, which act on microbes. However, our understanding of the responses of microbial communities to co-occurring climate change drivers is limited. We surveyed soil bacterial and fungal diversity and composition after a 1-year warming and altered precipitation manipulation in the Tibetan plateau alpine grassland. In isolation, warming and decreased precipitation treatments each had no significant effects on soil bacterial community structure; however, in combination of both treatments altered bacterial community structure (p = 0.03). The main effect of altered precipitation specifically impacted the relative abundances of Bacteroidetes and Gammaproteobacteria compared to the control, while the main effect of warming impacted the relative abundance of Betaproteobacteria. In contrast, the fungal community had no significant response to the treatments after 1-year. Using structural equation modeling (SEM), we found bacterial community composition was positively related to soil moisture. Our results indicate that short-term climate change could cause changes in soil bacterial community through taxonomic shifts. Our work provides new insights into immediate soil microbial responses to short-term stressors acting on an ecosystem that is particularly sensitive to global climate change. PMID:27446064

  1. Exposing to cadmium stress cause profound toxic effect on microbiota of the mice intestinal tract.

    Directory of Open Access Journals (Sweden)

    Yehao Liu

    Full Text Available Cadmium (Cd, one of the heavy metals, is an important environmental pollutant and a potent toxicant to organism. It poses a severe threat to the growth of the organism, and also has been recognized as a human carcinogen. However, the toxicity of cadmium and its influences on microbiota in mammal's intestine are still unclear. In our experiment, the changes of intestinal microbiota in two groups of mice were investigated, which were supplied with 20 and 100 mg kg(-1 cadmium chloride respectively for 3 weeks. The control group was treated with water free from cadmium chloride only. This study demonstrated that Cd accumulated in some tissues of mice after Cd administration and the gut barrier was impaired. Cd exposure also significantly elevated the colonic level of TNF-α. On the other hand, Cd-treatment could slow down the growth of gut microbiota and reduced the abundance of total intestinal bacteria of the mice. Among them, the growth of Bacteroidetes was significantly suppressed while Firmicutes growth was not. The probiotics including Lactobacillus and Bifidobacterium were notably inhibited. We also observed that the copies of key genes involved in the metabolism of carbohydrates to short-chain fatty acids (SCFAs were lower in Cd-treated groups than control. As a result, the levels of short-chain fatty acids in colonic decreased significantly. In summary, this study provides valuable insight into the effects of Cd intake on mice gut microbiota.

  2. Arabinogalactan and fructo-oligosaccharides have a different fermentation profile in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME ®).

    Science.gov (United States)

    Terpend, Kathleen; Possemiers, Sam; Daguet, David; Marzorati, Massimo

    2013-08-01

    Current prebiotics, such as fructo-oligosaccharides (FOS), are limited in their persistence in the distal colon and are predominantly fermented in the proximal colon. In order to identify a potential alternative, the differences in the fermentation profile of arabinogalactan (AG) and FOS have been assessed in the Simulator of the Human Intestinal Microbial Ecosystem. The effect of each product on the composition and activity of the microbial community was analysed during a 3-week treatment period at a dose of 5 g day(-1). While FOS indeed was mainly fermented in the simulated proximal colon, AG was still available for fermentation in the simulated distal colon as shown by pH profiles, size exclusion chromatography and analyses of specific enzymatic activities. As a consequence, the main effect of the products (increase in propionate and butyrate and decrease in ammonium production) occurred in different intestinal areas. DGGE and qPCR analyses confirmed that the main modulation of the microbiota by the two products occurred in different areas of the gut. AG was associated with a statistically significant increase in the concentration of total bacteria, Bacteroidetes, Faecalibacterium prausnitzii, a delayed bifidogenic effect and a decrease of the pathogenic Clostridium perfringens. FOS led to a strong lactobacillogenic effect. PMID:23864575

  3. Metagenomic insights into the effects of fructo-oligosaccharides (FOS) on the composition of fecal microbiota in mice.

    Science.gov (United States)

    Mao, Bingyong; Li, Dongyao; Zhao, Jianxin; Liu, Xiaoming; Gu, Zhennan; Chen, Yong Q; Zhang, Hao; Chen, Wei

    2015-01-28

    Fructo-oligosaccharides (FOS) are usually regarded as a type of prebiotic, favorably stimulating the growth of bifidobacteria and lactobacilli. However, they are not the specific substrates for these target species, and other bacteria, such as Streptococcus, Escherichia, and Clostridium, have been shown to be able to utilize FOS. Previous studies have mainly investigated only a few bacteria groups, and few reports analyzed the global effects of FOS on intestinal microbial communities. In this study the effects of FOS on gut bacteria in mice were investigated through a 16S rRNA metagenomic analysis. In the FOS-low group, the abundance of Actinobacteria significantly increased and that of Bacteroidetes decreased after FOS diet (5%) for 3 weeks. In the FOS-high group, Enterococcus was promoted and levels of Bifidobacterium and Olsenella both notably increased after FOS diet (25%) and the microbiota tended to revert to initial structure 2 weeks after FOS treatment ceased. The most striking observation was that Olsenella became a dominant genus comparable with Bifidobacterium after FOS treatment, and one strain of Olsenella, isolated from mice feces, was confirmed, for the first time, to be capable of using FOS. The results indicated that metagenomic analysis was helpful to reveal the FOS effects on the global composition of gut communities and new target for future studies. PMID:25598242

