WorldWideScience

Sample records for microbiome reveals forage

  1. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases.

    Science.gov (United States)

    Brulc, Jennifer M; Antonopoulos, Dionysios A; Miller, Margret E Berg; Wilson, Melissa K; Yannarell, Anthony C; Dinsdale, Elizabeth A; Edwards, Robert E; Frank, Edward D; Emerson, Joanne B; Wacklin, Pirjo; Coutinho, Pedro M; Henrissat, Bernard; Nelson, Karen E; White, Bryan A

    2009-02-10

    The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly sampled pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid sample (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood).

  2. Mucin glycan foraging in the human gut microbiome

    Science.gov (United States)

    Tailford, Louise E.; Crost, Emmanuelle H.; Kavanaugh, Devon; Juge, Nathalie

    2015-01-01

    The availability of host and dietary carbohydrates in the gastrointestinal (GI) tract plays a key role in shaping the structure-function of the microbiota. In particular, some gut bacteria have the ability to forage on glycans provided by the mucus layer covering the GI tract. The O-glycan structures present in mucin are diverse and complex, consisting predominantly of core 1-4 mucin-type O-glycans containing α- and β- linked N-acetyl-galactosamine, galactose and N-acetyl-glucosamine. These core structures are further elongated and frequently modified by fucose and sialic acid sugar residues via α1,2/3/4 and α2,3/6 linkages, respectively. The ability to metabolize these mucin O-linked oligosaccharides is likely to be a key factor in determining which bacterial species colonize the mucosal surface. Due to their proximity to the immune system, mucin-degrading bacteria are in a prime location to influence the host response. However, despite the growing number of bacterial genome sequences available from mucin degraders, our knowledge on the structural requirements for mucin degradation by gut bacteria remains fragmented. This is largely due to the limited number of functionally characterized enzymes and the lack of studies correlating the specificity of these enzymes with the ability of the strain to degrade and utilize mucin and mucin glycans. This review focuses on recent findings unraveling the molecular strategies used by mucin-degrading bacteria to utilize host glycans, adapt to the mucosal environment, and influence human health. PMID:25852737

  3. Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge.

    Science.gov (United States)

    Petri, Renee M; Schwaiger, Tyler; Penner, Greg B; Beauchemin, Karen A; Forster, Robert J; McKinnon, John J; McAllister, Tim A

    2013-01-01

    This study investigated the effect of diet and host on the rumen bacterial microbiome and the impact of an acidotic challenge on its composition. Using parallel pyrosequencing of the V3 hypervariable region of 16S rRNA gene, solid and liquid associated bacterial communities of 8 heifers were profiled. Heifers were exclusively fed forage, before being transitioned to a concentrate diet, subjected to an acidotic challenge and allowed to recover. Samples of rumen digesta were collected when heifers were fed forage, mixed forage, high grain, during challenge (4 h and 12 h) and recovery. A total of 560,994 high-quality bacterial sequences were obtained from the solid and liquid digesta. Using cluster analysis, prominent bacterial populations differed (P≤0.10) in solid and liquid fractions between forage and grain diets. Differences among hosts and diets were not revealed by DGGE, but real time qPCR showed that several bacteria taxon were impacted by changes in diet, with the exception of Streptococcus bovis. Analysis of the core rumen microbiome identified 32 OTU's representing 10 distinct bacterial taxa including Bacteroidetes (32.8%), Firmicutes (43.2%) and Proteobacteria (14.3%). Diversity of OTUs was highest with forage with 38 unique OTUs identified as compared to only 11 with the high grain diet. Comparison of the microbial profiles of clincial vs. subclinical acidotic heifers found a increases in the relative abundances of Acetitomaculum, Lactobacillus, Prevotella, and Streptococcus. Increases in Streptococcus and Lactobacillus likely reflect the tolerance of these species to low pH and their ability to proliferate on surplus fermentable carbohydrate. The acetogen, Acetitomaculum may thereforeplay a role in the conversion of lactate to acetate in acidotic animals. Further profiling of the bacterial populations associated with subclinical and clinical acidosis could establish a microbial fingerprint for these disorders and provide insight into whether there are

  4. Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis.

    Science.gov (United States)

    Wen, Chengping; Zheng, Zhijun; Shao, Tiejuan; Liu, Lin; Xie, Zhijun; Le Chatelier, Emmanuelle; He, Zhixing; Zhong, Wendi; Fan, Yongsheng; Zhang, Linshuang; Li, Haichang; Wu, Chunyan; Hu, Changfeng; Xu, Qian; Zhou, Jia; Cai, Shunfeng; Wang, Dawei; Huang, Yun; Breban, Maxime; Qin, Nan; Ehrlich, Stanislav Dusko

    2017-07-27

    The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. To investigate the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DNA from 211 Chinese individuals. A total of 23,709 genes and 12 metagenomic species were shown to be differentially abundant between ankylosing spondylitis patients and healthy controls. Patients were characterized by a form of gut microbial dysbiosis that is more prominent than previously reported cases with inflammatory bowel disease. Specifically, the ankylosing spondylitis patients demonstrated increases in the abundance of Prevotella melaninogenica, Prevotella copri, and Prevotella sp. C561 and decreases in Bacteroides spp. It is noteworthy that the Bifidobacterium genus, which is commonly used in probiotics, accumulated in the ankylosing spondylitis patients. Diagnostic algorithms were established using a subset of these gut microbial biomarkers. Alterations of the gut microbiome are associated with development of ankylosing spondylitis. Our data suggest biomarkers identified in this study might participate in the pathogenesis or development process of ankylosing spondylitis, providing new leads for the development of new diagnostic tools and potential treatments.

  5. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

    Science.gov (United States)

    Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

    2016-01-12

    Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of

  6. Foraging

    NARCIS (Netherlands)

    Ydenberg, R.C.; Prins, H.H.T.

    2012-01-01

    This chapter describes the role played by behavioural adjustments to foraging behaviour in accommodating rapid environmental change. It looks into the adjustments of foraging behaviour to predation danger as a result of changes in the type and array of food available. It investigates the effects of

  7. Individual foraging strategies reveal niche overlap between endangered galapagos pinnipeds.

    Directory of Open Access Journals (Sweden)

    Stella Villegas-Amtmann

    Full Text Available Most competition studies between species are conducted from a population-level approach. Few studies have examined inter-specific competition in conjunction with intra-specific competition, with an individual-based approach. To our knowledge, none has been conducted on marine top predators. Sympatric Galapagos fur seals (Arctocephalus galapagoensis and sea lions (Zalophus wollebaeki share similar geographic habitats and potentially compete. We studied their foraging niche overlap at Cabo Douglas, Fernandina Island from simultaneously collected dive and movement data to examine spatial and temporal inter- and intra-specific competition. Sea lions exhibited 3 foraging strategies (shallow, intermediate and deep indicating intra-specific competition. Fur seals exhibited one foraging strategy, diving predominantly at night, between 0-80 m depth and mostly at 19-22 h. Most sea lion dives also occurred at night (63%, between 0-40 m, within fur seals' diving depth range. 34% of sea lions night dives occurred at 19-22 h, when fur seals dived the most, but most of them occurred at dawn and dusk, when fur seals exhibited the least amount of dives. Fur seals and sea lions foraging behavior overlapped at 19 and 21 h between 0-30 m depths. Sea lions from the deep diving strategy exhibited the greatest foraging overlap with fur seals, in time (19 h, depth during overlapping time (21-24 m, and foraging range (37.7%. Fur seals foraging range was larger. Cabo Douglas northwest coastal area, region of highest diving density, is a foraging "hot spot" for both species. Fur seals and sea lions foraging niche overlap occurred, but segregation also occurred; fur seals primarily dived at night, while sea lions exhibited night and day diving. Both species exploited depths and areas exclusive to their species. Niche breadth generally increases with environmental uncertainty and decreased productivity. Potential competition between these species could be greater during

  8. Isotope analysis reveals foraging area dichotomy for atlantic leatherback turtles.

    Directory of Open Access Journals (Sweden)

    Stéphane Caut

    Full Text Available BACKGROUND: The leatherback turtle (Dermochelys coriacea has undergone a dramatic decline over the last 25 years, and this is believed to be primarily the result of mortality associated with fisheries bycatch followed by egg and nesting female harvest. Atlantic leatherback turtles undertake long migrations across ocean basins from subtropical and tropical nesting beaches to productive frontal areas. Migration between two nesting seasons can last 2 or 3 years, a time period termed the remigration interval (RI. Recent satellite transmitter data revealed that Atlantic leatherbacks follow two major dispersion patterns after nesting season, through the North Gulf Stream area or more eastward across the North Equatorial Current. However, information on the whole RI is lacking, precluding the accurate identification of feeding areas where conservation measures may need to be applied. METHODOLOGY/PRINCIPAL FINDINGS: Using stable isotopes as dietary tracers we determined the characteristics of feeding grounds of leatherback females nesting in French Guiana. During migration, 3-year RI females differed from 2-year RI females in their isotope values, implying differences in their choice of feeding habitats (offshore vs. more coastal and foraging latitude (North Atlantic vs. West African coasts, respectively. Egg-yolk and blood isotope values are correlated in nesting females, indicating that egg analysis is a useful tool for assessing isotope values in these turtles, including adults when not available. CONCLUSIONS/SIGNIFICANCE: Our results complement previous data on turtle movements during the first year following the nesting season, integrating the diet consumed during the year before nesting. We suggest that the French Guiana leatherback population segregates into two distinct isotopic groupings, and highlight the urgent need to determine the feeding habitats of the turtle in the Atlantic in order to protect this species from incidental take by

  9. Deep sequencing of the oral microbiome reveals signatures of periodontal disease.

    Directory of Open Access Journals (Sweden)

    Bo Liu

    Full Text Available The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease. While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Through the sequencing of the 16S rRNA gene and of whole community DNA we provide a glimpse at the global genetic, metabolic, and ecological changes associated with periodontitis in 15 subgingival plaque samples, four from each of two periodontitis patients, and the remaining samples from three healthy individuals. We also demonstrate the power of whole-metagenome sequencing approaches in characterizing the genomes of key players in the oral microbiome, including an unculturable TM7 organism. We reveal the disease microbiome to be enriched in virulence factors, and adapted to a parasitic lifestyle that takes advantage of the disrupted host homeostasis. Furthermore, diseased samples share a common structure that was not found in completely healthy samples, suggesting that the disease state may occupy a narrow region within the space of possible configurations of the oral microbiome. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease. Despite a modest level of sequencing (~2 lanes Illumina 76 bp PE and high human DNA contamination (up to ~90% we were able to partially reconstruct several oral microbes and to preliminarily characterize some systems-level differences between the healthy and diseased oral microbiomes.

  10. The microbiome of Brazilian mangrove sediments as revealed by metagenomics

    NARCIS (Netherlands)

    Andreote, Fernando Dini; Jiménez Avella, Diego; Chaves, Diego; Dias, Armando Cavalcante Franco; Luvizotto, Danice Mazzer; Dini-Andreote, Francisco; Fasanella, Cristiane Cipola; Lopez, Maryeimy Varon; Baena, Sandra; Taketani, Rodrigo Gouvêa; de Melo, Itamar Soares

    2012-01-01

    Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct

  11. Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies

    DEFF Research Database (Denmark)

    Campanaro, Stefano; Treu, Laura; Kougias, Panagiotis

    2018-01-01

    In the past few years, many studies investigated the anaerobic digestion microbiome by means of 16S rRNA amplicon sequencing. Results obtained from these studies were compared to each other without taking into consideration the followed procedure for amplicons preparation and data analysis...... specifically, the microbial compositions of three laboratory scale biogas reactors were analyzed before and after addition of sodium oleate by sequencing the microbiome with three different approaches: 16S rRNA amplicon sequencing, shotgun DNA and shotgun RNA. This comparative analysis revealed that......, in amplicon sequencing, abundance of some taxa (Euryarchaeota and Spirochaetes) was biased by the inefficiency of universal primers to hybridize all the templates. Reliability of the results obtained was also influenced by the number of hypervariable regions under investigation. Finally, amplicon sequencing...

  12. The microbiome of Brazilian mangrove sediments as revealed by metagenomics.

    Directory of Open Access Journals (Sweden)

    Fernando Dini Andreote

    Full Text Available Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04 in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H(2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.

  13. The microbiome of Brazilian mangrove sediments as revealed by metagenomics.

    Science.gov (United States)

    Andreote, Fernando Dini; Jiménez, Diego Javier; Chaves, Diego; Dias, Armando Cavalcante Franco; Luvizotto, Danice Mazzer; Dini-Andreote, Francisco; Fasanella, Cristiane Cipola; Lopez, Maryeimy Varon; Baena, Sandra; Taketani, Rodrigo Gouvêa; de Melo, Itamar Soares

    2012-01-01

    Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H(2)S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.

  14. Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis.

    Science.gov (United States)

    Noyes, Noelle; Cho, Kyu-Chul; Ravel, Jacques; Forney, Larry J; Abdo, Zaid

    2018-01-01

    The vaginal microbiome plays an influential role in several disease states in reproductive age women, including bacterial vaginosis (BV). While demographic characteristics are associated with differences in vaginal microbiome community structure, little is known about the influence of sexual and hygiene habits. Furthermore, associations between the vaginal microbiome and risk symptoms of bacterial vaginosis have not been fully elucidated. Using Bayesian network (BN) analysis of 16S rRNA gene sequence results, demographic and extensive questionnaire data, we describe both novel and previously documented associations between habits of women and their vaginal microbiome. The BN analysis approach shows promise in uncovering complex associations between disparate data types. Our findings based on this approach support published associations between specific microbiome members (e.g., Eggerthella, Gardnerella, Dialister, Sneathia and Ruminococcaceae), the Nugent score (a BV diagnostic) and vaginal pH (a risk symptom of BV). Additionally, we found that several microbiome members were directly connected to other risk symptoms of BV (such as vaginal discharge, odor, itch, irritation, and yeast infection) including L. jensenii, Corynebacteria, and Proteobacteria. No direct connections were found between the Nugent Score and risk symptoms of BV other than pH, indicating that the Nugent Score may not be the most useful criteria for assessment of clinical BV. We also found that demographics (i.e., age, ethnicity, previous pregnancy) were associated with the presence/absence of specific vaginal microbes. The resulting BN revealed several as-yet undocumented associations between birth control usage, menstrual hygiene practices and specific microbiome members. Many of these complex relationships were not identified using common analytical methods, i.e., ordination and PERMANOVA. While these associations require confirmatory follow-up study, our findings strongly suggest that future

  15. Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis.

    Directory of Open Access Journals (Sweden)

    Noelle Noyes

    Full Text Available The vaginal microbiome plays an influential role in several disease states in reproductive age women, including bacterial vaginosis (BV. While demographic characteristics are associated with differences in vaginal microbiome community structure, little is known about the influence of sexual and hygiene habits. Furthermore, associations between the vaginal microbiome and risk symptoms of bacterial vaginosis have not been fully elucidated. Using Bayesian network (BN analysis of 16S rRNA gene sequence results, demographic and extensive questionnaire data, we describe both novel and previously documented associations between habits of women and their vaginal microbiome. The BN analysis approach shows promise in uncovering complex associations between disparate data types. Our findings based on this approach support published associations between specific microbiome members (e.g., Eggerthella, Gardnerella, Dialister, Sneathia and Ruminococcaceae, the Nugent score (a BV diagnostic and vaginal pH (a risk symptom of BV. Additionally, we found that several microbiome members were directly connected to other risk symptoms of BV (such as vaginal discharge, odor, itch, irritation, and yeast infection including L. jensenii, Corynebacteria, and Proteobacteria. No direct connections were found between the Nugent Score and risk symptoms of BV other than pH, indicating that the Nugent Score may not be the most useful criteria for assessment of clinical BV. We also found that demographics (i.e., age, ethnicity, previous pregnancy were associated with the presence/absence of specific vaginal microbes. The resulting BN revealed several as-yet undocumented associations between birth control usage, menstrual hygiene practices and specific microbiome members. Many of these complex relationships were not identified using common analytical methods, i.e., ordination and PERMANOVA. While these associations require confirmatory follow-up study, our findings strongly

  16. Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis

    Science.gov (United States)

    Noyes, Noelle; Cho, Kyu-Chul; Ravel, Jacques; Forney, Larry J.

    2018-01-01

    The vaginal microbiome plays an influential role in several disease states in reproductive age women, including bacterial vaginosis (BV). While demographic characteristics are associated with differences in vaginal microbiome community structure, little is known about the influence of sexual and hygiene habits. Furthermore, associations between the vaginal microbiome and risk symptoms of bacterial vaginosis have not been fully elucidated. Using Bayesian network (BN) analysis of 16S rRNA gene sequence results, demographic and extensive questionnaire data, we describe both novel and previously documented associations between habits of women and their vaginal microbiome. The BN analysis approach shows promise in uncovering complex associations between disparate data types. Our findings based on this approach support published associations between specific microbiome members (e.g., Eggerthella, Gardnerella, Dialister, Sneathia and Ruminococcaceae), the Nugent score (a BV diagnostic) and vaginal pH (a risk symptom of BV). Additionally, we found that several microbiome members were directly connected to other risk symptoms of BV (such as vaginal discharge, odor, itch, irritation, and yeast infection) including L. jensenii, Corynebacteria, and Proteobacteria. No direct connections were found between the Nugent Score and risk symptoms of BV other than pH, indicating that the Nugent Score may not be the most useful criteria for assessment of clinical BV. We also found that demographics (i.e., age, ethnicity, previous pregnancy) were associated with the presence/absence of specific vaginal microbes. The resulting BN revealed several as-yet undocumented associations between birth control usage, menstrual hygiene practices and specific microbiome members. Many of these complex relationships were not identified using common analytical methods, i.e., ordination and PERMANOVA. While these associations require confirmatory follow-up study, our findings strongly suggest that future

  17. Fecal microbiome of growing pigs fed a cereal based diet including chicory (Cichorium intybus L.) or ribwort (Plantago lanceolata L.) forage

    Energy Technology Data Exchange (ETDEWEB)

    Dicksved, Johan; Jansson, Janet K.; Lindberg, Jan Erik

    2015-12-01

    BACKGROUND: The purpose of this study was to investigate how inclusion of chicory forage or ribwort forage in a cereal-based diet influenced the fecal microbial community (microbiome) in newly weaned (35 days of age) piglets. The piglets were fed a cereal-based diet without (B) and with inclusion (80 and 160 g/kg air-dry forage) of vegetative shoots of chicory (C) and leaves of ribwort (R) forage in a 35-day growth trial. Fecal samples were collected at the start (D0), 17 (D17) and 35 (D35) days after weaning and profiles of the microbial consortia were generated using terminal restriction fragment length polymorphism (T-RFLP). 454-FLX pyrosequencing of 16S rRNA gene amplicons was used to analyze the microbial composition in a subset of the samples already analyzed with T-RFLP. RESULTS: The microbial clustering pattern was primarily dependent on age of the pigs, but diet effects could also be observed. Lactobacilli and enterobacteria were more abundant at D0, whereas the genera Streptococcus, Treponema, Clostridium, Clostridiaceae1 and Coprococcus were present in higher abundances at D35. Pigs fed ribwort had an increased abundance of sequences classified as Treponema and a reduction in lactobacilli. However, the abundance of Prevotellaceae increased with age in on both the chicory and the ribwort diet. Moreover, there were significant correlations between the abundance of Bacteroides and the digested amount of galactose, uronic acids and total non-starch polysaccharides, and between the abundance of Bacteroidales and the digested amount of xylose. CONCLUSION: This study demonstrated that both chicory and ribwort inclusion in the diet of newly weaned pigs influenced the composition of the fecal microbiota and that digestion of specific dietary components was correlated with species composition of the microbiota. Moreover, this study showed that the gut will be exposed to a dramatic shift in the microbial community structure several weeks after weaning.

  18. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease.

    Science.gov (United States)

    Greenblum, Sharon; Turnbaugh, Peter J; Borenstein, Elhanan

    2012-01-10

    The human microbiome plays a key role in a wide range of host-related processes and has a profound effect on human health. Comparative analyses of the human microbiome have revealed substantial variation in species and gene composition associated with a variety of disease states but may fall short of providing a comprehensive understanding of the impact of this variation on the community and on the host. Here, we introduce a metagenomic systems biology computational framework, integrating metagenomic data with an in silico systems-level analysis of metabolic networks. Focusing on the gut microbiome, we analyze fecal metagenomic data from 124 unrelated individuals, as well as six monozygotic twin pairs and their mothers, and generate community-level metabolic networks of the microbiome. Placing variations in gene abundance in the context of these networks, we identify both gene-level and network-level topological differences associated with obesity and inflammatory bowel disease (IBD). We show that genes associated with either of these host states tend to be located at the periphery of the metabolic network and are enriched for topologically derived metabolic "inputs." These findings may indicate that lean and obese microbiomes differ primarily in their interface with the host and in the way they interact with host metabolism. We further demonstrate that obese microbiomes are less modular, a hallmark of adaptation to low-diversity environments. We additionally link these topological variations to community species composition. The system-level approach presented here lays the foundation for a unique framework for studying the human microbiome, its organization, and its impact on human health.

  19. Xenobiotics and the Human Gut Microbiome: Metatranscriptomics Reveal the Active Players

    OpenAIRE

    Ursell, Luke K.; Knight, Rob

    2013-01-01

    The human gut microbiome plays an important role in the metabolism of xenobiotics. In a recent issue of Cell, Maurice et al. identify the active members of the gut microbiome and show how gene expression profiles change within the gut microbial community in response to antibiotics and host-targeted xenobiotics.

  20. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

    NARCIS (Netherlands)

    Zhernakova, A.; Kurilshikov, Alexander; Bonder, Marc Jan; Feskens, E.J.M.

    2016-01-01

    Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These

  1. 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.

  2. Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome

    DEFF Research Database (Denmark)

    Xie, Hailiang; Guo, Ruijin; Zhong, Huanzi

    2016-01-01

    The gut microbiota has been typically viewed as an environmental factor for human health. Twins are well suited for investigating the concordance of their gut microbiomes and decomposing genetic and environmental influences. However, existing twin studies utilizing metagenomic shotgun sequencing...... have included only a few samples. Here, we sequenced fecal samples from 250 adult twins in the TwinsUK registry and constructed a comprehensive gut microbial reference gene catalog. We demonstrate heritability of many microbial taxa and functional modules in the gut microbiome, including those...... associated with diseases. Moreover, we identified 8 million SNPs in the gut microbiome and observe a high similarity in microbiome SNPs between twins that slowly decreases after decades of living apart. The results shed new light on the genetic and environmental influences on the composition and function...

  3. Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients

    DEFF Research Database (Denmark)

    Jitwasinkul, Tossawan; Suriyaphol, Prapat; Tangphatsornruang, Sithichoke

    2016-01-01

    Antibiotic resistance genes are rapidly spread between pathogens and the normal flora, with plasmids playing an important role in their circulation. This study aimed to investigate antibiotic resistance plasmids in the gut microbiome of hospitalised patients. Stool samples were collected from seven...... inpatients at Siriraj Hospital (Bangkok, Thailand) and were compared with a sample from a healthy volunteer. Plasmids from the gut microbiomes extracted from the stool samples were subjected to high-throughput DNA sequencing (GS Junior). Newbler-assembled DNA reads were categorised into known and unknown...... in the gut microbiome; however, it was difficult to link these to the antibiotic resistance genes identified. That the antibiotic resistance genes came from hospital and community environments is worrying....

  4. Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome.

    Directory of Open Access Journals (Sweden)

    Jens Christian Claussen

    2017-06-01

    Full Text Available The analysis of microbiome compositions in the human gut has gained increasing interest due to the broader availability of data and functional databases and substantial progress in data analysis methods, but also due to the high relevance of the microbiome in human health and disease. While most analyses infer interactions among highly abundant species, the large number of low-abundance species has received less attention. Here we present a novel analysis method based on Boolean operations applied to microbial co-occurrence patterns. We calibrate our approach with simulated data based on a dynamical Boolean network model from which we interpret the statistics of attractor states as a theoretical proxy for microbiome composition. We show that for given fractions of synergistic and competitive interactions in the model our Boolean abundance analysis can reliably detect these interactions. Analyzing a novel data set of 822 microbiome compositions of the human gut, we find a large number of highly significant synergistic interactions among these low-abundance species, forming a connected network, and a few isolated competitive interactions.

  5. Pyrosequencing reveals the predominance of Pseudomonadaceae in gut microbiome of a Gall Midge

    Science.gov (United States)

    Gut microbes are known to play various roles in insects such as digestion of inaccessible nutrients, synthesis of deficient amino acids, and interaction with ecological environments, including host plants. Here, we analyzed the gut microbiome in Hessian fly, a serious pest of wheat. A total of 3,654...

  6. Autonomous gliders reveal features of the water column associated with foraging by adelie penguins.

    Science.gov (United States)

    Kahl, L Alex; Schofield, Oscar; Fraser, William R

    2010-12-01

    Despite their strong dependence on the pelagic environment, seabirds and other top predators in polar marine ecosystems are generally studied during their reproductive phases in terrestrial environments. As a result, a significant portion of their life history is understudied which in turn has led to limited understanding. Recent advances in autonomous underwater vehicle (AUV) technologies have allowed satellite-tagged Adélie penguins to guide AUV surveys of the marine environment at the Palmer Long-Term Ecological Research (LTER) site on the western Antarctic Peninsula. Near real-time data sent via Iridium satellites from the AUVs to a centralized control center thousands of miles away allowed scientists to adapt AUV sampling strategies to meet the changing conditions of the subsurface. Such AUV data revealed the water masses and fine-scale features associated with Adélie penguin foraging trips. During this study, the maximum concentration of chlorophyll was between 30 and 50 m deep. Encompassing this peak in the chlorophyll concentration, within the water-column, was a mixture of nutrient-laden Upper Circumpolar Deep (UCDW) and western Antarctic Peninsula winter water (WW). Together, data from the AUV survey and penguin dives reveal that 54% of foraging by Adélie penguins occurs immediately below the chlorophyll maximum. These data demonstrate how bringing together emerging technologies, such as AUVs, with established methods such as the radio-tagging of penguins can provide powerful tools for monitoring and hypothesis testing of previously inaccessible ecological processes. Ocean and atmosphere temperatures are expected to continue increasing along the western Antarctic Peninsula, which will undoubtedly affect regional marine ecosystems. New and emerging technologies such as unmanned underwater vehicles and individually mounted satellite tracking devices will provide the tools critical to documenting and understanding the widespread ecological change

  7. GPS tracking devices reveal foraging strategies of black-legged kittiwakes

    Science.gov (United States)

    Kotzerka, Jana; Garthe, Stefan; Hatch, Scott A.

    2010-01-01

    The Black-legged Kittiwake Rissa tridactyla is the most abundant gull species in the world, but some populations have declined in recent years, apparently due to food shortage. Kittiwakes are surface feeders and thus can compensate for low food availability only by increasing their foraging range and/or devoting more time to foraging. The species is widely studied in many respects, but long-distance foraging and the limitations of conventional radio telemetry have kept its foraging behavior largely out of view. The development of Global Positioning System (GPS) loggers is advancing rapidly. With devices as small as 8 g now available, it is possible to use this technology for tracking relatively small species of oceanic birds like kittiwakes. Here we present the first results of GPS telemetry applied to Black-legged Kittiwakes in 2007 in the North Pacific. All but one individual foraged in the neritic zone north of the island. Three birds performed foraging trips only close to the colony (within 13 km), while six birds had foraging ranges averaging about 40 km. The maximum foraging range was 59 km, and the maximum distance traveled was 165 km. Maximum trip duration was 17 h (mean 8 h). An apparently bimodal distribution of foraging ranges affords new insight on the variable foraging behaviour of Black-legged Kittiwakes. Our successful deployment of GPS loggers on kittiwakes holds much promise for telemetry studies on many other bird species of similar size and provides an incentive for applying this new approach in future studies.

  8. Pyrosequencing Reveals the Predominance of Pseudomonadaceae in Gut Microbiome of a Gall Midge

    Directory of Open Access Journals (Sweden)

    Raman Bansal

    2014-06-01

    Full Text Available Gut microbes are known to play various roles in insects such as digestion of inaccessible nutrients, synthesis of deficient amino acids, and interaction with ecological environments, including host plants. Here, we analyzed the gut microbiome in Hessian fly, a serious pest of wheat. A total of 3,654 high quality sequences of the V3 hypervariable region of the 16S rRNA gene were obtained through 454-pyrosequencing. From these sequences, 311 operational taxonomic units (OTUs were obtained at the >97% similarity cutoff. In the gut of 1st instar, otu01, a member of Pseudomonas, was predominant, representing 90.2% of total sequences. otu13, an unidentified genus in the Pseudomonadaceae family, represented 1.9% of total sequences. The remaining OTUs were each less than 1%. In the gut of the 2nd instar, otu01 and otu13 decreased to 85.5% and 1.5%, respectively. otu04, a member of Buttiauxella, represented 9.7% of total sequences. The remaining OTUs were each less than 1%. In the gut of the 3rd instar, otu01 and otu13 further decreased to 29.0% and 0%, respectively. otu06, otu08, and otu16, also three members of the Pseudomonadaceae family were 13.2%, 8.6%, and 2.3%, respectively. In addition, otu04 and otu14, two members of the Enterobacteriaceae family, were 4.7% and 2.5%; otu18 and otu20, two members of the Xanthomonadaceae family, were 1.3% and 1.2%, respectively; otu12, a member of Achromobacter, was 4.2%; otu19, a member of Undibacterium, was 1.4%; and otu9, otu10, and otu15, members of various families, were 6.1%, 6.3%, and 1.9%, respectively. The investigation into dynamics of Pseudomonas, the most abundant genera, revealed that its population level was at peak in freshly hatched or 1 day larvae as well as in later developmental stages, thus suggesting a prominent role for this bacterium in Hessian fly development and in its interaction with host plants. This study is the first comprehensive survey on bacteria associated with the gut of a gall

  9. Diet and exercise orthogonally alter the gut microbiome and reveal independent associations with anxiety and cognition.

    Science.gov (United States)

    Kang, Silvia S; Jeraldo, Patricio R; Kurti, Aishe; Miller, Margret E Berg; Cook, Marc D; Whitlock, Keith; Goldenfeld, Nigel; Woods, Jeffrey A; White, Bryan A; Chia, Nicholas; Fryer, John D

    2014-09-13

    The ingestion of a high-fat diet (HFD) and the resulting obese state can exert a multitude of stressors on the individual including anxiety and cognitive dysfunction. Though many studies have shown that exercise can alleviate the negative consequences of a HFD using metabolic readouts such as insulin and glucose, a paucity of well-controlled rodent studies have been published on HFD and exercise interactions with regard to behavioral outcomes. This is a critical issue since some individuals assume that HFD-induced behavioral problems such as anxiety and cognitive dysfunction can simply be exercised away. To investigate this, we analyzed mice fed a normal diet (ND), ND with exercise, HFD diet, or HFD with exercise. We found that mice on a HFD had robust anxiety phenotypes but this was not rescued by exercise. Conversely, exercise increased cognitive abilities but this was not impacted by the HFD. Given the importance of the gut microbiome in shaping the host state, we used 16S rRNA hypervariable tag sequencing to profile our cohorts and found that HFD massively reshaped the gut microbial community in agreement with numerous published studies. However, exercise alone also caused massive shifts in the gut microbiome at nearly the same magnitude as diet but these changes were surprisingly orthogonal. Additionally, specific bacterial abundances were directly proportional to measures of anxiety or cognition. Thus, behavioral domains and the gut microbiome are both impacted by diet and exercise but in unrelated ways. These data have important implications for obesity research aimed at modifications of the gut microbiome and suggest that specific gut microbes could be used as a biomarker for anxiety or cognition or perhaps even targeted for therapy.

  10. Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

    Science.gov (United States)

    Lowrey, Liam; Woodhams, Douglas C.; Tacchi, Luca

    2015-01-01

    The mucosal surfaces of wild and farmed aquatic vertebrates face the threat of many aquatic pathogens, including fungi. These surfaces are colonized by diverse symbiotic bacterial communities that may contribute to fight infection. Whereas the gut microbiome of teleosts has been extensively studied using pyrosequencing, this tool has rarely been employed to study the compositions of the bacterial communities present on other teleost mucosal surfaces. Here we provide a topographical map of the mucosal microbiome of an aquatic vertebrate, the rainbow trout (Oncorhynchus mykiss). Using 16S rRNA pyrosequencing, we revealed novel bacterial diversity at each of the five body sites sampled and showed that body site is a strong predictor of community composition. The skin exhibited the highest diversity, followed by the olfactory organ, gills, and gut. Flectobacillus was highly represented within skin and gill communities. Principal coordinate analysis and plots revealed clustering of external sites apart from internal sites. A highly diverse community was present within the epithelium, as demonstrated by confocal microscopy and pyrosequencing. Using in vitro assays, we demonstrated that two Arthrobacter sp. skin isolates, a Psychrobacter sp. strain, and a combined skin aerobic bacterial sample inhibit the growth of Saprolegnia australis and Mucor hiemalis, two important aquatic fungal pathogens. These results underscore the importance of symbiotic bacterial communities of fish and their potential role for the control of aquatic fungal diseases. PMID:26209676

  11. Stable Isotopes Reveal Long-Term Fidelity to Foraging Grounds in the Galapagos Sea Lion (Zalophus wollebaeki.

    Directory of Open Access Journals (Sweden)

    Massimiliano Drago

    Full Text Available Most otariids have colony-specific foraging areas during the breeding season, when they behave as central place foragers. However, they may disperse over broad areas after the breeding season and individuals from different colonies may share foraging grounds at that time. Here, stable isotope ratios in the skull bone of adult Galapagos sea lions (Zalophus wollebaeki were used to assess the long-term fidelity of both sexes to foraging grounds across the different regions of the Galapagos archipelago. Results indicated that the stable isotope ratios (δ(13C and δ(15N of sea lion bone significantly differed among regions of the archipelago, without any significant difference between sexes and with a non significant interaction between sex and region. Moreover, standard ellipses, estimated by Bayesian inference and used as a measure of the isotopic resource use area at the population level, overlapped widely for the sea lions from the southern and central regions, whereas the overlap of the ellipses for sea lions from the central and western regions was small and non-existing for those from the western and southern regions. These results suggest that males and females from the same region within the archipelago use similar foraging grounds and have similar diets. Furthermore, they indicate that the exchange of adults between regions is limited, thus revealing a certain degree of foraging philopatry at a regional scale within the archipelago. The constraints imposed on males by an expanded reproductive season (~ 6 months, resulting from the weak reproductive synchrony among females, and those imposed on females by a very long lactation period (at least one year but up to three years, may explain the limited mobility of adult Galapagos sea lions of both sexes across the archipelago.

  12. The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants.

    Science.gov (United States)

    Mustafa, Ghada A; Abd-Elgawad, Amr; Ouf, Amged; Siam, Rania

    2016-07-01

    The Red Sea is considered one of the youngest oceanic systems, with unique physical, geochemical and biological characteristics. Tourism, industrialization, extensive fishing, oil processing and shipping are extensive sources of pollution in the Red Sea. We analyzed the geochemical characteristics and microbial community of sediments along the Egyptian coast of the Red Sea. Our sites mainly included 1) four ports used for shipping aluminum, ilmenite and phosphate; 2) a site previously reported to have suffered extensive oil spills; and 3) a site impacted by tourism. Two major datasets for the sediment of ten Red Sea coastal sites were generated; i) a chemical dataset included measurements of carbon, hydrogen, nitrogen and sulfur, metals and selected semi-volatile oil; and ii) a 16S rRNA Pyrotags bacterial metagenomic dataset. Based on the taxonomic assignments of the 16S rRNA Pyrotags to major bacterial groups, we report 30 taxa constituting an Egyptian Red Sea Coastal Microbiome. Bacteria that degrade hydrocarbons were predominant in the majority of the sites, particularly in two ports where they reached up to 76% of the total identified genera. In contrast, sulfate-reducing and sulfate-oxidizing bacteria dominated two lakes at the expense of other hydrocarbon metabolizers. Despite the reported "Egyptian Red Sea Coastal Microbiome," sites with similar anthropogenic pollutants showed unique microbial community abundances. This suggests that the abundance of a specific bacterial community is an evolutionary mechanism induced in response to selected anthropogenic pollutants. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism.

    Science.gov (United States)

    Bao, Yun-Juan; Xu, Zixiang; Li, Yang; Yao, Zhi; Sun, Jibin; Song, Hui

    2017-06-01

    The soil with petroleum contamination is one of the most studied soil ecosystems due to its rich microorganisms for hydrocarbon degradation and broad applications in bioremediation. However, our understanding of the genomic properties and functional traits of the soil microbiome is limited. In this study, we used high-throughput metagenomic sequencing to comprehensively study the microbial community from petroleum-contaminated soils near Tianjin Dagang oilfield in eastern China. The analysis reveals that the soil metagenome is characterized by high level of community diversity and metabolic versatility. The metageome community is predominated by γ-Proteobacteria and α-Proteobacteria, which are key players for petroleum hydrocarbon degradation. The functional study demonstrates over-represented enzyme groups and pathways involved in degradation of a broad set of xenobiotic aromatic compounds, including toluene, xylene, chlorobenzoate, aminobenzoate, DDT, methylnaphthalene, and bisphenol. A composite metabolic network is proposed for the identified pathways, thus consolidating our identification of the pathways. The overall data demonstrated the great potential of the studied soil microbiome in the xenobiotic aromatics degradation. The results not only establish a rich reservoir for novel enzyme discovery but also provide putative applications in bioremediation. Copyright © 2016. Published by Elsevier B.V.

  14. Oligotyping reveals differences between gut-microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas on a bacterial species-like level

    Directory of Open Access Journals (Sweden)

    Sebastian eMenke

    2014-10-01

    Full Text Available Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs based on a similarity threshold (e.g. 97%. This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from abnormal microbial compositions that affect host health requires knowledge of the normal microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus and the black-backed jackal (Canis mesomelas. Bacterial phyla with proportions > 0.2 % were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥ 0.1 %, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3 % OTUs, oligotyping can detect fine-scale taxonomic differences between

  15. Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level.

    Science.gov (United States)

    Menke, Sebastian; Wasimuddin; Meier, Matthias; Melzheimer, Jörg; Mfune, John K E; Heinrich, Sonja; Thalwitzer, Susanne; Wachter, Bettina; Sommer, Simone

    2014-01-01

    Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from "abnormal" microbial compositions that affect host health requires knowledge of the "normal" microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.

  16. Puffins reveal contrasting relationships between forage fish and ocean climate in the North Pacific

    Science.gov (United States)

    Sydeman, William J.; Piatt, John F.; Thompson, Sarah Ann; Garcia-Reyes, Marisol; Hatch, Scott A.; Arimitsu, Mayumi L.; Slater, Leslie; Williams, Jeffrey C.; Rojek, Nora A.; Zador, Stephani G.; Renner, Heather M.

    2017-01-01

    Long-term studies of predator food habits (i.e., ‘predator-based sampling’) are useful for identifying patterns of spatial and temporal variability of forage nekton in marine ecosystems. We investigated temporal changes in forage fish availability and relationships to ocean climate by analyzing diet composition of three puffin species (horned puffin Fratercula corniculata, tufted puffin Fratercula cirrhata, and rhinoceros auklet Cerorhinca monocerata) from five sites in the North Pacific from 1978–2012. Dominant forage species included squids and hexagrammids in the western Aleutians, gadids and Pacific sand lance (Ammodytes personatus) in the eastern Aleutians and western Gulf of Alaska (GoA), and sand lance and capelin (Mallotus villosus) in the northern and eastern GoA. Interannual fluctuations in forage availability dominated variability in the western Aleutians, whereas lower-frequency shifts in forage fish availability dominated elsewhere. We produced regional multivariate indicators of sand lance, capelin, and age-0 gadid availability by combining data across species and sites using Principal Component Analysis, and related these indices to environmental factors including sea level pressure (SPL), winds, and sea surface temperature (SST). There was coherence in the availability of sand lance and capelin across the study area. Sand lance availability increased linearly with environmental conditions leading to warmer ocean temperatures, whereas capelin availability increased in a non-linear manner when environmental changes led to lower ocean temperatures. Long-term studies of puffin diet composition appear to be a promising tool for understanding the availability of these difficult-to-survey forage nekton in remote regions of the North Pacific.

  17. Comparative genomic analysis of the microbiome [corrected] of herbivorous insects reveals eco-environmental adaptations: biotechnology applications.

    Directory of Open Access Journals (Sweden)

    Weibing Shi

    Full Text Available Metagenome analysis of the gut symbionts of three different insects was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts. A second goal was the discovery of novel biocatalysts for biorefinery applications. Grasshopper and cutworm gut symbionts were sequenced and compared with the previously identified metagenome of termite gut microbiota. These insect hosts represent three different insect orders and specialize on different food types. The comparative analysis revealed dramatic differences among the three insect species in the abundance and taxonomic composition of the symbiont populations present in the gut. The composition and abundance of symbionts was correlated with their previously identified capacity to degrade and utilize the different types of food consumed by their hosts. The metabolic reconstruction revealed that the gut metabolome of cutworms and grasshoppers was more enriched for genes involved in carbohydrate metabolism and transport than wood-feeding termite, whereas the termite gut metabolome was enriched for glycosyl hydrolase (GH enzymes relevant to lignocellulosic biomass degradation. Moreover, termite gut metabolome was more enriched with nitrogen fixation genes than those of grasshopper and cutworm gut, presumably due to the termite's adaptation to the high fiber and less nutritious food types. In order to evaluate and exploit the insect symbionts for biotechnology applications, we cloned and further characterized four biomass-degrading enzymes including one endoglucanase and one xylanase from both the grasshopper and cutworm gut symbionts. The results indicated that the grasshopper symbiont enzymes were generally more efficient in biomass degradation than the homologous enzymes from cutworm symbionts. Together, these results demonstrated a correlation between the composition and putative metabolic functionality of the gut microbiome and host

  18. Spatio-temporal dynamics of ocean conditions and forage taxa reveal regional structuring of seabird–prey relationships.

    Science.gov (United States)

    Santora, Jarrod A; Schroeder, Isaac D; Field, John C; Wells, Brian K; Sydeman, William J

    Studies of predator–prey demographic responses and the physical drivers of such relationships are rare, yet essential for predicting future changes in the structure and dynamics of marine ecosystems. Here, we hypothesize that predator–prey relationships vary spatially in association with underlying physical ocean conditions, leading to observable changes in demographic rates, such as reproduction. To test this hypothesis, we quantified spatio-temporal variability in hydrographic conditions, krill, and forage fish to model predator (seabird) demographic responses over 18 years (1990–2007). We used principal component analysis and spatial correlation maps to assess coherence among ocean conditions, krill, and forage fish, and generalized additive models to quantify interannual variability in seabird breeding success relative to prey abundance. The first principal component of four hydrographic measurements yielded an index that partitioned “warm/weak upwelling” and “cool/strong upwelling” years. Partitioning of krill and forage fish time series among shelf and oceanic regions yielded spatially explicit indicators of prey availability. Krill abundance within the oceanic region was remarkably consistent between years, whereas krill over the shelf showed marked interannual fluctuations in relation to ocean conditions. Anchovy abundance varied on the shelf, and was greater in years of strong stratification, weak upwelling and warmer temperatures. Spatio-temporal variability of juvenile forage fish co-varied strongly with each other and with krill, but was weakly correlated with hydrographic conditions. Demographic responses between seabirds and prey availability revealed spatially variable associations indicative of the dynamic nature of “predator–habitat” relationships. Quantification of spatially explicit demographic responses, and their variability through time, demonstrate the possibility of delineating specific critical areas where the

  19. Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism.

    Science.gov (United States)

    Mohammed, Akram; Guda, Chittibabu

    2015-01-01

    Enzymes are known as the molecular machines that drive the metabolism of an organism; hence identification of the full enzyme complement of an organism is essential to build the metabolic blueprint of that species as well as to understand the interplay of multiple species in an ecosystem. Experimental characterization of the enzymatic reactions of all enzymes in a genome is a tedious and expensive task. The problem is more pronounced in the metagenomic samples where even the species are not adequately cultured or characterized. Enzymes encoded by the gut microbiota play an essential role in the host metabolism; thus, warranting the need to accurately identify and annotate the full enzyme complements of species in the genomic and metagenomic projects. To fulfill this need, we develop and apply a method called ECemble, an ensemble approach to identify enzymes and enzyme classes and study the human gut metabolic pathways. ECemble method uses an ensemble of machine-learning methods to accurately model and predict enzymes from protein sequences and also identifies the enzyme classes and subclasses at the finest resolution. A tenfold cross-validation result shows accuracy between 97 and 99% at different levels in the hierarchy of enzyme classification, which is superior to comparable methods. We applied ECemble to predict the entire complements of enzymes from ten sequenced proteomes including the human proteome. We also applied this method to predict enzymes encoded by the human gut microbiome from gut metagenomic samples, and to study the role played by the microbe-derived enzymes in the human metabolism. After mapping the known and predicted enzymes to canonical human pathways, we identified 48 pathways that have at least one bacteria-encoded enzyme, which demonstrates the complementary role of gut microbiome in human gut metabolism. These pathways are primarily involved in metabolizing dietary nutrients such as carbohydrates, amino acids, lipids, cofactors and

  20. Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism

    Science.gov (United States)

    2015-01-01

    Background Enzymes are known as the molecular machines that drive the metabolism of an organism; hence identification of the full enzyme complement of an organism is essential to build the metabolic blueprint of that species as well as to understand the interplay of multiple species in an ecosystem. Experimental characterization of the enzymatic reactions of all enzymes in a genome is a tedious and expensive task. The problem is more pronounced in the metagenomic samples where even the species are not adequately cultured or characterized. Enzymes encoded by the gut microbiota play an essential role in the host metabolism; thus, warranting the need to accurately identify and annotate the full enzyme complements of species in the genomic and metagenomic projects. To fulfill this need, we develop and apply a method called ECemble, an ensemble approach to identify enzymes and enzyme classes and study the human gut metabolic pathways. Results ECemble method uses an ensemble of machine-learning methods to accurately model and predict enzymes from protein sequences and also identifies the enzyme classes and subclasses at the finest resolution. A tenfold cross-validation result shows accuracy between 97 and 99% at different levels in the hierarchy of enzyme classification, which is superior to comparable methods. We applied ECemble to predict the entire complements of enzymes from ten sequenced proteomes including the human proteome. We also applied this method to predict enzymes encoded by the human gut microbiome from gut metagenomic samples, and to study the role played by the microbe-derived enzymes in the human metabolism. After mapping the known and predicted enzymes to canonical human pathways, we identified 48 pathways that have at least one bacteria-encoded enzyme, which demonstrates the complementary role of gut microbiome in human gut metabolism. These pathways are primarily involved in metabolizing dietary nutrients such as carbohydrates, amino acids, lipids

  1. Viromes of one year old infants reveal the impact of birth mode on microbiome diversity.

    LENUS (Irish Health Repository)

    McCann, Angela

    2018-05-01

    Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome\\/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU\\'s (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.

  2. Brazilian Microbiome Project: revealing the unexplored microbial diversity--challenges and prospects.

    Science.gov (United States)

    Pylro, Victor Satler; Roesch, Luiz Fernando Wurdig; Ortega, José Miguel; do Amaral, Alexandre Morais; Tótola, Marcos Rogério; Hirsch, Penny Ruth; Rosado, Alexandre Soares; Góes-Neto, Aristóteles; da Costa da Silva, Artur Luiz; Rosa, Carlos Augusto; Morais, Daniel Kumazawa; Andreote, Fernando Dini; Duarte, Gabriela Frois; de Melo, Itamar Soares; Seldin, Lucy; Lambais, Márcio Rodrigues; Hungria, Mariangela; Peixoto, Raquel Silva; Kruger, Ricardo Henrique; Tsai, Siu Mui; Azevedo, Vasco

    2014-02-01

    The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world's macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world's catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.

  3. Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

    Directory of Open Access Journals (Sweden)

    Angela McCann

    2018-05-01

    Full Text Available Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD or caesarean section (CS influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU’s (operational taxonomic units identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.

  4. Biogeographic Comparison of Lophelia-Associated Bacterial Communities in the Western Atlantic Reveals Conserved Core Microbiome

    Directory of Open Access Journals (Sweden)

    Christina A. Kellogg

    2017-05-01

    sequences, whereas open Atlantic samples had a much higher proportion of locally consistent bacteria. Further, predictive functional profiling highlights the potential for the L. pertusa microbiome to contribute to chemoautotrophy, nutrient cycling, and antibiotic production.

  5. Following a Foraging Fish-Finder: Diel Habitat Use of Blainville's Beaked Whales Revealed by Echolocation

    Science.gov (United States)

    Arranz, Patricia; de Soto, Natacha Aguilar; Madsen, Peter T.; Brito, Alberto; Bordes, Fernando; Johnson, Mark P.

    2011-01-01

    Simultaneous high resolution sampling of predator behavior and habitat characteristics is often difficult to achieve despite its importance in understanding the foraging decisions and habitat use of predators. Here we tap into the biosonar system of Blainville's beaked whales, Mesoplodon densirostris, using sound and orientation recording tags to uncover prey-finding cues available to echolocating predators in the deep-sea. Echolocation sounds indicate where whales search and encounter prey, as well as the altitude of whales above the sea-floor and the density of organisms around them, providing a link between foraging activity and the bio-physical environment. Tagged whales (n = 9) hunted exclusively at depth, investing most of their search time either in the lower part of the deep scattering layer (DSL) or near the sea-floor with little diel change. At least 43% (420/974) of recorded prey-capture attempts were performed within the benthic boundary layer despite a wide range of dive depths, and many dives included both meso- and bentho-pelagic foraging. Blainville's beaked whales only initiate searching when already deep in the descent and encounter prey suitable for capture within 2 min of the start of echolocation, suggesting that these whales are accessing prey in reliable vertical strata. Moreover, these prey resources are sufficiently dense to feed the animals in what is effectively four hours of hunting per day enabling a strategy in which long dives to exploit numerous deep-prey with low nutritional value require protracted recovery periods (average 1.5 h) between dives. This apparent searching efficiency maybe aided by inhabiting steep undersea slopes with access to both the DSL and the sea-floor over small spatial scales. Aggregations of prey in these biotopes are located using biosonar-derived landmarks and represent stable and abundant resources for Blainville's beaked whales in the otherwise food-limited deep-ocean. PMID:22163295

  6. Videography reveals in-water behavior of loggerhead turtles (Caretta caretta at a foraging ground

    Directory of Open Access Journals (Sweden)

    Samir Harshad Patel

    2016-12-01

    Full Text Available Assessing sea turtle behavior at the foraging grounds has been primarily limited to the interpretation of remotely-sensed data. As a result, there is a general lack of detailed understanding regarding the habitat use of sea turtles during a phase that accounts for a majority of their lives. Thus, this study aimed to fill these data gaps by providing detailed information about the feeding habits, prey availability, buoyancy control and water column usage by 73 loggerhead turtles across 45.7 hours of video footage obtained from a remotely operated vehicle (ROV from 2008 – 2014. We developed an ethogram to account for 27 potential environmental and behavioral parameters. Turtles were filmed through the entire water column and we quantified the frequency of behaviors such as flipper beats, breaths, defecations, feedings and reactions to the ROV. We used the ROV’s depth sensor and visible cues (i.e. water surface or benthic zone in view to distinguish depth zones and assess the turtles’ use of the water column. We also quantified interactions with sympatric biota, including potential gelatinous and non-gelatinous prey species, fish (including sharks, marine mammals and other sea turtles. We discovered that turtles tended to remain within the near surface and surface zones of the water column through the majority of the footage. During benthic dives, turtles consistently exhibited negative buoyancy and some turtles exhibited a dichotomous foraging behavior, first foraging within the water column, then diving to the benthic environment. Videography allowed us to combine behavioral observations and habitat features that cannot be captured by traditional telemetry methods, resulting in a broader understanding of loggerheads’ ecological role in the U.S. Mid-Atlantic.