  4. Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke

    Science.gov (United States)

    Yang, Hui; Hu, Jinxiang; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-01-01

    The interaction between roots and bacterial communities in halophytic species is poorly understood. Here, we used Jerusalem artichoke cultivar Nanyu 1 (NY-1) to characterise root distribution patterns and determine diversity and abundance of bacteria in the rhizosphere soil under variable salinity. Root growth was not inhibited within the salinity range 1.2 to 1.9 g salt/kg, but roots were mainly confined to 0–20 cm soil layer vertically and 0–30 cm horizontally from the plant centre. Root concentrations of K+, Na+, Mg2+ and particularly Ca2+ were relatively high under salinity stress. High salinity stress decreased soil invertase and catalase activity. Using a next-generation, Illumina-based sequencing approach, we determined higher diversity of bacteria in the rhizosphere soil at high than low salinity. More than 15,500 valid reads were obtained, and Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria predominated in all samples, accounting for >80% of the reads. On a genus level, 636 genera were common to the low and high salinity treatments at 0–5 cm and 5–10 cm depth. The abundance of Steroidobacter and Sphingomonas was significantly decreased by increasing salinity. Higher Shannon and Chao 1 indices with increasing severity of salt stress indicated that high salt stress increased diversity in the bacterial communities. PMID:26852800

  5. A three-scale analysis of bacterial communities involved in rocks colonization and soil formation in high mountain environments.

    Science.gov (United States)

    Esposito, Alfonso; Ciccazzo, Sonia; Borruso, Luigimaria; Zerbe, Stefan; Daffonchio, Daniele; Brusetti, Lorenzo

    2013-10-01

    Alpha and beta diversities of the bacterial communities growing on rock surfaces, proto-soils, riparian sediments, lichen thalli, and water springs biofilms in a glacier foreland were studied. We used three molecular based techniques to allow a deeper investigation at different taxonomic resolutions: denaturing gradient gel electrophoresis, length heterogeneity-PCR, and automated ribosomal intergenic spacer analysis. Bacterial communities were mainly composed of Acidobacteria, Proteobacteria, and Cyanobacteria with distinct variations among sites. Proteobacteria were more represented in sediments, biofilms, and lichens; Acidobacteria were mostly found in proto-soils; and Cyanobacteria on rocks. Firmicutes and Bacteroidetes were mainly found in biofilms. UniFrac P values confirmed a significant difference among different matrices. Significant differences (P < 0.001) in beta diversity were observed among the different matrices at the genus-species level, except for lichens and rocks which shared a more similar community structure, while at deep taxonomic resolution two distinct bacterial communities between lichens and rocks were found. PMID:23712376

  6. The effect of carbon nanotubes and titanium dioxide incorporated in PDMS on biofilm community composition and subsequent mussel plantigrade settlement.

    Science.gov (United States)

    Yang, Jin-Long; Li, Yi-Feng; Guo, Xing-Pan; Liang, Xiao; Xu, Yue-Feng; Ding, De-Wen; Bao, Wei-Yang; Dobretsov, Sergey

    2016-08-01

    This study investigated the effect of carbon nanotubes (CNTs) and titanium dioxide (TiO2) incorporated in PDMS on biofilm formation and plantigrade settlement of Mytilus coruscus. TiO2 increased bacterial density, and CNTs also increased bacterial density but reduced diatom density in biofilms after 28 days. Further analysis was conducted between bacterial communities on glass, PDMS, CNTs (0.5 wt%) and TiO2 (7.5 wt%). ANOSIM analysis revealed significant differences (R > 0.9) between seven, 14, 21 and 28 day-old bacterial communities. MiSeq sequencing showed that CNTs and TiO2 impacted the composition of 28 day-old bacterial communities by increasing the abundance of Proteobacteria and decreasing the abundance of Bacteroidetes. The maximum decreased settlement rate in 28 day-old biofilms on CNTs and TiO2 was > 50% in comparison to those on glass and PDMS. Thus, CNTs and TiO2 incorporated in PDMS altered the biomass and community composition of biofilms, and subsequently decreased mussel settlement. PMID:27348759

  7. Monitoring bacterial diversity of the marine sponge Ircinia strobilina upon transfer into aquaculture.

    Science.gov (United States)

    Mohamed, Naglaa M; Rao, Venkateswara; Hamann, Mark T; Kelly, Michelle; Hill, Russell T