  7. Following a foraging fish-finder: diel habitat use of Blainville's beaked whales revealed by echolocation.

    Directory of Open Access Journals (Sweden)

    Patricia Arranz

    Full Text Available Simultaneous high resolution sampling of predator behavior and habitat characteristics is often difficult to achieve despite its importance in understanding the foraging decisions and habitat use of predators. Here we tap into the biosonar system of Blainville's beaked whales, Mesoplodon densirostris, using sound and orientation recording tags to uncover prey-finding cues available to echolocating predators in the deep-sea. Echolocation sounds indicate where whales search and encounter prey, as well as the altitude of whales above the sea-floor and the density of organisms around them, providing a link between foraging activity and the bio-physical environment. Tagged whales (n = 9 hunted exclusively at depth, investing most of their search time either in the lower part of the deep scattering layer (DSL or near the sea-floor with little diel change. At least 43% (420/974 of recorded prey-capture attempts were performed within the benthic boundary layer despite a wide range of dive depths, and many dives included both meso- and bentho-pelagic foraging. Blainville's beaked whales only initiate searching when already deep in the descent and encounter prey suitable for capture within 2 min of the start of echolocation, suggesting that these whales are accessing prey in reliable vertical strata. Moreover, these prey resources are sufficiently dense to feed the animals in what is effectively four hours of hunting per day enabling a strategy in which long dives to exploit numerous deep-prey with low nutritional value require protracted recovery periods (average 1.5 h between dives. This apparent searching efficiency maybe aided by inhabiting steep undersea slopes with access to both the DSL and the sea-floor over small spatial scales. Aggregations of prey in these biotopes are located using biosonar-derived landmarks and represent stable and abundant resources for Blainville's beaked whales in the otherwise food-limited deep-ocean.

  8. Dental calculus reveals Mesolithic foragers in the Balkans consumed domesticated plant foods.

    Science.gov (United States)

    Cristiani, Emanuela; Radini, Anita; Edinborough, Marija; Borić, Dušan

    2016-09-13

    Researchers agree that domesticated plants were introduced into southeast Europe from southwest Asia as a part of a Neolithic "package," which included domesticated animals and artifacts typical of farming communities. It is commonly believed that this package reached inland areas of the Balkans by ∼6200 calibrated (cal.) BC or later. Our analysis of the starch record entrapped in dental calculus of Mesolithic human teeth at the site of Vlasac in the Danube Gorges of the central Balkans provides direct evidence that already by ∼6600 cal. BC, if not earlier, Late Mesolithic foragers of this region consumed domestic cereals, such as Triticum monococcum, Triticum dicoccum, and Hordeum distichon, which were also the main crops found among Early Neolithic communities of southeast Europe. We infer that "exotic" Neolithic domesticated plants were introduced to southern Europe independently almost half a millennium earlier than previously thought, through networks that enabled exchanges between inland Mesolithic foragers and early farming groups found along the Aegean coast of Turkey.

  9. The foraging ecology of the mountain long-eared bat Plecotus macrobullaris revealed with DNA mini-barcodes.

    Directory of Open Access Journals (Sweden)

    Antton Alberdi

    Full Text Available Molecular analysis of diet overcomes the considerable limitations of traditional techniques for identifying prey remains in bat faeces. We collected faeces from individual Mountain Long-eared Bats Plecotus macrobullaris trapped using mist nets during the summers of 2009 and 2010 in the Pyrenees. We analysed their diet using DNA mini-barcodes to identify prey species. In addition, we inferred some basic features of the bat's foraging ecology that had not yet been addressed. P. macrobullaris fed almost exclusively on moths (97.8%. As prey we detected one dipteran genus (Tipulidae and 29 moth taxa: 28 were identified at species level (23 Noctuidae, 1 Crambidae, 1 Geometridae, 1 Pyralidae, 1 Sphingidae, 1 Tortricidae, and one at genus level (Rhyacia sp., Noctuidae. Known ecological information about the prey species allowed us to determine that bats had foraged at elevations between 1,500 and 2,500 m amsl (above mean sea level, mostly in subalpine meadows, followed by other open habitats such as orophilous grasslands and alpine meadows. No forest prey species were identified in the diet. As 96.4% of identified prey species were tympanate moths and no evidence of gleaning behaviour was revealed, we suggest P. macrobullaris probably forages by aerial hawking using faint echolocation pulses to avoid detection by hearing moths. As we could identify 87.8% of the analysed sequences (64.1% of the MOTUs, Molecular Operational Taxonomic Units at species level, we conclude that DNA mini-barcodes are a very useful tool to analyse the diet of moth-specialist bats.

  10. Towards the human colorectal cancer microbiome.

    Directory of Open Access Journals (Sweden)

    Julian R Marchesi

    Full Text Available Multiple factors drive the progression from healthy mucosa towards sporadic colorectal carcinomas and accumulating evidence associates intestinal bacteria with disease initiation and progression. Therefore, the aim of this study was to provide a first high-resolution map of colonic dysbiosis that is associated with human colorectal cancer (CRC. To this purpose, the microbiomes colonizing colon tumor tissue and adjacent non-malignant mucosa were compared by deep rRNA sequencing. The results revealed striking differences in microbial colonization patterns between these two sites. Although inter-individual colonization in CRC patients was variable, tumors consistently formed a niche for Coriobacteria and other proposed probiotic bacterial species, while potentially pathogenic Enterobacteria were underrepresented in tumor tissue. As the intestinal microbiota is generally stable during adult life, these findings suggest that CRC-associated physiological and metabolic changes recruit tumor-foraging commensal-like bacteria. These microbes thus have an apparent competitive advantage in the tumor microenvironment and thereby seem to replace pathogenic bacteria that may be implicated in CRC etiology. This first glimpse of the CRC microbiome provides an important step towards full understanding of the dynamic interplay between intestinal microbial ecology and sporadic CRC, which may provide important leads towards novel microbiome-related diagnostic tools and therapeutic interventions.

  11. Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization.

    Science.gov (United States)

    Slaby, Beate M; Hackl, Thomas; Horn, Hannes; Bayer, Kristina; Hentschel, Ute

    2017-11-01

    Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts. A within-symbionts genome comparison revealed a nutritional specialization of at least two symbiont guilds, where one appears to metabolize carnitine and the other sulfated polysaccharides, both of which are abundant molecules in the sponge extracellular matrix. A third guild of symbionts may be viewed as nutritional generalists that perform largely the same metabolic pathways but lack such extraordinary numbers of the relevant genes. This study characterizes the genomic repertoire of sponge symbionts at an unprecedented resolution and it provides greater insights into the molecular mechanisms underlying microbial-sponge symbiosis.

  12. An abundance of Epsilonproteobacteria revealed in the gut microbiome of the laboratory cultured sea urchin, Lytechinus variegatus

    Science.gov (United States)

    Hakim, Joseph A.; Koo, Hyunmin; Dennis, Lacey N.; Kumar, Ranjit; Ptacek, Travis; Morrow, Casey D.; Lefkowitz, Elliot J.; Powell, Mickie L.; Bej, Asim K.; Watts, Stephen A.

    2015-01-01

    In this study, we have examined the bacterial community composition of the laboratory cultured sea urchin Lytechinus variegatus gut microbiome and its culture environment using NextGen amplicon sequencing of the V4 segment of the 16S rRNA gene, and downstream bioinformatics tools. Overall, the gut and tank water was dominated by Proteobacteria, whereas the feed consisted of a co-occurrence of Proteobacteria and Firmicutes at a high abundance. The gut tissue represented Epsilonproteobacteria as dominant, with order Campylobacterales at the highest relative abundance (>95%). However, the pharynx tissue was dominated by class Alphaproteobacteria. The gut digesta and egested fecal pellets had a high abundance of class Gammaproteobacteria, from which Vibrio was found to be the primary genus, and Epsilonproteobacteria, with genus Arcobacter occurring at a moderate level. At the class level, the tank water was dominated by Gammaproteobacteria, and the feed by Alphaproteobacteria. Multi-Dimensional Scaling analysis showed that the microbial community of the gut tissue clustered together, as did the pharynx tissue to the feed. The gut digesta and egested fecal pellets showed a similarity relationship to the tank water. Further analysis of Campylobacterales at a lower taxonomic level using the oligotyping method revealed 37 unique types across the 10 samples, where Oligotype 1 was primarily represented in the gut tissue. BLAST analysis identified Oligotype 1 to be Arcobacter sp., Sulfuricurvum sp., and Arcobacter bivalviorum at an identity level >90%. This study showed that although distinct microbial communities are evident across multiple components of the sea urchin gut ecosystem, there is a noticeable correlation between the overall microbial communities of the gut with the sea urchin L. variegatus culture environment. PMID:26528245

  13. An abundance of Epsilonproteobacteria revealed in the gut microbiome of the laboratory cultured sea urchin, Lytechinus variegatus

    Directory of Open Access Journals (Sweden)

    Joseph Antoine Hakim

    2015-10-01

    Full Text Available In this study, we have examined the bacterial community composition in the laboratory cultured sea urchin Lytechinus variegatus gut microbiome and its culture environment using NextGen amplicon sequencing of the V4 segment of the 16S rRNA gene, and downstream bioinformatics tools. Overall, the gut and tank water was dominated by Proteobacteria, whereas the feed consisted of a co-occurrence of Proteobacteria and Firmicutes at a high abundance. The gut tissue represented Epsilonproteobacteria as dominant, with order Campylobacterales at the highest relative abundance (>95%. However, the pharynx tissue was dominated by class Alphaproteobacteria. The gut digesta and egested fecal pellets had a high abundance of class Gammaproteobacteria, from which Vibrio was found to be the primary genus, and Epsilonproteobacteria, with genus Arcobacter occurring at a moderate level. At the class level, the tank water was dominated by Gammaproteobacteria, and the feed by Alphaproteobacteria. Multi-Dimensional Scaling analysis showed that the microbial community of the gut tissue clustered together, as did the pharynx tissue to the feed. The gut digesta and egested fecal pellets showed a similar relationship to the tank water. Further analysis of Campylobacterales at a lower taxonomic level using the oligotyping method revealed 37 unique types across the ten samples, where Oligotype 1 was primarily represented in the gut tissue. BLAST analysis identified Oligotype 1 to be Arcobacter sp., Sulfuricurvum sp., and Arcobacter bivalviorum at an identity level >90%. This study showed that although distinct microbial communities were evident across multiple components of the sea urchin gut ecosystem, there is a noticeable correlation between the overall microbial communities of the gut with the sea urchin L. variegatus culture environment.

  14. Foraging through multiple target categories reveals the flexibility of visual working memory.

    Science.gov (United States)

    Kristjánsson, Tómas; Kristjánsson, Árni

    2018-02-01

    A key assumption in the literature on visual attention is that templates, actively maintained in visual working memory (VWM), guide visual attention. An important question therefore involves the nature and capacity of VWM. According to load theories, more than one search template can be active at the same time and capacity is determined by the total load rather than a precise number of templates. By an alternative account only one search template can be active within visual working memory at any given time, while other templates are in an accessory state - but do not affect visual selection. We addressed this question by varying the number of targets and distractors in a visual foraging task for 40 targets among 40 distractors in two ways: 1) Fixed-distractor-number, involving two distractor types while target categories varied from one to four. 2) Fixed-color-number (7), so that if the target types were two, distractors types were five, while if target number increased to three, distractor types were four (etc.). The two accounts make differing predictions. Under the single-template account, we should expect large switch costs as target types increase to two, but switch-costs should not increase much as target types increase beyond two. Load accounts predict an approximately linear increase in switch costs with increased target type number. The results were that switch costs increased roughly linearly in both conditions, in line with load accounts. The results are discussed in light of recent proposals that working memory reflects lingering neural activity at various sites that operate on the stimuli in each case and findings showing neurally silent working memory representations. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Cross-kingdom similarities in microbiome functions

    NARCIS (Netherlands)

    Mendes, R.; Raaijmakers, J.M.

    2015-01-01

    Recent advances in medical research have revealed how humans rely on their microbiome for diverse traits and functions. Similarly, microbiomes of other higher organisms play key roles in disease, health, growth and development of their host. Exploring microbiome functions across kingdoms holds

  16. Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes.

    Science.gov (United States)

    Zhu, Lifeng; Wu, Qi; Deng, Cao; Zhang, Mengjie; Zhang, Chenglin; Chen, Hua; Lu, Guoqing; Wei, Fuwen

    2018-05-01

    Carnivorous members of the Carnivora reside at the apex of food chains and consume meat-only diets, rich in purine, fats and protein. Here, we aimed to identify potential adaptive evolutionary signatures compatible with high purine and fat metabolism based on analysis of host genomes and symbiotic gut microbial metagenomes. We found that the gut microbiomes of carnivorous Carnivora (e.g., Felidae, Canidae) clustered in the same clade, and other clades comprised omnivorous and herbivorous Carnivora (e.g., badgers, bears and pandas). The relative proportions of genes encoding enzymes involved in uric acid degradation were higher in the gut microbiomes of meat-eating carnivorans than plant-eating species. Adaptive amino acid substitutions in two enzymes, carnitine O-palmitoyltransferase 1 (CPT1A) and lipase F (LIPF), which play a role in fat digestion, were identified in Felidae-Candidae species. Carnivorous carnivorans appear to endure diets high in purines and fats via gut microbiomic and genomic adaptations. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

  17. Hot topic: 16S rRNA gene sequencing reveals the microbiome of the virgin and pregnant bovine uterus.

    Science.gov (United States)

    Moore, S G; Ericsson, A C; Poock, S E; Melendez, P; Lucy, M C

    2017-06-01

    We tested the hypothesis that the uterus of virgin heifers and pregnant cows possessed a resident microbiome by 16S rRNA gene sequencing of the virgin and pregnant bovine uterus. The endometrium of 10 virgin heifers in estrus and the amniotic fluid, placentome, intercotyledonary placenta, cervical lumen, and external cervix surface (control) of 5 pregnant cows were sampled using aseptic techniques. The DNA was extracted, the V4 hypervariable region of the 16S rRNA gene was amplified, and amplicons were sequenced using Illumina MiSeq technology (Illumina Inc., San Diego, CA). Operational taxonomic units (OTU) were generated from the sequences using Qiime v1.8 software, and taxonomy was assigned using the Greengenes database. The effect of tissue on the microbial composition within the pregnant uterus was tested using univariate (mixed model) and multivariate (permutational multivariate ANOVA) procedures. Amplicons of 16S rRNA gene were generated in all samples, supporting the contention that the uterus of virgin heifers and pregnant cows contained a microbiome. On average, 53, 199, 380, 382, 525, and 13,589 reads annotated as 16, 35, 43, 63, 48, and 176 OTU in the placentome, virgin endometrium, amniotic fluid, cervical lumen, intercotyledonary placenta, and external surface of the cervix, respectively, were generated. The 3 most abundant phyla in the uterus of the virgin heifers and pregnant cows were Firmicutes, Bacteroidetes, and Proteobacteria, and they accounted for approximately 40, 35, and 10% of the sequences, respectively. Phyla abundance was similar between the tissues of the pregnant uterus. Principal component analysis, one-way PERMANOVA analysis of the Bray-Curtis similarity index, and mixed model analysis of the Shannon diversity index and Chao1 index demonstrated that the microbiome of the control tissue (external surface of the cervix) was significantly different from that of the amniotic fluid, intercotyledonary placenta, and placentome tissues

  18. Stable isotopes (δ13C, δ15N combined with conventional dietary approaches reveal plasticity in central-place foraging behaviour of little penguins (Eudyptula minor

    Directory of Open Access Journals (Sweden)

    Andre eChiaradia

    2016-01-01

    reveal an otherwise intractable ecological issue of different constrains of being a central-place forager, such as the little penguin, which could be applied to other marine species.

  19. Moonlight avoidance in gerbils reveals a sophisticated interplay among time allocation, vigilance and state-dependent foraging.

    Science.gov (United States)

    Kotler, Burt P; Brown, Joel; Mukherjee, Shomen; Berger-Tal, Oded; Bouskila, Amos

    2010-05-22

    Foraging animals have several tools for managing the risk of predation, and the foraging games between them and their predators. Among these, time allocation is foremost, followed by vigilance and apprehension. Together, their use influences a forager's time allocation and giving-up density (GUD) in depletable resource patches. We examined Allenby's gerbils (Gerbilus andersoni allenbyi) exploiting seed resource patches in a large vivarium under varying moon phases in the presence of a red fox (Vulpes vulpes). We measured time allocated to foraging patches electronically and GUDs from seeds left behind in resource patches. From these, we estimated handling times, attack rates and quitting harvest rates (QHRs). Gerbils displayed greater vigilance (lower attack rates) at brighter moon phases (full full > new > wane). Finally, gerbils displayed higher QHRs at new and waxing moon phases. Differences across moon phases not only reflect changing time allocation and vigilance, but changes in the state of the foragers and their marginal value of energy. Early in the lunar cycle, gerbils rely on vigilance and sacrifice state to avoid risk; later they defend state at the cost of increased time allocation; finally their state can recover as safe opportunities expand. In the predator-prey foraging game, foxes may contribute to these patterns of behaviours by modulating their own activity in response to the opportunities presented in each moon phase.

  20. GPS-tracking and colony observations reveal variation in offshore habitat use and foraging ecology of breeding Sandwich Terns

    Science.gov (United States)

    Fijn, R. C.; de Jong, J.; Courtens, W.; Verstraete, H.; Stienen, E. W. M.; Poot, M. J. M.

    2017-09-01

    Breeding success of seabirds critically depends on their foraging success offshore. However, studies combining at-sea tracking and visual provisioning observations are scarce, especially for smaller species of seabirds. This study is the first in which breeding Sandwich Terns were tracked with GPS-loggers to collect detailed data on foraging habitat use in four breeding seasons. The maximum home range of individual Sandwich Terns comprised approximately 1900 km2 and the average foraging range was 27 km. Trip durations were on average 135 min with average trip lengths of 67 km. Actual foraging behaviour comprised 35% of the time budget of a foraging trip. Substantial year-to-year variation was found in habitat use and trip variables, yet with the exception of 2012, home range size remained similar between years. Food availability, chick age and environmental conditions are proposed as the main driving factors between inter- and intra-annual variations in trip variables. Our multi-method approach also provided geo-referenced information on prey presence and we conclude that future combining of colony observations and GPS-loggers deployments can potentially provide a near complete insight into the feeding ecology of breeding Sandwich Terns, including the behaviour of birds at sea.

  1. Cannabis microbiome sequencing reveals several mycotoxic fungi native to dispensary grade Cannabis flowers [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Kevin McKernan

    2016-05-01

    Full Text Available The Center for Disease Control estimates 128,000 people in the U.S. are hospitalized annually due to food borne illnesses. This has created a demand for food safety testing targeting the detection of pathogenic mold and bacteria on agricultural products. This risk extends to medical Cannabis and is of particular concern with inhaled, vaporized and even concentrated Cannabis products . As a result, third party microbial testing has become a regulatory requirement in the medical and recreational Cannabis markets, yet knowledge of the Cannabis microbiome is limited. Here we describe the first next generation sequencing survey of the fungal communities found in dispensary based Cannabis flowers by ITS2 sequencing, and demonstrate the sensitive detection of several toxigenic Penicillium and Aspergillus species, including P. citrinum and P. paxilli, that were not detected by one or more culture-based methods currently in use for safety testing.

  2. A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types

    Science.gov (United States)

    Wagner, Emily C.; Schellenberg, John J.; Links, Matthew G.; van Schalkwyk, Julie; Reid, Gregor; Hemmingsen, Sean M.; Hill, Janet E.; Money, Deborah

    2015-01-01

    The vaginal microbiota is important in women’s reproductive and overall health. However, the relationships between the structure, function and dynamics of this complex microbial community and health outcomes remain elusive. The objective of this study was to determine the phylogenetic range and abundance of prokaryotes in the vaginal microbiota of healthy, non-pregnant, ethnically diverse, reproductive-aged Canadian women. Socio-demographic, behavioural and clinical data were collected and vaginal swabs were analyzed from 310 women. Detailed profiles of their vaginal microbiomes were generated by pyrosequencing of the chaperonin-60 universal target. Six community state types (CST) were delineated by hierarchical clustering, including three Lactobacillus-dominated CST (L. crispatus, L. iners, L. jensenii), two Gardnerella-dominated (subgroups A and C) and an “intermediate” CST which included a small number of women with microbiomes dominated by seven other species or with no dominant species but minority populations of Streptococcus, Staphylococcus, Peptoniphilus, E. coli and various Proteobacteria in co-dominant communities. The striking correspondence between Nugent score and deep sequencing CST continues to reinforce the basic premise provided by the simpler Gram stain method, while additional analyses reveal detailed cpn60-based phylogeny and estimated abundance in microbial communities from vaginal samples. Ethnicity was the only demographic or clinical characteristic predicting CST, with differences in Asian and White women (p = 0.05). In conclusion, this study confirms previous work describing four cpn60-based subgroups of Gardnerella, revealing previously undescribed CST. The data describe the range of bacterial communities seen in Canadian women presenting with no specific vaginal health concerns, and provides an important baseline for future investigations of clinically important cohorts. PMID:26266808

  3. Second generation sequencing and morphological faecal analysis reveal unexpected foraging behaviour by Myotis nattereri (Chiroptera, Vespertilionidae) in winter

    DEFF Research Database (Denmark)

    Hope, Paul R; Bohmann, Kristine; Gilbert, M. Thomas P.

    2014-01-01

    BACKGROUND: Temperate winters produce extreme energetic challenges for small insectivorous mammals. Some bat species inhabiting locations with mild temperate winters forage during brief inter-torpor normothermic periods of activity. However, the winter diet of bats in mild temperate locations is ...

  4. Bovine teat microbiome analysis revealed reduced alpha diversity and significant changes in taxonomic profiles in quarters with a history of mastitis

    Directory of Open Access Journals (Sweden)

    Helene eFalentin

    2016-04-01

    Full Text Available Mastitis is a mammary gland inflammatory disease often due to bacterial infections. Like many other infections, it used to be considered as a host-pathogen interaction driven by host and bacterial determinants. Until now, the involvement of the bovine mammary gland microbiota in the host-pathogen interaction has been poorly investigated, and mainly during the infectious episode. In this study, the bovine teat microbiome was investigated in 31 quarters corresponding to 27 animals, which were all free of inflammation at sampling time but which had different histories regarding mastitis: from no episode of mastitis on all the previous lactations (Healthy quarter, Hq to one or several clinical mastitis events (Mastitic quarter, Mq. Several quarters whose status was unclear (possible history of subclinical mastitis were classified as NDq. Total bacterial DNA was extracted from foremilk samples and swab samples of the teat canal. Taxonomic profiles were determined by pyrosequencing on 16s amplicons of the V3-4 region. Hq quarters showed a higher diversity compared to Mq ones (Shannon index: ~8 and 6, respectively. Clustering of the quarters based on their bacterial composition made it possible to separate Mq and Hq quarters into two separate clusters (C1 and C2, respectively. Discriminant analysis of taxonomic profiles between these clusters revealed several differences and allowed the identification of taxonomic markers in relation to mastitis history. C2 quarters were associated with a higher proportion of the Clostridia class (including genera such as Ruminococcus, Oscillospira, Roseburia, Dorea, etc., the Bacteroidetes phylum (Prevotella, Bacteroides, Paludibacter, etc., and the Bifidobacteriales order (Bifidobacterium, whereas C1 quarters showed a higher proportion of the Bacilli class (Staphylococcus and Chlamydiia class. These results indicate that microbiota is altered in udders which have already developed mastitis, even far from the

  5. Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia

    Science.gov (United States)

    Engel, Juan C.; Ruby, J. Graham; Ganem, Donald; Andino, Raul; DeRisi, Joseph L.

    2011-01-01

    Honey bees (Apis mellifera) play a critical role in global food production as pollinators of numerous crops. Recently, honey bee populations in the United States, Canada, and Europe have suffered an unexplained increase in annual losses due to a phenomenon known as Colony Collapse Disorder (CCD). Epidemiological analysis of CCD is confounded by a relative dearth of bee pathogen field studies. To identify what constitutes an abnormal pathophysiological condition in a honey bee colony, it is critical to have characterized the spectrum of exogenous infectious agents in healthy hives over time. We conducted a prospective study of a large scale migratory bee keeping operation using high-frequency sampling paired with comprehensive molecular detection methods, including a custom microarray, qPCR, and ultra deep sequencing. We established seasonal incidence and abundance of known viruses, Nosema sp., Crithidia mellificae, and bacteria. Ultra deep sequence analysis further identified four novel RNA viruses, two of which were the most abundant observed components of the honey bee microbiome (∼1011 viruses per honey bee). Our results demonstrate episodic viral incidence and distinct pathogen patterns between summer and winter time-points. Peak infection of common honey bee viruses and Nosema occurred in the summer, whereas levels of the trypanosomatid Crithidia mellificae and Lake Sinai virus 2, a novel virus, peaked in January. PMID:21687739

  6. Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia.

    Directory of Open Access Journals (Sweden)

    Charles Runckel

    Full Text Available Honey bees (Apis mellifera play a critical role in global food production as pollinators of numerous crops. Recently, honey bee populations in the United States, Canada, and Europe have suffered an unexplained increase in annual losses due to a phenomenon known as Colony Collapse Disorder (CCD. Epidemiological analysis of CCD is confounded by a relative dearth of bee pathogen field studies. To identify what constitutes an abnormal pathophysiological condition in a honey bee colony, it is critical to have characterized the spectrum of exogenous infectious agents in healthy hives over time. We conducted a prospective study of a large scale migratory bee keeping operation using high-frequency sampling paired with comprehensive molecular detection methods, including a custom microarray, qPCR, and ultra deep sequencing. We established seasonal incidence and abundance of known viruses, Nosema sp., Crithidia mellificae, and bacteria. Ultra deep sequence analysis further identified four novel RNA viruses, two of which were the most abundant observed components of the honey bee microbiome (∼10(11 viruses per honey bee. Our results demonstrate episodic viral incidence and distinct pathogen patterns between summer and winter time-points. Peak infection of common honey bee viruses and Nosema occurred in the summer, whereas levels of the trypanosomatid Crithidia mellificae and Lake Sinai virus 2, a novel virus, peaked in January.

  7. Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation.

    Science.gov (United States)

    Kim, Sang Hu; Clark, Shawn T; Surendra, Anuradha; Copeland, Julia K; Wang, Pauline W; Ammar, Ron; Collins, Cathy; Tullis, D Elizabeth; Nislow, Corey; Hwang, David M; Guttman, David S; Cowen, Leah E

    2015-11-01

    The microbiome shapes diverse facets of human biology and disease, with the importance of fungi only beginning to be appreciated. Microbial communities infiltrate diverse anatomical sites as with the respiratory tract of healthy humans and those with diseases such as cystic fibrosis, where chronic colonization and infection lead to clinical decline. Although fungi are frequently recovered from cystic fibrosis patient sputum samples and have been associated with deterioration of lung function, understanding of species and population dynamics remains in its infancy. Here, we coupled high-throughput sequencing of the ribosomal RNA internal transcribed spacer 1 (ITS1) with phenotypic and genotypic analyses of fungi from 89 sputum samples from 28 cystic fibrosis patients. Fungal communities defined by sequencing were concordant with those defined by culture-based analyses of 1,603 isolates from the same samples. Different patients harbored distinct fungal communities. There were detectable trends, however, including colonization with Candida and Aspergillus species, which was not perturbed by clinical exacerbation or treatment. We identified considerable inter- and intra-species phenotypic variation in traits important for host adaptation, including antifungal drug resistance and morphogenesis. While variation in drug resistance was largely between species, striking variation in morphogenesis emerged within Candida species. Filamentation was uncoupled from inducing cues in 28 Candida isolates recovered from six patients. The filamentous isolates were resistant to the filamentation-repressive effects of Pseudomonas aeruginosa, implicating inter-kingdom interactions as the selective force. Genome sequencing revealed that all but one of the filamentous isolates harbored mutations in the transcriptional repressor NRG1; such mutations were necessary and sufficient for the filamentous phenotype. Six independent nrg1 mutations arose in Candida isolates from different patients

  8. Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation.

    Directory of Open Access Journals (Sweden)

    Sang Hu Kim

    2015-11-01

    Full Text Available The microbiome shapes diverse facets of human biology and disease, with the importance of fungi only beginning to be appreciated. Microbial communities infiltrate diverse anatomical sites as with the respiratory tract of healthy humans and those with diseases such as cystic fibrosis, where chronic colonization and infection lead to clinical decline. Although fungi are frequently recovered from cystic fibrosis patient sputum samples and have been associated with deterioration of lung function, understanding of species and population dynamics remains in its infancy. Here, we coupled high-throughput sequencing of the ribosomal RNA internal transcribed spacer 1 (ITS1 with phenotypic and genotypic analyses of fungi from 89 sputum samples from 28 cystic fibrosis patients. Fungal communities defined by sequencing were concordant with those defined by culture-based analyses of 1,603 isolates from the same samples. Different patients harbored distinct fungal communities. There were detectable trends, however, including colonization with Candida and Aspergillus species, which was not perturbed by clinical exacerbation or treatment. We identified considerable inter- and intra-species phenotypic variation in traits important for host adaptation, including antifungal drug resistance and morphogenesis. While variation in drug resistance was largely between species, striking variation in morphogenesis emerged within Candida species. Filamentation was uncoupled from inducing cues in 28 Candida isolates recovered from six patients. The filamentous isolates were resistant to the filamentation-repressive effects of Pseudomonas aeruginosa, implicating inter-kingdom interactions as the selective force. Genome sequencing revealed that all but one of the filamentous isolates harbored mutations in the transcriptional repressor NRG1; such mutations were necessary and sufficient for the filamentous phenotype. Six independent nrg1 mutations arose in Candida isolates from

  9. The functional microbiome of arthropods.

    Science.gov (United States)

    Degli Esposti, Mauro; Martinez Romero, Esperanza

    2017-01-01

    Many studies on the microbiome of animals have been reported but a comprehensive analysis is lacking. Here we present a meta-analysis on the microbiomes of arthropods and their terrestrial habitat, focusing on the functional profile of bacterial communities derived from metabolic traits that are essential for microbial life. We report a detailed analysis of probably the largest set of biochemically defined functional traits ever examined in microbiome studies. This work deals with the phylum proteobacteria, which is usually dominant in marine and terrestrial environments and covers all functions associated with microbiomes. The considerable variation in the distribution and abundance of proteobacteria in microbiomes has remained fundamentally unexplained. This analysis reveals discrete functional groups characteristic for adaptation to anaerobic conditions, which appear to be defined by environmental filtering of taxonomically related taxa. The biochemical diversification of the functional groups suggests an evolutionary trajectory in the structure of arthropods' microbiome, from metabolically versatile to specialized proteobacterial organisms that are adapted to complex environments such as the gut of social insects. Bacterial distribution in arthropods' microbiomes also shows taxonomic clusters that do not correspond to functional groups and may derive from other factors, including common contaminants of soil and reagents.

  10. Animal-Borne Imaging Reveals Novel Insights into the Foraging Behaviors and Diel Activity of a Large-Bodied Apex Predator, the American Alligator (Alligator mississippiensis)

    Science.gov (United States)

    Nifong, James C.; Nifong, Rachel L.; Silliman, Brian R.; Lowers, Russell H.; Guillette, Louis J.; Ferguson, Jake M.; Welsh, Matthew; Abernathy, Kyler; Marshall, Greg

    2014-01-01

    Large-bodied, top- and apex predators (e.g., crocodilians, sharks, wolves, killer whales) can exert strong top-down effects within ecological communities through their interactions with prey. Due to inherent difficulties while studying the behavior of these often dangerous predatory species, relatively little is known regarding their feeding behaviors and activity patterns, information that is essential to understanding their role in regulating food web dynamics and ecological processes. Here we use animal-borne imaging systems (Crittercam) to study the foraging behavior and activity patterns of a cryptic, large-bodied predator, the American alligator (Alligator mississippiensis) in two estuaries of coastal Florida, USA. Using retrieved video data we examine the variation in foraging behaviors and activity patterns due to abiotic factors. We found the frequency of prey-attacks (mean = 0.49 prey attacks/hour) as well as the probability of prey-capture success (mean = 0.52 per attack) were significantly affected by time of day. Alligators attempted to capture prey most frequently during the night. Probability of prey-capture success per attack was highest during morning hours and sequentially lower during day, night, and sunset, respectively. Position in the water column also significantly affected prey-capture success, as individuals’ experienced two-fold greater success when attacking prey while submerged. These estimates are the first for wild adult American alligators and one of the few examples for any crocodilian species worldwide. More broadly, these results reveal that our understandings of crocodilian foraging behaviors are biased due to previous studies containing limited observations of cryptic and nocturnal foraging interactions. Our results can be used to inform greater understanding regarding the top-down effects of American alligators in estuarine food webs. Additionally, our results highlight the importance and power of using animal

  11. Microbes Persist: Using a Systems Biology Approach to Reveal How the Soil Microbiome Shapes Soil Organic Matter

    Science.gov (United States)

    Pett-Ridge, J.

    2017-12-01

    Soils store more carbon than the atmosphere and terrestrial vegetation combined, yet the factors that control its persistence remain elusive. Recent insights have overturned the long-held assumption that carbon stability depends mostly on chemical `recalcitrance' of soil organic matter (SOM). Instead, an emerging paradigm emphasizes how environmental drivers like temperature and moisture, soil minerals, and microbial ecology interact to control SOM formation, stabilization, and turnover. Detailed spectroscopic and isotopic (14C) analyses of mineral-associated SOM show that the oldest carbon in soil may be easily broken down and respired in the laboratory, and that it biochemically resembles microbial cells and metabolites far more than plant material. This places microbial ecophysiology at the center of the soil carbon persistence question. Microbial cells likely interact with mineral surfaces as part of an ecological strategy to condition their environment (e.g. biofilm formation or extracellular enzyme production), and their diverse cellular components likely associate with minerals after cells die. Collectively, these microbial characteristics - metabolic activities, population growth strategies, and cellular biochemistry - can be thought of as `soil ecophysiological traits'. This presentation will explore potential traits that may be fruitful targets for studies evaluating the persistence and importance of microbial products as SOM precursors, and will highlight results showing that soil mineral type influences the microbial communities that colonize mineral surfaces, as well as the quantity and type of mineral-associated carbon that accumulates. I will propose a series of integrated approaches that used together can examine how genomic capacity and activities of soil microbiomes are shaped by edaphic conditions (moisture, temperature, redox regimes) and fundamentally affect the terrestrial soil C pool.

  12. Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds

    Science.gov (United States)

    Links, Matthew G; Demeke, Tigst; Gräfenhan, Tom; Hill, Janet E; Hemmingsen, Sean M; Dumonceaux, Tim J

    2014-01-01

    In order to address the hypothesis that seeds from ecologically and geographically diverse plants harbor characteristic epiphytic microbiota, we characterized the bacterial and fungal microbiota associated with Triticum and Brassica seed surfaces. The total microbial complement was determined by amplification and sequencing of a fragment of chaperonin 60 (cpn60). Specific microorganisms were quantified by qPCR. Bacteria and fungi corresponding to operational taxonomic units (OTU) that were identified in the sequencing study were isolated and their interactions examined. A total of 5477 OTU were observed from seed washes. Neither total epiphytic bacterial load nor community richness/evenness was significantly different between the seed types; 578 OTU were shared among all samples at a variety of abundances. Hierarchical clustering revealed that 203 were significantly different in abundance on Triticum seeds compared with Brassica. Microorganisms isolated from seeds showed 99–100% identity between the cpn60 sequences of the isolates and the OTU sequences from this shared microbiome. Bacterial strains identified as Pantoea agglomerans had antagonistic properties toward one of the fungal isolates (Alternaria sp.), providing a possible explanation for their reciprocal abundances on both Triticum and Brassica seeds. cpn60 enabled the simultaneous profiling of bacterial and fungal microbiota and revealed a core seed-associated microbiota shared between diverse plant genera. PMID:24444052

  13. Different foraging preferences of hummingbirds on artificial and natural flowers reveal mechanisms structuring plant-pollinator interactions.

    Science.gov (United States)

    Maglianesi, María A; Böhning-Gaese, Katrin; Schleuning, Matthias

    2015-05-01

    In plant-pollinator networks, the floral morphology of food plants is an important determinant of the interaction niche of pollinators. Studies on foraging preferences of pollinators combining experimental and observational approaches may help to understand the mechanisms behind patterns of interactions and niche partitioning within pollinator communities. In this study, we tested whether morphological floral traits were associated with foraging preferences of hummingbirds for artificial and natural flower types in Costa Rica. We performed field experiments with artificial feeders, differing in length and curvature of flower types, to quantify the hummingbirds' interaction niche under unlimited nectar resources. To quantify the interaction niche under real-world conditions of limited nectar resources, we measured foraging preferences of hummingbirds for a total of 34 plant species. Artificial feeders were visited by Eupherusa nigriventris and Phaethornis guy in the pre-montane forest, and Lampornis calolaemus in the lower montane forest. Under experimental conditions, all three hummingbird species overlapped their interaction niches and showed a preference for the short artificial flower type over the long-straight and the long-curved flower types. Under natural conditions, the two co-occurring hummingbird species preferred to feed on plant species with floral traits corresponding to their bill morphology. The short-billed hummingbird E. nigriventris preferred to feed on short and straight flowers, whereas the long- and curved-billed P. guy preferred long and curved natural flowers. The medium-size billed species L. calolaemus preferred to feed on flowers of medium length and did not show preferences for plant species with specific corolla curvature. Our results show that floral morphological traits constrain access by short-billed hummingbird species to nectar resources. Morphological constraints, therefore, represent one important mechanism structuring trophic

  14. On revealing the gene targets of Ebola virus microRNAs involved in the human skin microbiome

    Directory of Open Access Journals (Sweden)

    Pei-Chun Hsu

    2018-01-01

    Full Text Available Ebola virus, a negative-sense single-stranded RNA virus, causes severe viral hemorrhagic fever and has a high mortality rate. Histopathological and immunopathological analyses of Ebola virus have revealed that histopathological changes in skin tissue are associated with various degrees of endothelial cell swelling and necrosis. The interactions of microbes within or on a host are a crucial for the skin immune shield. The discovery of microRNAs (miRNAs in Ebola virus implies that immune escape, endothelial cell rupture, and tissue dissolution during Ebola virus infection are a result of the effects of Ebola virus miRNAs. Keratinocytes obtained from normal skin can attach and spread through expression of the thrombospondin family of proteins, playing a role in initiation of cell-mediated immune responses in the skin. Several miRNAs have been shown to bind the 3′ untranslated region of thrombospondin mRNA, thereby controlling its stability and translational activity. In this study, we discovered short RNA sequences that may act as miRNAs from Propionibacterium acnes using a practical workflow of bioinformatics methods. Subsequently, we deciphered the common target gene. These RNA sequences tended to bind to the same thrombospondin protein, THSD4, emphasizing the potential importance of the synergistic binding of miRNAs from Ebola virus, Propionibacterium acnes, and humans to the target. These results provide important insights into the molecular mechanisms of thrombospondin proteins and miRNAs in Ebola virus infection.

  15. The Microbiome of Seriola lalandi of Wild and Aquaculture Origin Reveals Differences in Composition and Potential Function

    Directory of Open Access Journals (Sweden)

    Carolina Ramírez

    2017-09-01

    Full Text Available Seriola lalandi is an economically important species that is globally distributed in temperate and subtropical marine waters. Aquaculture production of this species has had problems associated with intensive fish farming, such as disease outbreaks or nutritional deficiencies causing high mortalities. Intestinal microbiota has been involved in many processes that benefit the host, such as disease control, stimulation of the immune response, and the promotion of nutrient metabolism, among others. However, little is known about the potential functionality of the microbiota and the differences in the composition between wild and aquacultured fish. Here, we assayed the V4-region of the 16S rRNA gene using high-throughput sequencing. Our results showed that there are significant differences between S. lalandi of wild and aquaculture origin (ANOSIM and PERMANOVA, P < 0.05. At the genus level, a total of 13 genera were differentially represented between the two groups, all of which have been described as beneficial microorganisms that have an antagonistic effect against pathogenic bacteria, improve immunological parameters and growth performance, and contribute to nutrition. Additionally, the changes in the presumptive functions of the intestinal microbiota of yellowtail were examined by predicting the metagenomes using PICRUSt. The most abundant functional categories were those corresponding to the metabolism of cofactors and vitamins, amino acid metabolism and carbohydrate metabolism, revealing differences in the contribution of the microbiota depending on the origin of the animals. To our knowledge, this is the first study to characterize and compare the intestinal microbiota of S. lalandi of wild and aquaculture origin using high-throughput sequencing.

  16. The Microbiome of Seriola lalandi of Wild and Aquaculture Origin Reveals Differences in Composition and Potential Function.

    Science.gov (United States)

    Ramírez, Carolina; Romero, Jaime

    2017-01-01

    Seriola lalandi is an economically important species that is globally distributed in temperate and subtropical marine waters. Aquaculture production of this species has had problems associated with intensive fish farming, such as disease outbreaks or nutritional deficiencies causing high mortalities. Intestinal microbiota has been involved in many processes that benefit the host, such as disease control, stimulation of the immune response, and the promotion of nutrient metabolism, among others. However, little is known about the potential functionality of the microbiota and the differences in the composition between wild and aquacultured fish. Here, we assayed the V4-region of the 16S rRNA gene using high-throughput sequencing. Our results showed that there are significant differences between S. lalandi of wild and aquaculture origin (ANOSIM and PERMANOVA, P < 0.05). At the genus level, a total of 13 genera were differentially represented between the two groups, all of which have been described as beneficial microorganisms that have an antagonistic effect against pathogenic bacteria, improve immunological parameters and growth performance, and contribute to nutrition. Additionally, the changes in the presumptive functions of the intestinal microbiota of yellowtail were examined by predicting the metagenomes using PICRUSt. The most abundant functional categories were those corresponding to the metabolism of cofactors and vitamins, amino acid metabolism and carbohydrate metabolism, revealing differences in the contribution of the microbiota depending on the origin of the animals. To our knowledge, this is the first study to characterize and compare the intestinal microbiota of S. lalandi of wild and aquaculture origin using high-throughput sequencing.

  17. Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

    DEFF Research Database (Denmark)

    Thorsen, Jonathan; Brejnrod, Asker Daniel; Mortensen, Martin Steen

    2016-01-01

    BACKGROUND: There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of 16S rRNA gene hypervariable regions, aggregating sequence-similar amplicons...

  18. Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level

    Czech Academy of Sciences Publication Activity Database

    Menke, S.; Wasimuddin, Wasimuddin; Meier, M.; Melzheimer, J.; Mfune, J. K. E.; Heinrich, S.; Thalwitzer, S.; Wachter, B.; Sommer, S.

    2014-01-01

    Roč. 5, č. 526 (2014), s. 526 ISSN 1664-302X R&D Projects: GA MŠk EE2.3.20.0303 Institutional support: RVO:68081766 Keywords : gut microbiome * bacteria * oligotyping * carnivores * cheetah (Acinonyx jubatus) * black-backed jackal (Canis mesomelas) * Namibia Subject RIV: EG - Zoology Impact factor: 3.989, year: 2014

  19. Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits

    Directory of Open Access Journals (Sweden)

    Thangasamy Saminathan

    2018-01-01

    Full Text Available The plant microbiome is a key determinant of plant health and productivity, and changes in the plant microbiome can alter the tolerance to biotic and abiotic stresses and the quality of end produce. Little is known about the microbial diversity and its effect on carbohydrate metabolism in ripe fruits. In this study, we aimed to understand the diversity and function of microorganisms in relation to carbohydrate metabolism of ripe watermelon fruits. We used 16S metagenomics and RNAseq metatranscriptomics for analysis of red (PI459074, Congo, and SDRose and yellow fruit-flesh cultivars (PI227202, PI435990, and JBush of geographically and metabolically diverse watermelon cultivars. Metagenomics data showed that Proteobacteria were abundant in SDRose and PI227202, whereas Cyanobacteria were most abundant in Congo and PI4559074. In the case of metatranscriptome data, Proteobacteria was the most abundant in all cultivars. High expression of genes linked to infectious diseases and the expression of peptidoglycan hydrolases associated to pathogenicity of eukaryotic hosts was observed in SDRose, which could have resulted in low microbial diversity in this cultivar. The presence of GH28, associated with polygalacturonase activity in JBush and SDRose could be related to cell wall modifications including de-esterification and depolymerization, and consequent loss of galacturonic acid and neutral sugars. Moreover, based on the KEGG annotation of the expressed genes, nine α-galactosidase genes involved in key processes of galactosyl oligosaccharide metabolism, such as raffinose family were identified and galactose metabolism pathway was reconstructed. Results of this study underline the links between the host and fruit-associated microbiome in carbohydrate metabolism of the ripe fruits. The cultivar difference in watermelon reflects the quantum and diversity of the microbiome, which would benefit watermelon and other plant breeders aiming at the holobiont

  20. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

    2017-08-05

    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HED N/OM ), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Methodology and Ontology in Microbiome Research

    OpenAIRE

    Huss, John

    2014-01-01

    Research on the human microbiome has generated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and enterotype—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statistical methods, coupled with a translational imperative, are the pr...

  2. The Plastisphere "Microbiome"

    Science.gov (United States)

    Amaral-Zettler, L. A.; Dupont, C. L.; Zettler, E. R.; Slikas, B.; Kaul, D.; Mincer, T. J.

    2016-02-01

    Alongside other ocean stressors, plastic marine debris (PMD) is now considered a major source of marine pollution and potential source of invasive alien species, two important ocean health index criteria. While macroplastics are recognized as a visible problem in coastal environments, the less conspicuous microplastics (impact is much less understood. Central to biological interactions with plastic is the almost instant colonization upon entry into the sea by a thin film of microorganisms, the Plastisphere microbiome. While the phylogenetic diversity of the Plastisphere is now recognized to be highly variable and diverse in nature, less is known about its metabolic potential. Using shotgun metagenomics techniques, we characterized the metabolic potential of Plastisphere microbiomes from ocean gyre-collected microplastics and contrasted it with those of known biotic substrates such as macroalgae. Our data reveal that microbial eukaryotic assemblages dominate some Plastisphere communities, and bacteria dominate others, while archaea appear to be consistently rare inhabitants. We have successfully recovered dozens of draft bacterial genomes and several partial eukaryotic genomes from our libraries. Our data allow us to conduct comparative genomics on commonly occurring Plastisphere residents, further gaining insights into their physiology, ecology, pathogenicity, and substrate transformation potential.

  3. Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species.

    Directory of Open Access Journals (Sweden)

    Alexander J Probst

    Full Text Available Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses.

  4. Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens.

    Directory of Open Access Journals (Sweden)

    Oliver Deusch

    Full Text Available Previously, we demonstrated that dietary protein:carbohydrate ratio dramatically affects the fecal microbial taxonomic structure of kittens using targeted 16S gene sequencing. The present study, using the same fecal samples, applied deep Illumina shotgun sequencing to identify the diet-associated functional potential and analyze taxonomic changes of the feline fecal microbiome.Fecal samples from kittens fed one of two diets differing in protein and carbohydrate content (high-protein, low-carbohydrate, HPLC; and moderate-protein, moderate-carbohydrate, MPMC were collected at 8, 12 and 16 weeks of age (n = 6 per group. A total of 345.3 gigabases of sequence were generated from 36 samples, with 99.75% of annotated sequences identified as bacterial. At the genus level, 26% and 39% of reads were annotated for HPLC- and MPMC-fed kittens, with HPLC-fed cats showing greater species richness and microbial diversity. Two phyla, ten families and fifteen genera were responsible for more than 80% of the sequences at each taxonomic level for both diet groups, consistent with the previous taxonomic study. Significantly different abundances between diet groups were observed for 324 genera (56% of all genera identified demonstrating widespread diet-induced changes in microbial taxonomic structure. Diversity was not affected over time. Functional analysis identified 2,013 putative enzyme function groups were different (p<0.000007 between the two dietary groups and were associated to 194 pathways, which formed five discrete clusters based on average relative abundance. Of those, ten contained more (p<0.022 enzyme functions with significant diet effects than expected by chance. Six pathways were related to amino acid biosynthesis and metabolism linking changes in dietary protein with functional differences of the gut microbiome.These data indicate that feline feces-derived microbiomes have large structural and functional differences relating to the dietary

  5. The role of microbiome in central nervous system disorders

    Science.gov (United States)

    Wang, Yan; Kasper, Lloyd H.

    2014-01-01

    Mammals live in a co-evolutionary association with the plethora of microorganisms that reside at a variety of tissue microenvironments. The microbiome represents the collective genomes of these co-existing microorganisms, which is shaped by host factors such as genetics and nutrients but in turn is able to influence host biology in health and disease. Niche-specific microbiome, prominently the gut microbiome, has the capacity to effect both local and distal sites within the host. The gut microbiome has played a crucial role in the bidirectional gut-brain axis that integrates the gut and central nervous system (CNS) activities, and thus the concept of microbiome-gut-brain axis is emerging. Studies are revealing how diverse forms of neuro-immune and neuro-psychiatric disorders are correlated with or modulated by variations of microbiome, microbiota-derived products and exogenous antibiotics and probiotics. The microbiome poises the peripheral immune homeostasis and predisposes host susceptibility to CNS autoimmune diseases such as multiple sclerosis. Neural, endocrine and metabolic mechanisms are also critical mediators of the microbiome-CNS signaling, which are more involved in neuro-psychiatric disorders such as autism, depression, anxiety, stress. Research on the role of microbiome in CNS disorders deepens our academic knowledge about host-microbiome commensalism in central regulation and in practicality, holds conceivable promise for developing novel prognostic and therapeutic avenues for CNS disorders. PMID:24370461

  6. Breaking down the gut microbiome composition in multiple sclerosis.

    Science.gov (United States)

    Budhram, Adrian; Parvathy, Seema; Kremenchutzky, Marcelo; Silverman, Michael

    2017-04-01

    The gut microbiome, which consists of a highly diverse ecologic community of micro-organisms, has increasingly been studied regarding its role in multiple sclerosis (MS) immunopathogenesis. This review critically examines the literature investigating the gut microbiome in MS. A comprehensive search was performed of PubMed databases and ECTRIMS meeting abstracts for literature relating to the gut microbiome in MS. Controlled studies examining the gut microbiome in patients with MS were included for review. Identified studies were predominantly case-control in their design and consistently found differences in the gut microbiome of MS patients compared to controls. We examine plausible mechanistic links between these differences and MS immunopathogenesis, and discuss the therapeutic implications of these findings. Review of the available literature reveals potential immunopathogenic links between the gut microbiome and MS, identifies avenues for therapeutic advancement, and emphasizes the need for further systematic study in this emerging field.

  7. Deep Characterization of the Microbiomes of Calophya spp. (Hemiptera: Calophyidae) Gall-Inducing Psyllids Reveals the Absence of Plant Pathogenic Bacteria and Three Dominant Endosymbionts.

    Science.gov (United States)

    Overholt, Will A; Diaz, Rodrigo; Rosskopf, Erin; Green, Stefan J; Overholt, William A

    2015-01-01

    Bacteria associated with sap-feeding insect herbivores include not only symbionts that may increase their hosts' fitness but also harmful plant pathogens. Calophya spp. gall-inducing psyllids (Hemiptera: Calophyidae) are being investigated for their potential as biological control agents of the noxious weed, Brazilian peppertree (Schinus terebinthifolia), in Florida. Although there are no examples of plant pathogen transmission by members of the family Calophyidae, several insects in the superfamily Psylloidea are known to transmit pathogenic bacteria in the genera Candidatus Liberibacter and Candidatus Phytoplasma. To determine whether Calophya spp. harbor potentially harmful plant pathogenic bacteria, we sequenced small subunit (SSU) ribosomal RNA (rRNA) gene amplicons generated from individuals from four Calophya spp. populations: All microbial SSU gene sequences fell into the bacterial domain, with 98-99% belonging to the Proteobacteria. The Calophya microbiomes contained a relatively simple community, with 49-79 operational taxonomic units (OTUs; 97%) detected, and only 5-8 OTUs with greater than 1% abundance. Candidatus Carsonella showed the highest relative abundance, with OTUs from this candidate genus representing between 51-65% of all recovered sequences. The next most abundant clade observed was an unclassified Enterobacteriacae group closely related to bacteria from the genera Buchnera and Blochmannia that ranged from 20-31% in relative abundance. Wolbachia populations were the third most abundant group and represented 7-27% of the diversity in microbial OTUs. No SSU rRNA gene sequences from putative pathogenic bacteria from the genera Ca. Liberibacter or Ca. Phytoplasma were detected in the microbiomes of the four Calophya populations. The probability that infected psyllids were present in our colonies, but were not sampled, was extremley low (1.39 x 10(-10)). As far as we are aware, our study is the first to characterize the microbiome of a candidate

  8. Deep Characterization of the Microbiomes of Calophya spp. (Hemiptera: Calophyidae Gall-Inducing Psyllids Reveals the Absence of Plant Pathogenic Bacteria and Three Dominant Endosymbionts.

    Directory of Open Access Journals (Sweden)

    Will A Overholt

    Full Text Available Bacteria associated with sap-feeding insect herbivores include not only symbionts that may increase their hosts' fitness but also harmful plant pathogens. Calophya spp. gall-inducing psyllids (Hemiptera: Calophyidae are being investigated for their potential as biological control agents of the noxious weed, Brazilian peppertree (Schinus terebinthifolia, in Florida. Although there are no examples of plant pathogen transmission by members of the family Calophyidae, several insects in the superfamily Psylloidea are known to transmit pathogenic bacteria in the genera Candidatus Liberibacter and Candidatus Phytoplasma. To determine whether Calophya spp. harbor potentially harmful plant pathogenic bacteria, we sequenced small subunit (SSU ribosomal RNA (rRNA gene amplicons generated from individuals from four Calophya spp. populations: All microbial SSU gene sequences fell into the bacterial domain, with 98-99% belonging to the Proteobacteria. The Calophya microbiomes contained a relatively simple community, with 49-79 operational taxonomic units (OTUs; 97% detected, and only 5-8 OTUs with greater than 1% abundance. Candidatus Carsonella showed the highest relative abundance, with OTUs from this candidate genus representing between 51-65% of all recovered sequences. The next most abundant clade observed was an unclassified Enterobacteriacae group closely related to bacteria from the genera Buchnera and Blochmannia that ranged from 20-31% in relative abundance. Wolbachia populations were the third most abundant group and represented 7-27% of the diversity in microbial OTUs. No SSU rRNA gene sequences from putative pathogenic bacteria from the genera Ca. Liberibacter or Ca. Phytoplasma were detected in the microbiomes of the four Calophya populations. The probability that infected psyllids were present in our colonies, but were not sampled, was extremley low (1.39 x 10(-10. As far as we are aware, our study is the first to characterize the microbiome of

  9. Translating the human microbiome

    NARCIS (Netherlands)

    Brown, J.; Vos, de W.M.; Distefano, P.S.; Doré, J.; Huttenhower, C.; Knight, R.; Lawley, T.D.; Raes, J.; Turnbaugh, P.

    2013-01-01

    Over the past decade, an explosion of descriptive analyses from initiatives, such as the Human Microbiome Project (HMP) and the MetaHIT project, have begun to delineate the human microbiome. Inhabitants of the intestinal tract, nasal passages, oral cavities, skin, gastrointestinal tract and

  10. Diet may influence the oral microbiome composition in cats.

    Science.gov (United States)

    Adler, Christina J; Malik, Richard; Browne, Gina V; Norris, Jacqueline M

    2016-06-09

    Periodontal disease is highly prevalent amongst domestic cats, causing pain, gingival bleeding, reduced food intake, loss of teeth and possibly impacts on overall systemic health. Diet has been suggested to play a role in the development of periodontal disease in cats. There is a complete lack of information about how diet (composition and texture) affects the feline oral microbiome, the composition of which may influence oral health and the development of periodontal disease. We undertook a pilot study to assess if lifelong feeding of dry extruded kibble or wet (canned and/or fresh meat combinations) diets to cats (n = 10) with variable oral health affected the microbiome. Oral microbiome composition was assessed by amplifying the V1-V3 region of the 16S gene from supragingival dental plaque DNA extracts. These amplicons were sequenced using Illumina technology. This deep sequencing revealed the feline oral microbiome to be diverse, containing 411 bacterial species from 14 phyla. We found that diet had a significant influence on the overall diversity and abundance of specific bacteria in the oral environment. Cats fed a dry diet exclusively had higher bacterial diversity in their oral microbiome than wet-food diet cats (p microbiome between cats on the two diets assessed, the relationship between these differences and gingival health was unclear. Our preliminary results indicate that further analysis of the influence of dietary constituents and texture on the feline oral microbiome is required to reveal the relationship between diet, the oral microbiome and gingival health in cats.

  11. Gut microbiome and bone.

    Science.gov (United States)

    Ibáñez, Lidia; Rouleau, Matthieu; Wakkach, Abdelilah; Blin-Wakkach, Claudine

    2018-04-11

    The gut microbiome is now viewed as a tissue that interacts bidirectionally with the gastrointestinal, immune, endocrine and nervous systems, affecting the cellular responses in numerous organs. Evidence is accumulating of gut microbiome involvement in a growing number of pathophysiological processes, many of which are linked to inflammatory responses. More specifically, data acquired over the last decade point to effects of the gut microbiome on bone mass regulation and on the development of bone diseases (such as osteoporosis) and of inflammatory joint diseases characterized by bone loss. Mice lacking a gut microbiome have bone mass alteration that can be reversed by gut recolonization. Changes in the gut microbiome composition have been reported in mice with estrogen-deficiency osteoporosis and have also been found in a few studies in humans. Probiotic therapy decreases bone loss in estrogen-deficient animals. The effect of the gut microbiome on bone tissue involves complex mechanisms including modulation of CD4 + T cell activation, control of osteoclastogenic cytokine production and modifications in hormone levels. This complexity may contribute to explain the discrepancies observed betwwen some studies whose results vary depending on the age, gender, genetic background and treatment duration. Further elucidation of the mechanisms involved is needed. However, the available data hold promise that gut microbiome manipulation may prove of interest in the management of bone diseases. Copyright © 2018 Société française de rhumatologie. Published by Elsevier SAS. All rights reserved.

  12. Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases.

    Science.gov (United States)

    Gundogdu, Aycan; Nalbantoglu, Ufuk

    2017-04-01

    A short while ago, the human genome and microbiome were analysed simultaneously for the first time as a multi-omic approach. The analyses of heterogeneous population cohorts showed that microbiome components were associated with human genome variations. In-depth analysis of these results reveals that the majority of those relationships are between immune pathways and autoimmune disease-associated microbiome components. Thus, it can be hypothesized that autoimmunity may be associated with homeostatic disequilibrium of the human-microbiome interactome. Further analysis of human genome-human microbiome relationships in disease contexts with tailored systems biology approaches may yield insights into disease pathogenesis and prognosis.

  13. Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases

    Science.gov (United States)

    Nalbantoglu, Ufuk

    2017-01-01

    A short while ago, the human genome and microbiome were analysed simultaneously for the first time as a multi-omic approach. The analyses of heterogeneous population cohorts showed that microbiome components were associated with human genome variations. In-depth analysis of these results reveals that the majority of those relationships are between immune pathways and autoimmune disease-associated microbiome components. Thus, it can be hypothesized that autoimmunity may be associated with homeostatic disequilibrium of the human-microbiome interactome. Further analysis of human genome–human microbiome relationships in disease contexts with tailored systems biology approaches may yield insights into disease pathogenesis and prognosis. PMID:28785422

  14. Methodology and Ontology in Microbiome Research.

    Science.gov (United States)

    Huss, John

    2014-01-01

    Research on the human microbiome has generated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units-the metagenome, core microbiome, and enterotype-have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statistical methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing the dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely "hardening" into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a "core microbiome," typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of personalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM.

  15. USGS microbiome research

    Science.gov (United States)

    Kellogg, Christina A.; Hopkins, M. Camille

    2017-09-26

    Microbiomes are the communities of microorganisms (for example, bacteria, viruses, and fungi) that live on, in, and around people, plants, animals, soil, water, and the atmosphere. Microbiomes are active in the functioning of diverse ecosystems, for instance, by influencing water quality, nutrient acquisition 
and stress tolerance in plants, and stability of soil and aquatic environments. Microbiome research conducted by the U.S. Geological Survey spans many of our mission areas. Key research areas include water quality, understanding climate effects on soil and permafrost, ecosystem and wildlife health, invasive species, contaminated environments to improve bioremediation, and enhancing energy production. Microbiome research will fundamentally strengthen the ability to address the global challenges of maintaining clean water, ensuring adequate food supply, meeting energy needs, and preserving human and ecosystem health.

  16. Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns

    Czech Academy of Sciences Publication Activity Database

    Gomez, A.; Petrželková, Klára Judita; Burns, M. B.; Yeoman, C. J.; Amato, K. R.; Vlčková, K.; Modrý, David; Todd, A.; Robinson, C. A. J.; Remis, M. J.; Torralba, M.; Morton, E.; Umana, J. D.; Carbonero, F.; Gaskins, H. R.; Nelson, K. E.; Wilson, B. A.; Stumpf, R. M.; White, B. A.; Leigh, S. R.; Blekhman, R.

    2016-01-01

    Roč. 14, č. 9 (2016), s. 2142-2153 ISSN 2211-1247 Institutional support: RVO:60077344 Keywords : western lowland gorillas * microbiome * metabolomics * foraging ecology * anthropogenic interactions Subject RIV: EE - Microbiology, Virology Impact factor: 8.282, year: 2016

  17. Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns

    Czech Academy of Sciences Publication Activity Database

    Gomez, A.; Petrželková, Klára Judita; Burns, M. B.; Yeoman, C. J.; Amato, K. R.; Vlčková, K.; Modrý, D.; Todd, A.; Robinson, C. A. J.; Remis, M. J.; Torralba, M.; Morton, E.; Umana, J. D.; Carbonero, F.; Gaskins, H. R.; Nelson, K.; Wilson, B. A.; Stumpf, R. M.; White, B. A.; Leigh, S. R.; Blekhman, R.

    2016-01-01

    Roč. 14, č. 9 (2016), s. 2142-2153 ISSN 2211-1247 R&D Projects: GA ČR GA206/09/0927 Institutional support: RVO:68081766 Keywords : western lowland gorillas * microbiome * metabolomics * foraging ecology * anthropogenic interactions Subject RIV: EG - Zoology Impact factor: 8.282, year: 2016

  18. Gut microbiomes and their metabolites shape human and animal health.

    Science.gov (United States)

    Park, Woojun

    2018-03-01

    The host genetic background, complex surrounding environments, and gut microbiome are very closely linked to human and animal health and disease. Although significant correlations between gut microbiota and human and animal health have been revealed, the specific roles of each gut bacterium in shaping human and animal health and disease remain unclear. However, recent omics-based studies using experimental animals and surveys of gut microbiota from unhealthy humans have provided insights into the relationships among microbial community, their metabolites, and human and animal health. This editorial introduces six review papers that provide new discoveries of disease-associated microbiomes and suggest possible microbiome-based therapeutic approaches to human disease.

  19. Heat Damaged Forages: Effects on Forage Quality

    Science.gov (United States)

    Traditionally, heat damage in forages has been associated with alterations in forage protein quality as a result of Maillard reactions, and most producers and nutritionists are familiar with this concept. However, this is not necessarily the most important negative consequence of spontaneous heating...

  20. Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species

    Directory of Open Access Journals (Sweden)

    Lena Waidele

    2017-12-01

    Full Text Available The gut microbiome of lower termites comprises protists and bacteria that help these insects to digest cellulose and to thrive on wood. The composition of the termite gut microbiome correlates with phylogenetic distance of the animal host and host ecology (diet in termites collected from their natural environment. However, carryover of transient microbes from host collection sites are an experimental concern and might contribute to the ecological imprints on the termite gut microbiome. Here, we set out to test whether an ecological imprint on the termite gut microbiome remains, when focusing on the persistent microbiome. Therefore, we kept five termite species under strictly controlled dietary conditions and subsequently profiled their protist and bacterial gut microbial communities using 18S and 16S rRNA gene amplicon sequencing. The species differed in their ecology; while three of the investigated species were wood-dwellers that feed on the piece of wood they live in and never leave except for the mating flight, the other two species were foragers that regularly leave their nests to forage for food. Despite these prominent ecological differences, protist microbiome structure aligned with phylogenetic relatedness of termite host species. Conversely, bacterial communities seemed more flexible, suggesting that microbiome structure aligned more strongly with the foraging and wood-dwelling ecologies. Interestingly, protist and bacterial community alpha-diversity correlated, suggesting either putative interactions between protists and bacteria, or that both types of microbes in the termite gut follow shared structuring principles. Taken together, our results add to the notion that bacterial communities are more variable over evolutionary time than protist communities and might react more flexibly to changes in host ecology.

  1. Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species

    KAUST Repository

    Waidele, Lena

    2017-12-19

    The gut microbiome of lower termites comprises protists and bacteria that help these insects to digest cellulose and to thrive on wood. The composition of the termite gut microbiome correlates with phylogenetic distance of the animal host and host ecology (diet) in termites collected from their natural environment. However, carryover of transient microbes from host collection sites are an experimental concern and might contribute to the ecological imprints on the termite gut microbiome. Here, we set out to test whether an ecological imprint on the termite gut microbiome remains, when focusing on the persistent microbiome. Therefore, we kept five termite species under strictly controlled dietary conditions and subsequently profiled their protist and bacterial gut microbial communities using 18S and 16S rRNA gene amplicon sequencing. The species differed in their ecology; while three of the investigated species were wood-dwellers that feed on the piece of wood they live in and never leave except for the mating flight, the other two species were foragers that regularly leave their nests to forage for food. Despite these prominent ecological differences, protist microbiome structure aligned with phylogenetic relatedness of termite host species. Conversely, bacterial communities seemed more flexible, suggesting that microbiome structure aligned more strongly with the foraging and wood-dwelling ecologies. Interestingly, protist and bacterial community alpha-diversity correlated, suggesting either putative interactions between protists and bacteria, or that both types of microbes in the termite gut follow shared structuring principles. Taken together, our results add to the notion that bacterial communities are more variable over evolutionary time than protist communities and might react more flexibly to changes in host ecology.

  2. The Airplane Cabin Microbiome.

    Science.gov (United States)

    Weiss, Howard; Hertzberg, Vicki Stover; Dupont, Chris; Espinoza, Josh L; Levy, Shawn; Nelson, Karen; Norris, Sharon

    2018-06-06

    Serving over three billion passengers annually, air travel serves as a conduit for infectious disease spread, including emerging infections and pandemics. Over two dozen cases of in-flight transmissions have been documented. To understand these risks, a characterization of the airplane cabin microbiome is necessary. Our study team collected 229 environmental samples on ten transcontinental US flights with subsequent 16S rRNA sequencing. We found that bacterial communities were largely derived from human skin and oral commensals, as well as environmental generalist bacteria. We identified clear signatures for air versus touch surface microbiome, but not for individual types of touch surfaces. We also found large flight-to-flight beta diversity variations with no distinguishing signatures of individual flights, rather a high between-flight diversity for all touch surfaces and particularly for air samples. There was no systematic pattern of microbial community change from pre- to post-flight. Our findings are similar to those of other recent studies of the microbiome of built environments. In summary, the airplane cabin microbiome has immense airplane to airplane variability. The vast majority of airplane-associated microbes are human commensals or non-pathogenic, and the results provide a baseline for non-crisis-level airplane microbiome conditions.

  3. Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes: Deterministic assembly of hyporheic microbiomes

    Energy Technology Data Exchange (ETDEWEB)

    Graham, Emily B. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Crump, Alex R. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Resch, Charles T. [Geochemistry Department, Pacific Northwest National Laboratory, Richland WA USA; Fansler, Sarah [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Arntzen, Evan [Environmental Compliance and Emergency Preparation, Pacific Northwest National Laboratory, Richland WA USA; Kennedy, David W. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Fredrickson, Jim K. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Stegen, James C. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA

    2017-03-28

    Subsurface zones of groundwater and surface water mixing (hyporheic zones) are regions of enhanced rates of biogeochemical cycling, yet ecological processes governing hyporheic microbiome composition and function through space and time remain unknown. We sampled attached and planktonic microbiomes in the Columbia River hyporheic zone across seasonal hydrologic change, and employed statistical null models to infer mechanisms generating temporal changes in microbiomes within three hydrologically-connected, physicochemically-distinct geographic zones (inland, nearshore, river). We reveal that microbiomes remain dissimilar through time across all zones and habitat types (attached vs. planktonic) and that deterministic assembly processes regulate microbiome composition in all data subsets. The consistent presence of heterotrophic taxa and members of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum nonetheless suggests common selective pressures for physiologies represented in these groups. Further, co-occurrence networks were used to provide insight into taxa most affected by deterministic assembly processes. We identified network clusters to represent groups of organisms that correlated with seasonal and physicochemical change. Extended network analyses identified keystone taxa within each cluster that we propose are central in microbiome composition and function. Finally, the abundance of one network cluster of nearshore organisms exhibited a seasonal shift from heterotrophic to autotrophic metabolisms and correlated with microbial metabolism, possibly indicating an ecological role for these organisms as foundational species in driving biogeochemical reactions within the hyporheic zone. Taken together, our research demonstrates a predominant role for deterministic assembly across highly-connected environments and provides insight into niche dynamics associated with seasonal changes in hyporheic microbiome composition and metabolism.

  4. Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

    Directory of Open Access Journals (Sweden)

    Vinod K. Gupta

    2017-06-01

    Full Text Available One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats—Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT. The review focuses on the general trend in the human microbiome evolution—a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota—the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome—nature or nurture, host genetics

  5. Core microbiomes for sustainable agroecosystems.

    Science.gov (United States)

    Toju, Hirokazu; Peay, Kabir G; Yamamichi, Masato; Narisawa, Kazuhiko; Hiruma, Kei; Naito, Ken; Fukuda, Shinji; Ushio, Masayuki; Nakaoka, Shinji; Onoda, Yusuke; Yoshida, Kentaro; Schlaeppi, Klaus; Bai, Yang; Sugiura, Ryo; Ichihashi, Yasunori; Minamisawa, Kiwamu; Kiers, E Toby

    2018-05-01

    In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.

  6. Exploring coral microbiome assemblages in the South China Sea.

    Science.gov (United States)

    Cai, Lin; Tian, Ren-Mao; Zhou, Guowei; Tong, Haoya; Wong, Yue Him; Zhang, Weipeng; Chui, Apple Pui Yi; Xie, James Y; Qiu, Jian-Wen; Ang, Put O; Liu, Sheng; Huang, Hui; Qian, Pei-Yuan

    2018-02-05

    Coral reefs are significant ecosystems. The ecological success of coral reefs relies on not only coral-algal symbiosis but also coral-microbial partnership. However, microbiome assemblages in the South China Sea corals remain largely unexplored. Here, we compared the microbiome assemblages of reef-building corals Galaxea (G. fascicularis) and Montipora (M. venosa, M. peltiformis, M. monasteriata) collected from five different locations in the South China Sea using massively-parallel sequencing of 16S rRNA gene and multivariate analysis. The results indicated that microbiome assemblages for each coral species were unique regardless of location and were different from the corresponding seawater. Host type appeared to drive the coral microbiome assemblages rather than location and seawater. Network analysis was employed to explore coral microbiome co-occurrence patterns, which revealed 61 and 80 co-occurring microbial species assembling the Galaxea and Montipora microbiomes, respectively. Most of these co-occurring microbial species were commonly found in corals and were inferred to play potential roles in host nutrient metabolism; carbon, nitrogen, sulfur cycles; host detoxification; and climate change. These findings suggest that the co-occurring microbial species explored might be essential to maintain the critical coral-microbial partnership. The present study provides new insights into coral microbiome assemblages in the South China Sea.

  7. The Serpentinite Subsurface Microbiome

    Science.gov (United States)

    Schrenk, M. O.; Nelson, B. Y.; Brazelton, W. J.

    2011-12-01

    Microbial habitats hosted in ultramafic rocks constitute substantial, globally-distributed portions of the subsurface biosphere, occurring both on the continents and beneath the seafloor. The aqueous alteration of ultramafics, in a process known as serpentinization, creates energy rich, high pH conditions, with low concentrations of inorganic carbon which place fundamental constraints upon microbial metabolism and physiology. Despite their importance, very few studies have attempted to directly access and quantify microbial activities and distributions in the serpentinite subsurface microbiome. We have initiated microbiological studies of subsurface seeps and rocks at three separate continental sites of serpentinization in Newfoundland, Italy, and California and compared these results to previous analyses of the Lost City field, near the Mid-Atlantic Ridge. In all cases, microbial cell densities in seep fluids are extremely low, ranging from approximately 100,000 to less than 1,000 cells per milliliter. Culture-independent analyses of 16S rRNA genes revealed low-diversity microbial communities related to Gram-positive Firmicutes and hydrogen-oxidizing bacteria. Interestingly, unlike Lost City, there has been little evidence for significant archaeal populations in the continental subsurface to date. Culturing studies at the sites yielded numerous alkaliphilic isolates on nutrient-rich agar and putative iron-reducing bacteria in anaerobic incubations, many of which are related to known alkaliphilic and subsurface isolates. Finally, metagenomic data reinforce the culturing results, indicating the presence of genes associated with organotrophy, hydrogen oxidation, and iron reduction in seep fluid samples. Our data provide insight into the lifestyles of serpentinite subsurface microbial populations and targets for future quantitative exploration using both biochemical and geochemical approaches.

  8. The fish egg microbiome

    NARCIS (Netherlands)

    Liu, Y.

    2016-01-01

    Y. Liu

    Prof. dr. F. Govers (promotor); Prof. dr. J.M. Raaijmakers (promotor); Dr. I. de Bruijn (co-promotor); Wageningen University, 13 June 2016, 170 pp.

    The fish egg microbiome: diversity and activity against the oomycete pathogen

  9. Longitudinal Effects of Supplemental Forage on the Honey Bee (Apis mellifera) Microbiota and Inter- and Intra-Colony Variability.

    Science.gov (United States)

    Rothman, Jason A; Carroll, Mark J; Meikle, William G; Anderson, Kirk E; McFrederick, Quinn S

    2018-02-03

    Honey bees (Apis mellifera) provide vital pollination services for a variety of agricultural crops around the world and are known to host a consistent core bacterial microbiome. This symbiotic microbial community is essential to many facets of bee health, including likely nutrient acquisition, disease prevention and optimal physiological function. Being that the bee microbiome is likely involved in the digestion of nutrients, we either provided or excluded honey bee colonies from supplemental floral forage before being used for almond pollination. We then used 16S rRNA gene sequencing to examine the effects of forage treatment on the bees' microbial gut communities over four months. In agreement with previous studies, we found that the honey bee gut microbiota is quite stable over time. Similarly, we compared the gut communities of bees from separate colonies and sisters sampled from within the same hive over four months. Surprisingly, we found that the gut microbial communities of individual sisters from the same colony can exhibit as much variation as bees from different colonies. Supplemental floral forage had a subtle effect on the composition of the microbiome during the month of March only, with strains of Gilliamella apicola, Lactobacillus, and Bartonella being less proportionally abundant in bees exposed to forage in the winter. Collectively, our findings show that there is unexpected longitudinal variation within the gut microbial communities of sister honey bees and that supplemental floral forage can subtly alter the microbiome of managed honey bees.

  10. Optimally frugal foraging

    Science.gov (United States)

    Bénichou, O.; Bhat, U.; Krapivsky, P. L.; Redner, S.

    2018-02-01

    We introduce the frugal foraging model in which a forager performs a discrete-time random walk on a lattice in which each site initially contains S food units. The forager metabolizes one unit of food at each step and starves to death when it last ate S steps in the past. Whenever the forager eats, it consumes all food at its current site and this site remains empty forever (no food replenishment). The crucial property of the forager is that it is frugal and eats only when encountering food within at most k steps of starvation. We compute the average lifetime analytically as a function of the frugality threshold and show that there exists an optimal strategy, namely, an optimal frugality threshold k* that maximizes the forager lifetime.

  11. A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation

    Directory of Open Access Journals (Sweden)

    Hassan Brim

    2017-11-01

    Full Text Available Increasing evidence suggests a role of the gut microbiota in colorectal carcinogenesis (CRC. To detect bacterial markers of colorectal cancer in African Americans a metabolomic analysis was performed on fecal water extracts. DNA from stool samples of adenoma and healthy subjects and from colon cancer and matched normal tissues was analyzed to determine the microbiota composition (using 16S rDNA and genomic content (metagenomics. Metagenomic functions with discriminative power between healthy and neoplastic specimens were established. Quantitative Polymerase Chain Reaction (q-PCR using primers and probes specific to Streptococcus sp. VT_162 were used to validate this bacterium association with neoplastic transformation in stool samples from two independent cohorts of African Americans and Chinese patients with colorectal lesions. The metabolomic analysis of adenomas revealed low amino acids content. The microbiota in both cancer vs. normal tissues and adenoma vs. normal stool samples were different at the 16S rRNA gene level. Cross-mapping of metagenomic data led to 9 markers with significant discriminative power between normal and diseased specimens. These markers identified with Streptococcus sp. VT_162. Q-PCR data showed a statistically significant presence of this bacterium in advanced adenoma and cancer samples in an independent cohort of CRC patients. We defined metagenomic functions from Streptococcus sp. VT_162 with discriminative power among cancers vs. matched normal and adenomas vs. healthy subjects’ stools. Streptococcus sp. VT_162 specific 16S rDNA was validated in an independent cohort. These findings might facilitate non-invasive screening for colorectal cancer.

  12. Risso's dolphins plan foraging dives.

    Science.gov (United States)

    Arranz, Patricia; Benoit-Bird, Kelly J; Southall, Brandon L; Calambokidis, John; Friedlaender, Ari S; Tyack, Peter L

    2018-02-28

    Humans remember the past and use that information to plan future actions. Lab experiments that test memory for the location of food show that animals have a similar capability to act in anticipation of future needs, but less work has been done on animals foraging in the wild. We hypothesized that planning abilities are critical and common in breath-hold divers who adjust each dive to forage on prey varying in quality, location and predictability within constraints of limited oxygen availability. We equipped Risso's dolphins with sound-and-motion recording tags to reveal where they focus their attention through their externally observable echolocation and how they fine tune search strategies in response to expected and observed prey distribution. The information from the dolphins was integrated with synoptic prey data obtained from echosounders on an underwater vehicle. At the start of the dives, whales adjusted their echolocation inspection ranges in ways that suggest planning to forage at a particular depth. Once entering a productive prey layer, dolphins reduced their search range comparable to the scale of patches within the layer, suggesting that they were using echolocation to select prey within the patch. On ascent, their search range increased, indicating that they decided to stop foraging within that layer and started searching for prey in shallower layers. Information about prey, learned throughout the dive, was used to plan foraging in the next dive. Our results demonstrate that planning for future dives is modulated by spatial memory derived from multi-modal prey sampling (echoic, visual and capture) during earlier dives. © 2018. Published by The Company of Biologists Ltd.

  13. Antibiotics and the resistant microbiome

    DEFF Research Database (Denmark)

    Sommer, Morten; Dantas, Gautam

    2011-01-01

    . Less appreciated are the concomitant changes in the human microbiome in response to these assaults and their contribution to clinical resistance problems. Studies have shown that pervasive changes to the human microbiota result from antibiotic treatment and that resistant strains can persist for years....... Additionally, culture-independent functional characterization of the resistance genes from the microbiome has demonstrated a close evolutionary relationship between resistance genes in the microbiome and in pathogens. Application of these techniques and novel cultivation methods are expected to significantly...... expand our understanding of the interplay between antibiotics and the microbiome....

  14. Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology

    Czech Academy of Sciences Publication Activity Database

    Gomez, A.; Petrželková, Klára Judita; Yeoman, C. J.; Vlčková, K.; Mrázek, Jakub; Koppová, Ingrid; Carbonero, F.; Ulanov, A.; Modrý, D.; Todd, A.; Torralba, M.; Nelson, K.; Gaskins, H. R.; Wilson, B.; Stumpf, R. M.; White, B. A.; Leigh, S. R.

    2015-01-01

    Roč. 24, č. 10 (2015), s. 2551-2565 ISSN 0962-1083 R&D Projects: GA ČR GA206/09/0927 Institutional support: RVO:68081766 ; RVO:67985904 Keywords : western lowland gorillas * microbiome * metabolomics * foraging ecology * anthropogenic interactions Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 5.947, year: 2015

  15. Gut microbiome composition and metabolomic profiles/nof wild western lowland gorillas (Gorilla gorilla gorilla)/nreflect host ecology

    Czech Academy of Sciences Publication Activity Database

    Gomez, A.; Petrželková, Klára Judita; Yeoman, C. J.; Vlčková, K.; Mrázek, J.; Koppova, I.; Carbonero, F.; Ulanov, A.; Modrý, David; Todd, A.; Torralba, M.; Nelson, K. E.; Gaskins, H. R.; Wilson, B.; Stumpf, R. M.; White, B. A.; Leigh, S. R.

    2015-01-01

    Roč. 24, č. 10 (2015), s. 2551-2565 ISSN 0962-1083 R&D Projects: GA ČR GA206/09/0927 Institutional support: RVO:60077344 Keywords : anthropogenic interactions * foraging ecology * metabolomics * microbiome * western lowland gorillas Subject RIV: EG - Zoology Impact factor: 5.947, year: 2015

  16. The Sphagnum microbiome: new insights from an ancient plant lineage.

    Science.gov (United States)

    Kostka, Joel E; Weston, David J; Glass, Jennifer B; Lilleskov, Erik A; Shaw, A Jonathan; Turetsky, Merritt R

    2016-07-01

    57 I. 57 II. 58 III. 59 IV. 59 V. 61 VI. 62 63 References 63 SUMMARY: Peat mosses of the genus Sphagnum play a major role in global carbon storage and dominate many northern peatland ecosystems, which are currently being subjected to some of the most rapid climate changes on Earth. A rapidly expanding database indicates that a diverse community of microorganisms is intimately associated with Sphagnum, inhabiting the tissues and surface of the plant. Here we summarize the current state of knowledge regarding the Sphagnum microbiome and provide a perspective for future research directions. Although the majority of the microbiome remains uncultivated and its metabolic capabilities uncharacterized, prokaryotes and fungi have the potential to act as mutualists, symbionts, or antagonists of Sphagnum. For example, methanotrophic and nitrogen-fixing bacteria may benefit the plant host by providing up to 20-30% of Sphagnum carbon and nitrogen, respectively. Next-generation sequencing approaches have enabled the detailed characterization of microbiome community composition in peat mosses. However, as with other ecologically or economically important plants, our knowledge of Sphagnum-microbiome associations is in its infancy. In order to attain a predictive understanding of the role of the microbiome in Sphagnum productivity and ecosystem function, the mechanisms of plant-microbiome interactions and the metabolic potential of constituent microbial populations must be revealed. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  17. The plant microbiome explored: implications for experimental botany

    Energy Technology Data Exchange (ETDEWEB)

    Berg, Gabriele; Rybakova, Daria; Grube, Martin; Köberl, Martina

    2015-11-07

    The importance of microbial root inhabitants for plant growth and health was recognized as early as 100 years ago. Recent insights reveal a close symbiotic relationship between plants and their associated microorganisms, and high structural and functional diversity within plant microbiomes. Plants provide microbial communities with specific habitats, which can be broadly categorized as the rhizosphere, phyllosphere, and endosphere. Plant-associated microbes interact with their host in essential functional contexts. They can stimulate germination and growth, help plants fend off disease, promote stress resistance, and influence plant fitness. Therefore, plants have to be considered as metaorganisms within which the associated microbes usually outnumber the cells belonging to the plant host. The structure of the plant microbiome is determined by biotic and abiotic factors but follows ecological rules. Metaorganisms are coevolved species assemblages. The metabolism and morphology of plants and their microbiota are intensively connected with each other, and the interplay of both maintains the functioning and fitness of the holobiont. Our study of the current literature shows that analysis of plant microbiome data has brought about a paradigm shift in our understanding of the diverse structure and functioning of the plant microbiome with respect to the following: (i) the high interplay of bacteria, archaea, fungi, and protists; (ii) the high specificity even at cultivar level; (iii) the vertical transmission of core microbiomes; (iv) the extraordinary function of endophytes; and (v) several unexpected functions and metabolic interactions. The plant microbiome should be recognized as an additional factor in experimental botany and breeding strategies.

  18. The Perinatal Microbiome and Pregnancy: Moving Beyond the Vaginal Microbiome

    Science.gov (United States)

    Prince, Amanda L.; Chu, Derrick M.; Seferovic, Maxim D.; Antony, Kathleen M.; Ma, Jun; Aagaard, Kjersti M.

    2015-01-01

    The human microbiome, the collective genome of the microbial community that is on and within us, has recently been mapped. The initial characterization of healthy subjects has provided investigators with a reference population for interrogating the microbiome in metabolic, intestinal, and reproductive health and disease states. Although it is known that bacteria can colonize the vagina, recent metagenomic studies have shown that the vaginal microbiome varies among reproductive age women. Similarly, the richness and diversity of intestinal microbiota also naturally fluctuate among gravidae in both human and nonhuman primates, as well as mice. Moreover, recent evidence suggests that microbiome niches in pregnancy are not limited to maternal body sites, as the placenta appears to harbor a low biomass microbiome that is presumptively established in early pregnancy and varies in association with a remote history of maternal antenatal infection as well as preterm birth. In this article, we will provide a brief overview on metagenomics science as a means to investigate the microbiome, observations pertaining to both variation and the presumptive potential role of a varied microbiome during pregnancy, and how future studies of the microbiome in pregnancy may lend to a better understanding of human biology, reproductive health, and parturition. PMID:25775922

  19. Bioinformatics for discovery of microbiome variation

    DEFF Research Database (Denmark)

    Brejnrod, Asker Daniel

    of various molecular methods to build hypotheses about the impact of a copper contaminated soil. The introduction is a broad introduction to the field of microbiome research with a focus on the technologies that enable these discoveries and how some of the broader issues have related to this thesis......Sequencing based tools have revolutionized microbiology in recent years. Highthroughput DNA sequencing have allowed high-resolution studies on microbial life in many different environments and at unprecedented low cost. These culture-independent methods have helped discovery of novel bacteria...... 1 ,“Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies”, benchmarked the performance of a variety of popular statistical methods for discovering differentially abundant bacteria . between...

  20. The fecal microbiome in cats with diarrhea.

    Directory of Open Access Journals (Sweden)

    Jan S Suchodolski

    Full Text Available Recent studies have revealed that microbes play an important role in the pathogenesis of gastrointestinal (GI diseases in various animal species, but only limited data is available about the microbiome in cats with GI disease. The aim of this study was to evaluate the fecal microbiome in cats with diarrhea. Fecal samples were obtained from healthy cats (n = 21 and cats with acute (n = 19 or chronic diarrhea (n = 29 and analyzed by sequencing of 16S rRNA genes, and PICRUSt was used to predict the functional gene content of the microbiome. Linear discriminant analysis (LDA effect size (LEfSe revealed significant differences in bacterial groups between healthy cats and cats with diarrhea. The order Burkholderiales, the families Enterobacteriaceae, and the genera Streptococcus and Collinsella were significantly increased in diarrheic cats. In contrast the order Campylobacterales, the family Bacteroidaceae, and the genera Megamonas, Helicobacter, and Roseburia were significantly increased in healthy cats. Phylum Bacteroidetes was significantly decreased in cats with chronic diarrhea (>21 days duration, while the class Erysipelotrichi and the genus Lactobacillus were significantly decreased in cats with acute diarrhea. The observed changes in bacterial groups were accompanied by significant differences in functional gene contents: metabolism of fatty acids, biosynthesis of glycosphingolipids, metabolism of biotin, metabolism of tryptophan, and ascorbate and aldarate metabolism, were all significantly (p<0.001 altered in cats with diarrhea. In conclusion, significant differences in the fecal microbiomes between healthy cats and cats with diarrhea were identified. This dysbiosis was accompanied by changes in bacterial functional gene categories. Future studies are warranted to evaluate if these microbial changes correlate with changes in fecal concentrations of microbial metabolites in cats with diarrhea for the identification of potential diagnostic or

  1. Sex-Specific Effects of Organophosphate Diazinon on the Gut Microbiome and Its Metabolic Functions.

    Science.gov (United States)

    Gao, Bei; Bian, Xiaoming; Mahbub, Ridwan; Lu, Kun

    2017-02-01

    There is growing recognition of the significance of the gut microbiome to human health, and the association between a perturbed gut microbiome with human diseases has been established. Previous studies also show the role of environmental toxicants in perturbing the gut microbiome and its metabolic functions. The wide agricultural use of diazinon, an organophosphate insecticide, has raised serious environmental health concerns since it is a potent neurotoxicant. With studies demonstrating the presence of a microbiome-gut-brain axis, it is possible that gut microbiome perturbation may also contribute to diazinon toxicity. We investigated the impact of diazinon exposure on the gut microbiome composition and its metabolic functions in C57BL/6 mice. We used a combination of 16S rRNA gene sequencing, metagenomics sequencing, and mass spectrometry-based metabolomics profiling in a mouse model to examine the functional impact of diazinon on the gut microbiome. 16S rRNA gene sequencing revealed that diazinon exposure significantly perturbed the gut microbiome, and metagenomic sequencing found that diazinon exposure altered the functional metagenome. Moreover, metabolomics profiling revealed an altered metabolic profile arising from exposure. Of particular significance, these changes were more pronounced for male mice than for female mice. Diazinon exposure perturbed the gut microbiome community structure, functional metagenome, and associated metabolic profiles in a sex-specific manner. These findings may provide novel insights regarding perturbations of the gut microbiome and its functions as a potential new mechanism contributing to diazinon neurotoxicity and, in particular, its sex-selective effects. Citation: Gao B, Bian X, Mahbub R, Lu K. 2017. Sex-specific effects of organophosphate diazinon on the gut microbiome and its metabolic functions. Environ Health Perspect 125:198-206; http://dx.doi.org/10.1289/EHP202.

  2. Alterations of the Gut Microbiome in Hypertension

    Directory of Open Access Journals (Sweden)

    Qiulong Yan

    2017-08-01

    Full Text Available Introduction: Human gut microbiota is believed to be directly or indirectly involved in cardiovascular diseases and hypertension. However, the identification and functional status of the hypertension-related gut microbe(s have not yet been surveyed in a comprehensive manner.Methods: Here we characterized the gut microbiome in hypertension status by comparing fecal samples of 60 patients with primary hypertension and 60 gender-, age-, and body weight-matched healthy controls based on whole-metagenome shotgun sequencing.Results: Hypertension implicated a remarkable gut dysbiosis with significant reduction in within-sample diversity and shift in microbial composition. Metagenome-wide association study (MGWAS revealed 53,953 microbial genes that differ in distribution between the patients and healthy controls (false discovery rate, 0.05 and can be grouped into 68 clusters representing bacterial species. Opportunistic pathogenic taxa, such as, Klebsiella spp., Streptococcus spp., and Parabacteroides merdae were frequently distributed in hypertensive gut microbiome, whereas the short-chain fatty acid producer, such as, Roseburia spp. and Faecalibacterium prausnitzii, were higher in controls. The number of hypertension-associated species also showed stronger correlation to the severity of disease. Functionally, the hypertensive gut microbiome exhibited higher membrane transport, lipopolysaccharide biosynthesis and steroid degradation, while in controls the metabolism of amino acid, cofactors and vitamins was found to be higher. We further provided the microbial markers for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC of 0.78, demonstrating the potential of gut microbiota in prediction of hypertension.Conclusion: These findings represent specific alterations in microbial diversity, genes, species and functions of the hypertensive gut microbiome. Further studies on the causality relationship between

  3. Metagenomic Analysis of the Rumen Microbiome of Steers with Wheat-Induced Frothy Bloat

    OpenAIRE

    Pitta, D. W.; Pinchak, W. E.; Indugu, N.; Vecchiarelli, B.; Sinha, R.; Fulford, J. D.

    2016-01-01

    Frothy bloat is a serious metabolic disorder that affects stocker cattle grazing hard red winter wheat forage in the Southern Great Plains causing reduced performance, morbidity, and mortality. We hypothesize that a microbial dysbiosis develops in the rumen microbiome of stocker cattle when grazing on high quality winter wheat pasture that predisposes them to frothy bloat risk. In this study, rumen contents were harvested from six cannulated steers grazing hard red winter wheat (three with bl...

  4. Captivity humanizes the primate microbiome.

    Science.gov (United States)

    Clayton, Jonathan B; Vangay, Pajau; Huang, Hu; Ward, Tonya; Hillmann, Benjamin M; Al-Ghalith, Gabriel A; Travis, Dominic A; Long, Ha Thang; Tuan, Bui Van; Minh, Vo Van; Cabana, Francis; Nadler, Tilo; Toddes, Barbara; Murphy, Tami; Glander, Kenneth E; Johnson, Timothy J; Knights, Dan

    2016-09-13

    The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome.

  5. Phylotyping and functional analysis of two ancient human microbiomes.

    Directory of Open Access Journals (Sweden)

    Raúl Y Tito

    Full Text Available BACKGROUND: The Human Microbiome Project (HMP is one of the U.S. National Institutes of Health Roadmap for Medical Research. Primary interests of the HMP include the distinctiveness of different gut microbiomes, the factors influencing microbiome diversity, and the functional redundancies of the members of human microbiotas. In this present work, we contribute to these interests by characterizing two extinct human microbiotas. METHODOLOGY/PRINCIPAL FINDINGS: We examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago. Contamination control is a serious issue in ancient DNA research; we use a novel approach to control contamination. After we determined that each sample originated from a different human, we generated 45 thousand shotgun DNA sequencing reads. The phylotyping and functional analysis of these reads reveals a signature consistent with the modern gut ecology. Interestingly, inter-individual variability for phenotypes but not functional pathways was observed. The two ancient samples have more similar functional profiles to each other than to a recently published profile for modern humans. This similarity could not be explained by a chance sampling of the databases. CONCLUSIONS/SIGNIFICANCE: We conduct a phylotyping and functional analysis of ancient human microbiomes, while providing novel methods to control for DNA contamination and novel hypotheses about past microbiome biogeography. We postulate that natural selection has more of an influence on microbiome functional profiles than it does on the species represented in the microbial ecology. We propose that human microbiomes were more geographically structured during pre-Columbian times than today.

  6. Neural Mechanisms of Foraging

    OpenAIRE

    Kolling, Nils; Behrens, Timothy EJ; Mars, Rogier B; Rushworth, Matthew FS

    2012-01-01

    Behavioural economic studies, involving limited numbers of choices, have provided key insights into neural decision-making mechanisms. By contrast, animals’ foraging choices arise in the context of sequences of encounters with prey/food. On each encounter the animal chooses to engage or whether the environment is sufficiently rich that searching elsewhere is merited. The cost of foraging is also critical. We demonstrate humans can alternate between two modes of choice, comparative decision-ma...

  7. Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis.

    Directory of Open Access Journals (Sweden)

    Christopher J Stewart

    Full Text Available The preterm gut microbiome is a complex dynamic community influenced by genetic and environmental factors and is implicated in the pathogenesis of necrotising enterocolitis (NEC and sepsis. We aimed to explore the longitudinal development of the gut microbiome in preterm twins to determine how shared environmental and genetic factors may influence temporal changes and compared this to the expressed breast milk (EBM microbiome. Stool samples (n = 173 from 27 infants (12 twin pairs and 1 triplet set and EBM (n = 18 from 4 mothers were collected longitudinally. All samples underwent PCR-DGGE (denaturing gradient gel electrophoresis analysis and a selected subset underwent 454 pyrosequencing. Stool and EBM shared a core microbiome dominated by Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae. The gut microbiome showed greater similarity between siblings compared to unrelated individuals. Pyrosequencing revealed a reduction in diversity and increasing dominance of Escherichia sp. preceding NEC that was not observed in the healthy twin. Antibiotic treatment had a substantial effect on the gut microbiome, reducing Escherichia sp. and increasing other Enterobacteriaceae. This study demonstrates related preterm twins share similar gut microbiome development, even within the complex environment of neonatal intensive care. This is likely a result of shared genetic and immunomodulatory factors as well as exposure to the same maternal microbiome during birth, skin contact and exposure to EBM. Environmental factors including antibiotic exposure and feeding are additional significant determinants of community structure, regardless of host genetics.

  8. Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis.

    Science.gov (United States)

    Stewart, Christopher J; Marrs, Emma C L; Nelson, Andrew; Lanyon, Clare; Perry, John D; Embleton, Nicholas D; Cummings, Stephen P; Berrington, Janet E

    2013-01-01

    The preterm gut microbiome is a complex dynamic community influenced by genetic and environmental factors and is implicated in the pathogenesis of necrotising enterocolitis (NEC) and sepsis. We aimed to explore the longitudinal development of the gut microbiome in preterm twins to determine how shared environmental and genetic factors may influence temporal changes and compared this to the expressed breast milk (EBM) microbiome. Stool samples (n = 173) from 27 infants (12 twin pairs and 1 triplet set) and EBM (n = 18) from 4 mothers were collected longitudinally. All samples underwent PCR-DGGE (denaturing gradient gel electrophoresis) analysis and a selected subset underwent 454 pyrosequencing. Stool and EBM shared a core microbiome dominated by Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae. The gut microbiome showed greater similarity between siblings compared to unrelated individuals. Pyrosequencing revealed a reduction in diversity and increasing dominance of Escherichia sp. preceding NEC that was not observed in the healthy twin. Antibiotic treatment had a substantial effect on the gut microbiome, reducing Escherichia sp. and increasing other Enterobacteriaceae. This study demonstrates related preterm twins share similar gut microbiome development, even within the complex environment of neonatal intensive care. This is likely a result of shared genetic and immunomodulatory factors as well as exposure to the same maternal microbiome during birth, skin contact and exposure to EBM. Environmental factors including antibiotic exposure and feeding are additional significant determinants of community structure, regardless of host genetics.

  9. Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota.

    Science.gov (United States)

    van Veelen, H Pieter J; Salles, Joana Falcão; Tieleman, B Irene

    2018-05-01

    The microbiome is essential for development, health and homeostasis throughout an animal's life. Yet, the origins and transmission processes governing animal microbiomes remain elusive for non-human vertebrates, oviparous vertebrates in particular. Eggs may function as transgenerational carriers of the maternal microbiome, warranting characterisation of egg microbiome assembly. Here, we investigated maternal and environmental contributions to avian eggshell microbiota in wild passerine birds: woodlark Lullula arborea and skylark Alauda arvensis. Using 16S rRNA gene sequencing, we demonstrated in both lark species, at the population and within-nest levels, that bacterial communities of freshly laid eggs were distinct from the female cloacal microbiome. Instead, soil-borne bacteria appeared to thrive on freshly laid eggs, and eggshell microbiota composition strongly resembled maternal skin, body feather and nest material communities, sources in direct contact with laid eggs. Finally, phylogenetic structure analysis and microbial source tracking underscored species sorting from directly contacting sources rather than in vivo-transferred symbionts. The female-egg-nest system allowed an integrative assessment of avian egg microbiome assembly, revealing mixed modes of symbiont acquisition not previously documented for vertebrate eggs. Our findings illuminated egg microbiome origins, which suggested a limited potential of eggshells for transgenerational transmission, encouraging further investigation of eggshell microbiome functions in vertebrates.

  10. Eelgrass Leaf Surface Microbiomes Are Locally Variable and Highly Correlated with Epibiotic Eukaryotes

    Directory of Open Access Journals (Sweden)

    Mia M. Bengtsson

    2017-07-01

    Full Text Available Eelgrass (Zostera marina is a marine foundation species essential for coastal ecosystem services around the northern hemisphere. Like all macroscopic organisms, it possesses a microbiome (here defined as an associated prokaryotic community which may play critical roles in modulating the interaction of eelgrass with its environment. For example, its leaf surface microbiome could inhibit or attract eukaryotic epibionts which may overgrow the eelgrass leading to reduced primary productivity and subsequent eelgrass meadow decline. We used amplicon sequencing of the 16S and 18S rRNA genes of prokaryotes and eukaryotes to assess the leaf surface microbiome (prokaryotes as well as eukaryotic epibionts in- and outside lagoons on the German Baltic Sea coast. Prokaryote microbiomes varied substantially both between sites inside lagoons and between open coastal and lagoon sites. Water depth, leaf area and biofilm chlorophyll a concentration explained a large amount of variation in both prokaryotic and eukaryotic community composition. The prokaryotic microbiome and eukaryotic epibiont communities were highly correlated, and network analysis revealed disproportionate co-occurrence between a limited number of eukaryotic taxa and several bacterial taxa. This suggests that eelgrass leaf surfaces are home to a mosaic of microbiomes of several epibiotic eukaryotes, in addition to the microbiome of the eelgrass itself. Our findings thereby underline that eukaryotic diversity should be taken into account in order to explain prokaryotic microbiome assembly and dynamics in aquatic environments.

  11. Whose urban forest? The political ecology of foraging urban nontimber forest products

    Science.gov (United States)

    Patrick T. Hurley; Marla R. Emery; Rebecca McLain; Melissa Poe; Brian Grabbatin; Cari L. Goetcheus

    2015-01-01

    Drawing on case studies of foraging in Philadelphia, Pennsylvania and Mt. Pleasant, South Carolina, we point to foraging landscapes and practices within diverse urban forest spaces. We examine these spaces in relation to U.S. conservation and development processes and the effects of management and governance on species valued by foragers. These case studies reveal the...

  12. The skin microbiome: Associations between altered microbial communities and disease.

    Science.gov (United States)

    Weyrich, Laura S; Dixit, Shreya; Farrer, Andrew G; Cooper, Alan J; Cooper, Alan J

    2015-11-01

    A single square centimetre of the human skin can contain up to one billion microorganisms. These diverse communities of bacteria, fungi, mites and viruses can provide protection against disease, but can also exacerbate skin lesions, promote disease and delay wound healing. This review addresses the current knowledge surrounding the healthy skin microbiome and examines how different alterations to the skin microbial communities can contribute to disease. Current methodologies are considered, changes in microbial diversity and colonisation by specific microorganisms are discussed in the context of atopic dermatitis, psoriasis, acne vulgaris and chronic wounds. The recent impact of modern Westernised lifestyles on the human skin microbiome is also examined, as well as the potential benefits and pitfalls of novel therapeutic strategies. Further analysis of the human skin microbiome, and its interactions with the host immune system and other commensal microorganisms, will undoubtedly elucidate molecular mechanisms for disease and reveal gateways for novel therapeutic treatment strategies. © 2015 The Australasian College of Dermatologists.

  13. Sewage reflects the microbiomes of human populations.

    Science.gov (United States)

    Newton, Ryan J; McLellan, Sandra L; Dila, Deborah K; Vineis, Joseph H; Morrison, Hilary G; Eren, A Murat; Sogin, Mitchell L

    2015-02-24

    Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However

  14. Short Course in the Microbiome

    Directory of Open Access Journals (Sweden)

    Kimberly Falana

    2015-07-01

    Full Text Available Over the past decade, it has become evident that the microbiome is an important environmental factor that affects many physiological processes, such as cell proliferation and differentiation, behaviour, immune function and metabolism. More importantly, it may contribute to a wide variety of diseases, including cancer, inflammatory diseases, metabolic diseases and responses to pathogens. We expect that international, integrative and interdisciplinary translational research teams, along with the emergence of FDA-approved platforms, will set the framework for microbiome-based therapeutics and diagnostics. We recognize that the microbiome ecosystem offers new promise for personalized/precision medicine and targeted treatment for a variety of diseases. The short course was held as a four-session webinar series in April 2015, taught by pioneers and experts in the microbiome ecosystem, covering a broad range of topics from the healthy microbiome to the effects of an altered microbiome from neonates to adults and the long term effects as it is related to disease, from asthma to cancer. We have learned to appreciate how beneficial our microbes are in breaking down our food, fighting off infections and nurturing our immune system, and this information provides us with ideas as to how we can manipulate our microbiome to prevent certain diseases. However, given the variety of applications, there are scientific challenges, though there are very promising areas in reference to the clinical benefits of understanding more about our microbiome, whether in our gut or on our skin: the outlook is bright. A summary of the short course is presented as a meeting dispatch.