    2008-07-01

    Marine sponges in the genus Ircinia are known to be good sources of secondary metabolites with biological activities. A major obstacle in the development of sponge-derived metabolites is the difficulty in ensuring an economic, sustainable supply of the metabolites. A promising strategy is the ex situ culture of sponges in closed or semiclosed aquaculture systems. In this study, the marine sponge Ircinia strobilina (order Dictyoceratida: family Irciniidae) was collected from the wild and maintained for a year in a recirculating aquaculture system. Microbiological and molecular community analyses were performed on freshly collected sponges and sponges maintained in aquaculture for 3 months and 9 months. Chemical analyses were performed on wild collected sponges and individuals maintained in aquaculture for 3 months and 1 year. Denaturing gradient gel electrophoresis was used to assess the complexity of and to monitor changes in the microbial communities associated with I. strobilina. Culture-based and molecular techniques showed an increase in the Bacteroidetes and Alpha- and Gammaproteobacteria components of the bacterial community in aquaculture. Populations affiliated with Beta- and Deltaproteobacteria, Clostridia, and Planctomycetes emerged in sponges maintained in aquaculture. The diversity of bacterial communities increased upon transfer into aquaculture. PMID:18469126

  8. Quantitative role of shrimp fecal bacteria in organic matter fluxes in a recirculating shrimp aquaculture system.

    Science.gov (United States)

    Beardsley, Christine; Moss, Shaun; Malfatti, Francesca; Azam, Farooq

    2011-07-01

    Microorganisms play integral roles in the cycling of carbon (C) and nitrogen (N) in recirculating aquaculture systems (RAS) for fish and shellfish production. We quantified the pathways of shrimp fecal bacterial activities and their role in C- and N-flux partitioning relevant to culturing Pacific white shrimp, Penaeus (Litopenaeus) vannamei, in RAS. Freshly produced feces from P. vannamei contained 0.6-7 × 10(10) bacteria g(-1) dry wt belonging to Bacteroidetes (7%), Alphaproteobacteria (4%), and, within the Gammaproteobacteria, almost exclusively to the genus Vibrio (61%). Because of partial disintegration of the feces (up to 27% within 12 h), the experimental seawater became inoculated with fecal bacteria. Bacteria grew rapidly in the feces and in the seawater, and exhibited high levels of aminopeptidase, chitinase, chitobiase, alkaline phosphatase, α- and β-glucosidase, and lipase activities. Moreover, fecal bacteria enriched the protein content of the feces within 12 h, potentially enriching the feces for the coprophagous shrimp. The bacterial turnover time was much faster in feces (1-10 h) than in mature RAS water (350 h). Thus, shrimp fecal bacteria not only inoculate RAS water but also contribute to bacterial abundance and productivity, and regulate system processes important for shrimp health. PMID:21426366

  9. Characterizing the structural diversity of a bacterial community associated with filter materials in recirculating aquaculture systems of Scortum barcoo.

    Science.gov (United States)

    Zhu, Peng; Ye, Yangfang; Pei, Fangfang; Lu, Kaihong

    2012-03-01

    The bacterial community structure associated with filter materials in the recirculating aquaculture system of Scortum barcoo was investigated using the 16S rRNA gene clone library method. Preliminary results showed that the clone library constructed from the initial operation condition was characterized by 31 taxa of bacteria belonging to eight phyla including Proteobacteria, Acidobacteria, Firmicutes, Fusobacteria, Sphingobacteria, Bacteroidetes, Verrucomicrobiae, and Actinobacteria. There were 14 taxa of bacteria belonging to four phyla including Proteobacteria, Acidobacteria, Planctomycetacia, and Nitrospirae from the stable operation condition where the water quality was well maintained. Nitrospirae was only found under the stable operation condition in this study. Our results further indicated that Nitrospira was dominated by members of the Nitrospira sp. lineages, with a minor fraction related to Nitrospira moscoviensis and an unknown Nitrospira cluster. These great differences of both diversity and composition between two operation conditions suggested that the composition of the microbial community varied with the degree of water quality in the recirculating aquaculture system of S. barcoo. PMID:22339297

  10. [Nitrate removal from recirculating aquaculture system using polyhydroxybutyrate-co-hydroxyvalerate as carbon source ].

    Science.gov (United States)

    Zhang, Lanhe; Liu, Lili; Qiu, Tianlei; Gao, Min; Han, Meilin; Yuan, Ding; Wang, Xuming

    2014-09-01

    [ OBJECTIVE] Polyhydroxybutyrate-co-hydroxyvalerate (PHBV) was used as solid carbon source and biofilm carrier to remove nitrate from recirculating aquaculture system (RAS). Dynamics of microbial community structure in biofilm coating on carbon source packed into denitrification reactor were investigated. [METHODS] Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the microbial community in biofilm from denitrifiation reactor. Bacteria degrading PHBV were isolated from the reactor using pure culture method. [RESULTS] Nitrate decreased remarkably in the RAS connected with dentrification reactor. In contrast, Nitrate increased continuously in the conventional RAS without dentrification reactor. According to the phylogenetic analysis, the microbes in the biofilm samples from denitrification reactor were divided into Proteobacteria ( p-proteobacteria, γ-proteobacteria and δ- proteobacteria) , Firmicutes and Bacteroidetes. The major advantageous populations were Acidovorax and Bacillus in the 40-day reactor. The advantageous populat