  15. Quantitative microbiome profiling links gut community variation to microbial load.

    Science.gov (United States)

    Vandeputte, Doris; Kathagen, Gunter; D'hoe, Kevin; Vieira-Silva, Sara; Valles-Colomer, Mireia; Sabino, João; Wang, Jun; Tito, Raul Y; De Commer, Lindsey; Darzi, Youssef; Vermeire, Séverine; Falony, Gwen; Raes, Jeroen

    2017-11-23

    Current sequencing-based analyses of faecal microbiota quantify microbial taxa and metabolic pathways as fractions of the sample sequence library generated by each analysis. Although these relative approaches permit detection of disease-associated microbiome variation, they are limited in their ability to reveal the interplay between microbiota and host health. Comparative analyses of relative microbiome data cannot provide information about the extent or directionality of changes in taxa abundance or metabolic potential. If microbial load varies substantially between samples, relative profiling will hamper attempts to link microbiome features to quantitative data such as physiological parameters or metabolite concentrations. Saliently, relative approaches ignore the possibility that altered overall microbiota abundance itself could be a key identifier of a disease-associated ecosystem configuration. To enable genuine characterization of host-microbiota interactions, microbiome research must exchange ratios for counts. Here we build a workflow for the quantitative microbiome profiling of faecal material, through parallelization of amplicon sequencing and flow cytometric enumeration of microbial cells. We observe up to tenfold differences in the microbial loads of healthy individuals and relate this variation to enterotype differentiation. We show how microbial abundances underpin both microbiota variation between individuals and covariation with host phenotype. Quantitative profiling bypasses compositionality effects in the reconstruction of gut microbiota interaction networks and reveals that the taxonomic trade-off between Bacteroides and Prevotella is an artefact of relative microbiome analyses. Finally, we identify microbial load as a key driver of observed microbiota alterations in a cohort of patients with Crohn's disease, here associated with a low-cell-count Bacteroides enterotype (as defined through relative profiling).

  16. The microbiome of uncontacted Amerindians.

    Science.gov (United States)

    Clemente, Jose C; Pehrsson, Erica C; Blaser, Martin J; Sandhu, Kuldip; Gao, Zhan; Wang, Bin; Magris, Magda; Hidalgo, Glida; Contreras, Monica; Noya-Alarcón, Óscar; Lander, Orlana; McDonald, Jeremy; Cox, Mike; Walter, Jens; Oh, Phaik Lyn; Ruiz, Jean F; Rodriguez, Selena; Shen, Nan; Song, Se Jin; Metcalf, Jessica; Knight, Rob; Dantas, Gautam; Dominguez-Bello, M Gloria

    2015-04-03

    Most studies of the human microbiome have focused on westernized people with life-style practices that decrease microbial survival and transmission, or on traditional societies that are currently in transition to westernization. We characterize the fecal, oral, and skin bacterial microbiome and resistome of members of an isolated Yanomami Amerindian village with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group. Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements. These results suggest that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics. AR genes are likely poised for mobilization and enrichment upon exposure to pharmacological levels of antibiotics. Our findings emphasize the need for extensive characterization of the function of the microbiome and resistome in remote nonwesternized populations before globalization of modern practices affects potentially beneficial bacteria harbored in the human body.

  17. Adaptive Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2011-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a recently developed nature-inspired optimization algorithm, which is based on the foraging behavior of E. coli bacteria. Up to now, BFO has been applied successfully to some engineering problems due to its simplicity and ease of implementation. However, BFO possesses a poor convergence behavior over complex optimization problems as compared to other nature-inspired optimization techniques. This paper first analyzes how the run-length unit parameter of BFO controls the exploration of the whole search space and the exploitation of the promising areas. Then it presents a variation on the original BFO, called the adaptive bacterial foraging optimization (ABFO, employing the adaptive foraging strategies to improve the performance of the original BFO. This improvement is achieved by enabling the bacterial foraging algorithm to adjust the run-length unit parameter dynamically during algorithm execution in order to balance the exploration/exploitation tradeoff. The experiments compare the performance of two versions of ABFO with the original BFO, the standard particle swarm optimization (PSO and a real-coded genetic algorithm (GA on four widely-used benchmark functions. The proposed ABFO shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  18. Forage quantity and quality

    Science.gov (United States)

    Jorgenson, Janet C.; Udevitz, Mark S.; Felix, Nancy A.; Douglas, David C.; Reynolds, Patricia E.; Rhode, E.B.

    2002-01-01

    The Porcupine caribou herd has traditionally used the coastal plain of the Arctic National Wildlife Refuge, Alaska, for calving. Availability of nutritious forage has been hypothesized as one of the reasons the Porcupine caribou herd migrates hundreds of kilometers to reach the coastal plain for calving (Kuropat and Bryant 1980, Russell et al. 1993).Forage quantity and quality and the chronology of snowmelt (which determines availability and phenological stages of forage) have been suggested as important habitat attributes that lead calving caribou to select one area over another (Lent 1980, White and Trudell 1980, Eastland et al. 1989). A major question when considering the impact of petroleum development is whether potential displacement of the caribou from the 1002 Area to alternate calving habitat will limit access to high quantity and quality forage.Our study had the following objectives: 1) quantify snowmelt patterns by area; 2) quantify relationships among phenology, biomass, and nutrient content of principal forage species by vegetation type; and 3) determine if traditional concentrated calving areas differ from adjacent areas with lower calving densities in terms of vegetation characteristics.

  19. The sponge microbiome project.

    Science.gov (United States)

    Moitinho-Silva, Lucas; Nielsen, Shaun; Amir, Amnon; Gonzalez, Antonio; Ackermann, Gail L; Cerrano, Carlo; Astudillo-Garcia, Carmen; Easson, Cole; Sipkema, Detmer; Liu, Fang; Steinert, Georg; Kotoulas, Giorgos; McCormack, Grace P; Feng, Guofang; Bell, James J; Vicente, Jan; Björk, Johannes R; Montoya, Jose M; Olson, Julie B; Reveillaud, Julie; Steindler, Laura; Pineda, Mari-Carmen; Marra, Maria V; Ilan, Micha; Taylor, Michael W; Polymenakou, Paraskevi; Erwin, Patrick M; Schupp, Peter J; Simister, Rachel L; Knight, Rob; Thacker, Robert W; Costa, Rodrigo; Hill, Russell T; Lopez-Legentil, Susanna; Dailianis, Thanos; Ravasi, Timothy; Hentschel, Ute; Li, Zhiyong; Webster, Nicole S; Thomas, Torsten

    2017-10-01

    Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere. © The Authors 2017. Published by Oxford University Press.

  20. The sponge microbiome project

    KAUST Repository

    Moitinho-Silva, Lucas

    2017-08-16

    Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.

  1. Cooperative Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2009-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a novel optimization algorithm based on the social foraging behavior of E. coli bacteria. This paper presents a variation on the original BFO algorithm, namely, the Cooperative Bacterial Foraging Optimization (CBFO, which significantly improve the original BFO in solving complex optimization problems. This significant improvement is achieved by applying two cooperative approaches to the original BFO, namely, the serial heterogeneous cooperation on the implicit space decomposition level and the serial heterogeneous cooperation on the hybrid space decomposition level. The experiments compare the performance of two CBFO variants with the original BFO, the standard PSO and a real-coded GA on four widely used benchmark functions. The new method shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  2. Current state of knowledge: the canine gastrointestinal microbiome.

    Science.gov (United States)

    Hooda, Seema; Minamoto, Yasushi; Suchodolski, Jan S; Swanson, Kelly S

    2012-06-01

    Gastrointestinal (GI) microbes have important roles in the nutritional, immunological, and physiologic processes of the host. Traditional cultivation techniques have revealed bacterial density ranges from 10(4) to 10(5) colony forming units (CFU)/g in the stomach, from 10(5) to 10(7) CFU/g in the small intestine, and from 10(9) to 10(11) CFU/g in the colon of healthy dogs. As a small number of bacterial species can be grown and studied in culture, however, progress was limited until the recent emergence of DNA-based techniques. In recent years, DNA sequencing technology and bioinformatics have allowed for better phylogenetic and functional/metabolic characterization of the canine gut microbiome. Predominant phyla include Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, and Actinobacteria. Studies using 16S ribosomal RNA (rRNA) gene pyrosequencing have demonstrated spatial differences along the GI tract and among microbes adhered to the GI mucosa compared to those in intestinal contents or feces. Similar to humans, GI microbiome dysbiosis is common in canine GI diseases such as chronic diarrhea and inflammatory bowel diseases. DNA-based assays have also identified key pathogens contributing to such conditions, including various Clostridium, Campylobacter, Salmonella, and Escherichia spp. Moreover, nutritionists have applied DNA-based techniques to study the effects of dietary interventions such as dietary fiber, prebiotics, and probiotics on the canine GI microbiome and associated health indices. Despite recent advances in the field, the canine GI microbiome is far from being fully characterized and a deeper characterization of the phylogenetic and functional/metabolic capacity of the GI microbiome in health and disease is needed. This paper provides an overview of recent studies performed to characterize the canine GI microbiome.

  3. Stability of the Gorilla Microbiome Despite SIV Infection

    Science.gov (United States)

    Moeller, Andrew H.; Peeters, Martine; Ayouba, Ahidjo; Ngole, Eitel Mpoudi; Esteban, Amadine; Hahn, Beatrice H.; Ochman, Howard

    2015-01-01

    Simian Immunodeficiency Viruses (SIVs) have been discovered in over 45 primate species; however, the pathogenic potential of most SIV strains remains unknown due to difficulties inherent in observing wild populations. Because those SIV infections that are pathogenic have been shown to induce changes in the host's gut microbiome, monitoring the microbiota present in fecal samples can provide a noninvasive means for studying the effects of SIV infection on the health of wild-living primates. Here, we examine the effects of SIVgor, a close relative of SIVcpz of chimpanzees and HIV-1 of humans, on the gut bacterial communities residing within wild gorillas, revealing that gorilla gut microbiomes are exceptionally robust to SIV infection. In contrast to the microbiomes of HIV-1 infected humans and SIVcpz-infected chimpanzees, SIVgor-infected gorilla microbiomes exhibit neither rises in the frequencies of opportunistic pathogens nor elevated rates of microbial turnover within individual hosts. Regardless of SIV infection status, gorilla microbiomes assort into enterotypes, one of which is compositionally analogous to those identified in humans and chimpanzees. The other gorilla enterotype appears specialized for a leaf-based diet and is enriched in environmentally derived bacterial genera. We hypothesize that the acquisition of this gorilla-specific enterotype was enabled by lowered immune-system control over the composition of the microbiome. Our results indicate differences between the pathology of SIVgor and SIVcpz/HIV-1 infections, demonstrating the utility of investigating host microbial ecology as a means for studying disease in wild primates of high conservation priority. PMID:25545295

  4. Stability of the gorilla microbiome despite simian immunodeficiency virus infection.

    Science.gov (United States)

    Moeller, Andrew H; Peeters, Martine; Ayouba, Ahidjo; Ngole, Eitel Mpoudi; Esteban, Amadine; Hahn, Beatrice H; Ochman, Howard

    2015-02-01

    Simian immunodeficiency viruses (SIVs) have been discovered in over 45 primate species; however, the pathogenic potential of most SIV strains remains unknown due to difficulties inherent in observing wild populations. Because those SIV infections that are pathogenic have been shown to induce changes in the host's gut microbiome, monitoring the microbiota present in faecal samples can provide a noninvasive means for studying the effects of SIV infection on the health of wild-living primates. Here, we examine the effects of SIVgor, a close relative of SIVcpz of chimpanzees and HIV-1 of humans, on the gut bacterial communities residing within wild gorillas, revealing that gorilla gut microbiomes are exceptionally robust to SIV infection. In contrast to the microbiomes of HIV-1-infected humans and SIVcpz-infected chimpanzees, SIVgor-infected gorilla microbiomes exhibit neither rises in the frequencies of opportunistic pathogens nor elevated rates of microbial turnover within individual hosts. Regardless of SIV infection status, gorilla microbiomes assort into enterotypes, one of which is compositionally analogous to those identified in humans and chimpanzees. The other gorilla enterotype appears specialized for a leaf-based diet and is enriched in environmentally derived bacterial genera. We hypothesize that the acquisition of this gorilla-specific enterotype was enabled by lowered immune system control over the composition of the microbiome. Our results indicate differences between the pathology of SIVgor and SIVcpz/HIV-1 infections, demonstrating the utility of investigating host microbial ecology as a means for studying disease in wild primates of high conservation priority. © 2014 John Wiley & Sons Ltd.

  5. The plant microbiome explored: implications for experimental botany.

    Science.gov (United States)

    Berg, Gabriele; Rybakova, Daria; Grube, Martin; Köberl, Martina

    2016-02-01

    The importance of microbial root inhabitants for plant growth and health was recognized as early as 100 years ago. Recent insights reveal a close symbiotic relationship between plants and their associated microorganisms, and high structural and functional diversity within plant microbiomes. Plants provide microbial communities with specific habitats, which can be broadly categorized as the rhizosphere, phyllosphere, and endosphere. Plant-associated microbes interact with their host in essential functional contexts. They can stimulate germination and growth, help plants fend off disease, promote stress resistance, and influence plant fitness. Therefore, plants have to be considered as metaorganisms within which the associated microbes usually outnumber the cells belonging to the plant host. The structure of the plant microbiome is determined by biotic and abiotic factors but follows ecological rules. Metaorganisms are co-evolved species assemblages. The metabolism and morphology of plants and their microbiota are intensively connected with each other, and the interplay of both maintains the functioning and fitness of the holobiont. Our study of the current literature shows that analysis of plant microbiome data has brought about a paradigm shift in our understanding of the diverse structure and functioning of the plant microbiome with respect to the following: (i) the high interplay of bacteria, archaea, fungi, and protists; (ii) the high specificity even at cultivar level; (iii) the vertical transmission of core microbiomes; (iv) the extraordinary function of endophytes; and (v) several unexpected functions and metabolic interactions. The plant microbiome should be recognized as an additional factor in experimental botany and breeding strategies. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  6. New Developments in Forage Varieties

    Science.gov (United States)

    Forage crops harvested for hay or haylage or grazed support dairy, beef, sheep and horse production. Additional livestock production from reduced forage acreage supports the need for forage variety improvement. The Consortium for Alfalfa Improvement is a partnership model of government, private no...

  7. Optimal Foraging in Semantic Memory

    Science.gov (United States)

    Hills, Thomas T.; Jones, Michael N.; Todd, Peter M.

    2012-01-01

    Do humans search in memory using dynamic local-to-global search strategies similar to those that animals use to forage between patches in space? If so, do their dynamic memory search policies correspond to optimal foraging strategies seen for spatial foraging? Results from a number of fields suggest these possibilities, including the shared…

  8. The Microbiome and Sustainable Healthcare

    Science.gov (United States)

    Dietert, Rodney R.; Dietert, Janice M.

    2015-01-01

    Increasing prevalences, morbidity, premature mortality and medical needs associated with non-communicable diseases and conditions (NCDs) have reached epidemic proportions and placed a major drain on healthcare systems and global economies. Added to this are the challenges presented by overuse of antibiotics and increased antibiotic resistance. Solutions are needed that can address the challenges of NCDs and increasing antibiotic resistance, maximize preventative measures, and balance healthcare needs with available services and economic realities. Microbiome management including microbiota seeding, feeding, and rebiosis appears likely to be a core component of a path toward sustainable healthcare. Recent findings indicate that: (1) humans are mostly microbial (in terms of numbers of cells and genes); (2) immune dysfunction and misregulated inflammation are pivotal in the majority of NCDs; (3) microbiome status affects early immune education and risk of NCDs, and (4) microbiome status affects the risk of certain infections. Management of the microbiome to reduce later-life health risk and/or to treat emerging NCDs, to spare antibiotic use and to reduce the risk of recurrent infections may provide a more effective healthcare strategy across the life course particularly when a personalized medicine approach is considered. This review will examine the potential for microbiome management to contribute to sustainable healthcare. PMID:27417751

  9. Sewage Reflects the Microbiomes of Human Populations

    Science.gov (United States)

    Newton, Ryan J.; McLellan, Sandra L.; Dila, Deborah K.; Vineis, Joseph H.; Morrison, Hilary G.; Eren, A. Murat

    2015-01-01

    ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. PMID:25714718

  10. Exploring relationships between host genome and microbiome: new insights from genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Muslihudeen Abdul-Razaq Abdul-Aziz

    2016-10-01

    Full Text Available As our understanding of the human microbiome expands, impacts on health and disease continue to be revealed. Alterations in the microbiome can result in dysbiosis, which has now been linked to subsequent autoimmune and metabolic diseases, highlighting the need to identify factors that shape the microbiome. Research has identified that the composition and functions of the human microbiome can be influenced by diet, age, gender, and environment. More recently, studies have explored how human genetic variation may also influence the microbiome. Here, we review several recent analytical advances in this new research area, including those that use genome-wide association studies to examine host genome-microbiome interactions, while controlling for the influence of other factors. We find that current research is limited by small sample sizes, lack of cohort replication, and insufficient confirmatory mechanistic studies. In addition, we discuss the importance of understanding long-term interactions between the host genome and microbiome, as well as the potential impacts of disrupting this relationship, and explore new research avenues that may provide information about the co-evolutionary history of humans and their microorganisms.

  11. Metagenomic Analysis of the Rumen Microbiome of Steers with Wheat-Induced Frothy Bloat.

    Science.gov (United States)

    Pitta, D W; Pinchak, W E; Indugu, N; Vecchiarelli, B; Sinha, R; Fulford, J D

    2016-01-01

    Frothy bloat is a serious metabolic disorder that affects stocker cattle grazing hard red winter wheat forage in the Southern Great Plains causing reduced performance, morbidity, and mortality. We hypothesize that a microbial dysbiosis develops in the rumen microbiome of stocker cattle when grazing on high quality winter wheat pasture that predisposes them to frothy bloat risk. In this study, rumen contents were harvested from six cannulated steers grazing hard red winter wheat (three with bloat score "2" and three with bloat score "0"), extracted for genomic DNA and subjected to 16S rDNA and shotgun sequencing on 454/Roche platform. Approximately 1.5 million reads were sequenced, assembled and assigned for phylogenetic and functional annotations. Bacteria predominated up to 84% of the sequences while archaea contributed to nearly 5% of the sequences. The abundance of archaea was higher in bloated animals (P bloated samples. Co-occurrence analysis revealed syntrophic associations between bacteria and archaea in non-bloated samples, however; such interactions faded in bloated samples. Functional annotations of assembled reads to Subsystems database revealed the abundance of several metabolic pathways, with carbohydrate and protein metabolism well represented. Assignment of contigs to CaZy database revealed a greater diversity of Glycosyl Hydrolases dominated by oligosaccharide breaking enzymes (>70%) in non-bloated samples. However, the abundance and diversity of CaZymes were greatly reduced in bloated samples indicating the disruption of carbohydrate metabolism. We conclude that mild to moderate frothy bloat results from tradeoffs both within and between microbial domains due to greater competition for substrates that are of limited availability as a result of biofilm formation.

  12. Metagenomic Analysis of the Human Gut Microbiome

    DEFF Research Database (Denmark)

    dos Santos, Marcelo Bertalan Quintanilha

    Understanding the link between the human gut microbiome and human health is one of the biggest scientific challenges in our decade. Because 90% of our cells are bacteria, and the microbial genome contains 200 times more genes than the human genome, the study of the human microbiome has...... the potential to impact many areas of our health. This PhD thesis is the first study to generate a large amount of experimental data on the DNA and RNA of the human gut microbiome. This was made possible by our development of a human gut microbiome array capable of profiling any human gut microbiome. Analysis...... of our results changes the way we link the gut microbiome with diseases. Our results indicate that inflammatory diseases will affect the ecological system of the human gut microbiome, reducing its diversity. Classification analysis of healthy and unhealthy individuals demonstrates that unhealthy...

  13. Emerging Perspectives on the Natural Microbiome of Fresh Produce Vegetables

    Directory of Open Access Journals (Sweden)

    Colin R. Jackson

    2015-04-01

    Full Text Available Plants harbor a diverse microbiome existing as bacterial populations on the leaf surface (the phyllosphere and within plant tissues (endophytes. The composition of this microbiome has been largely unexplored in fresh produce vegetables, where studies have tended to focus on pathogen detection and survival. However, the application of next-generation 16S rRNA gene sequencing approaches is beginning to reveal the diversity of this produce-associated bacterial community. In this article we review what is known about the composition of the microbiome of fresh produce vegetables, placing it in the context of general phyllosphere research. We also demonstrate how next-generation sequencing can be used to assess the bacterial assemblages present on fresh produce, using fresh herbs as an example. That data shows how the use of such culture-independent approaches can detect groups of taxa (anaerobes, psychrophiles that may be missed by traditional culture-based techniques. Other issues discussed include questions as to whether to determine the microbiome during plant growth or at point of purchase or consumption, and the potential role of the natural bacterial community in mitigating pathogen survival.

  14. Genetic Characterization of the Gut Microbiome of Hajj Pilgrims

    KAUST Repository

    Beaudoin, Christopher

    2018-05-01

    Hajj, the annual Islamic pilgrimage to Makkah, Saudi Arabia, is a unique mass gathering event that brings more than 2 million individuals from around the world. Several public health considerations, such as the spread of infectious diseases, must be taken into account with this large temporary influx of people. Gastrointestinal diseases, such as diarrhea, are common at Hajj, yet little is known about the etiology. The human gut microbiome, collection of organisms residing within the intestinal tract, has been under intense study recently, since next generation DNA sequencing technologies allow for extensive surveying of genetic material found in complex biological samples, such as those containing many different organisms. Thus, using 16S rRNA and metagenomic shotgun sequencing, we have characterized the gut microbiome of over 612 pilgrims with and without diarrhea. Several metadata factors, such as hospitalization and different comorbidities, were found to have significant effects on the overall gut microbiome composition. Metagenomic shotgun sequencing efforts revealed the presence of antimicrobial resistance genes originating from disparate regions from around the world. This study provides a snapshot of information concerning the health status of the gut microbiome of Hajj pilgrims and provides more context to the investigation of how to best prepare for mass gathering events.

  15. Structure, function and diversity of the healthy human microbiome.

    Science.gov (United States)

    2012-06-13

    Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

  16. An integrated catalog of reference genes in the human gut microbiome

    DEFF Research Database (Denmark)

    Li, Junhua; Jia, Huijue; Cai, Xianghang

    2014-01-01

    Many analyses of the human gut microbiome depend on a catalog of reference genes. Existing catalogs for the human gut microbiome are based on samples from single cohorts or on reference genomes or protein sequences, which limits coverage of global microbiome diversity. Here we combined 249 newly...... signatures. This expanded catalog should facilitate quantitative characterization of metagenomic, metatranscriptomic and metaproteomic data from the gut microbiome to understand its variation across populations in human health and disease.......) comprising 9,879,896 genes. The catalog includes close-to-complete sets of genes for most gut microbes, which are also of considerably higher quality than in previous catalogs. Analyses of a group of samples from Chinese and Danish individuals using the catalog revealed country-specific gut microbial...

  17. Effect of forage quality in faeces from different ruminant species fed high and low quality forage

    DEFF Research Database (Denmark)

    Jalali, A R; Nørgaard, P; Nielsen, M O

    2010-01-01

    Effect of forage quality in faeces from different ruminant species fed high and low quality forage......Effect of forage quality in faeces from different ruminant species fed high and low quality forage...

  18. Characterization of the human gut microbiome during travelers' diarrhea.

    Science.gov (United States)

    Youmans, Bonnie P; Ajami, Nadim J; Jiang, Zhi-Dong; Campbell, Frederick; Wadsworth, W Duncan; Petrosino, Joseph F; DuPont, Herbert L; Highlander, Sarah K

    2015-01-01

    Alterations in the gut microbiota are correlated with ailments such as obesity, inflammatory bowel disease, and diarrhea. Up to 60% of individuals traveling from industrialized to developing countries acquire a form of secretory diarrhea known as travelers' diarrhea (TD), and enterotoxigenic Escherichia coli (ETEC) and norovirus (NoV) are the leading causative pathogens. Presumably, TD alters the gut microbiome, however the effect of TD on gut communities has not been studied. We report the first analysis of bacterial gut populations associated with TD. We examined and compared the gut microbiomes of individuals who developed TD associated with ETEC, NoV, or mixed pathogens, and TD with no pathogen identified, to healthy travelers. We observed a signature dysbiotic gut microbiome profile of high Firmicutes:Bacteroidetes ratios in the travelers who developed diarrhea, regardless of etiologic agent or presence of a pathogen. There was no significant difference in α-diversity among travelers. The bacterial composition of the microbiota of the healthy travelers was similar to the diarrheal groups, however the β-diversity of the healthy travelers was significantly different than any pathogen-associated TD group. Further comparison of the healthy traveler microbiota to those from healthy subjects who were part of the Human Microbiome Project also revealed a significantly higher Firmicutes:Bacteriodetes ratio in the healthy travelers and significantly different β-diversity. Thus, the composition of the gut microbiome in healthy, diarrhea-free travelers has characteristics of a dysbiotic gut, suggesting that these alterations could be associated with factors such as travel.

  19. The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions.

    Science.gov (United States)

    Bragina, Anastasia; Oberauner-Wappis, Lisa; Zachow, Christin; Halwachs, Bettina; Thallinger, Gerhard G; Müller, Henry; Berg, Gabriele

    2014-09-01

    Sphagnum-dominated bogs represent a unique yet widely distributed type of terrestrial ecosystem and strongly contribute to global biosphere functioning. Sphagnum is colonized by highly diverse microbial communities, but less is known about their function. We identified a high functional diversity within the Sphagnum microbiome applying an Illumina-based metagenomic approach followed by de novo assembly and MG-RAST annotation. An interenvironmental comparison revealed that the Sphagnum microbiome harbours specific genetic features that distinguish it significantly from microbiomes of higher plants and peat soils. The differential traits especially support ecosystem functioning by a symbiotic lifestyle under poikilohydric and ombrotrophic conditions. To realise a plasticity-stability balance, we found abundant subsystems responsible to cope with oxidative and drought stresses, to exchange (mobile) genetic elements, and genes that encode for resistance to detrimental environmental factors, repair and self-controlling mechanisms. Multiple microbe-microbe and plant-microbe interactions were also found to play a crucial role as indicated by diverse genes necessary for biofilm formation, interaction via quorum sensing and nutrient exchange. A high proportion of genes involved in nitrogen cycle and recycling of organic material supported the role of bacteria for nutrient supply. 16S rDNA analysis indicated a higher structural diversity than that which had been previously detected using PCR-dependent techniques. Altogether, the diverse Sphagnum microbiome has the ability to support the life of the host plant and the entire ecosystem under changing environmental conditions. Beyond this, the moss microbiome presents a promising bio-resource for environmental biotechnology - with respect to novel enzymes or stress-protecting bacteria. © 2014 John Wiley & Sons Ltd.

  20. Foraging niche segregation in Malaysian babblers (Family: Timaliidae)

    Science.gov (United States)

    Mansor, Mohammad Saiful; Ramli, Rosli

    2017-01-01

    Tropical rainforests are considered as hotspots for bird diversity, yet little is known about the system that upholds the coexistence of species. Differences in body size that are associated with foraging strategies and spatial distribution are believed to promote the coexistence of closely related species by reducing competition. However, the fact that many babbler species do not differ significantly in their morphology has challenged this view. We studied the foraging ecology of nine sympatric babbler species (i.e., Pellorneum capistratum, P. bicolor, P. malaccense, Malacopteron cinereum, M. magnum, Stachyris nigriceps, S. nigricollis, S. maculata, and Cyanoderma erythropterum) in the Krau Wildlife Reserve in Peninsular Malaysia. We investigated; i) how these babblers forage in the wild and use vegetation to obtain food, and ii) how these trophically similar species differ in spatial distribution and foraging tactics. Results indicated that most babblers foraged predominantly on aerial leaf litter and used gleaning manoeuvre in intermediate-density foliage but exhibited wide ranges of vertical strata usage, thus reducing interspecific competition. The principal component analysis indicated that two components, i.e., foraging height and substrate are important as mechanisms to allow the coexistence of sympatric babblers. The present findings revealed that these bird species have unique foraging niches that are distinct from each other, and this may apply to other insectivorous birds inhabiting tropical forests. This suggests that niche separation does occur among coexisting birds, thus following Gause’ law of competitive exclusion, which states two species occupying the same niche will not stably coexist. PMID:28253284

  1. Foraging niche segregation in Malaysian babblers (Family: Timaliidae.

    Directory of Open Access Journals (Sweden)

    Mohammad Saiful Mansor

    Full Text Available Tropical rainforests are considered as hotspots for bird diversity, yet little is known about the system that upholds the coexistence of species. Differences in body size that are associated with foraging strategies and spatial distribution are believed to promote the coexistence of closely related species by reducing competition. However, the fact that many babbler species do not differ significantly in their morphology has challenged this view. We studied the foraging ecology of nine sympatric babbler species (i.e., Pellorneum capistratum, P. bicolor, P. malaccense, Malacopteron cinereum, M. magnum, Stachyris nigriceps, S. nigricollis, S. maculata, and Cyanoderma erythropterum in the Krau Wildlife Reserve in Peninsular Malaysia. We investigated; i how these babblers forage in the wild and use vegetation to obtain food, and ii how these trophically similar species differ in spatial distribution and foraging tactics. Results indicated that most babblers foraged predominantly on aerial leaf litter and used gleaning manoeuvre in intermediate-density foliage but exhibited wide ranges of vertical strata usage, thus reducing interspecific competition. The principal component analysis indicated that two components, i.e., foraging height and substrate are important as mechanisms to allow the coexistence of sympatric babblers. The present findings revealed that these bird species have unique foraging niches that are distinct from each other, and this may apply to other insectivorous birds inhabiting tropical forests. This suggests that niche separation does occur among coexisting birds, thus following Gause' law of competitive exclusion, which states two species occupying the same niche will not stably coexist.

  2. Foraging niche segregation in Malaysian babblers (Family: Timaliidae).

    Science.gov (United States)

    Mansor, Mohammad Saiful; Ramli, Rosli

    2017-01-01

    Tropical rainforests are considered as hotspots for bird diversity, yet little is known about the system that upholds the coexistence of species. Differences in body size that are associated with foraging strategies and spatial distribution are believed to promote the coexistence of closely related species by reducing competition. However, the fact that many babbler species do not differ significantly in their morphology has challenged this view. We studied the foraging ecology of nine sympatric babbler species (i.e., Pellorneum capistratum, P. bicolor, P. malaccense, Malacopteron cinereum, M. magnum, Stachyris nigriceps, S. nigricollis, S. maculata, and Cyanoderma erythropterum) in the Krau Wildlife Reserve in Peninsular Malaysia. We investigated; i) how these babblers forage in the wild and use vegetation to obtain food, and ii) how these trophically similar species differ in spatial distribution and foraging tactics. Results indicated that most babblers foraged predominantly on aerial leaf litter and used gleaning manoeuvre in intermediate-density foliage but exhibited wide ranges of vertical strata usage, thus reducing interspecific competition. The principal component analysis indicated that two components, i.e., foraging height and substrate are important as mechanisms to allow the coexistence of sympatric babblers. The present findings revealed that these bird species have unique foraging niches that are distinct from each other, and this may apply to other insectivorous birds inhabiting tropical forests. This suggests that niche separation does occur among coexisting birds, thus following Gause' law of competitive exclusion, which states two species occupying the same niche will not stably coexist.

  3. Five decades on: Use of historical weaning size data reveals that a decrease in maternal foraging success underpins the long-term decline in population of southern elephant seals (Mirounga leonina.

    Directory of Open Access Journals (Sweden)

    Ella Clausius

    Full Text Available The population of Southern elephant seals (Mirounga leonina at Macquarie Island has declined since the 1960s, and is thought to be due to changing oceanic conditions leading to reductions in the foraging success of Macquarie Island breeding females. To test this hypothesis, we used a 55-year-old data set on weaning size of southern elephant seals to quantify a decrease in weaning size from a period of population stability in 1950s to its present state of on-going decline. Being capital breeders, the size of elephant seal pups at weaning is a direct consequence of maternal foraging success in the preceding year. During the 1940-1950s, the mean of female pups at weaning was similar between the Heard and Macquarie Island populations, while the snout-tail-length length of male weaners from Heard Island were longer than their conspecifics at Macquarie Island. Additionally, the snout-tail-length of pups at weaning decreased by 3cm between the 1950s and 1990s in the Macquarie Island population, concurrent with the observed population decline. Given the importance of weaning size in determining first-year survival and recruitment rates, the decline in the size at weaning suggests that the decline in the Macquarie Island population has, to some extent, been driven by reduced maternal foraging success, consequent declines in the size of pups at weaning, leading to reduced first-year survival rates and recruitment of breeding females into the population 3 to 4 years later.

  4. Review: Maternal health and the placental microbiome.

    Science.gov (United States)

    Pelzer, Elise; Gomez-Arango, Luisa F; Barrett, Helen L; Nitert, Marloes Dekker

    2017-06-01

    Over the past decade, the role of the microbiome in regulating metabolism, immune function and behavior in humans has become apparent. It has become clear that the placenta is not a sterile organ, but rather has its own endogenous microbiome. The composition of the placental microbiome is distinct from that of the vagina and has been reported to resemble the oral microbiome. Compared to the gut microbiome, the placental microbiome exhibits limited microbial diversity. This review will focus on the current understanding of the placental microbiota in normal healthy pregnancy and also in disease states including preterm birth, chorioamnionitis and maternal conditions such as obesity, gestational diabetes mellitus and preeclampsia. Factors known to alter the composition of the placental microbiota will be discussed in the final part of this review. Copyright © 2016. Published by Elsevier Ltd.

  5. Microbiome in parturition and preterm birth.

    Science.gov (United States)

    Mysorekar, Indira U; Cao, Bin

    2014-01-01

    Preterm parturition is a one of the most significant global maternal-child health problem. In recent years, there has been an explosion in reports on a role for microbiomes (i.e., a microbial biomass) on a plethora of physiologic and pathologic human conditions. This review aims to describe our current understanding of the microbiome and its impact on parturition, with particular emphasis on preterm birth. We will focus on the roles of vaginal and oral mucosal microbiomes in premature parturition and describe the state-of-the-art methodologies used in microbiome studies. Next, we will present new studies on a potential microbiome in the placenta and how it may affect pregnancy outcomes. Finally, we will propose that host genetic factors can perturb the normal "pregnancy microbiome" and trigger adverse pregnancy outcomes. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  6. The microbiome of New World vultures.

    Science.gov (United States)

    Roggenbuck, Michael; Bærholm Schnell, Ida; Blom, Nikolaj; Bælum, Jacob; Bertelsen, Mads Frost; Sicheritz-Pontén, Thomas; Pontén, Thomas Sicheritz; Sørensen, Søren Johannes; Gilbert, M Thomas P; Graves, Gary R; Hansen, Lars H

    2014-11-25

    Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the facial skin. Clostridia and Fusobacteria, widely pathogenic to other vertebrates, dominate the vulture's gut microbiota. We reveal a likely faecal-oral-gut route for their origin. DNA of prey species detectable on facial swabs was completely degraded in the gut samples from most vultures, suggesting that the gastrointestinal tracts of vultures are extremely selective. Our findings show a strong adaption of vultures and their bacteria to their food source, exemplifying a specialized host-microbial alliance.

  7. The microbiome of New World vultures

    DEFF Research Database (Denmark)

    Roggenbuck, Michael; Schnell, Ida Baerholm; Blom, Nikolaj

    2014-01-01

    Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we...... demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the facial skin. Clostridia and Fusobacteria, widely pathogenic to other vertebrates, dominate the vulture's gut...... microbiota. We reveal a likely faecal-oral-gut route for their origin. DNA of prey species detectable on facial swabs was completely degraded in the gut samples from most vultures, suggesting that the gastrointestinal tracts of vultures are extremely selective. Our findings show a strong adaption of vultures...

  8. forage systems mixed with forage legumes grazed by lactating cows

    Directory of Open Access Journals (Sweden)

    Clair Jorge Olivo

    2017-02-01

    Full Text Available Current research evaluates productivity, stocking and nutritional rates of three forage systems with Elephant Grass (EG + Italian Ryegrass (IR + Spontaneous Growth Species (SGS, without forage legumes; EG + IR + SGS + Forage Peanut (FP, mixed with FP; and EG + IR + SGS + Red Clover (RC, mixed with RC, in rotational grazing method by lactating cows. IR developed between rows of EG. FP was maintained, whilst RC was sow to respective forage systems. The experimental design was completely randomized, with three treatments and two replication, subdivided into parcels over time. Mean rate for forage yield and average stocking rate were 10.6, 11.6 and 14.4 t ha-1; 3.0, 2.8 and 3.1 animal unit ha-1 day-1, for the respective systems. Levels of crude protein and total digestible nutrients were 17.8, 18.7 and 17.5%; 66.5, 66.8 and 64.8%, for the respective forage systems. The presence of RC results in better and higher forage yield in the mixture, whilst FP results in greater control of SGS. The inclusion of forage legumes in pasture systems provides better nutritional rates.

  9. Applying the design-build-test paradigm in microbiome engineering.

    Science.gov (United States)

    Pham, Hoang Long; Ho, Chun Loong; Wong, Adison; Lee, Yung Seng; Chang, Matthew Wook

    2017-12-01

    The recently discovered roles of human microbiome in health and diseases have inspired research efforts across many disciplines to engineer microbiome for health benefits. In this review, we highlight recent progress in human microbiome research and how modifications to the microbiome could result in implications to human health. Furthermore, we discuss the application of a 'design-build-test' framework to expedite microbiome engineering efforts by reviewing current literature on three key aspects: design principles to engineer the human microbiome, methods to engineer microbiome with desired functions, and analytical techniques to examine complex microbiome samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Childhood Malnutrition and the Intestinal Microbiome Malnutrition and the microbiome

    OpenAIRE

    Kane, Anne V.; Dinh, Duy M.; Ward, Honorine D.

    2014-01-01

    Malnutrition contributes to almost half of all deaths in children under the age of 5 years, particularly those who live in resource-constrained areas. Those who survive frequently suffer from long-term sequelae including growth failure and neurodevelopmental impairment. Malnutrition is part of a vicious cycle of impaired immunity, recurrent infections and worsening malnutrition. Recently, alterations in the gut microbiome have also been strongly implicated in childhood malnutrition. It has be...

  11. Novel Insights into The Human Microbiome

    Indian Academy of Sciences (India)

    PPM

    Microbiome. Individual genetic background. What we eat. (diet). Homeostasis. Health. Perturbation. Diseases. Low risk of allergies. Infection resistance. Allergies. Metabolic syndrome. Obesity. Infections ...

  12. Forage evaluation by analysis after

    African Journals Online (AJOL)

    by forages, can be estimated by amino acid analysis of the products of fermentation in vitro. Typical results of such analyses are presented in Table 1. These results indicate that after fermentation the amino acid balance of forages is not optimal for either milk or meat production, with histidine usually being the first limiting.

  13. The organophosphate malathion disturbs gut microbiome development and the quorum-Sensing system.

    Science.gov (United States)

    Gao, Bei; Chi, Liang; Tu, Pengcheng; Bian, Xiaoming; Thomas, Jesse; Ru, Hongyu; Lu, Kun

    2018-02-01

    The gut microbiome has tremendous potential to impact health and disease. Various environmental toxicants, including insecticides, have been shown to alter gut microbiome community structures. However, the mechanism that compositionally and functionally regulates gut microbiota remains unclear. Quorum sensing is known to modulate intra- and interspecies gene expression and coordinate population responses. It is unknown whether quorum sensing is disrupted when environmental toxicants cause perturbations in the gut microbiome community structure. To reveal the response of the quorum-sensing system to environmental exposure, we use a combination of Illumina-based 16S rRNA gene amplicon and shotgun metagenome sequencing to examine the impacts of a widely used organophosphate insecticide, malathion, on the gut microbiome trajectory, quorum sensing system and behaviors related to quorum sensing, such as motility and pathogenicity. Our results demonstrated that malathion perturbed the gut microbiome development, quorum sensing and quorum sensing related behaviors. These findings may provide a novel mechanistic understanding of the role of quorum-sensing in the gut microbiome toxicity of malathion. Copyright © 2017. Published by Elsevier B.V.

  14. The Murine Lung Microbiome Changes During Lung Inflammation and Intranasal Vancomycin Treatment

    Science.gov (United States)

    Barfod, Kenneth Klingenberg; Vrankx, Katleen; Mirsepasi-Lauridsen, Hengameh Chloé; Hansen, Jitka Stilund; Hougaard, Karin Sørig; Larsen, Søren Thor; Ouwenhand, Arthur C.; Krogfelt, Karen Angeliki

    2015-01-01

    Most microbiome research related to airway diseases has focused on the gut microbiome. This is despite advances in culture independent microbial identification techniques revealing that even healthy lungs possess a unique dynamic microbiome. This conceptual change raises the question; if lung diseases could be causally linked to local dysbiosis of the local lung microbiota. Here, we manipulate the murine lung and gut microbiome, in order to show that the lung microbiota can be changed experimentally. We have used four different approaches: lung inflammation by exposure to carbon nano-tube particles, oral probiotics and oral or intranasal exposure to the antibiotic vancomycin. Bacterial DNA was extracted from broncho-alveolar and nasal lavage fluids, caecum samples and compared by DGGE. Our results show that: the lung microbiota is sex dependent and not just a reflection of the gut microbiota, and that induced inflammation can change lung microbiota. This change is not transferred to offspring. Oral probiotics in adult mice do not change lung microbiome detectible by DGGE. Nasal vancomycin can change the lung microbiome preferentially, while oral exposure does not. These observations should be considered in future studies of the causal relationship between lung microbiota and lung diseases. PMID:26668669

  15. The "most wanted" taxa from the human microbiome for whole genome sequencing.

    Directory of Open Access Journals (Sweden)

    Anthony A Fodor

    Full Text Available The goal of the Human Microbiome Project (HMP is to generate a comprehensive catalog of human-associated microorganisms including reference genomes representing the most common species. Toward this goal, the HMP has characterized the microbial communities at 18 body habitats in a cohort of over 200 healthy volunteers using 16S rRNA gene (16S sequencing and has generated nearly 1,000 reference genomes from human-associated microorganisms. To determine how well current reference genome collections capture the diversity observed among the healthy microbiome and to guide isolation and future sequencing of microbiome members, we compared the HMP's 16S data sets to several reference 16S collections to create a 'most wanted' list of taxa for sequencing. Our analysis revealed that the diversity of commonly occurring taxa within the HMP cohort microbiome is relatively modest, few novel taxa are represented by these OTUs and many common taxa among HMP volunteers recur across different populations of healthy humans. Taken together, these results suggest that it should be possible to perform whole-genome sequencing on a large fraction of the human microbiome, including the 'most wanted', and that these sequences should serve to support microbiome studies across multiple cohorts. Also, in stark contrast to other taxa, the 'most wanted' organisms are poorly represented among culture collections suggesting that novel culture- and single-cell-based methods will be required to isolate these organisms for sequencing.

  16. High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism

    Science.gov (United States)

    McCann, Joshua C.; Wickersham, Tryon A.; Loor, Juan J.

    2014-01-01

    Diversity in the forestomach microbiome is one of the key features of ruminant animals. The diverse microbial community adapts to a wide array of dietary feedstuffs and management strategies. Understanding rumen microbiome composition, adaptation, and function has global implications ranging from climatology to applied animal production. Classical knowledge of rumen microbiology was based on anaerobic, culture-dependent methods. Next-generation sequencing and other molecular techniques have uncovered novel features of the rumen microbiome. For instance, pyrosequencing of the 16S ribosomal RNA gene has revealed the taxonomic identity of bacteria and archaea to the genus level, and when complemented with barcoding adds multiple samples to a single run. Whole genome shotgun sequencing generates true metagenomic sequences to predict the functional capability of a microbiome, and can also be used to construct genomes of isolated organisms. Integration of high-throughput data describing the rumen microbiome with classic fermentation and animal performance parameters has produced meaningful advances and opened additional areas for study. In this review, we highlight recent studies of the rumen microbiome in the context of cattle production focusing on nutrition, rumen development, animal efficiency, and microbial function. PMID:24940050

  17. Microbiome Tools for Forensic Science.

    Science.gov (United States)

    Metcalf, Jessica L; Xu, Zhenjiang Z; Bouslimani, Amina; Dorrestein, Pieter; Carter, David O; Knight, Rob

    2017-09-01

    Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and computational approaches have led to recent breakthroughs in the use of microbiome approaches for forensic science, particularly in the areas of estimating postmortem intervals (PMIs), locating clandestine graves, and obtaining soil and skin trace evidence. Low-cost, high-throughput technologies allow us to accumulate molecular data quickly and to apply sophisticated machine-learning algorithms, building generalizable predictive models that will be useful in the criminal justice system. In particular, integrating microbiome and metabolomic data has excellent potential to advance microbial forensics. Copyright © 2017. Published by Elsevier Ltd.

  18. Menopause and the vaginal microbiome.

    Science.gov (United States)

    Muhleisen, Alicia L; Herbst-Kralovetz, Melissa M

    2016-09-01

    For over a century it has been well documented that bacteria in the vagina maintain vaginal homeostasis, and that an imbalance or dysbiosis may be associated with poor reproductive and gynecologic health outcomes. Vaginal microbiota are of particular significance to postmenopausal women and may have a profound effect on vulvovaginal atrophy, vaginal dryness, sexual health and overall quality of life. As molecular-based techniques have evolved, our understanding of the diversity and complexity of this bacterial community has expanded. The objective of this review is to compare the changes that have been identified in the vaginal microbiota of menopausal women, outline alterations in the microbiome associated with specific menopausal symptoms, and define how hormone replacement therapy impacts the vaginal microbiome and menopausal symptoms; it concludes by considering the potential of probiotics to reinstate vaginal homeostasis following menopause. This review details the studies that support the role of Lactobacillus species in maintaining vaginal homeostasis and how the vaginal microbiome structure in postmenopausal women changes with decreasing levels of circulating estrogen. In addition, the associated transformations in the microanatomical features of the vaginal epithelium that can lead to vaginal symptoms associated with menopause are described. Furthermore, hormone replacement therapy directly influences the dominance of Lactobacillus in the microbiota and can resolve vaginal symptoms. Oral and vaginal probiotics hold great promise and initial studies complement the findings of previous research efforts concerning menopause and the vaginal microbiome; however, additional trials are required to determine the efficacy of bacterial therapeutics to modulate or restore vaginal homeostasis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. Exploring the Cultivable Ectocarpus Microbiome

    OpenAIRE

    KleinJan, Hetty; Jeanthon, Christian; Boyen, Catherine; Dittami, Simon M.

    2017-01-01

    Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being develope...

  20. Esophageal microbiome in eosinophilic esophagitis.

    Directory of Open Access Journals (Sweden)

    J Kirk Harris

    Full Text Available The microbiome has been implicated in the pathogenesis of a number of allergic and inflammatory diseases. The mucosa affected by eosinophilic esophagitis (EoE is composed of a stratified squamous epithelia and contains intraepithelial eosinophils. To date, no studies have identified the esophageal microbiome in patients with EoE or the impact of treatment on these organisms. The aim of this study was to identify the esophageal microbiome in EoE and determine whether treatments change this profile. We hypothesized that clinically relevant alterations in bacterial populations are present in different forms of esophagitis.In this prospective study, secretions from the esophageal mucosa were collected from children and adults with EoE, Gastroesophageal Reflux Disease (GERD and normal mucosa using the Esophageal String Test (EST. Bacterial load was determined using quantitative PCR. Bacterial communities, determined by 16S rRNA gene amplification and 454 pyrosequencing, were compared between health and disease.Samples from a total of 70 children and adult subjects were examined. Bacterial load was increased in both EoE and GERD relative to normal subjects. In subjects with EoE, load was increased regardless of treatment status or degree of mucosal eosinophilia compared with normal. Haemophilus was significantly increased in untreated EoE subjects as compared with normal subjects. Streptococcus was decreased in GERD subjects on proton pump inhibition as compared with normal subjects.Diseases associated with mucosal eosinophilia are characterized by a different microbiome from that found in the normal mucosa. Microbiota may contribute to esophageal inflammation in EoE and GERD.

  1. Microbiome/microbiota and allergies.

    Science.gov (United States)

    Inoue, Yuzaburo; Shimojo, Naoki

    2015-01-01

    Allergies are characterized by a hypersensitive immune reaction to originally harmless antigens. In recent decades, the incidence of allergic diseases has markedly increased, especially in developed countries. The increase in the frequency of allergic diseases is thought to be primarily due to environmental changes related to a westernized lifestyle, which affects the commensal microbes in the human body. The human gut is the largest organ colonized by bacteria and contains more than 1000 bacterial species, called the "gut microbiota." The recent development of sequencing technology has enabled researchers to genetically investigate and clarify the diversity of all species of commensal microbes. The collective genomes of commensal microbes are together called the "microbiome." Although the detailed mechanisms remain unclear, it has been proposed that the microbiota/microbiome, especially that in the gut, impacts the systemic immunity and metabolism, thus affecting the development of various immunological diseases, including allergies. In this review, we summarize the recent findings regarding the importance of the microbiome/microbiota in the development of allergic diseases and also the results of interventional studies using probiotics or prebiotics to prevent allergies.

  2. Xenobiotic Metabolism and Gut Microbiomes.

    Directory of Open Access Journals (Sweden)

    Anubhav Das

    Full Text Available Humans are exposed to numerous xenobiotics, a majority of which are in the form of pharmaceuticals. Apart from human enzymes, recent studies have indicated the role of the gut bacterial community (microbiome in metabolizing xenobiotics. However, little is known about the contribution of the plethora of gut microbiome in xenobiotic metabolism. The present study reports the results of analyses on xenobiotic metabolizing enzymes in various human gut microbiomes. A total of 397 available gut metagenomes from individuals of varying age groups from 8 nationalities were analyzed. Based on the diversities and abundances of the xenobiotic metabolizing enzymes, various bacterial taxa were classified into three groups, namely, least versatile, intermediately versatile and highly versatile xenobiotic metabolizers. Most interestingly, specific relationships were observed between the overall drug consumption profile and the abundance and diversity of the xenobiotic metabolizing repertoire in various geographies. The obtained differential abundance patterns of xenobiotic metabolizing enzymes and bacterial genera harboring them, suggest their links to pharmacokinetic variations among individuals. Additional analyses of a few well studied classes of drug modifying enzymes (DMEs also indicate geographic as well as age specific trends.

  3. The inside tract: The appendicular, cecal, and colonic microbiome of captive aye-ayes.

    Science.gov (United States)

    Greene, Lydia K; McKenney, Erin A

    2018-04-17

    The aye-aye (Daubentonia madagascariensis) is famous for its feeding strategies that target structurally defended, but high-quality resources. Nonetheless, the influence of this digestible diet on gut microbial contributions to aye-aye metabolism and nutrition remains unexplored. When four captive aye-ayes were unexpectedly lost to persin toxicity, we opportunistically collected samples along the animals' gastrointestinal tracts. Here we describe the diversity and composition of appendicular, cecal, and colonic consortia relative to the aye-aye's unusual feeding ecology. During necropsies, we collected digestive content from the appendix, cecum, and distal colon. We determined microbiome structure at these sites via amplicon sequencing of the 16S rRNA gene and an established bioinformatics pipeline. The aye-ayes' microbiomes exhibited low richness and diversity compared to the consortia of other lemurs housed at the same facility, and were dominated by a single genus, Prevotella. Appendicular microbiomes were differentiated from more homogenized cecal and colonic consortia by lower richness and diversity, greater evenness, and a distinct taxonomic composition. The simplicity of the aye-aye's gut microbiome could be attributed to captivity-induced dysbiosis, or it may reflect this species' extreme foraging investment in a digestible diet that requires little microbial metabolism. Site-specific appendicular consortia, but more similar cecal and colonic consortia, support the theory that the appendix functions as a safe-house for beneficial bacteria, and confirm fecal communities as fairly reliable proxies for consortia along the lower gut. We encourage others to make similar use of natural or accidental losses for probing the primate gut microbiome. © 2018 Wiley Periodicals, Inc.

  4. Attention in Urban Foraging

    Directory of Open Access Journals (Sweden)

    Malcolm McCullough

    2013-05-01

    Full Text Available This position paper argues how there has to be much more to smart city learning than just wayshowing, and something better as augmented reality than covering the world with instructions. Attention has become something for many people to know better in an age of information superabundance. Embodied cognition explains how the work-ings of attention are not solely a foreground task, as if attention is something to pay. As digital media appear in ever more formats and contexts, their hybrids with physical form increasing influence how habitual engagement with persistent situations creates learning. Ambient information can just add to the distraction by multitasking, or it can support more favorable processes of shifting among different kinds of information with a particular intent. As one word for this latter process, foraging deserves more consideration in smart city learning

  5. Biodiversity and Seasonal Changes of the Microbiome in Chernozem Agroecosystem

    Science.gov (United States)

    Kutovaya, Olga; Chernov, Timofey; Tkhakakhova, Azida; Ivanova, Ekaterina

    2016-04-01

    environmental changes were representatives of the Taumarchaeota, Acidobacteria, Bacteroides, Firmicutes, and Verrucomicrobia groups. The differences in the structure of the soil prokaryotic communities were more significant between seasons than those related to different systems of land use. It is noteworthy that the UniFrac analysis did not practically reveal differences in the prokaryotic communities between the fertilized and unfertilized arable soils, since it was difficult to distinguish them from the differences related to the natural heterogeneity of the soil samples (replicates) analyzed. It is probably related to the high buffer capacity and the high adaptive potential of chernozems. In this experiment, even taking into account the 30-year history, the application of fertilizers is a less significant factor affecting the structure of the microbiome than the type of land use or seasonal climate changes. The phylogenetic diversity estimated by the Shannon index, the number of the operating taxonomic units found, and the Chao1 index little depends on the rate of the fertilizers applied and the type of land use; however, one can mention a rather higher diversity of the microbiomes in the summer and autumn periods compared to the spring one.

  6. The microbiome-systemic diseases connection

    NARCIS (Netherlands)

    van der Meulen, T. A.; Harmsen, H. J. M.; Bootsma, H.; Spijkervet, F. K. L.; Kroese, F. G. M.; Vissink, A.

    2016-01-01

    The human microbiome consists of all microorganisms occupying the skin, mucous membranes and intestinal tract of the human body. The contact of the mucosal immune system with the human microbiome is a balanced interplay between defence mechanisms of the immune system and symbiotic or pathogenic

  7. Microbiome Data Science: Understanding Our Microbial Planet.

    Science.gov (United States)

    Kyrpides, Nikos C; Eloe-Fadrosh, Emiley A; Ivanova, Natalia N

    2016-06-01

    Microbiology is experiencing a revolution brought on by recent developments in sequencing technology. The unprecedented volume of microbiome data being generated poses significant challenges that are currently hindering progress in the field. Here, we outline the major bottlenecks and propose a vision to advance microbiome research as a data-driven science. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Road MAPs to engineer host microbiomes

    NARCIS (Netherlands)

    Oyserman, B. O.; Medema, Marnix H; Raaijmakers, J.M.

    2018-01-01

    Microbiomes contribute directly or indirectly to host health and fitness. Thus far, investigations into these emergent traits, referred to here as microbiome-associated phenotypes (MAPs), have been primarily qualitative and taxonomy-driven rather than quantitative and trait-based. We present the

  9. Emerging Technologies for Gut Microbiome Research

    Science.gov (United States)

    Arnold, Jason W.; Roach, Jeffrey; Azcarate-Peril, M. Andrea

    2016-01-01

    Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches will improve the efficiency and quality of microbiome research. Here, we will discuss emerging technologies and their potential impact on gut microbiome studies. PMID:27426971

  10. Variability in individual activity bursts improves ant foraging success.

    Science.gov (United States)

    Campos, Daniel; Bartumeus, Frederic; Méndez, Vicenç; Andrade, José S; Espadaler, Xavier

    2016-12-01

    Using experimental and computational methods, we study the role of behavioural variability in activity bursts (or temporal activity patterns) for individual and collective regulation of foraging in A. senilis ants. First, foraging experiments were carried out under special conditions (low densities of ants and food and absence of external cues or stimuli) where individual-based strategies are most prevalent. By using marked individuals and recording all foraging trajectories, we were then able to precisely quantify behavioural variability among individuals. Our main conclusions are that (i) variability of ant trajectories (turning angles, speed, etc.) is low compared with variability of temporal activity profiles, and (ii) this variability seems to be driven by plasticity of individual behaviour through time, rather than the presence of fixed behavioural stereotypes or specialists within the group. The statistical measures obtained from these experimental foraging patterns are then used to build a general agent-based model (ABM) which includes the most relevant properties of ant foraging under natural conditions, including recruitment through pheromone communication. Using the ABM, we are able to provide computational evidence that the characteristics of individual variability observed in our experiments can provide a functional advantage (in terms of foraging success) to the group; thus, we propose the biological basis underpinning our observations. Altogether, our study reveals the potential utility of experiments under simplified (laboratory) conditions for understanding information-gathering in biological systems. © 2016 The Author(s).

  11. Hologenome analysis of two marine sponges with different microbiomes

    KAUST Repository

    Ryu, Tae Woo

    2016-02-29

    Background Sponges (Porifera) harbor distinct microbial consortia within their mesohyl interior. We herein analysed the hologenomes of Stylissa carteri and Xestospongia testudinaria, which notably differ in their microbiome content. Results Our analysis revealed that S. carteri has an expanded repertoire of immunological domains, specifically Scavenger Receptor Cysteine-Rich (SRCR)-like domains, compared to X. testudinaria. On the microbial side, metatranscriptome analyses revealed an overrepresentation of potential symbiosis-related domains in X. testudinaria. Conclusions Our findings provide genomic insights into the molecular mechanisms underlying host-symbiont coevolution and may serve as a roadmap for future hologenome analyses.

  12. Evaluating the impact of domestication and captivity on the horse gut microbiome.

    Science.gov (United States)

    Metcalf, Jessica L; Song, Se Jin; Morton, James T; Weiss, Sophie; Seguin-Orlando, Andaine; Joly, Frédéric; Feh, Claudia; Taberlet, Pierre; Coissac, Eric; Amir, Amnon; Willerslev, Eske; Knight, Rob; McKenzie, Valerie; Orlando, Ludovic

    2017-11-14

    The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly modified. We investigated fecal microbiomes of Przewalski's horse (PH; Equus ferus przewalskii), the only horses alive today not successfully domesticated by humans, and herded, domestic horse (E. f. caballus) living in adjacent natural grasslands. We discovered PH fecal microbiomes hosted a distinct and more diverse community of bacteria compared to domestic horses, which is likely partly explained by different plant diets as revealed by trnL maker data. Within the PH population, four individuals were born in captivity in European zoos and hosted a strikingly low diversity of fecal microbiota compared to individuals born in natural reserves in France and Mongolia. These results suggest that anthropogenic forces can dramatically reshape equid gastrointestinal microbiomes, which has broader implications for the conservation management of endangered mammals.

  13. Exploring the Cultivable Ectocarpus Microbiome.

    Science.gov (United States)

    KleinJan, Hetty; Jeanthon, Christian; Boyen, Catherine; Dittami, Simon M

    2017-01-01

    Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus -associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal-bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E . subulatus -associated bacteria. To meet the variety of metabolic demands of Ectocarpus -associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas ( Gammaproteobacteria ), Bosea ( Alphaproteobacteria ), and Limnobacter ( Betaproteobacteria ) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part

  14. Exploring the Cultivable Ectocarpus Microbiome

    Directory of Open Access Journals (Sweden)

    Hetty KleinJan

    2017-12-01

    Full Text Available Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal–bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains, of which Halomonas (Gammaproteobacteria, Bosea (Alphaproteobacteria, and Limnobacter (Betaproteobacteria were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%, although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered

  15. Multiple-stage decisions in a marine central-place forager.

    Science.gov (United States)

    Friedlaender, Ari S; Johnston, David W; Tyson, Reny B; Kaltenberg, Amanda; Goldbogen, Jeremy A; Stimpert, Alison K; Curtice, Corrie; Hazen, Elliott L; Halpin, Patrick N; Read, Andrew J; Nowacek, Douglas P

    2016-05-01

    Air-breathing marine animals face a complex set of physical challenges associated with diving that affect the decisions of how to optimize feeding. Baleen whales (Mysticeti) have evolved bulk-filter feeding mechanisms to efficiently feed on dense prey patches. Baleen whales are central place foragers where oxygen at the surface represents the central place and depth acts as the distance to prey. Although hypothesized that baleen whales will target the densest prey patches anywhere in the water column, how depth and density interact to influence foraging behaviour is poorly understood. We used multi-sensor archival tags and active acoustics to quantify Antarctic humpback whale foraging behaviour relative to prey. Our analyses reveal multi-stage foraging decisions driven by both krill depth and density. During daylight hours when whales did not feed, krill were found in deep high-density patches. As krill migrated vertically into larger and less dense patches near the surface, whales began to forage. During foraging bouts, we found that feeding rates (number of feeding lunges per hour) were greatest when prey was shallowest, and feeding rates decreased with increasing dive depth. This strategy is consistent with previous models of how air-breathing diving animals optimize foraging efficiency. Thus, humpback whales forage mainly when prey is more broadly distributed and shallower, presumably to minimize diving and searching costs and to increase feeding rates overall and thus foraging efficiency. Using direct measurements of feeding behaviour from animal-borne tags and prey availability from echosounders, our study demonstrates a multi-stage foraging process in a central place forager that we suggest acts to optimize overall efficiency by maximizing net energy gain over time. These data reveal a previously unrecognized level of complexity in predator-prey interactions and underscores the need to simultaneously measure prey distribution in marine central place forager

  16. Multiple-stage decisions in a marine central-place forager

    Science.gov (United States)

    Friedlaender, Ari S.; Johnston, David W.; Tyson, Reny B.; Kaltenberg, Amanda; Goldbogen, Jeremy A.; Stimpert, Alison K.; Curtice, Corrie; Hazen, Elliott L.; Halpin, Patrick N.; Read, Andrew J.; Nowacek, Douglas P.

    2016-05-01

    Air-breathing marine animals face a complex set of physical challenges associated with diving that affect the decisions of how to optimize feeding. Baleen whales (Mysticeti) have evolved bulk-filter feeding mechanisms to efficiently feed on dense prey patches. Baleen whales are central place foragers where oxygen at the surface represents the central place and depth acts as the distance to prey. Although hypothesized that baleen whales will target the densest prey patches anywhere in the water column, how depth and density interact to influence foraging behaviour is poorly understood. We used multi-sensor archival tags and active acoustics to quantify Antarctic humpback whale foraging behaviour relative to prey. Our analyses reveal multi-stage foraging decisions driven by both krill depth and density. During daylight hours when whales did not feed, krill were found in deep high-density patches. As krill migrated vertically into larger and less dense patches near the surface, whales began to forage. During foraging bouts, we found that feeding rates (number of feeding lunges per hour) were greatest when prey was shallowest, and feeding rates decreased with increasing dive depth. This strategy is consistent with previous models of how air-breathing diving animals optimize foraging efficiency. Thus, humpback whales forage mainly when prey is more broadly distributed and shallower, presumably to minimize diving and searching costs and to increase feeding rates overall and thus foraging efficiency. Using direct measurements of feeding behaviour from animal-borne tags and prey availability from echosounders, our study demonstrates a multi-stage foraging process in a central place forager that we suggest acts to optimize overall efficiency by maximizing net energy gain over time. These data reveal a previously unrecognized level of complexity in predator-prey interactions and underscores the need to simultaneously measure prey distribution in marine central place forager

  17. The lung microbiome in health and disease.

    Science.gov (United States)

    Moffatt, Miriam F; Cookson, William Ocm

    2017-12-01

    The Human Microbiome Project began 10 years ago, leading to a significant growth in understanding of the role the human microbiome plays in health and disease. In this article, we explain with an emphasis on the lung, the origins of microbiome research. We discuss how 16S rRNA gene sequencing became the first major molecular tool to examine the bacterial communities present within the human body. We highlight the pitfalls of molecular-based studies, such as false findings resulting from contamination, and the limitations of 16S rRNA gene sequencing. Knowledge about the lung microbiome has evolved from initial scepticism to the realisation that it might have a significant influence on many illnesses. We also discuss the lung microbiome in the context of disease by giving examples of important respiratory conditions. In addition, we draw attention to the challenges for metagenomic studies of respiratory samples and the importance of systematic bacterial isolation to enable host-microbiome interactions to be understood. We conclude by discussing how knowledge of the lung microbiome impacts current clinical diagnostics. © Royal College of Physicians 2017. All rights reserved.

  18. Modeling the Dynamic Digestive System Microbiome

    Directory of Open Access Journals (Sweden)

    Anne M. Estes

    2015-08-01

    Full Text Available “Modeling the Dynamic Digestive System Microbiome” is a hands-on activity designed to demonstrate the dynamics of microbiome ecology using dried pasta and beans to model disturbance events in the human digestive system microbiome. This exercise demonstrates how microbiome diversity is influenced by: 1 niche availability and habitat space and 2 a major disturbance event, such as antibiotic use. Students use a pictorial key to examine prepared models of digestive system microbiomes to determine what the person with the microbiome “ate.” Students then model the effect of taking antibiotics by removing certain “antibiotic sensitive” pasta. Finally, they add in “environmental microbes” or “native microbes” to recolonize the digestive system, determine how resilient their model microbome community is to disturbance, and discuss the implications. Throughout the exercise, students discuss differences in the habitat space available and microbiome community diversity. This exercise can be modified to discuss changes in the microbiome due to diet shifts and the emergence of antibiotic resistance in more depth.

  19. The microbiome in PTEN hamartoma tumor syndrome.

    Science.gov (United States)

    Byrd, Victoria; Getz, Ted; Padmanabhan, Roshan; Arora, Hans; Eng, Charis

    2018-03-01

    Germline PTEN mutations defining PTEN hamartoma tumor syndrome (PHTS) confer heritable predisposition to breast, endometrial, thyroid and other cancers with known age-related risks, but it remains impossible to predict if any individual will develop cancer. In the general population, gut microbial dysbiosis has been linked to cancer, yet is unclear whether these are associated in PHTS patients. In this pilot study, we aimed to characterize microbial composition of stool, urine, and oral wash from 32 PTEN mutation-positive individuals using 16S rRNA gene sequencing. PCoA revealed clustering of the fecal microbiome by cancer history ( P  = 0.03, R 2  = 0.04). Fecal samples from PHTS cancer patients had relatively more abundant operational taxonomic units (OTUs) from family Rikenellaceae and unclassified members of Clostridia compared to those from non-cancer patients, whereas families Peptostreptococcaceae, Enterobacteriaceae, and Bifidobacteriaceae represented relatively more abundant OTUs among fecal samples from PHTS non-cancer patients. Functional metagenomic prediction revealed enrichment of the folate biosynthesis, genetic information processing and cell growth and death pathways among fecal samples from PHTS cancer patients compared to non-cancer patients. We found no major shifts in overall diversity and no clustering by cancer history among oral wash or urine samples. Our observations suggest the utility of an expanded study to interrogate gut dysbiosis as a potential cancer risk modifier in PHTS patients. © 2018 The authors.

  20. The skin microbiome in healthy and allergic dogs.

    Directory of Open Access Journals (Sweden)

    Aline Rodrigues Hoffmann

    Full Text Available BACKGROUND: Changes in the microbial populations on the skin of animals have traditionally been evaluated using conventional microbiology techniques. The sequencing of bacterial 16S rRNA genes has revealed that the human skin is inhabited by a highly diverse and variable microbiome that had previously not been demonstrated by culture-based methods. The goals of this study were to describe the microbiome inhabiting different areas of the canine skin, and to compare the skin microbiome of healthy and allergic dogs. METHODOLOGY/PRINCIPAL FINDINGS: DNA extracted from superficial skin swabs from healthy (n = 12 and allergic dogs (n = 6 from different regions of haired skin and mucosal surfaces were used for 454-pyrosequencing of the 16S rRNA gene. Principal coordinates analysis revealed clustering for the different skin sites across all dogs, with some mucosal sites and the perianal regions clustering separately from the haired skin sites. The rarefaction analysis revealed high individual variability between samples collected from healthy dogs and between the different skin sites. Higher species richness and microbial diversity were observed in the samples from haired skin when compared to mucosal surfaces or mucocutaneous junctions. In all examined regions, the most abundant phylum and family identified in the different regions of skin and mucosal surfaces were Proteobacteria and Oxalobacteriaceae. The skin of allergic dogs had lower species richness when compared to the healthy dogs. The allergic dogs had lower proportions of the Betaproteobacteria Ralstonia spp. when compared to the healthy dogs. CONCLUSIONS/SIGNIFICANCE: The study demonstrates that the skin of dogs is inhabited by much more rich and diverse microbial communities than previously thought using culture-based methods. Our sequence data reveal high individual variability between samples collected from different patients. Differences in species richness was also seen between

  1. Antibiotic use and microbiome function.

    Science.gov (United States)

    Ferrer, Manuel; Méndez-García, Celia; Rojo, David; Barbas, Coral; Moya, Andrés

    2017-06-15

    Our microbiome should be understood as one of the most complex components of the human body. The use of β-lactam antibiotics is one of the microbiome covariates that influence its composition. The extent to which our microbiota changes after an antibiotic intervention depends not only on the chemical nature of the antibiotic or cocktail of antibiotics used to treat specific infections, but also on the type of administration, duration and dose, as well as the level of resistance that each microbiota develops. We have begun to appreciate that not all bacteria within our microbiota are vulnerable or reactive to different antibiotic interventions, and that their influence on both microbial composition and metabolism may differ. Antibiotics are being used worldwide on a huge scale and the prescription of antibiotics is continuing to rise; however, their effects on our microbiota have been reported for only a limited number of them. This article presents a critical review of the antibiotics or antibiotic cocktails whose use in humans has been linked to changes in the composition of our microbial communities, with a particular focus on the gut, oral, respiratory, skin and vaginal microbiota, and on their molecular agents (genes, proteins and metabolites). We review the state of the art as of June 2016, and cover a total of circa 68 different antibiotics. The data herein are the first to compile information about the bacteria, fungi, archaea and viruses most influenced by the main antibiotic treatments prescribed nowadays. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Does greed help a forager survive?

    Science.gov (United States)

    Bhat, U.; Redner, S.; Bénichou, O.

    2017-06-01

    We investigate the role of greed on the lifetime of a random-walking forager on an initially resource-rich lattice. Whenever the forager lands on a food-containing site, all the food there is eaten and the forager can hop S more steps without food before starving. Upon reaching an empty site, the forager comes one time unit closer to starvation. The forager is also greedy—given a choice to move to an empty or to a food-containing site in its local neighborhood, the forager moves preferentially toward food. Surprisingly, the forager lifetime varies nonmonotonically with greed, with different senses of the nonmonotonicity in one and two dimensions. Also unexpectedly, the forager lifetime in one dimension has a huge peak for very negative greed where the forager is food averse.

  3. Tributyltin exposure induces gut microbiome dysbiosis with increased body weight gain and dyslipidemia in mice.

    Science.gov (United States)

    Guo, Hao; Yan, Haotian; Cheng, Dong; Wei, Xinglong; Kou, Ruirui; Si, Jiliang

    2018-05-03

    Gut microbiome dysbiosis plays a profound role in the pathogenesis of obesity and tributyltin (TBT) has been found as an environmental obesogen. However, whether TBT could disturb gut microbiome and the relationship between obesity induced by TBT exposure and alteration in gut microbiota are still unknown. In order to assess the association between them, mice were exposed to TBTCl (50 μg kg -1 ) once every three days from postnatal days (PNDs) 24 to 54. The results demonstrated that TBT exposure resulted in increased body weight gain, lager visceral fat accumulation and dyslipidemia in male mice on PND 84. Correspondingly, 16S rRNA gene sequencing revealed that TBT treatment decreased gut microbial species and perturbed the microbiome composition in mice. Furthermore, Pearson's corelation coefficient analysis showed a significantly negative correlation between the body weight and the alpha diversity of gut microbiome. These results suggested that TBT exposure could induce gut microbiome dysbiosis in mice, which might contribute to the obesity pathogenesis. Copyright © 2018 Elsevier B.V. All rights reserved.

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

    KAUST Repository

    Alzubaidy, Hanin S.

    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.

  5. Analyses of the microbial diversity across the human microbiome.

    Directory of Open Access Journals (Sweden)

    Kelvin Li

    Full Text Available Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, S(max, and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, ("τ", based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ's greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for

  6. Embracing community ecology in plant microbiome research

    NARCIS (Netherlands)

    Dini-Andreote, F.; Raaijmakers, J.M.

    2018-01-01

    Community assembly is mediated by selection, dispersal, drift, and speciation. Environmental selection is mostly used to date to explain patterns in plant microbiome assembly, whereas the influence of the other processes remains largely elusive. Recent studies highlight that adopting community

  7. Road MAPs to engineer host microbiomes.

    Science.gov (United States)

    Oyserman, Ben O; Medema, Marnix H; Raaijmakers, Jos M

    2017-12-02

    Microbiomes contribute directly or indirectly to host health and fitness. Thus far, investigations into these emergent traits, referred to here as microbiome-associated phenotypes (MAPs), have been primarily qualitative and taxonomy-driven rather than quantitative and trait-based. We present the MAPs-first approach, a theoretical and experimental roadmap that involves quantitative profiling of MAPs across genetically variable hosts and subsequent identification of the underlying mechanisms. We outline strategies for developing 'modular microbiomes'-synthetic microbial consortia that are engineered in concert with the host genotype to confer different but mutually compatible MAPs to a single host or host population. By integrating host and microbial traits, these strategies will facilitate targeted engineering of microbiomes to the benefit of agriculture, human/animal health and biotechnology. Copyright © 2017. Published by Elsevier Ltd.

  8. The Placenta Harbors a Unique Microbiome

    OpenAIRE

    Aagaard, Kjersti; Ma, Jun; Antony, Kathleen M.; Ganu, Radhika; Petrosino, Joseph; Versalovic, James

    2014-01-01

    Humans and their microbiomes have coevolved as a physiologic community composed of distinct body site niches with metabolic and antigenic diversity. The placental microbiome has not been robustly interrogated, despite recent demonstrations of intracellular bacteria with diverse metabolic and immune regulatory functions. A population-based cohort of placental specimens collected under sterile conditions from 320 subjects with extensive clinical data was established for comparative 16S ribosoma...

  9. The intestinal microbiome of fish under starvation

    OpenAIRE

    Xia, Jun Hong; Lin, Grace; Fu, Gui Hong; Wan, Zi Yi; Lee, May; Wang, Le; Liu, Xiao Jun; Yue, Gen Hua

    2014-01-01

    Background Starvation not only affects the nutritional and health status of the animals, but also the microbial composition in the host’s intestine. Next-generation sequencing provides a unique opportunity to explore gut microbial communities and their interactions with hosts. However, studies on gut microbiomes have been conducted predominantly in humans and land animals. Not much is known on gut microbiomes of aquatic animals and their changes under changing environmental conditions. To add...

  10. Upper ocean stratification and sea ice growth rates during the summer-fall transition, as revealed by Elephant seal foraging in the Adélie Depression, East Antarctica

    Directory of Open Access Journals (Sweden)

    G. D. Williams

    2011-03-01

    Full Text Available Southern elephant seals (Mirounga leonina, fitted with Conductivity-Temperature-Depth sensors at Macquarie Island in January 2005 and 2010, collected unique oceanographic observations of the Adélie and George V Land continental shelf (140–148° E during the summer-fall transition (late February through April. This is a key region of dense shelf water formation from enhanced sea ice growth/brine rejection in the local coastal polynyas. In 2005, two seals occupied the continental shelf break near the grounded icebergs at the northern end of the Mertz Glacier Tongue for several weeks from the end of February. One of the seals migrated west to the Dibble Ice Tongue, apparently utilising the Antarctic Slope Front current near the continental shelf break. In 2010, immediately after that year's calving of the Mertz Glacier Tongue, two seals migrated to the same region but penetrated much further southwest across the Adélie Depression and sampled the Commonwealth Bay polynya from March through April. Here we present observations of the regional oceanography during the summer-fall transition, in particular (i the zonal distribution of modified Circumpolar Deep Water exchange across the shelf break, (ii the upper ocean stratification across the Adélie Depression, including alongside iceberg C-28 that calved from the Mertz Glacier and (iii the convective overturning of the deep remnant seasonal mixed layer in Commonwealth Bay from sea ice growth. Heat and freshwater budgets to 200–300 m are used to estimate the ocean heat content (400→50 MJ m−2, flux (50–200 W m−2 loss and sea ice growth rates (maximum of 7.5–12.5 cm day−1. Mean seal-derived sea ice growth rates were within the range of satellite-derived estimates from 1992–2007 using ERA-Interim data. We speculate that the continuous foraging by the seals within Commonwealth Bay during the summer/fall transition was due to favorable feeding

  11. Upper ocean stratification and sea ice growth rates during the summer-fall transition, as revealed by Elephant seal foraging in the Adélie Depression, East Antarctica

    Science.gov (United States)

    Williams, G. D.; Hindell, M.; Houssais, M.-N.; Tamura, T.; Field, I. C.

    2011-03-01

    Southern elephant seals (Mirounga leonina), fitted with Conductivity-Temperature-Depth sensors at Macquarie Island in January 2005 and 2010, collected unique oceanographic observations of the Adélie and George V Land continental shelf (140-148° E) during the summer-fall transition (late February through April). This is a key region of dense shelf water formation from enhanced sea ice growth/brine rejection in the local coastal polynyas. In 2005, two seals occupied the continental shelf break near the grounded icebergs at the northern end of the Mertz Glacier Tongue for several weeks from the end of February. One of the seals migrated west to the Dibble Ice Tongue, apparently utilising the Antarctic Slope Front current near the continental shelf break. In 2010, immediately after that year's calving of the Mertz Glacier Tongue, two seals migrated to the same region but penetrated much further southwest across the Adélie Depression and sampled the Commonwealth Bay polynya from March through April. Here we present observations of the regional oceanography during the summer-fall transition, in particular (i) the zonal distribution of modified Circumpolar Deep Water exchange across the shelf break, (ii) the upper ocean stratification across the Adélie Depression, including alongside iceberg C-28 that calved from the Mertz Glacier and (iii) the convective overturning of the deep remnant seasonal mixed layer in Commonwealth Bay from sea ice growth. Heat and freshwater budgets to 200-300 m are used to estimate the ocean heat content (400→50 MJ m-2), flux (50-200 W m-2 loss) and sea ice growth rates (maximum of 7.5-12.5 cm day-1). Mean seal-derived sea ice growth rates were within the range of satellite-derived estimates from 1992-2007 using ERA-Interim data. We speculate that the continuous foraging by the seals within Commonwealth Bay during the summer/fall transition was due to favorable feeding conditions resulting from the convective overturning of the deep

  12. Foraging in corallivorous butterflyfish varies with wave exposure

    Science.gov (United States)

    Noble, Mae M.; Pratchett, Morgan S.; Coker, Darren J.; Cvitanovic, Christopher; Fulton, Christopher J.

    2014-06-01

    Understanding the foraging patterns of reef fishes is crucial for determining patterns of resource use and the sensitivity of species to environmental change. While changes in prey availability and interspecific competition have been linked to patterns of prey selection, body condition, and survival in coral reef fishes, rarely has the influence of abiotic environmental conditions on foraging been considered. We used underwater digital video to explore how prey availability and wave exposure influence the behavioural time budgets and prey selectivity of four species of obligate coral-feeding butterflyfishes. All four species displayed high selectivity towards live hard corals, both in terms of time invested and frequency of searching and feeding events. However, our novel analysis revealed that such selectivity was sensitive to wave exposure in some species, despite there being no significant differences in the availability of each prey category across exposures. In most cases, these obligate corallivores increased their selectivity towards their most favoured prey types at sites of high wave exposure. This suggests there are costs to foraging under different wave environments that can shape the foraging patterns of butterflyfishes in concert with other conditions such as prey availability, interspecific competition, and territoriality. Given that energy acquisition is crucial to the survival and fitness of fishes, we highlight how such environmental forcing of foraging behaviour may influence the ecological response of species to the ubiquitous and highly variable wave climates of shallow coral reefs.

  13. Arsenic induces structural and compositional colonic microbiome change and promotes host nitrogen and amino acid metabolism

    International Nuclear Information System (INIS)

    Dheer, Rishu; Patterson, Jena; Dudash, Mark; Stachler, Elyse N.; Bibby, Kyle J.; Stolz, Donna B.; Shiva, Sruti; Wang, Zeneng; Hazen, Stanley L.; Barchowsky, Aaron; Stolz, John F.

    2015-01-01

    Chronic exposure to arsenic in drinking water causes cancer and non-cancer diseases. However, mechanisms for chronic arsenic-induced pathogenesis, especially in response to lower exposure levels, are unclear. In addition, the importance of health impacts from xeniobiotic-promoted microbiome changes is just being realized and effects of arsenic on the microbiome with relation to disease promotion are unknown. To investigate impact of arsenic exposure on both microbiome and host metabolism, the stucture and composition of colonic microbiota, their metabolic phenotype, and host tissue and plasma metabolite levels were compared in mice exposed for 2, 5, or 10 weeks to 0, 10 (low) or 250 (high) ppb arsenite (As(III)). Genotyping of colonic bacteria revealed time and arsenic concentration dependent shifts in community composition, particularly the Bacteroidetes and Firmicutes, relative to those seen in the time-matched controls. Arsenic-induced erosion of bacterial biofilms adjacent to the mucosal lining and changes in the diversity and abundance of morphologically distinct species indicated changes in microbial community structure. Bacterical spores increased in abundance and intracellular inclusions decreased with high dose arsenic. Interestingly, expression of arsenate reductase (arsA) and the As(III) exporter arsB, remained unchanged, while the dissimilatory nitrite reductase (nrfA) gene expression increased. In keeping with the change in nitrogen metabolism, colonic and liver nitrite and nitrate levels and ratios changed with time. In addition, there was a concomitant increase in pathogenic arginine metabolites in the mouse circulation. These data suggest that arsenic exposure impacts the microbiome and microbiome/host nitrogen metabolism to support disease enhancing pathogenic phenotypes. - Highlights: • Arsenic exposure induces changes in host and host nitrogen metabolism that cause progresive change in the microbiome. • A polyphasic approach reveals changes

  14. Arsenic induces structural and compositional colonic microbiome change and promotes host nitrogen and amino acid metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Dheer, Rishu; Patterson, Jena; Dudash, Mark [Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282 (United States); Stachler, Elyse N.; Bibby, Kyle J. [Department of Civil and Environmental Engineering, University of Pittsburgh Swanson School of Engineering, Pittsburgh, PA 15261 (United States); Stolz, Donna B. [Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 (United States); Shiva, Sruti [Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh 15261 (United States); Vascular Medicine Institute, University of Pittsburgh, Pittsburgh 15261 (United States); Wang, Zeneng; Hazen, Stanley L. [Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195 (United States); Barchowsky, Aaron, E-mail: aab20@pitt.edu [Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh 15261 (United States); Vascular Medicine Institute, University of Pittsburgh, Pittsburgh 15261 (United States); Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219 (United States); Stolz, John F. [Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282 (United States)

    2015-12-15

    Chronic exposure to arsenic in drinking water causes cancer and non-cancer diseases. However, mechanisms for chronic arsenic-induced pathogenesis, especially in response to lower exposure levels, are unclear. In addition, the importance of health impacts from xeniobiotic-promoted microbiome changes is just being realized and effects of arsenic on the microbiome with relation to disease promotion are unknown. To investigate impact of arsenic exposure on both microbiome and host metabolism, the stucture and composition of colonic microbiota, their metabolic phenotype, and host tissue and plasma metabolite levels were compared in mice exposed for 2, 5, or 10 weeks to 0, 10 (low) or 250 (high) ppb arsenite (As(III)). Genotyping of colonic bacteria revealed time and arsenic concentration dependent shifts in community composition, particularly the Bacteroidetes and Firmicutes, relative to those seen in the time-matched controls. Arsenic-induced erosion of bacterial biofilms adjacent to the mucosal lining and changes in the diversity and abundance of morphologically distinct species indicated changes in microbial community structure. Bacterical spores increased in abundance and intracellular inclusions decreased with high dose arsenic. Interestingly, expression of arsenate reductase (arsA) and the As(III) exporter arsB, remained unchanged, while the dissimilatory nitrite reductase (nrfA) gene expression increased. In keeping with the change in nitrogen metabolism, colonic and liver nitrite and nitrate levels and ratios changed with time. In addition, there was a concomitant increase in pathogenic arginine metabolites in the mouse circulation. These data suggest that arsenic exposure impacts the microbiome and microbiome/host nitrogen metabolism to support disease enhancing pathogenic phenotypes. - Highlights: • Arsenic exposure induces changes in host and host nitrogen metabolism that cause progresive change in the microbiome. • A polyphasic approach reveals changes

  15. The Gut Commensal Microbiome of Drosophila melanogaster Is Modified by the Endosymbiont Wolbachia.

    Science.gov (United States)

    Simhadri, Rama K; Fast, Eva M; Guo, Rong; Schultz, Michaela J; Vaisman, Natalie; Ortiz, Luis; Bybee, Joanna; Slatko, Barton E; Frydman, Horacio M

    2017-01-01

    and parasitic nematodes. They can block mosquitos' ability to transmit several infectious disease-causing pathogens, including Zika, dengue, chikungunya, and West Nile viruses and malaria parasites. Certain extracellular bacteria present in the gut lumen of these insects can also block pathogen transmission. However, our understanding of interactions between Wolbachia and gut bacteria and how they influence each other is limited. Here we show that the presence of Wolbachia strain w Mel changes the composition of gut commensal bacteria in the fruit fly. Our findings implicate interactions between bacterial species as a key factor in determining the overall composition of the microbiome and thus reveal new paradigms to consider in the development of disease control strategies.

  16. Emerging roles of the microbiome in cancer

    Science.gov (United States)

    Bultman, Scott J.

    2014-01-01

    Gene–environment interactions underlie cancer susceptibility and progression. Yet, we still have limited knowledge of which environmental factors are important and how they function during tumorigenesis. In this respect, the microbial communities that inhabit our gastrointestinal tract and other body sites have been unappreciated until recently. However, our microbiota are environmental factors that we are exposed to continuously, and human microbiome studies have revealed significant differences in the relative abundance of certain microbes in cancer cases compared with controls. To characterize the function of microbiota in carcinogenesis, mouse models of cancer have been treated with antibiotics. They have also been maintained in a germfree state or have been colonized with specific bacteria in specialized (gnotobiotic) facilities. These studies demonstrate that microbiota can increase or decrease cancer susceptibility and progression by diverse mechanisms such as by modulating inflammation, influencing the genomic stability of host cells and producing metabolites that function as histone deacetylase inhibitors to epigenetically regulate host gene expression. One might consider microbiota as tractable environmental factors because they are highly quantifiable and relatively stable within an individual compared with our exposures to external agents. At the same time, however, diet can modulate the composition of microbial communities within our gut, and this supports the idea that probiotics and prebiotics can be effective chemoprevention strategies. The trajectory of where the current work is headed suggests that microbiota will continue to provide insight into the basic mechanisms of carcinogenesis and that microbiota will also become targets for therapeutic intervention. PMID:24302613

  17. Resource diversity and landscape-level homogeneity drive native bee foraging.

    Science.gov (United States)

    Jha, Shalene; Kremen, Claire

    2013-01-08

    Given widespread declines in pollinator communities and increasing global reliance on pollinator-dependent crops, there is an acute need to develop a mechanistic understanding of native pollinator population and foraging biology. Using a population genetics approach, we determine the impact of habitat and floral resource distributions on nesting and foraging patterns of a critical native pollinator, Bombus vosnesenskii. Our findings demonstrate that native bee foraging is far more plastic and extensive than previously believed and does not follow a simple optimal foraging strategy. Rather, bumble bees forage further in pursuit of species-rich floral patches and in landscapes where patch-to-patch variation in floral resources is less, regardless of habitat composition. Thus, our results reveal extreme foraging plasticity and demonstrate that floral diversity, not density, drives bee foraging distance. Furthermore, we find a negative impact of paved habitat and a positive impact of natural woodland on bumble bee nesting densities. Overall, this study reveals that natural and human-altered landscapes can be managed for increased native bee nesting and extended foraging, dually enhancing biodiversity and the spatial extent of pollination services.

  18. Metabolome of human gut microbiome is predictive of host dysbiosis.

    Science.gov (United States)

    Larsen, Peter E; Dai, Yang

    2015-01-01

    Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. However, the community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome's interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent on its community metabolome; an emergent property of the microbiome. Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles. Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome-host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.

  19. Comparative Effect of Sole Forage and Mixed Concentrate-Forage ...

    African Journals Online (AJOL)

    There was no statistical (P>0.05) difference in average intake of forage between the two treatment groups. Economically, Treatment 1 proves to be better for the enhancement of body weight in growing rabbits than Treatment 2. Key words: Weaner rabbits,Poultry grower mesh, Tridax procumbens, Feed intake,Body weight ...

  20. Foraging task specialisation and foraging labour allocation in stingless bees

    NARCIS (Netherlands)

    Hofstede, Frouke Elisabeth

    2006-01-01

    Social bees collect nectar and pollen from flowering plants for energy of the adult bees and for feeding the larvae in the colony. The flowering patterns of plants imply that periods of high food availability are often followed by periods of meagre foraging conditions. Being dependent on such a

  1. Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption.

    Directory of Open Access Journals (Sweden)

    Jeremiah J Minich

    Full Text Available Global climate change includes rising temperatures and increased pCO2 concentrations in the ocean, with potential deleterious impacts on marine organisms. In this case study we conducted a four-week climate change incubation experiment, and tested the independent and combined effects of increased temperature and partial pressure of carbon dioxide (pCO2, on the microbiomes of a foundation species, the giant kelp Macrocystis pyrifera, and the surrounding water column. The water and kelp microbiome responded differently to each of the climate stressors. In the water microbiome, each condition caused an increase in a distinct microbial order, whereas the kelp microbiome exhibited a reduction in the dominant kelp-associated order, Alteromondales. The water column microbiomes were most disrupted by elevated pCO2, with a 7.3 fold increase in Rhizobiales. The kelp microbiome was most influenced by elevated temperature and elevated temperature in combination with elevated pCO2. Kelp growth was negatively associated with elevated temperature, and the kelp microbiome showed a 5.3 fold increase Flavobacteriales and a 2.2 fold increase alginate degrading enzymes and sulfated polysaccharides. In contrast, kelp growth was positively associated with the combination of high temperature and high pCO2 'future conditions', with a 12.5 fold increase in Planctomycetales and 4.8 fold increase in Rhodobacteriales. Therefore, the water and kelp microbiomes acted as distinct communities, where the kelp was stabilizing the microbiome under changing pCO2 conditions, but lost control at high temperature. Under future conditions, a new equilibrium between the kelp and the microbiome was potentially reached, where the kelp grew rapidly and the commensal microbes responded to an increase in mucus production.

  2. Execution Plans for Cyber Foraging

    DEFF Research Database (Denmark)

    Kristensen, Mads Darø

    2008-01-01

    Cyber foraging helps small devices perform heavy tasks by opportunistically discovering and utilising available resources (such as computation, storage, bandwidth, etc.) held by larger, nearby peers. This offloading is done in an ad-hoc manner, as larger machines will not always be within reach...

  3. Triticale for dairy forage systems

    Science.gov (United States)

    Triticale forages have become increasingly important components of dairy-cropping systems. In part, this trend has occurred in response to environmental pressures, specifically a desire to capture N and other nutrients from land-applied manure, and/or to improve stewardship of the land by providing ...

  4. Execution Plans for Cyber Foraging

    DEFF Research Database (Denmark)

    Kristensen, Mads Darø

    2008-01-01

    Cyber foraging helps small devices perform heavy tasks by opportunistically discovering and utilising available resources (such as computation, storage, bandwidth, etc.) held by larger, nearby peers. This offloading is done in an ad-hoc manner, as larger machines will not always be within reach. ...

  5. Final Report: The Human Microbiome as a Multipurpose Biomarker

    Science.gov (United States)

    2015-11-23

    Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 microbiome, biomarker, microbial forensics, microbial ecology , identifiability REPORT...temporal variation in the ecology of the human microbiome, this work demonstrated the feasibility of microbiome-based identifiability for the first time...a result with important ethical implications for microbiome study design. In order to construct metagenomic codes that are stable over time, we

  6. Potential contribution of the uterine microbiome in the development of endometrial cancer

    Directory of Open Access Journals (Sweden)

    Marina R. S. Walther-António

    2016-11-01

    Full Text Available Abstract Background Endometrial cancer studies have led to a number of well-defined but mechanistically unconnected genetic and environmental risk factors. One of the emerging modulators between environmental triggers and genetic expression is the microbiome. We set out to inquire about the composition of the uterine microbiome and its putative role in endometrial cancer. Methods We undertook a study of the microbiome in samples taken from different locations along the female reproductive tract in patients with endometrial cancer (n = 17, patients with endometrial hyperplasia (endometrial cancer precursor, n = 4, and patients afflicted with benign uterine conditions (n = 10. Vaginal, cervical, Fallopian, ovarian, peritoneal, and urine samples were collected aseptically both in the operating room and the pathology laboratory. DNA extraction was followed by amplification and high-throughput next generation sequencing (MiSeq of the 16S rDNA V3-V5 region to identify the microbiota present. Microbiota data were summarized using both α-diversity to reflect species richness and evenness within bacterial populations and β-diversity to reflect the shared diversity between bacterial populations. Statistical significance was determined through the use of multiple testing, including the generalized mixed-effects model. Results The microbiome sequencing (16S rDNA V3-V5 region revealed that the microbiomes of all organs (vagina, cervix, Fallopian tubes, and ovaries are significantly correlated (p 4.5. Conclusions Our results suggest that the detection of A. vaginae and the identified Porphyromonas sp. in the gynecologic tract combined with a high vaginal pH is statistically associated with the presence of endometrial cancer. Given the documented association of the identified microorganisms with other pathologies, these findings raise the possibility of a microbiome role in the manifestation, etiology, or progression of endometrial cancer that

  7. Understanding the microbiome: Emerging biomarkers for exploiting the microbiota for personalized medicine against cancer.

    Science.gov (United States)

    Rajpoot, Meenakshi; Sharma, Anil K; Sharma, Anil; Gupta, Girish Kumar

    2018-02-06

    The human body is a home to more than 1 trillion microbes with a diverse variety of commensal microbes that play a crucial role towards the health of the individual. These microbes occupy different habitats such as gut, skin, vagina, oral etc. Not only the types and abundance of microbes are different in different organs, but also these may differ in different individuals. The genome of these microbiota and their ecosystem constitute to form a microbiome. Factors such as diet, environment, host genetics etc. may be the reason behind the wide microbial diversity. A number of studies performed on human microbiome have revealed that microbiota present in healthy and diseased individuals are distinct. Altered microbiome is many a times the reason behind the overexpression of genes which may cause complex diseases including cancer. Manipulation of the human microbiome can be done by microbial supplements such as probiotics or synbiotics, diet or prebiotics and microbial suppression strategies using antibiotics. Recent advances in genome sequencing technologies and metagenomic analysis provide us the broader understanding of these commensal microbes and highlighting the distinctive features of microbiome during healthy and disease states. Molecular pathological epidemiology (MPE) studies have been very helpful in providing insights into the pathological process behind disease evolution and progression by determining the specific etiological factors. New emerging field of research targets the microbiome for therapeutic purposes by which personalized medicines can be made for treating various types of tumors. Screening programmes might be helpful in identifying patients who are at the verge of developing cancer and in delivering appropriate approaches according to individual risk modes so that disease could be prevented. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. Differential regulation of the foraging gene associated with task behaviors in harvester ants

    Directory of Open Access Journals (Sweden)

    Kleeman Lindsay

    2011-08-01

    Full Text Available Abstract Background The division of labor in social insect colonies involves transitions by workers from one task to another and is critical to the organization and ecological success of colonies. The differential regulation of genetic pathways is likely to be a key mechanism involved in plasticity of social insect task behavior. One of the few pathways implicated in social organization involves the cGMP-activated protein kinase gene, foraging, a gene associated with foraging behavior in social insect species. The association of the foraging gene with behavior is conserved across diverse species, but the observed expression patterns and proposed functions of this gene vary across taxa. We compared the protein sequence of foraging across social insects and explored whether the differential regulation of this gene is associated with task behaviors in the harvester ant, Pogonomyrmex occidentalis. Results Phylogenetic analysis of the coding region of the foraging gene reveals considerable conservation in protein sequence across insects, particularly among hymenopteran species. The absence of amino acid variation in key active and binding sites suggests that differences in behaviors associated with this gene among species may be the result of changes in gene expression rather than gene divergence. Using real time qPCR analyses with a harvester ant ortholog to foraging (Pofor, we found that the brains of harvester ant foragers have a daily fluctuation in expression of foraging with mRNA levels peaking at midday. In contrast, young workers inside the nest have low levels of Pofor mRNA with no evidence of daily fluctuations in expression. As a result, the association of foraging expression with task behavior within a species changes depending on the time of day the individuals are sampled. Conclusions The amino acid protein sequence of foraging is highly conserved across social insects. Differences in foraging behaviors associated with this gene among

  9. Gut Microbiome of the Canadian Arctic Inuit

    Science.gov (United States)

    Tromas, Nicolas; Amyot, Marc

    2017-01-01

    ABSTRACT Diet is a major determinant of community composition in the human gut microbiome, and “traditional” diets have been associated with distinct and highly diverse communities, compared to Western diets. However, most traditional diets studied have been those of agrarians and hunter-gatherers consuming fiber-rich diets. In contrast, the Inuit of the Canadian Arctic have been consuming a traditional diet low in carbohydrates and rich in animal fats and protein for thousands of years. We hypothesized that the Inuit diet and lifestyle would be associated with a distinct microbiome. We used deep sequencing of the 16S rRNA gene to compare the gut microbiomes of Montrealers with a Western diet to those of the Inuit consuming a range of traditional and Western diets. At the overall microbial community level, the gut microbiomes of Montrealers and Inuit were indistinguishable and contained similar levels of microbial diversity. However, we observed significant differences in the relative abundances of certain microbial taxa down to the subgenus level using oligotyping. For example, Prevotella spp., which have been previously associated with high-fiber diets, were enriched in Montrealers and among the Inuit consuming a Western diet. The gut microbiomes of Inuit consuming a traditional diet also had significantly less genetic diversity within the Prevotella genus, suggesting that a low-fiber diet might not only select against Prevotella but also reduce its diversity. Other microbes, such as Akkermansia, were associated with geography as well as diet, suggesting limited dispersal to the Arctic. Our report provides a snapshot of the Inuit microbiome as Western-like in overall community structure but distinct in the relative abundances and diversity of certain genera and strains. IMPORTANCE Non-Western populations have been shown to have distinct gut microbial communities shaped by traditional diets. The hitherto-uncharacterized microbiome of the Inuit may help us to

  10. Evaluation of the microbiome in children's appendicitis.

    Science.gov (United States)

    Salö, Martin; Marungruang, Nittaya; Roth, Bodil; Sundberg, Tiia; Stenström, Pernilla; Arnbjörnsson, Einar; Fåk, Frida; Ohlsson, Bodil

    2017-01-01

    The role of the microbiome has been widely discussed in the etiology of appendicitis. The primary aim was to evaluate the microbiome in the normal appendix and in appendicitis specifically divided into the three clinically and histopathologically defined grades of inflammation. Secondary aims were to examine whether there were any microbiome differences between proximal and distal appendices, and relate the microbiome with histopathological findings. A prospective pilot study was conducted of children undergoing appendectomy for appendicitis. The diagnosis was based on histopathological analysis. Children with incidental appendectomy were used as controls. The proximal and distal mucosa from the appendices were analyzed with 16S rRNA gene sequencing. A total of 22 children, 3 controls and 19 appendicitis patients; 11 phlegmonous, 4 gangrenous, and 4 perforated appendices, were prospectively included. The amount of Fusobacterium increased and Bacteroides decreased in phlegmonous and perforated appendicitis compared to controls, but statistical significance was not reached, and this pattern was not seen in gangrenous appendicitis. No relation could be seen between different bacteria and the grade of inflammation, and there was a wide variation of abundances at phylum, genus, and species level within every specific group of patients. Further, no significant differences could be detected when comparing the microbiome in proximal and distal mucosa, which may be because the study was underpowered. A trend with more abundance of Fusobacteria in the distal mucosa was seen in appendicitis patients with obstruction (25 and 13 %, respectively, p = 0.06). The pattern of microbiome differed not only between groups, but also within groups. However, no statistically significant differences could be found in the microbiome between groups or clinical conditions. No correlation between a specific bacteria and grade of inflammation was found. In the vast majority of cases of

  11. Microbial co-occurrence relationships in the human microbiome.

    Directory of Open Access Journals (Sweden)

    Karoline Faust

    Full Text Available The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs to taxonomic marker (16S rRNA gene profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut often compete, while potential pathogens (e.g. Treponema and

  12. Microbial Co-occurrence Relationships in the Human Microbiome

    Science.gov (United States)

    Izard, Jacques; Segata, Nicola; Gevers, Dirk

    2012-01-01

    The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecological relationships (both oppositional and symbiotic) between microbial inhabitants are important contributors to this variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons. The initial Human Microbiome Project (HMP) cohort, comprising 239 individuals and 18 different microbial habitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort, resulting in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome. This network revealed strong niche specialization, with most microbial associations occurring within body sites and a number of accompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselves showed no direct influence on the composition of the gut microbiota. Conversely, niches such as the vagina demonstrated little to no decomposition into region-specific interactions. Diverse mechanisms underlay individual interactions, with some such as the co-exclusion of Porphyromonaceae family members and Streptococcus in the subgingival plaque supported by known biochemical dependencies. These differences varied among broad phylogenetic groups as well, with the Bacilli and Fusobacteria, for example, both enriched for exclusion of taxa from other clades. Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. Treponema and Prevotella in the

  13. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

    Directory of Open Access Journals (Sweden)

    Christopher L Hemme

    2015-10-01

    Full Text Available To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301 and contaminated groundwater (FW106 samples from the Oak Ridge Integrated Field Research Center (OR-IFRC were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas are the most abundant lineages in the pristine community, though a significant proportion (>55% of the community is composed of poorly characterized low abundance (individually <1% lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. These results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.

  14. Corn in consortium with forages

    Directory of Open Access Journals (Sweden)

    Cássia Maria de Paula Garcia

    2013-12-01

    Full Text Available The basic premises for sustainable agricultural development with focus on rural producers are reducing the costs of production and aggregation of values through the use crop-livestock system (CLS throughout the year. The CLS is based on the consortium of grain crops, especially corn with tropical forages, mainly of the genus Panicum and Urochloa. The study aimed to evaluate the grain yield of irrigated corn crop intercropped with forage of the genus Panicum and Urochloa. The experiment was conducted at the Fazenda de Ensino, Pesquisa e Extensão – FEPE  of the Faculdade de Engenharia - UNESP, Ilha Solteira in an Oxisol in savannah conditions and in the autumn winter of 2009. The experimental area was irrigated by a center pivot and had a history of no-tillage system for 8 years. The corn hybrid used was simple DKB 390 YG at distances of 0.90 m. The seeds of grasses were sown in 0.34 m spacing in the amount of 5 kg ha-1, they were mixed with fertilizer minutes before sowing  and placed in a compartment fertilizer seeder and fertilizers were mechanically deposited in the soil at a depth of 0.03 m. The experimental design used was a randomized block with four replications and five treatments: Panicum maximum cv. Tanzania sown during the nitrogen fertilization (CTD of the corn; Panicum maximum cv. Mombaça sown during the nitrogen fertilization (CMD of the corn; Urochloa brizantha cv. Xaraés sown during the occasion of nitrogen fertilization (CBD of the corn; Urochloa ruziziensis cv. Comumsown during the nitrogen fertilization (CRD of the corn and single corn (control. The production components of corn: plant population per hectare (PlPo, number of ears per hectare (NE ha-1, number of rows per ear (NRE, number of kernels per row on the cob (NKR, number of grain in the ear (NGE and mass of 100 grains (M100G were not influenced by consortium with forage. Comparing grain yield (GY single corn and maize intercropped with forage of the genus Panicum

  15. The gut microbiome in atherosclerotic cardiovascular disease

    DEFF Research Database (Denmark)

    Jie, Zhuye; Xia, Huihua; Zhong, Shi-Long

    2017-01-01

    The gut microbiota has been linked to cardiovascular diseases. However, the composition and functional capacity of the gut microbiome in relation to cardiovascular diseases have not been systematically examined. Here, we perform a metagenome-wide association study on stools from 218 individuals...... with atherosclerotic cardiovascular disease (ACVD) and 187 healthy controls. The ACVD gut microbiome deviates from the healthy status by increased abundance of Enterobacteriaceae and Streptococcus spp. and, functionally, in the potential for metabolism or transport of several molecules important for cardiovascular......), with liver cirrhosis, and rheumatoid arthritis. Our data represent a comprehensive resource for further investigations on the role of the gut microbiome in promoting or preventing ACVD as well as other related diseases.The gut microbiota may play a role in cardiovascular diseases. Here, the authors perform...

  16. The gut microbiome in atherosclerotic cardiovascular disease

    DEFF Research Database (Denmark)

    Jie, Zhuye; Xia, Huihua; Zhong, Shi-Long

    2017-01-01

    The gut microbiota has been linked to cardiovascular diseases. However, the composition and functional capacity of the gut microbiome in relation to cardiovascular diseases have not been systematically examined. Here, we perform a metagenome-wide association study on stools from 218 individuals...... with atherosclerotic cardiovascular disease (ACVD) and 187 healthy controls. The ACVD gut microbiome deviates from the healthy status by increased abundance of Enterobacteriaceae and Streptococcus spp. and, functionally, in the potential for metabolism or transport of several molecules important for cardiovascular...... health. Although drug treatment represents a confounding factor, ACVD status, and not current drug use, is the major distinguishing feature in this cohort. We identify common themes by comparison with gut microbiome data associated with other cardiometabolic diseases (obesity and type 2 diabetes...

  17. Deciphering conjugative plasmid permissiveness in wastewater microbiomes

    DEFF Research Database (Denmark)

    Jacquiod, Samuel Jehan Auguste; Brejnrod, Asker Daniel; Milani, Stefan Morberg

    2017-01-01

    Wastewater treatment plants (WWTPs) are designed to robustly treat polluted water. They are characterized by ceaseless flows of organic, chemical and microbial matter, followed by treatment steps before environmental release. WWTPs are hotspots of horizontal gene transfer between bacteria via...... still remains largely uncharted. Furthermore, current in vitro methods used to assess conjugation in complex microbiomes do not include in situ behaviours of recipient cells, resulting in partial understanding of transfers. We investigated the in vitro conjugation capacities of WWTP microbiomes from...... inlet sewage and outlet treated water using the broad-host range IncP-1 conjugative plasmid, pKJK5. A thorough molecular approach coupling metagenomes to 16S rRNA DNA/cDNA amplicon sequencing was established to characterize microbiomes using the ecological concept of functional response groups. A broad...

  18. A neural coding scheme reproducing foraging trajectories

    Science.gov (United States)

    Gutiérrez, Esther D.; Cabrera, Juan Luis

    2015-12-01

    The movement of many animals may follow Lévy patterns. The underlying generating neuronal dynamics of such a behavior is unknown. In this paper we show that a novel discovery of multifractality in winnerless competition (WLC) systems reveals a potential encoding mechanism that is translatable into two dimensional superdiffusive Lévy movements. The validity of our approach is tested on a conductance based neuronal model showing WLC and through the extraction of Lévy flights inducing fractals from recordings of rat hippocampus during open field foraging. Further insights are gained analyzing mice motor cortex neurons and non motor cell signals. The proposed mechanism provides a plausible explanation for the neuro-dynamical fundamentals of spatial searching patterns observed in animals (including humans) and illustrates an until now unknown way to encode information in neuronal temporal series.

  19. The gut mycobiome of the Human Microbiome Project healthy cohort.

    Science.gov (United States)

    Nash, Andrea K; Auchtung, Thomas A; Wong, Matthew C; Smith, Daniel P; Gesell, Jonathan R; Ross, Matthew C; Stewart, Christopher J; Metcalf, Ginger A; Muzny, Donna M; Gibbs, Richard A; Ajami, Nadim J; Petrosino, Joseph F

    2017-11-25

    Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene. Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents. Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual's mycobiome is no more similar to itself over time than to another person's. Nonetheless, several fungal species persisted across a majority of samples, evidence that

  20. Intrinsic association between diet and the gut microbiome: current evidence

    Directory of Open Access Journals (Sweden)

    Winglee K

    2015-10-01

    Full Text Available Kathryn Winglee, Anthony A Fodor Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA Abstract: The gut microbiome performs many crucial functions for the human host, but the molecular mechanisms by which host, microbe, and diet interact to mediate health and disease are only starting to be revealed. Here, we review the literature on how changes in the diet affect the microbiome. A number of studies have shown that within a geographic region, different diets (such as vegan vs omnivore are associated with differences in a modest number of taxa, but do not reliably produce radical differences within the gut microbial community. In contrast, studies that look across continents consistently find profoundly different microbial communities between Westernized and traditional populations, although it remains unclear to what extent diet or other differences in lifestyle drive these distinct microbial community structures. Furthermore, studies that place subjects on controlled short-term experimental diets have found the resulting alterations to the gut microbial community to generally be small in scope, with changes that do not overcome initial individual differences in microbial community structure. These results emphasize that the human gut microbial community is relatively stable over time. In contrast, short-term changes in diet can cause large changes in metabolite profiles, including metabolites processed by the gut microbial community. These results suggest that commensal gut microbes have a great deal of genetic plasticity and can activate different metabolic pathways independent of changes to microbial community composition. Thus, future studies of how the diet impacts host health via the microbiome may wish to focus on functional assays such as transcriptomics and metabolomics, in addition to 16S rRNA and whole-genome metagenome shotgun analyses of DNA. Taken together, the literature is most

  1. Subgingival Microbiome of Gingivitis in Chinese Undergraduates.

    Science.gov (United States)

    Deng, Ke; Ouyang, Xiang Ying; Chu, Yi; Zhang, Qian

    To analyse the microbiome composition of health and gingivitis in Chinese undergraduates with high-throughput sequencing. Sequencing of 16S rRNA gene amplicons was performed with the MiSeq system to compare subgingival bacterial communities from 54 subjects with gingivitis and 12 periodontally healthy controls. A total of 1,967,372 sequences representing 14 phyla, 104 genera, and 96 species were detected. Analysis of similarities (Anosim) test and Principal Component Analysis (PCA) showed significantly different community profiles between the health control and the subjects with gingivitis. Alpha-diversity metrics were significantly higher in the subgingival plaque of the subjects with gingivitis compared with that of the healthy control. Overall, the relative abundance of 35 genera and 46 species were significantly different between the two groups, among them 28 genera and 45 species showed higher relative abundance in the subjects with gingivitis, whereas seven genera and one species showed a higher relative abundance in the healthy control. The genera Porphyromonas, Treponema, and Tannerella showed higher relative abundance in the subjects with gingivitis, while the genera Capnocytophaga showed higher proportions in health controls. Porphyromonas gingivalis, Prevotella intermedia and Porphyromonas endodontalis had higher relative abundance in gingivitis. Among them, Porphyromonas gingivalis was most abundant. Our results revealed significantly different microbial community composition and structures of subgingival plaque between subjects with gingivitis and healthy controls. Subjects with gingivitis showed greater taxonomic diversity compared with periodontally healthy subjects. The proportion of Porphyromonas, especially Porphyromonas gingivalis, may be associated with gingivitis subjects aged between 18 and 21 years old in China. Adults with gingivitis in this age group may have a higher risk of developing periodontitis.

  2. Metabolome of human gut microbiome is predictive of host dysbiosis

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, Peter E.; Dai, Yang

    2015-09-14

    Background: Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. However, the community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome’s interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent on its community metabolome; an emergent property of the microbiome. Results: Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles. Conclusions: Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome–host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.

  3. Current understanding of the human microbiome

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, Jack A.; Blaser, Martin J.; Caporaso, J. Gregory; Jansson, Janet K.; Lynch, Susan V.; Knight, Rob

    2018-04-10

    Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes, and mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this Review we focus on studies in humans to describe these challenges, and propose strategies that leverage existing knowledge to move rapidly from correlation to causation, and ultimately to translation.

  4. Rapid changes in the gut microbiome during human evolution.

    Science.gov (United States)

    Moeller, Andrew H; Li, Yingying; Mpoudi Ngole, Eitel; Ahuka-Mundeke, Steve; Lonsdorf, Elizabeth V; Pusey, Anne E; Peeters, Martine; Hahn, Beatrice H; Ochman, Howard

    2014-11-18

    Humans are ecosystems containing trillions of microorganisms, but the evolutionary history of this microbiome is obscured by a lack of knowledge about microbiomes of African apes. We sequenced the gut communities of hundreds of chimpanzees, bonobos, and gorillas and developed a phylogenetic approach to reconstruct how present-day human microbiomes have diverged from those of ancestral populations. Compositional change in the microbiome was slow and clock-like during African ape diversification, but human microbiomes have deviated from the ancestral state at an accelerated rate. Relative to the microbiomes of wild apes, human microbiomes have lost ancestral microbial diversity while becoming specialized for animal-based diets. Individual wild apes cultivate more phyla, classes, orders, families, genera, and species of bacteria than do individual humans across a range of societies. These results indicate that humanity has experienced a depletion of the gut flora since diverging from Pan.

  5. Geographic profiling and animal foraging.

    Science.gov (United States)

    Le Comber, Steven C; Nicholls, Barry; Rossmo, D Kim; Racey, Paul A

    2006-05-21

    Geographic profiling was originally developed as a statistical tool for use in criminal cases, particularly those involving serial killers and rapists. It is designed to help police forces prioritize lists of suspects by using the location of crime scenes to identify the areas in which the criminal is most likely to live. Two important concepts are the buffer zone (criminals are less likely to commit crimes in the immediate vicinity of their home) and distance decay (criminals commit fewer crimes as the distance from their home increases). In this study, we show how the techniques of geographic profiling may be applied to animal data, using as an example foraging patterns in two sympatric colonies of pipistrelle bats, Pipistrellus pipistrellus and P. pygmaeus, in the northeast of Scotland. We show that if model variables are fitted to known roost locations, these variables may be used as numerical descriptors of foraging patterns. We go on to show that these variables can be used to differentiate patterns of foraging in these two species.

  6. Season and landscape composition affect pollen foraging distances and habitat use of honey bees.

    Science.gov (United States)

    Danner, Nadja; Molitor, Anna Maria; Schiele, Susanne; Härtel, Stephan; Steffan-Dewenter, Ingolf

    2016-09-01

    Honey bees (Apis mellifera L.) show a large variation in foraging distances and use a broad range of plant species as pollen resources, even in regions with intensive agriculture. However, it is unknown how increasing areas of mass-flowering crops like oilseed rape (Brassica napus; OSR) or a decrease of seminatural habitats (SNH) change the temporal and spatial availability of pollen resources for honey bee colonies, and thus foraging distances and frequency in different habitat types. We studied pollen foraging of honey bee colonies in 16 agricultural landscapes with independent gradients of OSR and SNH area within 2 km and used waggle dances and digital geographic maps with major land cover types to reveal the distance and visited habitat type on a landscape level. Mean pollen foraging distance of 1347 decoded bee dances was 1015 m (± 26 m; SEM). In spring, increasing area of flowering OSR within 2 km reduced mean pollen foraging distances from 1324 m to only 435 m. In summer, increasing cover of SNH areas close to the colonies (within 200 m radius) reduced mean pollen foraging distances from 846 to 469 m. Frequency of pollen foragers per habitat type, measured as the number of dances per hour and hectare, was equally high for SNH, grassland, and OSR fields, but lower for other crops and forests. In landscapes with a small proportion of SNH a significantly higher density of pollen foragers on SNH was observed, indicating that pollen resources in such simple agricultural landscapes are more limited. Overall, we conclude that SNH and mass-flowering crops can reduce foraging distances of honey bee colonies at different scales and seasons with possible benefits for the performance of honey bee colonies. Further, mixed agricultural landscapes with a high proportion of SNH reduce foraging densities of honey bees in SNH and thus possible competition for pollen resources. © 2016 by the Ecological Society of America.

  7. Feeding-Related Traits Are Affected by Dosage of the foraging Gene in Drosophila melanogaster.

    Science.gov (United States)

    Allen, Aaron M; Anreiter, Ina; Neville, Megan C; Sokolowski, Marla B

    2017-02-01

    Nutrient acquisition and energy storage are critical parts of achieving metabolic homeostasis. The foraging gene in Drosophila melanogaster has previously been implicated in multiple feeding-related and metabolic traits. Before foraging's functions can be further dissected, we need a precise genetic null mutant to definitively map its amorphic phenotypes. We used homologous recombination to precisely delete foraging, generating the for 0 null allele, and used recombineering to reintegrate a full copy of the gene, generating the {for BAC } rescue allele. We show that a total loss of foraging expression in larvae results in reduced larval path length and food intake behavior, while conversely showing an increase in triglyceride levels. Furthermore, varying foraging gene dosage demonstrates a linear dose-response on these phenotypes in relation to foraging gene expression levels. These experiments have unequivocally proven a causal, dose-dependent relationship between the foraging gene and its pleiotropic influence on these feeding-related traits. Our analysis of foraging's transcription start sites, termination sites, and splicing patterns using rapid amplification of cDNA ends (RACE) and full-length cDNA sequencing, revealed four independent promoters, pr1-4, that produce 21 transcripts with nine distinct open reading frames (ORFs). The use of alternative promoters and alternative splicing at the foraging locus creates diversity and flexibility in the regulation of gene expression, and ultimately function. Future studies will exploit these genetic tools to precisely dissect the isoform- and tissue-specific requirements of foraging's functions and shed light on the genetic control of feeding-related traits involved in energy homeostasis. Copyright © 2017 by the Genetics Society of America.

  8. Starvation dynamics of a greedy forager

    Science.gov (United States)

    Bhat, U.; Redner, S.; Bénichou, O.

    2017-07-01

    We investigate the dynamics of a greedy forager that moves by random walking in an environment where each site initially contains one unit of food. Upon encountering a food-containing site, the forager eats all the food there and can subsequently hop an additional S steps without food before starving to death. Upon encountering an empty site, the forager goes hungry and comes one time unit closer to starvation. We investigate the new feature of forager greed; if the forager has a choice between hopping to an empty site or to a food-containing site in its nearest neighborhood, it hops preferentially towards food. If the neighboring sites all contain food or are all empty, the forager hops equiprobably to one of these neighbors. Paradoxically, the lifetime of the forager can depend non-monotonically on greed, and the sense of the non-monotonicity is opposite in one and two dimensions. Even more unexpectedly, the forager lifetime in one dimension is substantially enhanced when the greed is negative; here the forager tends to avoid food in its local neighborhood. We also determine the average amount of food consumed at the instant when the forager starves. We present analytic, heuristic, and numerical results to elucidate these intriguing phenomena.

  9. Circadian Disruption Changes Gut Microbiome Taxa and Functional Gene Composition.

    Science.gov (United States)

    Deaver, Jessica A; Eum, Sung Y; Toborek, Michal

    2018-01-01

    Disrupted circadian rhythms and alterations of the gut microbiome composition were proposed to affect host health. Therefore, the aim of this research was to identify whether these events are connected and if circadian rhythm disruption by abnormal light-dark (LD) cycles affects microbial community gene expression and host vulnerability to intestinal dysfunction. Mice were subjected to either a 4-week period of constant 24-h light or of normal 12-h LD cycles. Stool samples were collected at the beginning and after the circadian rhythm disruption. A metatranscriptomic analysis revealed an increase in Ruminococcus torques , a bacterial species known to decrease gut barrier integrity, and a decrease in Lactobacillus johnsonii , a bacterium that helps maintain the intestinal epithelial cell layer, after circadian rhythm disruption. In addition, genes involved in pathways promoting host beneficial immune responses were downregulated, while genes involved in the synthesis and transportation of the endotoxin lipopolysaccharide were upregulated in mice with disrupted circadian cycles. Importantly, these mice were also more prone to dysfunction of the intestinal barrier. These results further elucidate the impact of light-cycle disruption on the gut microbiome and its connection with increased incidence of disease in response to circadian rhythm disturbances.

  10. Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America.

    Science.gov (United States)

    Köberl, Martina; Dita, Miguel; Martinuz, Alfonso; Staver, Charles; Berg, Gabriele

    2015-01-01

    Bananas (Musa spp.) belong to the most important global food commodities, and their cultivation represents the world's largest monoculture. Although the plant-associated microbiome has substantial influence on plant growth and health, there is a lack of knowledge of the banana microbiome and its influencing factors. We studied the impact of (i) biogeography, and (ii) agroforestry on the banana-associated gammaproteobacterial microbiome analyzing plants grown in smallholder farms in Nicaragua and Costa Rica. Profiles of 16S rRNA genes revealed high abundances of Pseudomonadales, Enterobacteriales, Xanthomonadales, and Legionellales. An extraordinary high diversity of the gammaproteobacterial microbiota was observed within the endophytic microenvironments (endorhiza and pseudostem), which was similar in both countries. Enterobacteria were identified as dominant group of above-ground plant parts (pseudostem and leaves). Neither biogeography nor agroforestry showed a statistically significant impact on the gammaproteobacterial banana microbiome in general. However, indicator species for each microenvironment and country, as well as for plants grown in Coffea intercropping systems with and without agri-silvicultural production of different Fabaceae trees (Inga spp. in Nicaragua and Erythrina poeppigiana in Costa Rica) could be identified. For example, banana plants grown in agroforestry systems were characterized by an increase of potential plant-beneficial bacteria, like Pseudomonas and Stenotrophomonas, and on the other side by a decrease of Erwinia. Hence, this study could show that as a result of legume-based agroforestry the indigenous banana-associated gammaproteobacterial community noticeably shifted.

  11. An Insect Herbivore Microbiome with High Plant Biomass-Degrading Capacity

    Energy Technology Data Exchange (ETDEWEB)

    Suen, Garret; Barry, Kerrie; Goodwin, Lynne; Scott, Jarrod; Aylward, Frank; Adams, Sandra; Pinto-Tomas, Adrian; Foster, Clifton; Pauly, Markus; Weimer, Paul; Bouffard, Pascal; Li, Lewyn; Osterberger, Jolene; Harkins, Timothy; Slater, Steven; Donohue, Timothy; Currie, Cameron; Tringe, Susannah G.

    2010-09-23

    Herbivores can gain indirect access to recalcitrant carbon present in plant cell walls through symbiotic associations with lignocellulolytic microbes. A paradigmatic example is the leaf-cutter ant (Tribe: Attini), which uses fresh leaves to cultivate a fungus for food in specialized gardens. Using a combination of sugar composition analyses, metagenomics, and whole-genome sequencing, we reveal that the fungus garden microbiome of leaf-cutter ants is composed of a diverse community of bacteria with high plant biomass-degrading capacity. Comparison of this microbiome?s predicted carbohydrate-degrading enzyme profile with other metagenomes shows closest similarity to the bovine rumen, indicating evolutionary convergence of plant biomass degrading potential between two important herbivorous animals. Genomic and physiological characterization of two dominant bacteria in the fungus garden microbiome provides evidence of their capacity to degrade cellulose. Given the recent interest in cellulosic biofuels, understanding how large-scale and rapid plant biomass degradation occurs in a highly evolved insect herbivore is of particular relevance for bioenergy.

  12. Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition

    Directory of Open Access Journals (Sweden)

    Emily B. Graham

    2018-04-01

    Full Text Available Recent advances have allowed for greater investigation into microbial regulation of mercury toxicity in the environment. In wetlands in particular, dissolved organic matter (DOM may influence methylmercury (MeHg production both through chemical interactions and through substrate effects on microbiomes. We conducted microcosm experiments in two disparate wetland environments (oligotrophic unvegetated and high-C vegetated sediments to examine the impacts of plant leachate and inorganic mercury loadings (20 mg/L HgCl2 on microbiomes and MeHg production in the St. Louis River Estuary. Our research reveals the greater relative capacity for mercury methylation in vegetated over unvegetated sediments. Further, our work shows how mercury cycling in oligotrophic unvegetated sediments may be susceptible to DOM inputs in the St. Louis River Estuary: unvegetated microcosms receiving leachate produced substantially more MeHg than unamended microcosms. We also demonstrate (1 changes in microbiome structure towards Clostridia, (2 metagenomic shifts toward fermentation, and (3 degradation of complex DOM; all of which coincide with elevated net MeHg production in unvegetated microcosms receiving leachate. Together, our work shows the influence of wetland vegetation in controlling MeHg production in the Great Lakes region and provides evidence that this may be due to both enhanced microbial activity as well as differences in microbiome composition.

  13. Impact of the Chromatin Remodeling Factor CHD1 on Gut Microbiome Composition of Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Johanna Sebald

    Full Text Available The composition of the intestinal microbiota of Drosophila has been studied in some detail in recent years. Environmental, developmental and host-specific genetic factors influence microbiome composition in the fly. Our previous work has indicated that intestinal bacterial load can be affected by chromatin-targeted regulatory mechanisms. Here we studied a potential role of the conserved chromatin assembly and remodeling factor CHD1 in the shaping of the gut microbiome in Drosophila melanogaster. Using high-throughput sequencing of 16S rRNA gene amplicons, we found that Chd1 deletion mutant flies exhibit significantly reduced microbial diversity compared to rescued control strains. Specifically, although Acetobacteraceae dominated the microbiota of both Chd1 wild-type and mutant guts, Chd1 mutants were virtually monoassociated with this bacterial family, whereas in control flies other bacterial taxa constituted ~20% of the microbiome. We further show age-linked differences in microbial load and microbiota composition between Chd1 mutant and control flies. Finally, diet supplementation experiments with Lactobacillus plantarum revealed that, in contrast to wild-type flies, Chd1 mutant flies were unable to maintain higher L. plantarum titres over time. Collectively, these data provide evidence that loss of the chromatin remodeler CHD1 has a major impact on the gut microbiome of Drosophila melanogaster.

  14. Metagenomic Systems Biology of the Human Microbiome

    DEFF Research Database (Denmark)

    Bonde, Ida

    The human microbiome is an integrated part of the human body, outnumbering the human cells by approximately a factor 10. These microorganisms are very important for human health, hence knowledge about this, ”our other genome”, has been growing rapidly in recent years. This is manly due to the adv...

  15. Phenylketonuria: central nervous system and microbiome interaction

    Directory of Open Access Journals (Sweden)

    Demian Arturo Herrera Morban

    2017-06-01

    Full Text Available Phenylketonuria (PKU is an autosomal recessive inborn error of metabolism characterized by increased phenylalanine (Phe levels causing an inadequate neurodevelopment; the treatment of PKU is a Phe-restricting diet, and as such it can modulate the intestinal microbiome of the individual, generating central nervous system secondary disturbances that, added to the baseline disturbance, can influence the outcome of the disease.

  16. Childhood malnutrition and the intestinal microbiome.

    Science.gov (United States)

    Kane, Anne V; Dinh, Duy M; Ward, Honorine D

    2015-01-01

    Malnutrition contributes to almost half of all deaths in children under the age of 5 y, particularly those who live in resource-constrained areas. Those who survive frequently suffer from long-term sequelae including growth failure and neurodevelopmental impairment. Malnutrition is part of a vicious cycle of impaired immunity, recurrent infections, and worsening malnutrition. Recently, alterations in the gut microbiome have also been strongly implicated in childhood malnutrition. It has been suggested that malnutrition may delay the normal development of the gut microbiota in early childhood or force it toward an altered composition that lacks the required functions for healthy growth and/or increases the risk for intestinal inflammation. This review addresses our current understanding of the beneficial contributions of gut microbiota to human nutrition (and conversely the potential role of changes in that community to malnutrition), the process of acquiring an intestinal microbiome, potential influences of malnutrition on the developing microbiota, and the evidence directly linking alterations in the intestinal microbiome to childhood malnutrition. We review recent studies on the association between alterations in the intestinal microbiome and early childhood malnutrition and discuss them in the context of implications for intervention or prevention of the devastation caused by malnutrition.

  17. Social attraction mediated by fruit flies' microbiome.

    Science.gov (United States)

    Venu, Isvarya; Durisko, Zachary; Xu, Jianping; Dukas, Reuven

    2014-04-15

    Larval and adult fruit flies are attracted to volatiles emanating from food substrates that have been occupied by larvae. We tested whether such volatiles are emitted by the larval gut bacteria by conducting tests under bacteria-free (axenic) conditions. We also tested attraction to two bacteria species, Lactobacillus brevis, which we cultured from larvae in our lab, and L. plantarum, a common constituent of fruit flies' microbiome in other laboratory populations and in wild fruit flies. Neither larvae nor adults showed attraction to axenic food that had been occupied by axenic larvae, but both showed the previously reported attraction to standard food that had been occupied by larvae with an intact microbiome. Larvae also showed significant attraction to volatiles from axenic food and larvae to which we added only either L. brevis or L. plantarum, and volatiles from L. brevis reared on its optimal growth medium. Controlled learning experiments indicated that larvae experienced with both standard and axenic used food do not perceive either as superior, while focal larvae experienced with simulated used food, which contains burrows, perceive it as superior to unused food. Our results suggest that flies rely on microbiome-derived volatiles for long-distance attraction to suitable food patches. Under natural settings, fruits often contain harmful fungi and bacteria, and both L. brevis and L. plantarum produce compounds that suppress the growth of some antagonistic fungi and bacteria. The larval microbiome volatiles may therefore lead prospective fruit flies towards substrates with a hospitable microbial environment.

  18. Metatranscriptomics of the human gut microbiome

    DEFF Research Database (Denmark)

    Sicheritz-Pontén, Thomas

    2011-01-01

    Our ‘other’ genome is the collective genetic information in all of the microorganisms that are living on and within us. Collectively known as the microbiome, these microbial cells outnumber human cells in the body by more than 10 to 1, and the genes carried by these organisms outnumber the genes ...... that there is a division of labor between the bacterial species in the human gut microbiome.......Our ‘other’ genome is the collective genetic information in all of the microorganisms that are living on and within us. Collectively known as the microbiome, these microbial cells outnumber human cells in the body by more than 10 to 1, and the genes carried by these organisms outnumber the genes...... in the human genome by more than 100 to 1. How these organisms contribute to and affect human health is poorly understood, but the emerging field of metagenomics promises a more comprehensive and complete understanding of the human microbiome. In the European-funded Metagenomics of the Human Intestinal Tract...

  19. Proton pump inhibitors affect the gut microbiome

    NARCIS (Netherlands)

    Imhann, Floris; Bonder, Marc Jan; Vich Vila, Arnau; Fu, Jingyuan; Mujagic, Zlatan; Vork, Lisa; Feenstra, Ettje T.; Jankipersadsing, Soesma A; Cenit, Maria Carmen; Harmsen, Hermie J M; Dijkstra, Gerard; Franke, Lude; Xavier, Ramnik J; Jonkers, Daisy; Wijmenga, Cisca; Weersma, Rinse K; Zhernakova, Alexandra

    BACKGROUND AND AIMS: Proton pump inhibitors (PPIs) are among the top 10 most widely used drugs in the world. PPI use has been associated with an increased risk of enteric infections, most notably Clostridium difficile. The gut microbiome plays an important role in enteric infections, by resisting or

  20. UNRAVELING THE FUNCTIONS OF THE MACROALGAL MICROBIOME

    Directory of Open Access Journals (Sweden)

    Ravindra Pal Singh

    2016-01-01

    Full Text Available Macroalgae are a diverse group of photosynthetic eukaryotic lower organisms and offer indispensable ecosystem services towards sustainable productivity of rocky coastal areas. The earlier studies have mainly focused on elucidation of the roles of the epiphytic bacterial communities in the ecophysiology of the host macroalga. However, mutualistic interactions have become topic of current interest. It is evident from recent studies that a fraction of epiphytic bacterial communities can be categorized as core microbial species, suggesting an obligate association. Epiphytic bacterial communities have also been reported to protect macroalgal surfaces from biofouling microorganisms through production of biologically active metabolites. Because of their intrinsic roles in the host life cycle, the host in turn may provide necessary organic nutrients in order to woo pelagic microbial communities to settle on the host surfaces. However, the precise composition of microbiomes and their functional partnership with hosts are hardly understood. In contrast, the microbial studies associated with human skin and gut and plants have significantly advanced our knowledge on microbiome and their functional interactions with the host. This has led to manipulation of the microbial flora of the human gut and of agricultural plants for improving health and performance. Therefore, it is highly imperative to investigate the functional microbiome that is closely involved in the life cycles of the host macroalgae using high-throughput techniques (metagenomics and metatranscriptomics. The findings from such investigations would help in promoting health and productivity in macroalgal species through regulation of functionally active microbiome.

  1. The Microbiome in Skin Health and Disease

    Indian Academy of Sciences (India)

    Souvik Mukherjee

    Differential Skin Microbiome profile in Caesarean babies is associated with risk of immune/metabolic .... Indicator. Genus. Cheek Sebum. (μg/cm2) p-value. Forehead Hydration. [Age adjusted] (a.u.) p-value .... Key Inferences. The Healthy Skin ...

  2. Visual Foraging With Fingers and Eye Gaze

    Directory of Open Access Journals (Sweden)

    Ómar I. Jóhannesson

    2016-03-01

    Full Text Available A popular model of the function of selective visual attention involves search where a single target is to be found among distractors. For many scenarios, a more realistic model involves search for multiple targets of various types, since natural tasks typically do not involve a single target. Here we present results from a novel multiple-target foraging paradigm. We compare finger foraging where observers cancel a set of predesignated targets by tapping them, to gaze foraging where observers cancel items by fixating them for 100 ms. During finger foraging, for most observers, there was a large difference between foraging based on a single feature, where observers switch easily between target types, and foraging based on a conjunction of features where observers tended to stick to one target type. The pattern was notably different during gaze foraging where these condition differences were smaller. Two conclusions follow: (a The fact that a sizeable number of observers (in particular during gaze foraging had little trouble switching between different target types raises challenges for many prominent theoretical accounts of visual attention and working memory. (b While caveats must be noted for the comparison of gaze and finger foraging, the results suggest that selection mechanisms for gaze and pointing have different operational constraints.

  3. Boa constrictor (Boa constrictor): foraging behavior

    Science.gov (United States)

    Sorrell, G.G.; Boback, M.S.; Reed, R.N.; Green, S.; Montgomery, Chad E.; DeSouza, L.S.; Chiaraviglio, M.

    2011-01-01

    Boa constrictor is often referred to as a sit-and-wait or ambush forager that chooses locations to maximize the likelihood of prey encounters (Greene 1983. In Janzen [ed.], Costa Rica Natural History, pp. 380-382. Univ. Chicago Press, Illinois). However, as more is learned about the natural history of snakes in general, the dichotomy between active versus ambush foraging is becoming blurred. Herein, we describe an instance of diurnal active foraging by a B. constrictor, illustrating that this species exhibits a range of foraging behaviors.

  4. U.S. DAIRY FORAGE RESEARCH CENTER

    Data.gov (United States)

    Federal Laboratory Consortium — Vision: Leading the world in integrated dairy forage systems research. Mission: Providing dairy industry solutions for food security, environmental sustainability,...

  5. U.S. Dairy Forage Research Center

    Data.gov (United States)

    Federal Laboratory Consortium — Vision: Leading the world in integrated dairy forage systems research. Mission: Providing dairy industry solutions for food security, environmental sustainability,...

  6. Foraging intention affects whether willow tits call to attract members of mixed-species flocks.

    Science.gov (United States)

    Suzuki, Toshitaka N; Kutsukake, Nobuyuki

    2017-06-01

    Understanding how individual behaviour influences the spatial and temporal distribution of other species is necessary to resolve the complex structure of species assemblages. Mixed-species bird flocks provide an ideal opportunity to investigate this issue, because members of the flocks are involved in a variety of behavioural interactions between species. Willow tits ( Poecile montanus ) often produce loud calls when visiting a new foraging patch to recruit other members of mixed-species flocks. The costs and benefits of flocking would differ with individual foraging behaviours (i.e. immediate consumption or caching); thus, willow tits may adjust the production of loud calls according to their foraging intention. In this study, we investigated the link between foraging decisions and calling behaviour in willow tits and tested its influence on the temporal cohesion with members of mixed-species flocks. Observations at experimental foraging patches showed that willow tits produced more calls when they consumed food items compared with when they cached them. Playback experiments revealed that these calls attracted flock members and helped to maintain their presence at foraging patches. Thus, willow tits adjusted calling behaviour according to their foraging intention, thereby coordinating the associations with members of mixed-species flocks. Our findings demonstrate the influence of individual decision-making on temporal cohesion with other species and highlight the importance of interspecific communication in mixed-species flocking dynamics.

  7. Pregnancy's stronghold on the vaginal microbiome.

    Directory of Open Access Journals (Sweden)

    Marina R S Walther-António

    Full Text Available To assess the vaginal microbiome throughout full-term uncomplicated pregnancy.Vaginal swabs were obtained from twelve pregnant women at 8-week intervals throughout their uncomplicated pregnancies. Patients with symptoms of vaginal infection or with recent antibiotic use were excluded. Swabs were obtained from the posterior fornix and cervix at 8-12, 17-21, 27-31, and 36-38 weeks of gestation. The microbial community was profiled using hypervariable tag sequencing of the V3-V5 region of the 16S rRNA gene, producing approximately 8 million reads on the Illumina MiSeq.Samples were dominated by a single genus, Lactobacillus, and exhibited low species diversity. For a majority of the patients (n = 8, the vaginal microbiome was dominated by Lactobacillus crispatus throughout pregnancy. Two patients showed Lactobacillus iners dominance during the course of pregnancy, and two showed a shift between the first and second trimester from L. crispatus to L. iners dominance. In all of the samples only these two species were identified, and were found at an abundance of higher than 1% in this study. Comparative analyses also showed that the vaginal microbiome during pregnancy is characterized by a marked dominance of Lactobacillus species in both Caucasian and African-American subjects. In addition, our Caucasian subject population clustered by trimester and progressed towards a common attractor while African-American women clustered by subject instead and did not progress towards a common attractor.Our analyses indicate normal pregnancy is characterized by a microbiome that has low diversity and high stability. While Lactobacillus species strongly dominate the vaginal environment during pregnancy across the two studied ethnicities, observed differences between the longitudinal dynamics of the analyzed populations may contribute to divergent risk for pregnancy complications. This helps establish a baseline for investigating the role of the microbiome in

  8. Brood ball-mediated transmission of microbiome members in the dung beetle, Onthophagus taurus (Coleoptera: Scarabaeidae.

    Directory of Open Access Journals (Sweden)

    Anne M Estes

    Full Text Available Insects feeding on plant sap, blood, and other nutritionally incomplete diets are typically associated with mutualistic bacteria that supplement missing nutrients. Herbivorous mammal dung contains more than 86% cellulose and lacks amino acids essential for insect development and reproduction. Yet one of the most ecologically necessary and evolutionarily successful groups of beetles, the dung beetles (Scarabaeinae feeds primarily, or exclusively, on dung. These associations suggest that dung beetles may benefit from mutualistic bacteria that provide nutrients missing from dung. The nesting behaviors of the female parent and the feeding behaviors of the larvae suggest that a microbiome could be vertically transmitted from the parental female to her offspring through the brood ball. Using sterile rearing and a combination of molecular and culture-based techniques, we examine transmission of the microbiome in the bull-headed dung beetle, Onthophagus taurus. Beetles were reared on autoclaved dung and the microbiome was characterized across development. A ~1425 bp region of the 16S rRNA identified Pseudomonadaceae, Enterobacteriaceae, and Comamonadaceae as the most common bacterial families across all life stages and populations, including cultured isolates from the 3(rd instar digestive system. Finer level phylotyping analyses based on lepA and gyrB amplicons of cultured isolates placed the isolates closest to Enterobacter cloacae, Providencia stuartii, Pusillimonas sp., Pedobacter heparinus, and Lysinibacillus sphaericus. Scanning electron micrographs of brood balls constructed from sterile dung reveals secretions and microbes only in the chamber the female prepares for the egg. The use of autoclaved dung for rearing, the presence of microbes in the brood ball and offspring, and identical 16S rRNA sequences in both parent and offspring suggests that the O. taurus female parent transmits specific microbiome members to her offspring through the brood

  9. Perturbations of gut microbiome genes in infants with atopic dermatitis according to feeding type.

    Science.gov (United States)

    Lee, Min-Jung; Kang, Mi-Jin; Lee, So-Yeon; Lee, Eun; Kim, Kangjin; Won, Sungho; Suh, Dong In; Kim, Kyung Won; Sheen, Youn Ho; Ahn, Kangmo; Kim, Bong-Soo; Hong, Soo-Jong

    2018-04-01

    Perturbations of the infant gut microbiota can shape development of the immune system and link to the risk of allergic diseases. We sought to understand the role of the gut microbiome in patients with atopic dermatitis (AD). The metagenome of the infant gut microbiome was analyzed according to feeding types. Composition of the gut microbiota was analyzed in fecal samples from 129 infants (6 months old) by using pyrosequencing, including 66 healthy infants and 63 infants with AD. The functional profile of the gut microbiome was analyzed by means of whole-metagenome sequencing (20 control subjects and 20 patients with AD). In addition, the total number of bacteria in the feces was determined by using real-time PCR. The gut microbiome of 6-month-old infants was different based on feeding types, and 2 microbiota groups (Bifidobacterium species-dominated and Escherichia/Veillonella species-dominated groups) were found in breast-fed and mixed-fed infants. Bacterial cell amounts in the feces were lower in infants with AD than in control infants. Although no specific taxa directly correlated with AD in 16S rRNA gene results, whole-metagenome analysis revealed differences in functional genes related to immune development. The reduction in genes for oxidative phosphorylation, phosphatidylinositol 3-kinase-Akt signaling, estrogen signaling, nucleotide-binding domain-like receptor signaling, and antigen processing and presentation induced by reduced colonization of mucin-degrading bacteria (Akkermansia muciniphila, Ruminococcus gnavus, and Lachnospiraceae bacterium 2_1_58FAA) was significantly associated with stunted immune development in the AD group compared with the control group (P gut microbiome can be associated with AD because of different bacterial genes that can modulate host immune cell function. Copyright © 2018 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  10. Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling.

    Science.gov (United States)

    d'Hennezel, Eva; Abubucker, Sahar; Murphy, Leon O; Cullen, Thomas W

    2017-01-01

    Cohabitation of microbial communities with the host enables the formation of a symbiotic relationship that maintains homeostasis in the gut and beyond. One prevailing model suggests that this relationship relies on the capacity of host cells and tissues to remain tolerant to the strong immune stimulation generated by the microbiota such as the activation of Toll-like receptor 4 (TLR4) pathways by lipopolysaccharide (LPS). Indeed, gut microbial LPS is thought to be one of the most potent activators of innate immune signaling and an important mediator of the microbiome's influence on host physiology. In this study, we performed computational and experimental analyses of healthy human fecal samples to examine the TLR4 signaling capacity of the gut microbiota. These analyses revealed that an immunoinhibitory activity of LPS, conserved across the members of the order Bacteroidales and derived from an underacylated structural feature, silences TLR4 signaling for the entire consortium of organisms inhabiting the human gut. Comparative analysis of metagenomic data from the Human Microbiome Project and healthy-donor samples indicates that immune silencing via LPS is a microbe-intrinsic feature in all healthy adults. These findings challenge the current belief that robust TLR4 signaling is a feature of the microbiome and demonstrate that microbiome-derived LPS has the ability to facilitate host tolerance of gut microbes. These findings have broad implications for how we model host-microbe interactions and for our understanding of microbiome-linked disease. IMPORTANCE While the ability for humans to host a complex microbial ecosystem is an essential property of life, the mechanisms allowing for immune tolerance of such a large microbial load are not completely understood and are currently the focus of intense research. This study shows that an important proinflammatory pathway that is commonly triggered by pathogenic bacteria upon interaction with the host is, in fact

  11. Subgingival Microbiome Colonization and Cytokine Production during Early Dental Implant Healing.

    Science.gov (United States)

    Payne, Jeffrey B; Johnson, Paul G; Kok, Car Reen; Gomes-Neto, João C; Ramer-Tait, Amanda E; Schmid, Marian J; Hutkins, Robert W

    2017-01-01

    Little is known about longitudinal development of the peri-implant subgingival microbiome and cytokine production as a new sulcus forms after dental implant placement. Therefore, the purpose of this observational study was to evaluate simultaneous longitudinal changes in the oral microbiome and cytokine production in the developing peri-implant sulcus compared to control natural teeth. Four and 12 weeks after implant placement and abutment connection, a dental implant and a natural tooth were sampled in 25 patients for subgingival plaque and gingival crevicular fluid (GCF [around teeth] and peri-implant crevicular fluid [PICF] around implants). DNA from plaque samples was extracted and sequenced using Illumina-based 16S rRNA sequencing. GCF and PICF samples were analyzed using a customized Milliplex human cytokine and chemokine magnetic bead panel. Beta diversity analysis revealed that natural teeth and implants had similar subgingival microbiomes, while teeth had greater alpha diversity than implants. At the genus level, however, few differences were noted between teeth and dental implants over 12 weeks. Specifically, Actinomyces and Selenomonas were significantly elevated around teeth versus dental implants at both 4 weeks and 12 weeks, while Corynebacterium and Campylobacter were significantly elevated only at 4 weeks around teeth. The only difference between PICF and GCF biomarkers was significantly elevated granulocyte-macrophage colony-stimulating factor levels around teeth versus dental implants at the 4-week visit. The subgingival microbiome and cytokine production were similar between teeth and implants during early healing, suggesting that these profiles are driven by the patient following dental implant placement and are not determined by anatomical niche. IMPORTANCE Dental implants are a common treatment option offered to patients for tooth replacement. However, little is known regarding initial colonization of the subgingival microbiome and

  12. Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome

    Directory of Open Access Journals (Sweden)

    Marchesi Julian R

    2010-01-01

    Full Text Available Abstract Background Little is known regarding the pool of mobile genetic elements associated with the human gut microbiome. In this study we employed the culture independent TRACA system to isolate novel plasmids from the human gut microbiota, and a comparative metagenomic analysis to investigate the distribution and relative abundance of functions encoded by these plasmids in the human gut microbiome. Results Novel plasmids were acquired from the human gut microbiome, and homologous nucleotide sequences with high identity (>90% to two plasmids (pTRACA10 and pTRACA22 were identified in the multiple human gut microbiomes analysed here. However, no homologous nucleotide sequences to these plasmids were identified in the murine gut or environmental metagenomes. Functions encoded by the plasmids pTRACA10 and pTRACA22 were found to be more prevalent in the human gut microbiome when compared to microbial communities from other environments. Among the most prevalent functions identified was a putative RelBE toxin-antitoxin (TA addiction module, and subsequent analysis revealed that this was most closely related to putative TA modules from gut associated bacteria belonging to the Firmicutes. A broad phylogenetic distribution of RelE toxin genes was observed in gut associated bacterial species (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria, but no RelE homologues were identified in gut associated archaeal species. We also provide indirect evidence for the horizontal transfer of these genes between bacterial species belonging to disparate phylogenetic divisions, namely Gram negative Proteobacteria and Gram positive species from the Firmicutes division. Conclusions The application of a culture independent system to capture novel plasmids from the human gut mobile metagenome, coupled with subsequent comparative metagenomic analysis, highlighted the unexpected prevalence of plasmid encoded functions in the gut microbial ecosystem. In

  13. Gut microbiome development along the colorectal adenoma-carcinoma sequence.

    Science.gov (United States)

    Feng, Qiang; Liang, Suisha; Jia, Huijue; Stadlmayr, Andreas; Tang, Longqing; Lan, Zhou; Zhang, Dongya; Xia, Huihua; Xu, Xiaoying; Jie, Zhuye; Su, Lili; Li, Xiaoping; Li, Xin; Li, Junhua; Xiao, Liang; Huber-Schönauer, Ursula; Niederseer, David; Xu, Xun; Al-Aama, Jumana Yousuf; Yang, Huanming; Wang, Jian; Kristiansen, Karsten; Arumugam, Manimozhiyan; Tilg, Herbert; Datz, Christian; Wang, Jun

    2015-03-11

    Colorectal cancer, a commonly diagnosed cancer in the elderly, often develops slowly from benign polyps called adenoma. The gut microbiota is believed to be directly involved in colorectal carcinogenesis. The identity and functional capacity of the adenoma- or carcinoma-related gut microbe(s), however, have not been surveyed in a comprehensive manner. Here we perform a metagenome-wide association study (MGWAS) on stools from advanced adenoma and carcinoma patients and from healthy subjects, revealing microbial genes, strains and functions enriched in each group. An analysis of potential risk factors indicates that high intake of red meat relative to fruits and vegetables appears to associate with outgrowth of bacteria that might contribute to a more hostile gut environment. These findings suggest that faecal microbiome-based strategies may be useful for early diagnosis and treatment of colorectal adenoma or carcinoma.

  14. Ocean plankton. Structure and function of the global ocean microbiome.

    Science.gov (United States)

    Sunagawa, Shinichi; Coelho, Luis Pedro; Chaffron, Samuel; Kultima, Jens Roat; Labadie, Karine; Salazar, Guillem; Djahanschiri, Bardya; Zeller, Georg; Mende, Daniel R; Alberti, Adriana; Cornejo-Castillo, Francisco M; Costea, Paul I; Cruaud, Corinne; d'Ovidio, Francesco; Engelen, Stefan; Ferrera, Isabel; Gasol, Josep M; Guidi, Lionel; Hildebrand, Falk; Kokoszka, Florian; Lepoivre, Cyrille; Lima-Mendez, Gipsi; Poulain, Julie; Poulos, Bonnie T; Royo-Llonch, Marta; Sarmento, Hugo; Vieira-Silva, Sara; Dimier, Céline; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Bowler, Chris; de Vargas, Colomban; Gorsky, Gabriel; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Jaillon, Olivier; Not, Fabrice; Ogata, Hiroyuki; Pesant, Stephane; Speich, Sabrina; Stemmann, Lars; Sullivan, Matthew B; Weissenbach, Jean; Wincker, Patrick; Karsenti, Eric; Raes, Jeroen; Acinas, Silvia G; Bork, Peer

    2015-05-22

    Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems. Copyright © 2015, American Association for the Advancement of Science.

  15. Developing Cyber Foraging Applications for Portable Devices

    DEFF Research Database (Denmark)

    Kristensen, Mads Darø; Bouvin, Niels Olof

    2008-01-01

    This paper presents the Locusts cyber foraging framework. Cyber foraging is the opportunistic use of computing resources available in the nearby environment, and using such resources thus fall into the category of distributed computing. Furthermore, for the resources to be used efficiently, paral...

  16. Dental Calculus and the Evolution of the Human Oral Microbiome.

    Science.gov (United States)

    Warinner, Christina

    2016-07-01

    Characterizing the evolution of the oral microbiome is a challenging, but increasingly feasible, task. Recently, dental calculus has been shown to preserve ancient biomolecules from the oral microbiota, host tissues and diet for tens of thousands of years. As such, it provides a unique window into the ancestral oral microbiome. This article reviews recent advancements in ancient dental calculus research and emerging insights into the evolution and ecology of the human oral microbiome.

  17. Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets

    OpenAIRE

    Li, Lianwei; Ma, Zhanshan (Sam)

    2016-01-01

    The human microbiome project (HMP) has made it possible to test important ecological theories for arguably the most important ecosystem to human health?the human microbiome. Existing limited number of studies have reported conflicting evidence in the case of the neutral theory; the present study aims to comprehensively test the neutral theory with extensive HMP datasets covering all five major body sites inhabited by the human microbiome. Utilizing 7437 datasets of bacterial community samples...

  18. Ruminal fermentation of Anti-methanogenic Nitrate- and Nitro-Containing Forages In Vitro

    Directory of Open Access Journals (Sweden)

    Robin C. Anderson

    2016-08-01

    Full Text Available Nitrate, 3-nitro-1-propionic acid (NPA and 3-nitro-1-propanol (NPOH can accumulate in forages and be poisonous to animals if consumed in high enough amounts. These chemicals are also recognized as potent anti-methanogenic compounds, but plants naturally containing these chemicals have been studied little in this regard. Presently, we found that nitrate-, NPA- or NPOH-containing forages effectively decreased methane production, by 35 to 87%, during in vitro fermentation by mixed cultures of ruminal microbes compared to fermentation by cultures incubated similarly with alfalfa. Methane production was further decreased during incubation of mixed cultures also inoculated with Denitrobacterium detoxificans, a ruminal bacterium known to metabolize nitrate, NPA and NPOH. Inhibition of methanogens within the mixed cultures was greatest with the NPA- and NPOH-containing forages. Hydrogen accumulated in all the mixed cultures incubated with forages containing nitrate, NPA or NPOH but was dramatically higher, exceeding 40 µmol hydrogen/mL, in mixed cultures incubated with NPA-containing forage but not inoculated with D. detoxificans. This possibly reflects the inhibition of hydrogenase-catalyzed uptake of hydrogen produced via conversion of 50 µmol added formate per mL to hydrogen. Accumulations of volatile fatty acids revealed compensatory changes in fermentation in mixed cultures incubated with the nitrate-, NPA- and NPOH-containing forages as evidenced by lower accumulations of acetate, and in some cases higher accumulations of butyrate and lower accumulations of ammonia, iso-buytrate and iso-valerate compared to cultures incubated with alfalfa. Results reveal that nitrate, NPA and NPOH that accumulate naturally in forages can be made available within ruminal incubations to inhibit methanogenesis. Further research is warranted to determine if diets can be formulated with nitrate-, NPA- and NPOH-containing forages to achieve efficacious mitigation in

  19. A global comparison of the nutritive values of forage plants grown in contrasting environments.

    Science.gov (United States)

    Lee, Mark A

    2018-03-17

    Forage plants are valuable because they maintain wild and domesticated herbivores, and sustain the delivery of meat, milk and other commodities. Forage plants contain different quantities of fibre, lignin, minerals and protein, and vary in the proportion of their tissue that can be digested by herbivores. These nutritive components are important determinants of consumer growth rates, reproductive success and behaviour. A dataset was compiled to quantify variation in forage plant nutritive values within- and between-plant species, and to assess variation between plant functional groups and bioclimatic zones. 1255 geo-located records containing 3774 measurements of nutritive values for 136 forage plant species grown in 30 countries were obtained from published articles. Spatial variability in forage nutritive values indicated that climate modified plant nutritive values. Forage plants grown in arid and equatorial regions generally contained less digestible material than those grown in temperate and tundra regions; containing more fibre and lignin, and less protein. These patterns may reveal why herbivore body sizes, digestion and migration strategies are different in warmer and drier regions. This dataset also revealed the capacity for variation in the nutrition provided by forage plants, which may drive consumer species coexistence. The proportion of the plant tissue that was digestible ranged between species from 2 to 91%. The amount of fibre contained within plant material ranged by 23-90%, protein by 2-36%, lignin by 1-21% and minerals by 2-22%. On average, grasses and tree foliage contained the most fibre, whilst herbaceous legumes contained the most protein and tree foliage contained the most lignin. However, there were individual species within each functional group that were highly nutritious. This dataset may be used to identify forage plant species or mixtures of species from different functional groups with useful nutritional traits which can be cultivated

  20. The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition.

    Science.gov (United States)

    Cremers, Amelieke Jh; Zomer, Aldert L; Gritzfeld, Jenna F; Ferwerda, Gerben; van Hijum, Sacha Aft; Ferreira, Daniela M; Shak, Joshua R; Klugman, Keith P; Boekhorst, Jos; Timmerman, Harro M; de Jonge, Marien I; Gordon, Stephen B; Hermans, Peter Wm

    2014-01-01

    Several cohort studies have indicated associations between S. pneumoniae and other microbes in the nasopharynx. To study causal relationships between the nasopharyngeal microbiome and pneumococcal carriage, we employed an experimental human pneumococcal carriage model. Healthy adult volunteers were assessed for pneumococcal carriage by culture of nasal wash samples (NWS). Those without natural pneumococcal carriage received an intranasal pneumococcal inoculation with serotype 6B or 23F. The composition of the nasopharyngeal microbiome was longitudinally studied by 16S rDNA pyrosequencing on NWS collected before and after challenge. Among 40 selected volunteers, 10 were natural carriers and 30 were experimentally challenged. At baseline, five distinct nasopharyngeal microbiome profiles were identified. The phylogenetic distance between microbiomes of natural pneumococcal carriers was particularly large compared to non-carriers. A more diverse microbiome prior to inoculation was associated with the establishment of pneumococcal carriage. Perturbation of microbiome diversity upon pneumococcal challenge was strain specific. Shifts in microbiome profile occurred after pneumococcal exposure, and those volunteers who acquired carriage more often diverted from their original profile. S. pneumoniae was little prominent in the microbiome of pneumococcal carriers. Pneumococcal acquisition in healthy adults is more likely to occur in a diverse microbiome and appears to promote microbial heterogeneity.

  1. Microbiome, Metabolome and Inflammatory Bowel Disease

    Directory of Open Access Journals (Sweden)

    Ishfaq Ahmed

    2016-06-01

    Full Text Available Inflammatory Bowel Disease (IBD is a multifactorial disorder that conceptually occurs as a result of altered immune responses to commensal and/or pathogenic gut microbes in individuals most susceptible to the disease. During Crohn’s Disease (CD or Ulcerative Colitis (UC, two components of the human IBD, distinct stages define the disease onset, severity, progression and remission. Epigenetic, environmental (microbiome, metabolome and nutritional factors are important in IBD pathogenesis. While the dysbiotic microbiota has been proposed to play a role in disease pathogenesis, the data on IBD and diet are still less convincing. Nonetheless, studies are ongoing to examine the effect of pre/probiotics and/or FODMAP reduced diets on both the gut microbiome and its metabolome in an effort to define the healthy diet in patients with IBD. Knowledge of a unique metabolomic fingerprint in IBD could be useful for diagnosis, treatment and detection of disease pathogenesis.

  2. Advancing gut microbiome research using cultivation

    DEFF Research Database (Denmark)

    Sommer, Morten OA

    2015-01-01

    Culture-independent approaches have driven the field of microbiome research and illuminated intricate relationships between the gut microbiota and human health. However, definitively associating phenotypes to specific strains or elucidating physiological interactions is challenging for metagenomic...... approaches. Recently a number of new approaches to gut microbiota cultivation have emerged through the integration of high-throughput phylogenetic mapping and new simplified cultivation methods. These methodologies are described along with their potential use within microbiome research. Deployment of novel...... cultivation approaches should enable improved studies of xenobiotic tolerance and modification phenotypes and allow a drastic expansion of the gut microbiota reference genome catalogues. Furthermore, the new cultivation methods should facilitate systematic studies of the causal relationship between...

  3. Seven Billion Microcosms: Evolution within Human Microbiomes.

    Science.gov (United States)

    Lieberman, Tami D

    2018-01-01

    Rational microbiome-based therapies may one day treat a wide range of diseases and promote wellness. Yet, we are still limited in our abilities to employ such therapies and to predict which bacterial strains have the potential to stably colonize a person. The Lieberman laboratory is working to close this knowledge gap and to develop an understanding of how individual species and strains behave in the human microbiome, including with regard to their niche ranges, survival strategies, and the degree to which they adapt to individual people. We employ system-level approaches, with a particular emphasis on using de novo mutations and evolutionary inference to reconstruct the history of bacterial lineages within individuals.

  4. Enterotypes of the human gut microbiome

    DEFF Research Database (Denmark)

    Arumugam, Manimozhiyan; Raes, Jeroen; Pelletier, Eric

    2011-01-01

    Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previou......Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries....... This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species...

  5. Factors Affecting Gastrointestinal Microbiome Development in Neonates

    Directory of Open Access Journals (Sweden)

    Clara Yieh Lin Chong

    2018-02-01

    Full Text Available The gut microbiome is established in the newborn period and is recognised to interact with the host to influence metabolism. Different environmental factors that are encountered during this critical period may influence the gut microbial composition, potentially impacting upon later disease risk, such as asthma, metabolic disorder, and inflammatory bowel disease. The sterility dogma of the foetus in utero is challenged by studies that identified bacteria, bacterial DNA, or bacterial products in meconium, amniotic fluid, and the placenta; indicating the initiation of maternal-to-offspring microbial colonisation in utero. This narrative review aims to provide a better understanding of factors that affect the development of the gastrointestinal (GI microbiome during prenatal, perinatal to postnatal life, and their reciprocal relationship with GI tract development in neonates.

  6. The microbiome of New World vultures

    OpenAIRE

    Roggenbuck, Michael; Schnell, Ida Baerholm; Blom, Nikolaj; Bælum, Jacob; Bertelsen, Mads Frost; Sicheritz-Pontén, Thomas; Sørensen, Søren Johannes; Gilbert, M. Thomas P.; Graves, Gary R.; Hansen, Lars Henrik

    2014-01-01

    Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the fa...

  7. The oral microbiome and adverse pregnancy outcomes

    Directory of Open Access Journals (Sweden)

    Cobb CM

    2017-08-01

    Full Text Available Charles M Cobb,1 Patricia J Kelly,2 Karen B Williams,3 Shilpa Babbar,4 Mubashir Angolkar,5 Richard J Derman6 1Department of Periodontics, School of Dentistry, 2Department of Public Health Nursing, School of Nursing and Health Studies, 3Department of Biomedical & Health Informatics, School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 4Department of Obstetrics, Gynecology & Women’s Health, Division of Maternal & Fetal Medicine, School of Medicine, Saint Louis University, St Louis, MO, USA; 5Department of Public Health, Jawaharlal Nehru Medical College (JNMC, KLE University, Karnataka, India; 6Department of Obstetrics & Gynecology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA Abstract: Significant evidence supports an association between periodontal pathogenic bacteria and preterm birth and preeclampsia. The virulence properties assigned to specific oral pathogenic bacteria, for example, Fusobacterium nucleatum, Porphyromonas gingivalis, Filifactor alocis, Campylobacter rectus, and others, render them as potential collaborators in adverse outcomes of pregnancy. Several pathways have been suggested for this association: 1 hematogenous spread (bacteremia of periodontal pathogens; 2 hematogenous spread of multiple mediators of inflammation that are generated by the host and/or fetal immune response to pathogenic bacteria; and 3 the possibility of oral microbial pathogen transmission, with subsequent colonization, in the vaginal microbiome resulting from sexual practices. As periodontal disease is, for the most part, preventable, the medical and dental public health communities can address intervention strategies to control oral inflammatory disease, lessen the systemic inflammatory burden, and ultimately reduce the potential for adverse pregnancy outcomes. This article reviews the oral, vaginal, and placental microbiomes, considers their potential impact on preterm labor, and the future

  8. Municipal Solid Waste Landfills Harbor Distinct Microbiomes

    Directory of Open Access Journals (Sweden)

    Blake Warren Stamps

    2016-04-01

    Full Text Available Landfills are the final repository for most of the discarded material from human society and its built environments. Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2 and a complex mixture of soluble chemical compounds in leachate. Characterization of landfill microbiomes and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.

  9. Forest microbiome: diversity, complexity and dynamics

    Czech Academy of Sciences Publication Activity Database

    Baldrian, Petr

    2017-01-01

    Roč. 41, č. 2 (2017), s. 109-130 ISSN 0168-6445 R&D Projects: GA ČR GA13-06763S; GA ČR GA13-27454S; GA MŠk(CZ) LD15086 Institutional support: RVO:61388971 Keywords : forests * microbiome * habitat Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 12.198, year: 2016

  10. Effects of forage provision to dairy calves on growth performance and rumen fermentation: A meta-analysis and meta-regression.

    Science.gov (United States)

    Imani, M; Mirzaei, M; Baghbanzadeh-Nobari, B; Ghaffari, M H

    2017-02-01

    A meta-analysis of the potential effect of forage provision on growth performance and rumen fermentation of dairy calves was conducted using published data from the literature (1998-2016). Meta-regression was used to evaluate the effects of different forage levels, forage sources, forage offering methods, physical forms of starter, and grain sources on the heterogeneity of the results. We considered 27 studies that reported the effects of forage provision to dairy calves. Estimated effect sizes of forage were calculated on starter feed intake, average daily gain (ADG), feed efficiency (FE), body weight (BW), and rumen fermentation parameters. Intake of starter feed, ADG, BW, ruminal pH, and rumen molar proportion of acetate increased when supplementing forage but FE decreased. Heterogeneity (the amount of variation among studies) was significant for intake of starter feed, ADG, FE, final BW, and rumen fermentation parameters. Improving overall starter feed intake was greater in calves offered alfalfa hay compared with those offered other types of forages. During the milk feeding and overall periods, improving ADG was greater for calves fed a high level of forage (>10% in dry matter) compared with those fed a low level of forage (≤10% in dry matter) diets. The advantages reported in weight gain at a high level of forage could be due to increased gut fill. Improving overall ADG was lower for calves offered forages with textured starter feed compared with ground starter feed. The meta-regression analysis revealed that changes associated with forage provision affect FE differently for various forage sources and forage offering methods during the milk-feeding period. Forage sources also modulated the effect of feeding forage on ruminal pH during the milk-feeding period. In conclusion, forage has the potential to affect starter feed intake and performance of dairy calves, but its effects depend on source, level, and method of forage feeding and physical form of starter

  11. Investigation of Arsenotrophic Microbiome in Arsenic-Affected Bangladesh Groundwater.

    Science.gov (United States)

    Sultana, Munawar; Mou, Taslin Jahan; Sanyal, Santonu Kumar; Diba, Farzana; Mahmud, Zahid Hayat; Parvez, Anowar Khasru; Hossain, M Anwar

    2017-09-01

    Arsenotrophic bacteria contribute to the nutrient cycling in arsenic (As) affected groundwater. This study employed a culture-independent and -dependent investigation of arsenotrophic microbiomes in As affected groundwater samples collected from Madhabpur, Sonatengra, and Union Porishod in Singair Upazila, Manikganj, Bangladesh. Total As contents, detected by Atomic Absorption Spectrophotometry (AAS) of the samples, were 47 µg/L (Madhabpur, SNGW-1), 53 µg/L (Sonatengra, SNGW-2), and 12 µg/L (Union porishod, SNGW-3), whereas the control well (SNGW-4; depths >150 m) showed As content of 6 µg/L. Denaturing Gradient Gel Electrophoresis (DGGE) analysis of the amplified 16S rRNA gene from As-affected groundwater samples revealed the dominance of aerobic bacteria Pseudomonas within heterogeneous bacterial populations. DGGE of heterotrophic enrichments supplemented with arsenite [As (III)] for 4 weeks showed the dominance of Chryseobacterium, Flavobacterium, and Aquabacterium, whereas the dominant genera in that of autotrophic enrichments were Aeromonas, Acinetobacter, and Pseudomonas. Cultured bacteria retrieved from both autotrophic and heterotrophic enrichments were distinguished into nine genotypes belonging to Chryseobacterium, Acinetobacter, Escherichia, Pseudomonas, Stenotrophomonas, Janibacter, Staphylococcus, and Bacillus. They exhibited varying range of As(III) tolerance from 4 to 27 mM. As(III) transformation potential was confirmed within the isolates with oxidation rate as high as 0.143 mM/h for Pseudomonas sp. Sn 28. The arsenotrophic microbiome specifies their potential role in groundwater As-cycling and their genetic information provide the scientific basis for As-bioremediation. © 2017, National Ground Water Association.

  12. Multiple model testing using Chernobyl fallout data of I-131 in forage and milk and Cs-137 in forage, milk, beef and grain. Pt. 1

    International Nuclear Information System (INIS)

    Koehler, H.; Peterson, S.R.; Owen Hoffman, F.

    1991-03-01

    Comprehensive measurements of I-131 and Cs-137 in the environment after the Chernobyl accident provided a unique opportunity for the collection of environmental transfer data sets. These come from 13 locations in the northern hemisphere which experienced levels of contamination that spanned approximately three orders of magnitude. Data have been compiled for radionuclide concentrations in air, rain, pasture vegetation, milk, beef and grain. In addition background information has been collated for factors such as prevailing meteorological conditions, location description, and local agricultural practices. Participants were asked to predict radionuclide concentrations in forage, milk, beef and grain from radionuclide concentrations in air, the daily amounts of precipitation and other pertinent information. This was a blind test in that the locations to which the input data referred were not revealed to the participants until after they had submitted their predictions. Twenty-three models were involved in the study. This report compares observations and predictions for deposition, time- integrated concentrations in forage, milk, beef and grain, to help assess understanding of individual processes, time-dependent concentrations in forage, milk and beef. In general, predictions of time-integrated concentration of I-131 and Cs-137 in forage, milk (normalized for forage) and beef are within a factor of 10 of the observations. About 50% of the predictions of I-131 and Cs-137 in forage and just over 30% of the predictions of those nuclides in milk (normalized for forage) fall within a factor of 2 of the observations. Documentation of the measurements, models, methods of analysis and model results is presented in the appendices. (au) (75 refs.)

  13. Forager bees (Apis mellifera) highly express immune and detoxification genes in tissues associated with nectar processing.

    Science.gov (United States)

    Vannette, Rachel L; Mohamed, Abbas; Johnson, Brian R

    2015-11-09

    Pollinators, including honey bees, routinely encounter potentially harmful microorganisms and phytochemicals during foraging. However, the mechanisms by which honey bees manage these potential threats are poorly understood. In this study, we examine the expression of antimicrobial, immune and detoxification genes in Apis mellifera and compare between forager and nurse bees using tissue-specific RNA-seq and qPCR. Our analysis revealed extensive tissue-specific expression of antimicrobial, immune signaling, and detoxification genes. Variation in gene expression between worker stages was pronounced in the mandibular and hypopharyngeal gland (HPG), where foragers were enriched in transcripts that encode antimicrobial peptides (AMPs) and immune response. Additionally, forager HPGs and mandibular glands were enriched in transcripts encoding detoxification enzymes, including some associated with xenobiotic metabolism. Using qPCR on an independent dataset, we verified differential expression of three AMP and three P450 genes between foragers and nurses. High expression of AMP genes in nectar-processing tissues suggests that these peptides may contribute to antimicrobial properties of honey or to honey bee defense against environmentally-acquired microorganisms. Together, these results suggest that worker role and tissue-specific expression of AMPs, and immune and detoxification enzymes may contribute to defense against microorganisms and xenobiotic compounds acquired while foraging.

  14. Determination of Tropical Forage Preferences Using Two Offering Methods in Rabbits

    Directory of Open Access Journals (Sweden)

    A. M. Safwat

    2014-04-01

    Full Text Available Two methods of feed preference trials were compared to evaluate the acceptability of 5 fresh foliages: Leucaena leucocephala, Moringa oleifera, Portulaca oleracea, Guazuma ulmifolia, and Brosimum alicastrum that was included as control. The evaluation included chemical analyses and forage intake by rabbits. The first method was a cafeteria trial; 12 California growing rabbits aged 8 wk, allocated in individual cages, were offered the five forage plants at the same time inside the cage, while in the second trial 60 California growing rabbits aged 8 wk, allocated individually, were randomly distributed into 5 experimental groups (n = 12/group; for each group just one forage species was offered at a time. The testing period for each method lasted for 7 d, preceded by one week of adaptation. The results showed that B. alicastrum and L. lecocephala were the most preferred forages while on the contrary G. ulmifolia was the least preferred one by rabbits. The results also revealed that the CV% value for the 2nd method (16.32%, which the tested forages were presented separately to rabbits, was lower and methodologically more acceptable than such value for the 1st method (34.28%, which all forages were presented together at the same time. It can be concluded that a range of tropical forages were consumed in acceptable quantities by rabbits, suggesting that diets based on such forages with a concentrate supplement could be used successfully for rabbit production. However, growth performance studies are still needed before recommendations could be made on appropriate ration formulations for commercial use.

  15. Sympatric cattle grazing and desert bighorn sheep foraging

    Science.gov (United States)

    Garrison, Kyle R.; Cain, James W.; Rominger, Eric M.; Goldstein, Elise J.

    2015-01-01

    Foraging behavior affects animal fitness and is largely dictated by the resources available to an animal. Understanding factors that affect forage resources is important for conservation and management of wildlife. Cattle sympatry is proposed to limit desert bighorn population performance, but few studies have quantified the effect of cattle foraging on bighorn forage resources or foraging behavior by desert bighorn. We estimated forage biomass for desert bighorn sheep in 2 mountain ranges: the cattle-grazed Caballo Mountains and the ungrazed San Andres Mountains, New Mexico. We recorded foraging bout efficiency of adult females by recording feeding time/step while foraging, and activity budgets of 3 age-sex classes (i.e., adult males, adult females, yearlings). We also estimated forage biomass at sites where bighorn were observed foraging. We expected lower forage biomass in the cattle-grazed Caballo range than in the ungrazed San Andres range and lower biomass at cattle-accessible versus inaccessible areas within the Caballo range. We predicted bighorn would be less efficient foragers in the Caballo range. Groundcover forage biomass was low in both ranges throughout the study (Jun 2012–Nov 2013). Browse biomass, however, was 4.7 times lower in the Caballo range versus the San Andres range. Bighorn in the Caballo range exhibited greater overall daily travel time, presumably to locate areas of higher forage abundance. By selecting areas with greater forage abundance, adult females in the Caballo range exhibited foraging bout efficiency similar to their San Andres counterparts but lower overall daily browsing time. We did not find a significant reduction in forage biomass at cattle-accessible areas in the Caballo range. Only the most rugged areas in the Caballo range had abundant forage, potentially a result of intensive historical livestock use in less rugged areas. Forage conditions in the Caballo range apparently force bighorn to increase foraging effort by

  16. CHEMICAL COMPOSITION OF CAATINGA POTENTIAL FORAGES SPECIES

    Directory of Open Access Journals (Sweden)

    Dynara Layza de Souza da Silva

    2015-12-01

    Full Text Available Chemical composition of some potential forages species, natives from Caatinga region, were evaluated. Samples of Macroptilium heterophyllum, Stylosanthes humilis, Rhynchosia mínima, Desmodium tortuosum Sw. Dc, Merremia aegyptia, Mimosa tenuiflora Wild, Bauhinia cheilantha and as well Macroptilium lathyroides, Caesalpinia pyramidalis and Mimosa tenuiflora hays were collected in Rio Grande do Norte Stated, during 2011 rainy season. The analyses: dry matter (DM, crude protein (CP mineral matter (MM ether extract  (EE neutral detergent fiber (NDF, acid detergent fiber (ADF, lignin (LIG, insoluble neutral detergent nitrogen, (INDN insoluble acid detergent nitrogen, (ADIN, total phenol (TF and total tannin (TT were done at Embrapa Caprinos e Ovinos in Ceará State. Plants analyzed, as expected, for tropical species, exhibited high level of cell wall constituents, high lignifications rate and revealed substantial presence of anti nutritional compounds. However, regardless of this data, the main problem, for grazing animals, is due to its xerophytes characteristics. Most of the shrubs and trees are deciduous, losing its leaves during the dry season. In addition, herbaceous presents a very rapid lifetime cycle, germinating and senescing during the brief wet season.

  17. Ocean acidification impairs crab foraging behaviour.

    Science.gov (United States)

    Dodd, Luke F; Grabowski, Jonathan H; Piehler, Michael F; Westfield, Isaac; Ries, Justin B

    2015-07-07

    Anthropogenic elevation of atmospheric CO2 is driving global-scale ocean acidification, which consequently influences calcification rates of many marine invertebrates and potentially alters their susceptibility to predation. Ocean acidification may also impair an organism's ability to process environmental and biological cues. These counteracting impacts make it challenging to predict how acidification will alter species interactions and community structure. To examine effects of acidification on consumptive and behavioural interactions between mud crabs (Panopeus herbstii) and oysters (Crassostrea virginica), oysters were reared with and without caged crabs for 71 days at three pCO2 levels. During subsequent predation trials, acidification reduced prey consumption, handling time and duration of unsuccessful predation attempt. These negative effects of ocean acidification on crab foraging behaviour more than offset any benefit to crabs resulting from a reduction in the net rate of oyster calcification. These findings reveal that efforts to evaluate how acidification will alter marine food webs should include quantifying impacts on both calcification rates and animal behaviour. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  18. Optimal Foraging by Birds: Experiments for Secondary & Postsecondary Students

    Science.gov (United States)

    Pecor, Keith W.; Lake, Ellen C.; Wund, Matthew A.

    2015-01-01

    Optimal foraging theory attempts to explain the foraging patterns observed in animals, including their choice of particular food items and foraging locations. We describe three experiments designed to test hypotheses about food choice and foraging habitat preference using bird feeders. These experiments can be used alone or in combination and can…

  19. BEE FORAGE MAPPING BASED ON MULTISPECTRAL IMAGES LANDSAT

    Directory of Open Access Journals (Sweden)

    A. Moskalenko

    2016-10-01

    Full Text Available Possibilities of bee forage identification and mapping based on multispectral images have been shown in the research. Spectral brightness of bee forage has been determined with the use of satellite images. The effectiveness of some methods of image classification for mapping of bee forage is shown. Keywords: bee forage, mapping, multispectral images, image classification.

  20. Acquiring and maintaining a normal oral microbiome: current perspective.

    NARCIS (Netherlands)

    Zaura, E.; Nicu, E.A.; Krom, B.P.; Keijser, B.J.

    2014-01-01

    The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis-a microbial shift

  1. Acquiring and maintaining a normal oral microbiome : Current perspective

    NARCIS (Netherlands)

    Zaura, E.; Nicu, E.A.; Krom, B.P.; Keijser, B.J.F.

    2014-01-01

    The oral microbiota survives daily physical and chemical perturbations from the intake of food and personal hygiene measures, resulting in a long-term stable microbiome. Biological properties that confer stability in the microbiome are important for the prevention of dysbiosis—a microbial shift

  2. Experimental metagenomics and ribosomal profiling of the human skin microbiome.

    Science.gov (United States)

    Ferretti, Pamela; Farina, Stefania; Cristofolini, Mario; Girolomoni, Giampiero; Tett, Adrian; Segata, Nicola

    2017-03-01

    The skin is the largest organ in the human body, and it is populated by a large diversity of microbes, most of which are co-evolved with the host and live in symbiotic harmony. There is increasing evidence that the skin microbiome plays a crucial role in the defense against pathogens, immune system training and homoeostasis, and microbiome perturbations have been associated with pathological skin conditions. Studying the skin resident microbial community is thus essential to better understand the microbiome-host crosstalk and to associate its specific configurations with cutaneous diseases. Several community profiling approaches have proved successful in unravelling the composition of the skin microbiome and overcome the limitations of cultivation-based assays, but these tools remain largely inaccessible to the clinical and medical dermatology communities. The study of the skin microbiome is also characterized by specific technical challenges, such as the low amount of microbial biomass and the extensive human DNA contamination. Here, we review the available community profiling approaches to study the skin microbiome, specifically focusing on the practical experimental and analytical tools necessary to generate and analyse skin microbiome data. We describe all the steps from the initial samples collection to the final data interpretation, with the goal of enabling clinicians and researchers who are not familiar with the microbiome field to perform skin profiling experiments. © 2016 The Authors. Experimental Dermatology Published by John Wiley & Sons Ltd.

  3. Functional variation in the gut microbiome of wild Drosophila populations.

    Science.gov (United States)

    Bost, Alyssa; Martinson, Vincent G; Franzenburg, Soeren; Adair, Karen L; Albasi, Alice; Wells, Martin T; Douglas, Angela E

    2018-05-26

    Most of the evidence that the gut microbiome of animals is functionally variable, with consequences for the health and fitness of the animal host, is based on laboratory studies, often using inbred animals under tightly controlled conditions. It is largely unknown whether these microbiome effects would be evident in outbred animal populations under natural conditions. In this study, we quantified the functional traits of the gut microbiota (metagenome) and host (gut transcriptome) and the taxonomic composition of the gut microorganisms (16S rRNA gene sequence) in natural populations of three mycophagous Drosophila species. Variation in microbiome function and composition was driven principally by the period of sample collection, while host function varied mostly with Drosophila species, indicating that variation in microbiome traits is determined largely by environmental factors, and not host taxonomy. Despite this, significant correlations between microbiome and host functional traits were obtained. In particular, microbiome functions dominated by metabolism were positively associated with host functions relating to gut epithelial turnover. Much of the functional variation in the microbiome could be attributed to variation in abundance of Bacteroidetes, rather than the two other abundant groups, the γ-Proteobacteria or Lactobacillales. We conclude that functional variation in the interactions between animals and their gut microbiome can be detectable in natural populations and, in mycophagous Drosophila, this variation relates primarily to metabolism and homeostasis of the gut epithelium. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  4. Gut microbiome and lipid metabolism : from associations to mechanisms

    NARCIS (Netherlands)

    Wang, Zheng; Koonen, Debby; Hofker, Marten; Fu, Jingyuan

    Purpose of review The gut microbiome has now been convincingly linked to human metabolic health but the underlying causality and mechanisms remain poorly understood. This review focuses on the recent progress in establishing the associations between gut microbiome species and lipid metabolism in

  5. Overweight and the feline gut microbiome - a pilot study

    DEFF Research Database (Denmark)

    Kieler, I. N.; Mølbak, Lars; Hansen, L. L.

    2016-01-01

    Compared with lean humans, the gut microbiota is altered in the obese. Whether these changes are due to an obesogenic diet, and whether the microbiota contributes to adiposity is currently discussed. In the cat population, where obesity is also prevalent, gut microbiome changes associated...... microbiome as compared to lean cats....

  6. Host Genetics and Gut Microbiome : Challenges and Perspectives

    NARCIS (Netherlands)

    Kurilshikov, Alexander; Wijmenga, Cisca; Fu, Jingyuan; Zhernakova, Alexandra

    The mammalian gut is colonized by trillions of microorganisms collectively called the microbiome. It is increasingly clear that this microbiome has a critical role of in many aspects of health including metabolism and immunity. While environmental factors such as diet and medications have been shown

  7. Metagenomic and metatranscriptomic analysis of the microbiome of watermelon fruits

    Science.gov (United States)

    The plant microbiome is a key determinant of plant health and productivity, and alteration of the plant microbiome can increase the quality of agricultural products. Little is known about the microbial population in fruit development of plants. In this study, we aimed to understand the function of m...

  8. Coral physiology and microbiome dynamics under combined warming and ocean acidification.

    Directory of Open Access Journals (Sweden)

    Andréa G Grottoli

    Full Text Available Rising seawater temperature and ocean acidification threaten the survival of coral reefs. The relationship between coral physiology and its microbiome may reveal why some corals are more resilient to these global change conditions. Here, we conducted the first experiment to simultaneously investigate changes in the coral microbiome and coral physiology in response to the dual stress of elevated seawater temperature and ocean acidification expected by the end of this century. Two species of corals, Acropora millepora containing the thermally sensitive endosymbiont C21a and Turbinaria reniformis containing the thermally tolerant endosymbiont Symbiodinium trenchi, were exposed to control (26.5°C and pCO2 of 364 μatm and treatment (29.0°C and pCO2 of 750 μatm conditions for 24 days, after which we measured the microbial community composition. These microbial findings were interpreted within the context of previously published physiological measurements from the exact same corals in this study (calcification, organic carbon flux, ratio of photosynthesis to respiration, photosystem II maximal efficiency, total lipids, soluble animal protein, soluble animal carbohydrates, soluble algal protein, soluble algal carbohydrate, biomass, endosymbiotic algal density, and chlorophyll a. Overall, dually stressed A. millepora had reduced microbial diversity, experienced large changes in microbial community composition, and experienced dramatic physiological declines in calcification, photosystem II maximal efficiency, and algal carbohydrates. In contrast, the dually stressed coral T. reniformis experienced a stable and more diverse microbiome community with minimal physiological decline, coupled with very high total energy reserves and particulate organic carbon release rates. Thus, the microbiome changed and microbial diversity decreased in the physiologically sensitive coral with the thermally sensitive endosymbiotic algae but not in the physiologically

  9. Coral physiology and microbiome dynamics under combined warming and ocean acidification.

    Science.gov (United States)

    Grottoli, Andréa G; Dalcin Martins, Paula; Wilkins, Michael J; Johnston, Michael D; Warner, Mark E; Cai, Wei-Jun; Melman, Todd F; Hoadley, Kenneth D; Pettay, D Tye; Levas, Stephen; Schoepf, Verena

    2018-01-01

    Rising seawater temperature and ocean acidification threaten the survival of coral reefs. The relationship between coral physiology and its microbiome may reveal why some corals are more resilient to these global change conditions. Here, we conducted the first experiment to simultaneously investigate changes in the coral microbiome and coral physiology in response to the dual stress of elevated seawater temperature and ocean acidification expected by the end of this century. Two species of corals, Acropora millepora containing the thermally sensitive endosymbiont C21a and Turbinaria reniformis containing the thermally tolerant endosymbiont Symbiodinium trenchi, were exposed to control (26.5°C and pCO2 of 364 μatm) and treatment (29.0°C and pCO2 of 750 μatm) conditions for 24 days, after which we measured the microbial community composition. These microbial findings were interpreted within the context of previously published physiological measurements from the exact same corals in this study (calcification, organic carbon flux, ratio of photosynthesis to respiration, photosystem II maximal efficiency, total lipids, soluble animal protein, soluble animal carbohydrates, soluble algal protein, soluble algal carbohydrate, biomass, endosymbiotic algal density, and chlorophyll a). Overall, dually stressed A. millepora had reduced microbial diversity, experienced large changes in microbial community composition, and experienced dramatic physiological declines in calcification, photosystem II maximal efficiency, and algal carbohydrates. In contrast, the dually stressed coral T. reniformis experienced a stable and more diverse microbiome community with minimal physiological decline, coupled with very high total energy reserves and particulate organic carbon release rates. Thus, the microbiome changed and microbial diversity decreased in the physiologically sensitive coral with the thermally sensitive endosymbiotic algae but not in the physiologically tolerant coral with

  10. Computational Approaches for Integrative Analysis of the Metabolome and Microbiome

    Directory of Open Access Journals (Sweden)

    Jasmine Chong

    2017-11-01

    Full Text Available The study of the microbiome, the totality of all microbes inhabiting the host or an environmental niche, has experienced exponential growth over the past few years. The microbiome contributes functional genes and metabolites, and is an important factor for maintaining health. In this context, metabolomics is increasingly applied to complement sequencing-based approaches (marker genes or shotgun metagenomics to enable resolution of microbiome-conferred functionalities associated with health. However, analyzing the resulting multi-omics data remains a significant challenge in current microbiome studies. In this review, we provide an overview of different computational approaches that have been used in recent years for integrative analysis of metabolome and microbiome data, ranging from statistical correlation analysis to metabolic network-based modeling approaches. Throughout the process, we strive to present a unified conceptual framework for multi-omics integration and interpretation, as well as point out potential future directions.

  11. Group foraging increases foraging efficiency in a piscivorous diver, the African penguin

    Science.gov (United States)

    McGeorge, Cuan; Ginsberg, Samuel; Pichegru, Lorien; Pistorius, Pierre A.

    2017-01-01

    Marine piscivores have evolved a variety of morphological and behavioural adaptations, including group foraging, to optimize foraging efficiency when targeting shoaling fish. For penguins that are known to associate at sea and feed on these prey resources, there is nonetheless a lack of empirical evidence to support improved foraging efficiency when foraging with conspecifics. We examined the hunting strategies and foraging performance of breeding African penguins equipped with animal-borne video recorders. Individuals pursued both solitary as well as schooling pelagic fish, and demonstrated independent as well as group foraging behaviour. The most profitable foraging involved herding of fish schools upwards during the ascent phase of a dive where most catches constituted depolarized fish. Catch-per-unit-effort was significantly improved when targeting fish schools as opposed to single fish, especially when foraging in groups. In contrast to more generalist penguin species, African penguins appear to have evolved specialist hunting strategies closely linked to their primary reliance on schooling pelagic fish. The specialist nature of the observed hunting strategies further limits the survival potential of this species if Allee effects reduce group size-related foraging efficiency. This is likely to be exacerbated by diminishing fish stocks due to resource competition and environmental change. PMID:28989785

  12. Forage: a sensitive indicator of airborne radioactivity

    International Nuclear Information System (INIS)

    Jackson, W.M.; Noakes, J.E.; Spaulding, J.D.

    1981-01-01

    This paper presents the results of using Ge(Li) γ-ray spectroscopy to measure radioactivity concentration of forage in the vicinity of the Joseph M. Farley Nuclear Plant, Houston County, AL., over a 31/2 yr period. The report period includes 2 yr of pre-operational and 11/2 yr of operational sampling. Although the objective of forage sampling was the measurement of manmade airborne fallout radioactivity, several natural radioisotopes were also found to be present. A summary of natural radioactivity data for all samples measured during the period from August 1975 to December 1978 is given. Approximately 10 days after each of four Chinese atmospheric nuclear tests conducted during the sampling period fresh fission product fallout was measured on the forage. The information from these nuclear tests shows forage sampling to be a convenient and sensitive monitoring tool for airborne fallout radioactivity. (author)

  13. Cell Wall Diversity in Forage Maize

    NARCIS (Netherlands)

    Torres, A.F.; Noordam-Boot, C.M.M.; Dolstra, Oene; Weijde, van der Tim; Combes, Eliette; Dufour, Philippe; Vlaswinkel, Louis; Visser, R.G.F.; Trindade, L.M.

    2015-01-01

    Genetic studies are ideal platforms for assessing the extent of genetic diversity, inferring the genetic architecture, and evaluating complex trait interrelations for cell wall compositional and bioconversion traits relevant to bioenergy applications. Through the characterization of a forage

  14. African Journal of Range and Forage Science

    African Journals Online (AJOL)

    The African Journal of Range & Forage Science is the leading rangeland and pastoral journal in Africa. The Journal is dedicated to publishing quality original material that advances rangeland ecology and pasture management in Africa. Read more abou the journal here.

  15. Acquisition of Uropygial Gland Microbiome by Hoopoe Nestlings.

    Science.gov (United States)

    Martín-Vivaldi, Manuel; Soler, Juan José; Martínez-García, Ángela; Arco, Laura; Juárez-García-Pelayo, Natalia; Ruiz-Rodríguez, Magdalena; Martínez-Bueno, Manuel

    2017-12-18

    Mutualistic symbioses between animals and bacteria depend on acquisition of appropriate symbionts while avoiding exploitation by non-beneficial microbes. The mode of acquisition of symbionts would determine, not only the probability of encountering but also evolutionary outcomes of mutualistic counterparts. The microbiome inhabiting the uropygial gland of the European hoopoe (Upupa epops) includes a variety of bacterial strains, some of them providing antimicrobial benefits. Here, the mode of acquisition and stability of this microbiome is analyzed by means of Automated rRNA Intergenic Spacer Analysis and two different experiments. The first experiment impeded mothers' access to their glands, thus avoiding direct transmission of microorganisms from female to offspring secretions. The second experiment explored the stability of the microbiomes by inoculating glands with secretions from alien nests. The first experiment provoked a reduction in similarity of microbiomes of mother and nestlings. Interestingly, some bacterial strains were more often detected when females had not access to their glands, suggesting antagonistic effects among bacteria from different sources. The second experiment caused an increase in richness of the microbiome of receivers in terms of prevalence of Operational Taxonomic Units (OTUs) that reduced differences in microbiomes of donors and receivers. That occurred because OTUs that were present in donors but not in receivers incorporated to the microbiome of the latter, which provoked that cross-inoculated nestlings got similar final microbiomes that included the most prevalent OTUs. The results are therefore consistent with a central role of vertical transmission in bacterial acquisition by nestling hoopoes and support the idea that the typical composition of the hoopoe gland microbiome is reached by the incorporation of some bacteria during the nestling period. This scenario suggests the existence of a coevolved core microbiome composed by

  16. Host genetic variation impacts microbiome composition across human body sites.

    Science.gov (United States)

    Blekhman, Ran; Goodrich, Julia K; Huang, Katherine; Sun, Qi; Bukowski, Robert; Bell, Jordana T; Spector, Timothy D; Keinan, Alon; Ley, Ruth E; Gevers, Dirk; Clark, Andrew G

    2015-09-15

    The composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. While microbial communities are influenced by environmental factors, some degree of genetic influence of the host on the microbiome is also expected. This study is part of an expanding effort to comprehensively profile the interactions between human genetic variation and the composition of this microbial ecosystem on a genome- and microbiome-wide scale. Here, we jointly analyze the composition of the human microbiome and host genetic variation. By mining the shotgun metagenomic data from the Human Microbiome Project for host DNA reads, we gathered information on host genetic variation for 93 individuals for whom bacterial abundance data are also available. Using this dataset, we identify significant associations between host genetic variation and microbiome composition in 10 of the 15 body sites tested. These associations are driven by host genetic variation in immunity-related pathways, and are especially enriched in host genes that have been previously associated with microbiome-related complex diseases, such as inflammatory bowel disease and obesity-related disorders. Lastly, we show that host genomic regions associated with the microbiome have high levels of genetic differentiation among human populations, possibly indicating host genomic adaptation to environment-specific microbiomes. Our results highlight the role of host genetic variation in shaping the composition of the human microbiome, and provide a starting point toward understanding the complex interaction between human genetics and the microbiome in the context of human evolution and disease.

  17. Annual forage cropping-systems for midwestern ruminant livestock production

    OpenAIRE

    McMillan, John Ernest

    2016-01-01

    Annual forage cropping systems are a vital aspect of livestock forage production. One area where this production system can be enhanced is the integration of novel annual forages into conventional cropping systems. Two separate projects were conducted to investigate alternative forage options in annual forage production. In the first discussed research trial, two sets of crops were sown following soft red winter wheat (Triticum aestivum L.) grain harvest, at two nitrogen application rates 56 ...

  18. Agronomic and forage characteristics of Guazuma ulmifolia Lam.

    OpenAIRE

    Manríquez-Mendoza, Leonor Yalid; López-Ortíz, Silvia; Pérez-Hernández, Ponciano; Ortega- Jiménez, Eusebio; López-Tecpoyotl, Zenón Gerardo; Villarruel-Fuentes, Manuel

    2011-01-01

    Native trees are an important source of forage for livestock, particularly in regions having prolonged dry periods. Some tree species have fast growth rates, good nutritional quality, and the ability to produce forage during dry periods when the need for forage is greater. Guazuma ulmifolia Lam. is a tree native to tropical America that has a high forage potential. This species is mentioned in a number of studies assessing the forage potential of trees in a diverse array of environments and v...

  19. Supplementary Material for: Hologenome analysis of two marine sponges with different microbiomes

    KAUST Repository

    Ryu, Tae Woo; Seridi, Loqmane; Moitinho-Silva, Lucas; Oates, Matthew; Liew, Yi; Mavromatis, Charalampos Harris; Wang, Xiaolei; Haywood, Annika; Lafi, Feras; Kupresanin, Marija; Sougrat, Rachid; Alzahrani, Majed A.; Giles, Emily; Ghosheh, Yanal; Schunter, Celia Marei; Baumgarten, Sebastian; Berumen, Michael; Gao, Xin; Aranda, Manuel; Foret, Sylvain; Gough, Julian; Voolstra, Christian; Hentschel, Ute; Ravasi, Timothy

    2016-01-01

    Abstract Background Sponges (Porifera) harbor distinct microbial consortia within their mesohyl interior. We herein analysed the hologenomes of Stylissa carteri and Xestospongia testudinaria, which notably differ in their microbiome content. Results Our analysis revealed that S. carteri has an expanded repertoire of immunological domains, specifically Scavenger Receptor Cysteine-Rich (SRCR)-like domains, compared to X. testudinaria. On the microbial side, metatranscriptome analyses revealed an overrepresentation of potential symbiosis-related domains in X. testudinaria. Conclusions Our findings provide genomic insights into the molecular mechanisms underlying host-symbiont coevolution and may serve as a roadmap for future hologenome analyses.

  20. The Microbiome-Gut-Behavior Axis: Crosstalk Between the Gut Microbiome and Oligodendrocytes Modulates Behavioral Responses.

    Science.gov (United States)

    Ntranos, Achilles; Casaccia, Patrizia

    2018-01-01

    Environmental and dietary stimuli have always been implicated in brain development and behavioral responses. The gut, being the major portal of communication with the external environment, has recently been brought to the forefront of this interaction with the establishment of a gut-brain axis in health and disease. Moreover, recent breakthroughs in germ-free and antibiotic-treated mice have demonstrated the significant impact of the microbiome in modulating behavioral responses in mice and have established a more specific microbiome-gut-behavior axis. One of the mechanisms by which this axis affects social behavior is by regulating myelination at the prefrontal cortex, an important site for complex cognitive behavior planning and decision-making. The prefrontal cortex exhibits late myelination of its axonal projections that could extend into the third decade of life in humans, which make it susceptible to external influences, such as microbial metabolites. Changes in the gut microbiome were shown to alter the composition of the microbial metabolome affecting highly permeable bioactive compounds, such as p-cresol, which could impair oligodendrocyte differentiation. Dysregulated myelination in the prefrontal cortex is then able to affect behavioral responses in mice, shifting them towards social isolation. The reduced social interactions could then limit microbial exchange, which could otherwise pose a threat to the survival of the existing microbial community in the host and, thus, provide an evolutionary advantage to the specific microbial community. In this review, we will analyze the microbiome-gut-behavior axis, describe the interactions between the gut microbiome and oligodendrocytes and highlight their role in the modulation of social behavior.

  1. Evidence of trapline foraging in honeybees.

    Science.gov (United States)

    Buatois, Alexis; Lihoreau, Mathieu

    2016-08-15

    Central-place foragers exploiting floral resources often use multi-destination routes (traplines) to maximise their foraging efficiency. Recent studies on bumblebees have showed how solitary foragers can learn traplines, minimising travel costs between multiple replenishing feeding locations. Here we demonstrate a similar routing strategy in the honeybee (Apis mellifera), a major pollinator known to recruit nestmates to discovered food resources. Individual honeybees trained to collect sucrose solution from four artificial flowers arranged within 10 m of the hive location developed repeatable visitation sequences both in the laboratory and in the field. A 10-fold increase of between-flower distances considerably intensified this routing behaviour, with bees establishing more stable and more efficient routes at larger spatial scales. In these advanced social insects, trapline foraging may complement cooperative foraging for exploiting food resources near the hive (where dance recruitment is not used) or when resources are not large enough to sustain multiple foragers at once. © 2016. Published by The Company of Biologists Ltd.

  2. Interactions Increase Forager Availability and Activity in Harvester Ants.

    Directory of Open Access Journals (Sweden)

    Evlyn Pless

    Full Text Available Social insect colonies use interactions among workers to regulate collective behavior. Harvester ant foragers interact in a chamber just inside the nest entrance, here called the 'entrance chamber'. Previous studies of the activation of foragers in red harvester ants show that an outgoing forager inside the nest experiences an increase in brief antennal contacts before it leaves the nest to forage. Here we compare the interaction rate experienced by foragers that left the nest and ants that did not. We found that ants in the entrance chamber that leave the nest to forage experienced more interactions than ants that descend to the deeper nest without foraging. Additionally, we found that the availability of foragers in the entrance chamber is associated with the rate of forager return. An increase in the rate of forager return leads to an increase in the rate at which ants descend to the deeper nest, which then stimulates more ants to ascend into the entrance chamber. Thus a higher rate of forager return leads to more available foragers in the entrance chamber. The highest density of interactions occurs near the nest entrance and the entrances of the tunnels from the entrance chamber to the deeper nest. Local interactions with returning foragers regulate both the activation of waiting foragers and the number of foragers available to be activated.

  3. Microbial ecology of the salmon necrobiome: evidence salmon carrion decomposition influences aquatic and terrestrial insect microbiomes.

    Science.gov (United States)

    Pechal, Jennifer L; Benbow, M Eric

    2016-05-01

    Carrion decomposition is driven by complex relationships that affect necrobiome community (i.e. all organisms and their genes associated with a dead animal) interactions, such as insect species arrival time to carrion and microbial succession. Little is understood about how microbial communities interact with invertebrates at the aquatic-terrestrial habitat interface. The first objective of the study was to characterize internal microbial communities using high-throughput sequencing of 16S rRNA gene amplicons for aquatic insects (three mayfly species) in streams with salmon carcasses compared with those in streams without salmon carcasses. The second objective was to assess the epinecrotic microbial communities of decomposing salmon carcasses (Oncorhynchus keta) compared with those of terrestrial necrophagous insects (Calliphora terraenovae larvae and adults) associated with the carcasses. There was a significant difference in the internal microbiomes of mayflies collected in salmon carcass-bearing streams and in non-carcass streams, while the developmental stage of blow flies was the governing factor in structuring necrophagous insect internal microbiota. Furthermore, the necrophagous internal microbiome was influenced by the resource on which the larvae developed, and changes in the adult microbiome varied temporally. Overall, these carrion subsidy-driven networks respond to resource pulses with bottom-up effects on consumer microbial structure, as revealed by shifting communities over space and time. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  4. Potential NICU Environmental Influences on the Neonate's Microbiome: A Systematic Review.

    Science.gov (United States)

    Hartz, Lacey E; Bradshaw, Wanda; Brandon, Debra H

    2015-10-01

    To identify how the neonatal intensive care unit (NICU) environment potentially influences the microbiome high-risk term and preterm infants. Electronic databases utilized to identify studies published in English included PubMed, Google Scholar, Cumulative Index for Nursing and Allied Health Literature, and BioMedSearcher. Date of publication did not limit inclusion in the review. Two hundred fifty articles were assessed for relevance to the research question through title and abstract review. Further screening resulted in full review of 60 articles. An in-depth review of all 60 articles resulted in 39 articles that met inclusion criteria. Twenty-eight articles were eliminated on the basis of the type of study and subject of interest. Studies were reviewed for information related to environmental factors that influence microbial colonization of the neonatal microbiome. Environment was later defined as the physical environment of the NICU and nursery caregiving activities. Studies were characterized into factors that impacted the infant's microbiome—parental skin, feeding type, environmental surfaces and caregiving equipment, health care provider skin, and antibiotic use. Literature revealed that various aspects of living within the NICU environment do influence the microbiome of infants. Caregivers can implement strategies to prevent environment-associated nosocomial infection in the NICU such as implementing infection control measures, encouraging use of breast milk, and decreasing the empirical use of antibiotics.

  5. An insect herbivore microbiome with high plant biomass-degrading capacity.

    Directory of Open Access Journals (Sweden)

    Garret Suen

    2010-09-01

    Full Text Available Herbivores can gain indirect access to recalcitrant carbon present in plant cell walls through symbiotic associations with lignocellulolytic microbes. A paradigmatic example is the leaf-cutter ant (Tribe: Attini, which uses fresh leaves to cultivate a fungus for food in specialized gardens. Using a combination of sugar composition analyses, metagenomics, and whole-genome sequencing, we reveal that the fungus garden microbiome of leaf-cutter ants is composed of a diverse community of bacteria with high plant biomass-degrading capacity. Comparison of this microbiome's predicted carbohydrate-degrading enzyme profile with other metagenomes shows closest similarity to the bovine rumen, indicating evolutionary convergence of plant biomass degrading potential between two important herbivorous animals. Genomic and physiological characterization of two dominant bacteria in the fungus garden microbiome provides evidence of their capacity to degrade cellulose. Given the recent interest in cellulosic biofuels, understanding how large-scale and rapid plant biomass degradation occurs in a highly evolved insect herbivore is of particular relevance for bioenergy.

  6. Host-Specific and pH-Dependent Microbiomes of Copepods in an Extensive Rearing System.

    Science.gov (United States)

    Skovgaard, Alf; Castro-Mejia, Josue Leonardo; Hansen, Lars Hestbjerg; Nielsen, Dennis Sandris

    2015-01-01

    Copepods are to an increasing extent cultivated as feed for mariculture fish larvae with variable production success. In the temperate climate zone, this production faces seasonal limitation due to changing abiotic factors, in particular temperature and light. Furthermore, the production of copepods may be influenced by biotic factors of the culture systems, such as competing microorganisms, harmful algae, or other eukaryotes and prokaryotes that may be non-beneficial for the copepods. In this study, the composition of bacteria associated with copepods was investigated in an extensive outdoor copepod production system. Light microscopy and scanning electron microscopy revealed that bacteria were primarily found attached to the exoskeleton of copepods although a few bacteria were also found in the gut as well as internally in skeletal muscle tissue. Through 16S rRNA gene-targeted denaturing gradient gel electrophoresis (DGGE) analysis, a clear difference was found between the microbiomes of the two copepod species, Acartia tonsa and Centropages hamatus, present in the system. This pattern was corroborated through 454/FLX-based 16S rRNA gene amplicon sequencing of copepod microbiomes, which furthermore showed that the abiotic parameters pH and oxygen concentration in rearing tank water were the key factors influencing composition of copepod microbiomes.

  7. A Machine Learning Approach for Using the Postmortem Skin Microbiome to Estimate the Postmortem Interval.

    Directory of Open Access Journals (Sweden)

    Hunter R Johnson

    Full Text Available Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes of decomposing human cadavers, focusing on the skin microbiota found in the nasal and ear canals. We then developed several models of statistical regression to establish an algorithm for predicting the PMI of microbial samples. We found that the complete data set, rather than a curated list of indicator species, was preferred for training the regressor. We further found that genus and family, rather than species, are the most informative taxonomic levels. Finally, we developed a k-nearest- neighbor regressor, tuned with the entire data set from all nasal and ear samples, that predicts the PMI of unknown samples with an average error of ±55 accumulated degree days (ADD. This study outlines a machine learning approach for the use of necrobiome data in the prediction of the PMI and thereby provides a successful proof-of- concept that skin microbiota is a promising tool in forensic death investigations.

  8. Host-Specific and pH-Dependent Microbiomes of Copepods in an Extensive Rearing System.

    Directory of Open Access Journals (Sweden)

    Alf Skovgaard

    Full Text Available Copepods are to an increasing extent cultivated as feed for mariculture fish larvae with variable production success. In the temperate climate zone, this production faces seasonal limitation due to changing abiotic factors, in particular temperature and light. Furthermore, the production of copepods may be influenced by biotic factors of the culture systems, such as competing microorganisms, harmful algae, or other eukaryotes and prokaryotes that may be non-beneficial for the copepods. In this study, the composition of bacteria associated with copepods was investigated in an extensive outdoor copepod production system. Light microscopy and scanning electron microscopy revealed that bacteria were primarily found attached to the exoskeleton of copepods although a few bacteria were also found in the gut as well as internally in skeletal muscle tissue. Through 16S rRNA gene-targeted denaturing gradient gel electrophoresis (DGGE analysis, a clear difference was found between the microbiomes of the two copepod species, Acartia tonsa and Centropages hamatus, present in the system. This pattern was corroborated through 454/FLX-based 16S rRNA gene amplicon sequencing of copepod microbiomes, which furthermore showed that the abiotic parameters pH and oxygen concentration in rearing tank water were the key factors influencing composition of copepod microbiomes.

  9. [Review of the relation between gut microbiome, metabolic disease and hypertension].

    Science.gov (United States)

    Barna, István; Nyúl, Dóra; Szentes, Tamás; Schwab, Richárd

    2018-03-01

    Gut flora has personal characteristics for each individual, similar to the fingerprints, consisting of a special mixture of bacterial species living in the intestines, now referred to as the gut microbiome. There is a strong correlation between the loss of microbial diversity and the functional bowel disorders, obesity, type 2 diabetes and cardiovascular disease as well as many autoimmune disorders. With genetic testing of stool diversity of the gut microbiome and exact analysis of the species and phylogenetic classification of the gut flora, the changes of diversity can be identified and the overgrowth of some bacteria can be revealed. In cases with pre- and manifest hypertension, an overgrowth of species from the phylum Firmicutes has been reported along with the relative decline of the phylum Bacteroidetes as opposed with cases of normotension. At the same time, the physiological balance among bacterial families was lost. According to the first studies, there is a correlation between hypertension and the lost balance of the gut microflora, both in animal experiments and in the human clinical setting. This evidence also suggests that targeted dietary alteration of the gut microbiome can be a new innovative approach in the treatment of hypertension. Orv Hetil. 2018; 159(9): 346-351.

  10. Diverse CRISPRs evolving in human microbiomes.

    Directory of Open Access Journals (Sweden)

    Mina Rho

    Full Text Available CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats loci, together with cas (CRISPR-associated genes, form the CRISPR/Cas adaptive immune system, a primary defense strategy that eubacteria and archaea mobilize against foreign nucleic acids, including phages and conjugative plasmids. Short spacer sequences separated by the repeats are derived from foreign DNA and direct interference to future infections. The availability of hundreds of shotgun metagenomic datasets from the Human Microbiome Project (HMP enables us to explore the distribution and diversity of known CRISPRs in human-associated microbial communities and to discover new CRISPRs. We propose a targeted assembly strategy to reconstruct CRISPR arrays, which whole-metagenome assemblies fail to identify. For each known CRISPR type (identified from reference genomes, we use its direct repeat consensus sequence to recruit reads from each HMP dataset and then assemble the recruited reads into CRISPR loci; the unique spacer sequences can then be extracted for analysis. We also identified novel CRISPRs or new CRISPR variants in contigs from whole-metagenome assemblies and used targeted assembly to more comprehensively identify these CRISPRs across samples. We observed that the distributions of CRISPRs (including 64 known and 86 novel ones are largely body-site specific. We provide detailed analysis of several CRISPR loci, including novel CRISPRs. For example, known streptococcal CRISPRs were identified in most oral microbiomes, totaling ∼8,000 unique spacers: samples resampled from the same individual and oral site shared the most spacers; different oral sites from the same individual shared significantly fewer, while different individuals had almost no common spacers, indicating the impact of subtle niche differences on the evolution of CRISPR defenses. We further demonstrate potential applications of CRISPRs to the tracing of rare species and the virus exposure of individuals

  11. Municipal solid waste landfills harbor distinct microbiomes

    Science.gov (United States)

    Stamps, Blake W.; Lyles, Christopher N.; Suflita, Joseph M.; Masoner, Jason R.; Cozzarelli, Isabelle M.; Kolpin, Dana W.; Stevenson, Bradley S.

    2016-01-01

    Landfills are the final repository for most of the discarded material from human society and its “built environments.” Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH4 and CO2) and a complex mixture of soluble chemical compounds in leachate. Characterization of “landfill microbiomes” and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.

  12. Microbiomes associated with infective stages of root-knot and lesion nematodes in soil.

    Directory of Open Access Journals (Sweden)

    Ahmed Elhady

    Full Text Available Endoparasitic root-knot (Meloidogyne spp. and lesion (Pratylenchus spp. nematodes cause considerable damage in agriculture. Before they invade roots to complete their life cycle, soil microbes can attach to their cuticle or surface coat and antagonize the nematode directly or by induction of host plant defenses. We investigated whether the nematode-associated microbiome in soil differs between infective stages of Meloidogyne incognita and Pratylenchus penetrans, and whether it is affected by variation in the composition of microbial communities among soils. Nematodes were incubated in suspensions of five organically and two integrated horticultural production soils, recovered by sieving and analyzed for attached bacteria and fungi after washing off loosely adhering microbes. Significant effects of the soil type and nematode species on nematode-associated fungi and bacteria were revealed as analyzed by community profiling using denaturing gradient gel electrophoresis. Attached microbes represented a small specific subset of the soil microbiome. Two organic soils had very similar bacterial and fungal community profiles, but one of them was strongly suppressive towards root-knot nematodes. They were selected for deep amplicon sequencing of bacterial 16S rRNA genes and fungal ITS. Significant differences among the microbiomes associated with the two species in both soils suggested specific surface epitopes. Among the 28 detected bacterial classes, Betaproteobacteria, Bacilli and Actinobacteria were the most abundant. The most frequently detected fungal genera were Malassezia, Aspergillus and Cladosporium. Attached microbiomes did not statistically differ between these two soils. However, Malassezia globosa and four fungal species of the family Plectosphaerellaceae, and the bacterium Neorhizobium galegae were strongly enriched on M. incognita in the suppressive soil. In conclusion, the highly specific attachment of microbes to infective stages of

  13. Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing.

    Science.gov (United States)

    Lawrence, Kate; Hyde, Jeannette

    2017-01-01

    Manipulating gut bacteria in the microbiome, through the use of probiotics and prebiotics, has been found to have an influence on both physical and emotional wellbeing. This study uses a dietary manipulation 'The Gut Makeover' designed to elicit positive changes to the gut bacteria within the microbiome. 21 healthy participants undertook 'The Gut Makeover' for a four week period. Weight and various aspects of health were assessed pre and post intervention using the Functional Medicine Medical Symptoms Questionnaire (MSQ). Paired sample t-tests revealed a significant reduction in self-reported weight at the end of the intervention. Adverse medical symptoms related to digestion, cognition and physical and emotional wellbeing, were also significantly reduced during the course of the dietary intervention. The intervention, designed to manipulate gut bacteria, had a significant impact on digestion, reducing IBS type symptoms in this non-clinical population. There was also a striking reduction in negative symptoms related to cognition, memory and emotional wellbeing, including symptoms of anxiety and depression. Dietary gut microbiome manipulations may have the power to exert positive physical and psychological health benefits, of a similar nature to those reported in studies using pre and probiotics. The small sample size and lack of control over confounding variables means that it will be important to replicate these findings in larger-scale controlled, prospective, clinical trials. This dietary microbiome intervention has the potential to improve physical and emotional wellbeing in the general population but also to be investigated as a treatment option for individuals with conditions as diverse as IBS, anxiety, depression and Alzheimer's disease.

  14. The Gut Microbiome of the Vector Lutzomyia longipalpis Is Essential for Survival of Leishmania infantum.

    Science.gov (United States)

    Kelly, Patrick H; Bahr, Sarah M; Serafim, Tiago D; Ajami, Nadim J; Petrosino, Joseph F; Meneses, Claudio; Kirby, John R; Valenzuela, Jesus G; Kamhawi, Shaden; Wilson, Mary E

    2017-01-17

    The vector-borne disease leishmaniasis, caused by Leishmania species protozoa, is transmitted to humans by phlebotomine sand flies. Development of Leishmania to infective metacyclic promastigotes in the insect gut, a process termed metacyclogenesis, is an essential prerequisite for transmission. Based on the hypothesis that vector gut microbiota influence the development of virulent parasites, we sequenced midgut microbiomes in the sand fly Lutzomyia longipalpis with or without Leishmania infantum infection. Sucrose-fed sand flies contained a highly diverse, stable midgut microbiome. Blood feeding caused a decrease in microbial richness that eventually recovered. However, bacterial richness progressively decreased in L. infantum-infected sand flies. Acetobacteraceae spp. became dominant and numbers of Pseudomonadaceae spp. diminished coordinately as the parasite underwent metacyclogenesis and parasite numbers increased. Importantly, antibiotic-mediated perturbation of the midgut microbiome rendered sand flies unable to support parasite growth and metacyclogenesis. Together, these data suggest that the sand fly midgut microbiome is a critical factor for Leishmania growth and differentiation to its infective state prior to disease transmission. Leishmania infantum, a parasitic protozoan causing fatal visceral leishmaniasis, is transmitted to humans through the bite of the sand fly Lutzomyia longipalpis Development of the parasite to its virulent metacyclic state occurs in the sand fly gut. In this study, the microbiota within the Lu. longipalpis midgut was delineated by 16S ribosomal DNA (rDNA) sequencing, revealing a highly diverse community composition that lost diversity as parasites developed to their metacyclic state and increased in abundance in infected flies. Perturbing sand fly gut microbiota with an antibiotic cocktail, which alone had no effect on either the parasite or the fly, arrested both the development of virulent parasites and parasite expansion

  15. Individual lifetime pollen and nectar foraging preferences in bumble bees

    Science.gov (United States)

    Hagbery, Jessica; Nieh, James C.

    2012-10-01

    Foraging specialization plays an important role in the ability of social insects to efficiently allocate labor. However, relatively little is known about the degree to which individual bumble bees specialize on collecting nectar or pollen, when such preferences manifest, and if individuals can alter their foraging preferences in response to changes in the colony workforce. Using Bombus impatiens, we monitored all foraging visits made by every bee in multiple colonies and showed that individual foragers exhibit consistent lifetime foraging preferences. Based upon the distribution of foraging preferences, we defined three forager types (pollen specialists, nectar specialists, and generalists). In unmanipulated colonies, 16-36 % of individuals specialized (≥90 % of visits) on nectar or pollen only. On its first day of foraging, an individual's foraging choices (nectar only, pollen only, or nectar and pollen) significantly predicted its lifetime foraging preferences. Foragers that only collected pollen on their first day of foraging made 1.61- to 1.67-fold more lifetime pollen foraging visits (as a proportion of total trips) than foragers that only collected nectar on their first foraging day. Foragers were significantly larger than bees that stayed only in the nest. We also determined the effect of removing pollen specialists at early (brood present) or later (brood absent) stages in colony life. These results suggest that generalists can alter their foraging preferences in response to the loss of a small subset of foragers. Thus, bumble bees exhibit individual lifetime foraging preferences that are established early in life, but generalists may be able to adapt to colony needs.

  16. Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes.

    Science.gov (United States)

    Hehemann, Jan-Hendrik; Kelly, Amelia G; Pudlo, Nicholas A; Martens, Eric C; Boraston, Alisdair B

    2012-11-27

    Humans host an intestinal population of microbes--collectively referred to as the gut microbiome--which encode the carbohydrate active enzymes, or CAZymes, that are absent from the human genome. These CAZymes help to extract energy from recalcitrant polysaccharides. The question then arises as to if and how the microbiome adapts to new carbohydrate sources when modern humans change eating habits. Recent metagenome analysis of microbiomes from healthy American, Japanese, and Spanish populations identified putative CAZymes obtained by horizontal gene transfer from marine bacteria, which suggested that human gut bacteria evolved to degrade algal carbohydrates-for example, consumed in form of sushi. We approached this hypothesis by studying such a polysaccharide utilization locus (PUL) obtained by horizontal gene transfer by the gut bacterium Bacteroides plebeius. Transcriptomic and growth experiments revealed that the PUL responds to the polysaccharide porphyran from red algae, enabling growth on this carbohydrate but not related substrates like agarose and carrageenan. The X-ray crystallographic and biochemical analysis of two proteins encoded by this PUL, BACPLE_01689 and BACPLE_01693, showed that they are β-porphyranases belonging to glycoside hydrolase families 16 and 86, respectively. The product complex of the GH86 at 1.3 Å resolution highlights the molecular details of porphyran hydrolysis by this new porphyranase. Combined, these data establish experimental support for the argument that CAZymes and associated genes obtained from extrinsic microbes add new catabolic functions to the human gut microbiome.

  17. A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model

    Science.gov (United States)

    Martin, François-Pierre J; Dumas, Marc-Emmanuel; Wang, Yulan; Legido-Quigley, Cristina; Yap, Ivan K S; Tang, Huiru; Zirah, Séverine; Murphy, Gerard M; Cloarec, Olivier; Lindon, John C; Sprenger, Norbert; Fay, Laurent B; Kochhar, Sunil; van Bladeren, Peter; Holmes, Elaine; Nicholson, Jeremy K

    2007-01-01

    Symbiotic gut microorganisms (microbiome) interact closely with the mammalian host's metabolism and are important determinants of human health. Here, we decipher the complex metabolic effects of microbial manipulation, by comparing germfree mice colonized by a human baby flora (HBF) or a normal flora to conventional mice. We perform parallel microbiological profiling, metabolic profiling by 1H nuclear magnetic resonance of liver, plasma, urine and ileal flushes, and targeted profiling of bile acids by ultra performance liquid chromatography–mass spectrometry and short-chain fatty acids in cecum by GC-FID. Top-down multivariate analysis of metabolic profiles reveals a significant association of specific metabotypes with the resident microbiome. We derive a transgenomic graph model showing that HBF flora has a remarkably simple microbiome/metabolome correlation network, impacting directly on the host's ability to metabolize lipids: HBF mice present higher ileal concentrations of tauro-conjugated bile acids, reduced plasma levels of lipoproteins but higher hepatic triglyceride content associated with depletion of glutathione. These data indicate that the microbiome modulates absorption, storage and the energy harvest from the diet at the systems level. PMID:17515922

  18. Increasing evidence that bats actively forage at wind turbines.

    Science.gov (United States)

    Foo, Cecily F; Bennett, Victoria J; Hale, Amanda M; Korstian, Jennifer M; Schildt, Alison J; Williams, Dean A

    2017-01-01

    Although the ultimate causes of high bat fatalities at wind farms are not well understood, several lines of evidence suggest that bats are attracted to wind turbines. One hypothesis is that bats would be attracted to turbines as a foraging resource if the insects that bats prey upon are commonly present on and around the turbine towers. To investigate the role that foraging activity may play in bat fatalities, we conducted a series of surveys at a wind farm in the southern Great Plains of the US from 2011-2016. From acoustic monitoring we recorded foraging activity, including feeding buzzes indicative of prey capture, in the immediate vicinity of turbine towers from all six bat species known to be present at this site. From insect surveys we found Lepidoptera, Coleoptera, and Orthoptera in consistently high proportions over several years suggesting that food resources for bats were consistently available at wind turbines. We used DNA barcoding techniques to assess bat diet composition of (1) stomach contents from 47 eastern red bat ( Lasiurus borealis ) and 24 hoary bat ( Lasiurus cinereus ) carcasses collected in fatality searches, and (2) fecal pellets from 23 eastern red bats that were found on turbine towers, transformers, and tower doors. We found that the majority of the eastern red bat and hoary bat stomachs, the two bat species most commonly found in fatality searches at this site, were full or partially full, indicating that the bats were likely killed while foraging. Although Lepidoptera and Orthoptera dominated the diets of these two bat species, both consumed a range of prey items with individual bats having from one to six insect species in their stomachs at the time of death. The prey items identified from eastern red bat fecal pellets showed similar results. A comparison of the turbine insect community to the diet analysis results revealed that the most abundant insects at wind turbines, including terrestrial insects such as crickets and several

  19. Quitting time: When do honey bee foragers decide to stop foraging on natural resources?

    Directory of Open Access Journals (Sweden)

    Michael eRivera

    2015-05-01

    Full Text Available Honey bee foragers may use both personal and social information when making decisions about when to visit resources. In particular, foragers may stop foraging at resources when their own experience indicates declining resource quality, or when social information, namely the delay to being able to unload nectar to receiver bees, indicates that the colony has little need for the particular resource being collected. Here we test the relative importance of these two factors in a natural setting, where colonies are using many dynamically changing resources. We recorded detailed foraging histories of individually marked bees, and identified when they appeared to abandon any resources (such as flower patches that they had previously been collecting from consistently. As in previous studies, we recorded duration of trophallaxis events (unloading nectar to receiver bees as a proxy for resource quality and the delays before returning foragers started trophallaxis as a proxy for social need for the resource. If these proxy measures accurately reflect changes in resource quality and social need, they should predict whether bees continue foraging or not. However, neither factor predicted when individuals stopped foraging on a particular resource, nor did they explain changes in colony-level foraging activity. This may indicate that other, as yet unstudied processes also affect individual decisions to abandon particular resources.

  20. The Microbiome: a Revolution in Treatment for Rheumatic Diseases?

    Science.gov (United States)

    Rosenbaum, James T; Asquith, Mark J

    2016-10-01

    The microbiome is the term that describes the microbial ecosystem that cohabits an organism such as humans. The microbiome has been implicated in a long list of immune-mediated diseases which include rheumatoid arthritis, ankylosing spondylitis, and even gout. The mechanisms to account for this effect are multiple. The clinical implications from observations on the microbiome and disease are broad. A growing number of microbiota constituents such as Prevotella copri, Porphyromonas gingivalis, and Collinsella have been correlated or causally related to rheumatic disease. The microbiome has a marked effect on the immune system. Our understanding of immune pathways modulated by the microbiota such as the induction of T helper 17 (Th17) cells and secretory immunoglobulin A (IgA) responses to segmented filamentous bacteria continues to expand. In addition to the gut microbiome, bacterial communities of other sites such as the mouth, lung, and skin have also been associated with the pathogenesis of rheumatic diseases. Strategies to alter the microbiome or to alter the immune activation from the microbiome might play a role in the future therapy for rheumatic diseases.

  1. Immunomodulatory interplay of the microbiome and therapy of rheumatic diseases.

    Science.gov (United States)

    Ostrov, Barbara E; Amsterdam, Daniel

    2017-11-01

    Modulation of the immune system by microbes, especially from the gastrointestinal tract, is increasingly considered a key factor in the onset, course and outcome of rheumatic diseases. The interplay of the microbiome, along with genetic predisposition and environmental exposure, is thought to be an important trigger for rheumatic diseases. Improved identification of the relationship of disease-specific genetic alterations and rheumatic diseases has potential diagnostic and therapeutic applications. Treatment of rheumatic disorders is influenced by microbial actions but this interplay can be challenging due to variable and unpredictable responses to therapies. Expanded knowledge of the microbiome now allows clinicians to more precisely select ideal medication regimens and to predict response to and toxicity from drugs. Rheumatic diseases and associated therapies were among the earliest microbiome interactions investigated, yet it is notable that current research is focused on clinical and immunological associations but, in comparison, a limited number of studies regarding the microbiome's impact on treatment for rheumatic diseases have been published. In the coming years, further knowledge of immunomodulating interactions between the microbiome and the immune system will aid our understanding of autoimmunity and will be increasingly important in selection of therapeutic agents for patients with autoimmune and rheumatic diseases. In this review, recent literature regarding the bidirectional immunomodulatory effects of the microbiome with rheumatic diseases and current understanding and gaps regarding the drug-microbiome interface in the management of these disorders is presented.

  2. Interplay between the lung microbiome and lung cancer.

    Science.gov (United States)

    Mao, Qixing; Jiang, Feng; Yin, Rong; Wang, Jie; Xia, Wenjie; Dong, Gaochao; Ma, Weidong; Yang, Yao; Xu, Lin; Hu, Jianzhong

    2018-02-28

    The human microbiome confers benefits or disease susceptibility to the human body through multiple pathways. Disruption of the symbiotic balance of the human microbiome is commonly found in systematic diseases such as diabetes, obesity, and chronic gastric diseases. Emerging evidence has suggested that dysbiosis of the microbiota may also play vital roles in carcinogenesis at multiple levels, e.g., by affecting metabolic, inflammatory, or immune pathways. Although the impact of the gut microbiome on the digestive cancer has been widely explored, few studies have investigated the interplay between the microbiome and lung cancer. Some recent studies have shown that certain microbes and microbiota dysbiosis are correlated with development of lung cancer. In this mini-review, we briefly summarize current research findings describing the relationship between the lung microbiome and lung cancer. We further discuss the potential mechanisms through which the lung microbiome may play a role in lung carcinogenesis and impact lung cancer treatment. A better knowledge of the interplay between the lung microbiome and lung cancer may promote the development of innovative strategies for early prevention and personalized treatment in lung cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. The Urinary Tract Microbiome in Health and Disease.

    Science.gov (United States)

    Aragón, Isabel M; Herrera-Imbroda, Bernardo; Queipo-Ortuño, María I; Castillo, Elisabeth; Del Moral, Julia Sequeira-García; Gómez-Millán, Jaime; Yucel, Gozde; Lara, María F

    2016-11-14

    The urinary tract, previously considered a sterile body niche, has emerged as the host of an array of bacteria in healthy individuals, revolutionizing the urology research field. To review the literature on microbiome implications in the urinary tract and the usefulness of probiotics/prebiotics and diet as treatment for urologic disorders. A systematic review was conducted using PubMed and Medline from inception until July 2016. The initial search identified 1419 studies and 89 were included in this systematic review. Specific bacterial communities have been found in the healthy urinary tract. Changes in this microbiome have been observed in certain urologic disorders such as urinary incontinence, urologic cancers, interstitial cystitis, neurogenic bladder dysfunction, sexually transmitted infections, and chronic prostatitis/chronic pelvic pain syndrome. The role of probiotics, prebiotics, and diet as treatment or preventive agents for urologic disorders requires further investigation. There is a microbiome associated with the healthy urinary tract that can change in urologic disorders. This represents a propitious context to identify new diagnostic, prognostic, and predictive microbiome-based biomarkers that could be used in clinical urology practice. In addition, probiotics, prebiotics, and diet modifications appear to represent an opportunity to regulate the urinary microbiome. We review the urinary microbiome of healthy individuals and its changes in relation to urinary disorders. The question to resolve is how we can modulate the microbiome to improve urinary tract health. Copyright © 2016 European Association of Urology. Published by Elsevier B.V. All rights reserved.

  4. The Microbiome of Animals: Implications for Conservation Biology

    Directory of Open Access Journals (Sweden)

    Simon Bahrndorff

    2016-01-01

    Full Text Available In recent years the human microbiome has become a growing area of research and it is becoming clear that the microbiome of humans plays an important role for human health. Extensive research is now going into cataloging and annotating the functional role of the human microbiome. The ability to explore and describe the microbiome of any species has become possible due to new methods for sequencing. These techniques allow comprehensive surveys of the composition of the microbiome of nonmodel organisms of which relatively little is known. Some attention has been paid to the microbiome of insect species including important vectors of pathogens of human and veterinary importance, agricultural pests, and model species. Together these studies suggest that the microbiome of insects is highly dependent on the environment, species, and populations and affects the fitness of species. These fitness effects can have important implications for the conservation and management of species and populations. Further, these results are important for our understanding of invasion of nonnative species, responses to pathogens, and responses to chemicals and global climate change in the present and future.

  5. Dysbiosis of the microbiome in gastric carcinogenesis.

    Science.gov (United States)

    Castaño-Rodríguez, Natalia; Goh, Khean-Lee; Fock, Kwong Ming; Mitchell, Hazel M; Kaakoush, Nadeem O

    2017-11-21

    The gastric microbiome has been proposed as an etiological factor in gastric carcinogenesis. We compared the gastric microbiota in subjects presenting with gastric cancer (GC, n = 12) and controls (functional dyspepsia (FD), n = 20) from a high GC risk population in Singapore and Malaysia. cDNA from 16S rRNA transcripts were amplified (515F-806R) and sequenced using Illumina MiSeq 2 × 250 bp chemistry. Increased richness and phylogenetic diversity but not Shannon's diversity was found in GC as compared to controls. nMDS clustered GC and FD subjects separately, with PERMANOVA confirming a significant difference between the groups. H. pylori serological status had a significant impact on gastric microbiome α-diversity and composition. Several bacterial taxa were enriched in GC, including Lactococcus, Veilonella, and Fusobacteriaceae (Fusobacterium and Leptotrichia). Prediction of bacterial metabolic contribution indicated that serological status had a significant impact on metabolic function, while carbohydrate digestion and pathways were enriched in GC. Our findings highlight three mechanisms of interest in GC, including enrichment of pro-inflammatory oral bacterial species, increased abundance of lactic acid producing bacteria, and enrichment of short chain fatty acid production pathways.

  6. Bacterial microbiome of lungs in COPD

    Directory of Open Access Journals (Sweden)

    Sze MA

    2014-02-01

    Full Text Available Marc A Sze,1 James C Hogg,2 Don D Sin1 1Department of Medicine, 2Department of Pathology and Laboratory Medicine, The James Hogg Research Centre, Providence Heart-Lung Institute, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada Abstract: Chronic obstructive pulmonary disease (COPD is currently the third leading cause of death in the world. Although smoking is the main risk factor for this disease, only a minority of smokers develop COPD. Why this happens is largely unknown. Recent discoveries by the human microbiome project have shed new light on the importance and richness of the bacterial microbiota at different body sites in human beings. The microbiota plays a particularly important role in the development and functional integrity of the immune system. Shifts or perturbations in the microbiota can lead to disease. COPD is in part mediated by dysregulated immune responses to cigarette smoke and other environmental insults. Although traditionally the lung has been viewed as a sterile organ, by using highly sensitive genomic techniques, recent reports have identified diverse bacterial communities in the human lung that may change in COPD. This review summarizes the current knowledge concerning the lung microbiota in COPD and its potential implications for pathogenesis of the disease. Keywords: chronic obstructive pulmonary disease, bacterial microbiome, lungs

  7. Community assembly of the worm gut microbiome

    Science.gov (United States)

    Gore, Jeff

    It has become increasingly clear that human health is strongly influenced by the bacteria that live within the gut, known collectively as the gut microbiome. This complex community varies tremendously between individuals, but understanding the sources that lead to this heterogeneity is challenging. To address this challenge, we are using a bottom-up approach to develop a predictive understanding of how the microbiome assembles and functions within a simple and experimentally tractable gut, the gut of the worm C. elegans. We have found that stochastic community assembly in the C. elegansintestine is sufficient to produce strong inter-worm heterogeneity in community composition. When worms are fed with two neutrally-competing fluorescently labeled bacterial strains, we observe stochastically-driven bimodality in community composition, where approximately half of the worms are dominated by each bacterial strain. A simple model incorporating stochastic colonization suggests that heterogeneity between worms is driven by the low rate at which bacteria successfully establish new intestinal colonies. We can increase this rate experimentally by feeding worms at high bacterial density; in these conditions the bimodality disappears. We have also characterized all pairwise interspecies competitions among a set of eleven bacterial species, illuminating the rules governing interspecies community assembly. These results demonstrate the potential importance of stochastic processes in bacterial community formation and suggest a role for C. elegans as a model system for ecology of host-associated communities.

  8. The fecal microbiome of ALS patients.

    Science.gov (United States)

    Brenner, David; Hiergeist, Andreas; Adis, Carolin; Mayer, Benjamin; Gessner, André; Ludolph, Albert C; Weishaupt, Jochen H

    2018-01-01

    Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative motor neuron disease accompanied by both systemic and central nervous system-specific inflammation as well as deregulated energy metabolism. These potential pathogenetic factors have recently been found to mutually interact with the gut microbiota, raising the hypothesis of a link between microbiome alterations and ALS pathogenesis. The aim of our study was to assess whether ALS is associated with an altered composition of the fecal microbiota. We compared the fecal microbiota of 25 ALS patients with 32 age- and gender-matched healthy persons using 16S rRNA gene sequencing analysis. Confounding factors and secondary disease effects on the microbiome were minimized by selection of patients without dysphagia, gastrostomy, noninvasive ventilation, or reduced body mass index. Comparing the 2 carefully matched groups, the diversity and the abundance of the bacterial taxa on the different taxonomic levels as well as PICRUSt-predicted metagenomes were almost indistinguishable. Significant differences between ALS patients and healthy controls were only observed with regard to the overall number of microbial species (operational taxonomic units) and in the abundance of uncultured Ruminococcaceae. Conclusively, ALS patients do not exhibit a substantial alteration of the gut microbiota composition. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. The development of lower respiratory tract microbiome in mice.

    Science.gov (United States)

    Singh, Nisha; Vats, Asheema; Sharma, Aditi; Arora, Amit; Kumar, Ashwani

    2017-06-21

    Although culture-independent methods have paved the way for characterization of the lung microbiome, the dynamic changes in the lung microbiome from neonatal stage to adult age have not been investigated. In this study, we tracked changes in composition and diversity of the lung microbiome in C57BL/6N mice, starting from 1-week-old neonates to 8-week-old mice. Towards this, the lungs were sterilely excised from mice of different ages from 1 to 8 weeks. High-throughput DNA sequencing of the 16S rRNA gene followed by composition and diversity analysis was utilized to decipher the microbiome in these samples. Microbiome analysis suggests that the changes in the lung microbiome correlated with age. The lung microbiome was primarily dominated by phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria in all the stages from week 1 to week 8 after birth. Although Defluvibacter was the predominant genus in 1-week-old neonatal mice, Streptococcus became the dominant genus at the age of 2 weeks. Lactobacillus, Defluvibacter, Streptococcus, and Achromobacter were the dominant genera in 3-week-old mice, while Lactobacillus and Achromobacter were the most abundant genera in 4-week-old mice. Interestingly, relatively greater diversity (at the genus level) during the age of 5 to 6 weeks was observed as compared to the earlier weeks. The diversity of the lung microbiome remained stable between 6 and 8 weeks of age. In summary, we have tracked the development of the lung microbiome in mice from an early age of 1 week to adulthood. The lung microbiome is dominated by the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. However, dynamic changes were observed at the genus level. Relatively higher richness in the microbial diversity was achieved by age of 6 weeks and then maintained at later ages. We believe that this study improves our understanding of the development of the mice lung microbiome and will facilitate further analyses of the role of

  10. Assessing the Effects of Grassland Management on Forage Production and Environmental Quality to Identify Paths to Ecological Intensification in Mountain Grasslands.

    Science.gov (United States)

    Loucougaray, Grégory; Dobremez, Laurent; Gos, Pierre; Pauthenet, Yves; Nettier, Baptiste; Lavorel, Sandra

    2015-11-01

    Ecological intensification in grasslands can be regarded as a process for increasing forage production while maintaining high levels of ecosystem functions and biodiversity. In the mountain Vercors massif, where dairy cattle farming is the main component of agriculture, how to achieve forage autonomy at farm level while sustaining environmental quality for tourism and local dairy products has recently stimulated local debate. As specific management is one of the main drivers of ecosystem functioning, we assessed the response of forage production and environmental quality at grassland scale across a wide range of management practices. We aimed to determine which components of management can be harnessed to better match forage production and environmental quality. We sampled the vegetation of 51 grasslands stratified across 13 grassland types. We assessed each grassland for agronomic and environmental properties, measuring forage production, forage quality, and indices based on the abundance of particular plant species such as timing flexibility, apiarian potential, and aromatic plants. Our results revealed an expected trade-off between forage production and environmental quality, notably by stressing the contrasts between sown and permanent grasslands. However, strong within-type variability in both production and environmental quality as well as in flexibility of timing of use suggests possible ways to improve this trade-off at grassland and farm scales. As achieving forage autonomy relies on increasing both forage production and grassland resilience, our results highlight the critical role of the ratio between sown and permanent grasslands as a major path for ecological intensification in mountain grasslands.

  11. Factors influencing local ecological knowledge of forage resources: Ethnobotanical evidence from West Africa's savannas.

    Science.gov (United States)

    Naah, John-Baptist S N; Guuroh, Reginald T

    2017-03-01

    Recording local ecological knowledge (LEK) is a useful approach to understanding interactions of the complex social-ecological systems. In spite of the recent growing interest in LEK studies on the effects of climate and land use changes, livestock mobility decisions and other aspects of agro-pastoral systems, LEK on forage plants has still been vastly under-documented in the West African savannas. Using a study area ranging from northern Ghana to central Burkina Faso, we thus aimed at exploring how aridity and socio-demographic factors drive the distributional patterns of forage-related LEK among its holders. With stratified random sampling, we elicited LEK among 450 informants in 15 villages (seven in Ghana and eight in Burkina Faso) via free list tasks coupled with ethnobotanical walks and direct field observations. We performed generalized linear mixed-effects models (aridity- and ethnicity-based models) and robust model selection procedures. Our findings revealed that LEK for woody and herbaceous forage plants was strongly influenced by the ethnicity-based model, while aridity-based model performed better for LEK on overall forage resources and crop-related forage plants. We also found that climatic aridity had negative effect on the forage-related LEK across gender and age groups, while agro- and floristic diversity had positive effect on the body of LEK. About 135 species belonging to 95 genera and 52 families were cited. Our findings shed more light on how ethnicity and environmental harshness can markedly shape the body of LEK in the face of global climate change. Better understanding of such a place-based knowledge system is relevant for sustainable forage plants utilization and livestock production. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Beneficial Effects of a Dietary Weight Loss Intervention on Human Gut Microbiome Diversity and Metabolism Are Not Sustained during Weight Maintenance.

    Science.gov (United States)

    Heinsen, Femke-Anouska; Fangmann, Daniela; Müller, Nike; Schulte, Dominik M; Rühlemann, Malte C; Türk, Kathrin; Settgast, Ute; Lieb, Wolfgang; Baines, John F; Schreiber, Stefan; Franke, Andre; Laudes, Matthias

    2016-01-01

    In the present study, we examined the effect of a very low-calorie diet(VLCD)-based obesity program on human gut microbiome diversity and metabolism during weight loss and weight maintenance. Obese subjects underwent 3 months of VLCD followed by 3 months of weight maintenance. A lean and an obese control group were included. The microbiome was characterized by performing high-throughput dual-indexed 16S rDNA amplicon sequencing. At baseline, a significant difference in the Firmicutes/Bacteroidetes ratio between the lean and obese individuals was observed (p = 0.047). The VLCD resulted in significant alterations in gut microbiome diversity from baseline to 3 months (p = 0.0053). Acinetobacter represented an indicator species for the observed effect (indicator value = 0.998, p = 0.006). Metabolic analyses revealed alterations of the bacterial riboflavin pathway from baseline to 3 months (pnom = 0.0078). These changes in diversity and bacterial metabolism induced by VLCD diminished during the weight maintenance phase, despite sustained reductions in body weight and sustained improvements of insulin sensitivity. The present data show that a VLCD is able to beneficially alter both gut microbiome diversity and metabolism in obese humans, but that these changes are not sustained during weight maintenance. This finding might suggest that the microbiome should be targeted during obesity programs. © 2016 The Author(s) Published by S. Karger GmbH, Freiburg.

  13. Beneficial Effects of a Dietary Weight Loss Intervention on Human Gut Microbiome Diversity and Metabolism Are Not Sustained during Weight Maintenance

    Directory of Open Access Journals (Sweden)

    Femke-Anouska Heinsen

    2016-11-01

    Full Text Available Objective: In the present study, we examined the effect of a very low-calorie diet(VLCD-based obesity program on human gut microbiome diversity and metabolism during weight loss and weight maintenance. Methods: Obese subjects underwent 3 months of VLCD followed by 3 months of weight maintenance. A lean and an obese control group were included. The microbiome was characterized by performing high-throughput dual-indexed 16S rDNA amplicon sequencing. Results: At baseline, a significant difference in the Firmicutes/Bacteroidetes ratio between the lean and obese individuals was observed (p = 0.047. The VLCD resulted in significant alterations in gut microbiome diversity from baseline to 3 months (p = 0.0053. Acinetobacter represented an indicator species for the observed effect (indicator value = 0.998, p = 0.006. Metabolic analyses revealed alterations of the bacterial riboflavin pathway from baseline to 3 months (pnom = 0.0078. These changes in diversity and bacterial metabolism induced by VLCD diminished during the weight maintenance phase, despite sustained reductions in body weight and sustained improvements of insulin sensitivity. Conclusion: The present data show that a VLCD is able to beneficially alter both gut microbiome diversity and metabolism in obese humans, but that these changes are not sustained during weight maintenance. This finding might suggest that the microbiome should be targeted during obesity programs.

  14. A stochastic differential equation model for the foraging behavior of fish schools.

    Science.gov (United States)

    Tạ, Tôn Việt; Nguyen, Linh Thi Hoai

    2018-03-15

    Constructing models of living organisms locating food sources has important implications for understanding animal behavior and for the development of distribution technologies. This paper presents a novel simple model of stochastic differential equations for the foraging behavior of fish schools in a space including obstacles. The model is studied numerically. Three configurations of space with various food locations are considered. In the first configuration, fish swim in free but limited space. All individuals can find food with large probability while keeping their school structure. In the second and third configurations, they move in limited space with one and two obstacles, respectively. Our results reveal that the probability of foraging success is highest in the first configuration, and smallest in the third one. Furthermore, when school size increases up to an optimal value, the probability of foraging success tends to increase. When it exceeds an optimal value, the probability tends to decrease. The results agree with experimental observations.

  15. A stochastic differential equation model for the foraging behavior of fish schools

    Science.gov (United States)

    Tạ, Tôn ệt, Vi; Hoai Nguyen, Linh Thi

    2018-05-01

    Constructing models of living organisms locating food sources has important implications for understanding animal behavior and for the development of distribution technologies. This paper presents a novel simple model of stochastic differential equations for the foraging behavior of fish schools in a space including obstacles. The model is studied numerically. Three configurations of space with various food locations are considered. In the first configuration, fish swim in free but limited space. All individuals can find food with large probability while keeping their school structure. In the second and third configurations, they move in limited space with one and two obstacles, respectively. Our results reveal that the probability of foraging success is highest in the first configuration, and smallest in the third one. Furthermore, when school size increases up to an optimal value, the probability of foraging success tends to increase. When it exceeds an optimal value, the probability tends to decrease. The results agree with experimental observations.

  16. What do foraging wasps optimize in a variable environment, energy investment or body temperature?

    Science.gov (United States)

    Kovac, Helmut; Stabentheiner, Anton; Brodschneider, Robert

    2015-11-01

    Vespine wasps (Vespula sp.) are endowed with a pronounced ability of endothermic heat production. To show how they balance energetics and thermoregulation under variable environmental conditions, we measured the body temperature and respiration of sucrose foragers (1.5 M, unlimited flow) under variable ambient temperature (T a = 20-35 °C) and solar radiation (20-570 W m(-2)). Results revealed a graduated balancing of metabolic efforts with thermoregulatory needs. The thoracic temperature in the shade depended on ambient temperature, increasing from ~37 to 39 °C. However, wasps used solar heat gain to regulate their thorax temperature at a rather high level at low T a (mean T thorax ~ 39 °C). Only at high T a they used solar heat to reduce their metabolic rate remarkably. A high body temperature accelerated the suction speed and shortened foraging time. As the costs of foraging strongly depended on duration, the efficiency could be significantly increased with a high body temperature. Heat gain from solar radiation enabled the wasps to enhance foraging efficiency at high ambient temperature (T a = 30 °C) by up to 63 %. The well-balanced change of economic strategies in response to environmental conditions minimized costs of foraging and optimized energetic efficiency.

  17. Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

    Energy Technology Data Exchange (ETDEWEB)

    Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha; Theriot, Casey M.; Young, Vincent B.; Jansson, Janet K.; Fredricks, David N.; Borenstein, Elhanan; Sanchez, Laura M.

    2015-12-22

    ABSTRACT

    Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here, we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites’ abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributing to the shifts. Focusing on two independent vaginal microbiome data sets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that contribute significantly to these predictions. Interestingly, our analysis also detects metabolites for which the predicted variation negatively correlates with the measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome data sets reveals similar trends, including prediction of bile acid metabolite shifts. This framework is an important first step toward a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in

  18. Cognitive plasticity in foraging Vespula germanica wasps.

    Science.gov (United States)

    D'Adamo, Paola; Lozada, Mariana

    2011-01-01

    Vespula germanica (F.) (Hymenoptera: Vespidae) is a highly invasive social wasp that exhibits a rich behavioral repertoire in which learning and memory play a fundamental role in foraging. The learning abilities of these wasps were analyzed while relocating a food source and whether V. germanica foragers are capable of discriminating between different orientation patterns and generalizing their choice to a new pattern. Foraging wasps were trained to associate two different stripe orientation patterns with their respective food locations. Their response to a novel configuration that maintained the orientation of one of the learned patterns but differed in other aspects (e.g. width of stripes) was then evaluated. The results support the hypothesis that V. germanica wasps are able to associate a particular oriented pattern with the location of a feeder and to generalize their choice to a new pattern, which differed in quality, but presented the same orientation.

  19. Irf4-dependent CD103+CD11b+ dendritic cells and the intestinal microbiome regulate monocyte and macrophage activation and intestinal peristalsis in postoperative ileus

    DEFF Research Database (Denmark)

    Pohl, Judith Mira; Gutweiler, Sebastian; Thiebes, Stephanie

    2017-01-01

    and large intestinal POI suggested a potential role of the intestinal microbiota. Indeed, antibiotic treatment reduced iNOS levels and ameliorated POI. Conclusions: Our findings reveal that CD103+CD11b+ DCs and the intestinal microbiome are a prerequisite for the activation of intestinal monocytes...

  20. Forage production in mixed grazing systems of elephant grass with arrowleaf clover or forage peanut

    Directory of Open Access Journals (Sweden)

    Daiane Cristine Seibt

    Full Text Available ABSTRACT Most dairy production systems are pasture-based, usually consisting of sole grass species. This system facilitates pasture management, but results in high production costs, mainly because of nitrogen fertilizers. An alternative to making forage systems more sustainable is to introduce legumes into the pasture. Mixed pastures allow better forage distribution over time and reduce fertilization costs. Thus, the objective of this study was to evaluate, throughout the year, three forage systems (FS: FS1 (control - elephant grass (EG, ryegrass (RG, and spontaneous species (SS; FS2 - EG + RG + SS + arrowleaf clover; and FS3 - EG + RG + SS + forage peanut. Elephant grass was planted in rows spaced 4 m apart. Ryegrass was sown between the EG lines, in the winter. Arrowleaf clover was sown according to the respective treatments and forage peanut was preserved. Evaluation was carried out using Holstein cows. The experiment was arranged in a completely randomized design, with three treatments (FS, and three repetitions (paddocks with repeated measurements (grazing cycles. Forage mass achieved 3.46, 3.80, and 3.91 t ha-1 for the treatments FS1, FS2 and FS3, respectively. The forage systems intercropped with legumes produced the best results.

  1. Changes of Cattle Fecal Microbiome Under Field Conditions

    Science.gov (United States)

    Next generation sequencing (NGS) has been applied to study the microbiome in wastewater, sewage sludge, and feces. Previous microbial survival studies have shown different fecal-associated microbes have different decay rates and regrowth behaviors.

  2. The role of the skin microbiome in atopic dermatitis

    DEFF Research Database (Denmark)

    Bjerre, R. D.; Bandier, J.; Skov, L.

    2017-01-01

    Dysbiosis is a hallmark of atopic dermatitis (AD). The composition of skin microbiome communities and the causality of dysbiosis in eczema have not been well established. The objective of this review is to describe the skin microbiome profile in AD and address whether there is a causal relationship...... between dysbiosis and AD. The protocol is registered in PROSPERO (CRD42016035813). We searched PubMed, Embase, Scopus and ClinicalTrials.gov for primary research studies applying culture-independent analysis on the microbiome on AD skin of humans and animal models. Two authors independently screened...... of dysbiosis in eczema in mice should encourage future studies to investigate if this also applies to humans. Other important aspects are temporal dynamics and the influence of methodology on microbiome data....

  3. The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition

    NARCIS (Netherlands)

    Cremers, Amelieke Jh; Zomer, Aldert L; Gritzfeld, Jenna F; Ferwerda, Gerben; van Hijum, Sacha Aft; Ferreira, Daniela M; Shak, Joshua R; Klugman, Keith P; Boekhorst, Jos; Timmerman, Harro M; de Jonge, Marien I; Gordon, Stephen B; Hermans, Peter Wm

    2014-01-01

    BACKGROUND: Several cohort studies have indicated associations between S. pneumoniae and other microbes in the nasopharynx. To study causal relationships between the nasopharyngeal microbiome and pneumococcal carriage, we employed an experimental human pneumococcal carriage model. Healthy adult

  4. The placental microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis

    Science.gov (United States)

    Kannan, Paranthaman S.; Alvarez, Manuel; Gisslen, Tate; Harris, R. Alan; Sweeney, Emma L.; Knox, Christine L.; Lambers, Donna S.; Jobe, Alan H.; Chougnet, Claire A.; Kallapur, Suhas G.; Aagaard, Kjersti M.

    2016-01-01

    severity of histologic chorioamnionitis (permutational multivariate analysis of variance P = .005), there was no observable impact with either beta-methasone or antibiotic treatment. In preterm subjects with chorioamnionitis, we found a high abundance of both urogenital and oral commensal bacteria. These alterations in the microbiome were accompanied by significant variation (P < .05) in microbial metabolic pathways important in the glucose-fed pentose phosphate pathway (term subjects), or glycerophopholipid metabolism, and the biosynthesis of the siderophore group nonribosomal peptides (preterm subjects). CONCLUSION Consistent with ours and others previous findings, women who experienced spontaneous PTB harbor placental microbiota that further differed by severity of chorioamnionitis. Integrative meta-genomic analysis revealed significant variation in distinct bacterial metabolic pathways, which we speculate may contribute to risk of preterm birth with and without severe chorioamnionitis. PMID:26965447

  5. The placental membrane microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis.

    Science.gov (United States)

    Prince, Amanda L; Ma, Jun; Kannan, Paranthaman S; Alvarez, Manuel; Gisslen, Tate; Harris, R Alan; Sweeney, Emma L; Knox, Christine L; Lambers, Donna S; Jobe, Alan H; Chougnet, Claire A; Kallapur, Suhas G; Aagaard, Kjersti M

    2016-05-01

    (permutational multivariate analysis of variance P = .005), there was no observable impact with either betamethasone or antibiotic treatment. In preterm subjects with chorioamnionitis, we found a high abundance of both urogenital and oral commensal bacteria. These alterations in the microbiome were accompanied by significant variation (P < .05) in microbial metabolic pathways important in the glucose-fed pentose phosphate pathway (term subjects), or glycerophopholipid metabolism, and the biosynthesis of the siderophore group nonribosomal peptides (preterm subjects). Consistent with ours and others previous findings, women who experienced spontaneous PTB harbor placental microbiota that further differed by severity of chorioamnionitis. Integrative metagenomic analysis revealed significant variation in distinct bacterial metabolic pathways, which we speculate may contribute to risk of preterm birth with and without severe chorioamnionitis. Copyright © 2016. Published by Elsevier Inc.

  6. Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle

    OpenAIRE

    Jiachao Zhang; Chuanbiao Xu; Dongxue Huo; Qisong Hu; Qiannan Peng

    2017-01-01

    Previous studies suggested a close relationship between ruminant gut microbes and the mammary gland. In this study, shotgun metagenomic sequencing was used to reveal the differences in the intestinal microbiome potentially related to milk components in Murrah buffaloes and Chinese Holstein cattle. A PCoA based on the weighted Unifrac distances showed an apparent clustering pattern in the structure of intestinal microbiota between buffalo and cattle. We could attribute the structural differenc...

  7. Movement patterns for a critically endangered species, the leatherback turtle (Dermochelys coriacea), linked to foraging success and population status.

    Science.gov (United States)

    Bailey, Helen; Fossette, Sabrina; Bograd, Steven J; Shillinger, George L; Swithenbank, Alan M; Georges, Jean-Yves; Gaspar, Philippe; Strömberg, K H Patrik; Paladino, Frank V; Spotila, James R; Block, Barbara A; Hays, Graeme C

    2012-01-01

    Foraging success for pelagic vertebrates may be revealed by horizontal and vertical movement patterns. We show markedly different patterns for leatherback turtles in the North Atlantic versus Eastern Pacific, which feed on gelatinous zooplankton that are only occasionally found in high densities. In the Atlantic, travel speed was characterized by two modes, indicative of high foraging success at low speeds (turtles. The most parsimonious explanation for these findings is that Eastern Pacific turtles rarely achieve high foraging success. This is the first support for foraging behaviour differences between populations of this critically endangered species and suggests that longer periods searching for prey may be hindering population recovery in the Pacific while aiding population maintenance in the Atlantic.

  8. Negative binomial mixed models for analyzing microbiome count data.

    Science.gov (United States)

    Zhang, Xinyan; Mallick, Himel; Tang, Zaixiang; Zhang, Lei; Cui, Xiangqin; Benson, Andrew K; Yi, Nengjun

    2017-01-03

    Recent advances in next-generation sequencing (NGS) technology enable researchers to collect a large volume of metagenomic sequencing data. These data provide valuable resources for investigating interactions between the microbiome and host environmental/clinical factors. In addition to the well-known properties of microbiome count measurements, for example, varied total sequence reads across samples, over-dispersion and zero-inflation, microbiome studies usually collect samples with hierarchical structures, which introduce correlation among the samples and thus further complicate the analysis and interpretation of microbiome count data. In this article, we propose negative binomial mixed models (NBMMs) for detecting the association between the microbiome and host environmental/clinical factors for correlated microbiome count data. Although having not dealt with zero-inflation, the proposed mixed-effects models account for correlation among the samples by incorporating random effects into the commonly used fixed-effects negative binomial model, and can efficiently handle over-dispersion and varying total reads. We have developed a flexible and efficient IWLS (Iterative Weighted Least Squares) algorithm to fit the proposed NBMMs by taking advantage of the standard procedure for fitting the linear mixed models. We evaluate and demonstrate the proposed method via extensive simulation studies and the application to mouse gut microbiome data. The results show that the proposed method has desirable properties and outperform the previously used methods in terms of both empirical power and Type I error. The method has been incorporated into the freely available R package BhGLM ( http://www.ssg.uab.edu/bhglm/ and http://github.com/abbyyan3/BhGLM ), providing a useful tool for analyzing microbiome data.

  9. Breast tissue, oral and urinary microbiomes in breast cancer

    OpenAIRE

    Wang, Hannah; Altemus, Jessica; Niazi, Farshad; Green, Holly; Calhoun, Benjamin C.; Sturgis, Charles; Grobmyer, Stephen R.; Eng, Charis

    2017-01-01

    It has long been proposed that the gut microbiome contributes to breast carcinogenesis by modifying systemic estrogen levels. This is often cited as a possible mechanism linking breast cancer and high-fat, low-fiber diets as well as antibiotic exposure, associations previously identified in population-based studies. More recently, a distinct microbiome has been identified within breast milk and tissue, but few studies have characterized differences in the breast tissue microbiota of patients ...

  10. The Human Microbiome and Skin and Soft-Tissue Infections

    Science.gov (United States)

    2015-09-23

    purulent (ex. cutaneous abscess) or non-purulent (ex. cellulitis ). Furthermore, SSTIs can be caused by a wide array of bacterial pathogens such as...or cellulitis . Using a high-throughput sequencing approach, we found that the nasal microbiomes of trainees developed SSTI had significantly less...susceptibility to chlorhexidine. While S. aureus was typically associated with purulent abscess, cellulitis microbiomes were mostly composed of

  11. Information Foraging Theory: A Framework for Intelligence Analysis

    Science.gov (United States)

    2014-11-01

    oceanographic information, human intelligence (HUMINT), open-source intelligence ( OSINT ), and information provided by other governmental departments [1][5...Human Intelligence IFT Information Foraging Theory LSA Latent Semantic Similarity MVT Marginal Value Theorem OFT Optimal Foraging Theory OSINT

  12. A properly adjusted forage harvester can save time and money

    Science.gov (United States)

    A properly adjusted forage harvester can save fuel and increase the realizable milk per ton of your silage. This article details the adjustments necessary to minimize energy while maximizing productivity and forage quality....

  13. Social foraging by waterbirds in shallow coastal lagoons in Ghana

    NARCIS (Netherlands)

    Battley, PF; Poot, M; Wiersma, P; Gordon, C; Ntiamoa-Baidu, Y; Piersma, T; Battley, Phil F.

    Social foraging in waterbirds in Ghanaian coastal lagoons was studied during October and November 1994. Two types of foraging were social: directionally synchronized flocks (often involving distinctive feeding methods used in unison) and dense pecking aggregations. Social flocks were typically

  14. Transport infrastructure shapes foraging habitat in a raptor community.

    Science.gov (United States)

    Planillo, Aimara; Kramer-Schadt, Stephanie; Malo, Juan E

    2015-01-01

    Transport infrastructure elements are widespread and increasing in size and length in many countries, with the subsequent alteration of landscapes and wildlife communities. Nonetheless, their effects on habitat selection by raptors are still poorly understood. In this paper, we analyzed raptors' foraging habitat selection in response to conventional roads and high capacity motorways at the landscape scale, and compared their effects with those of other variables, such as habitat structure, food availability, and presence of potential interspecific competitors. We also analyzed whether the raptors' response towards infrastructure depends on the spatial scale of observation, comparing the attraction or avoidance behavior of the species at the landscape scale with the response of individuals observed in the proximity of the infrastructure. Based on ecological hypotheses for foraging habitat selection, we built generalized linear mixed models, selected the best models according to Akaike Information Criterion and assessed variable importance by Akaike weights. At the community level, the traffic volume was the most relevant variable in the landscape for foraging habitat selection. Abundance, richness, and diversity values reached their maximum at medium traffic volumes and decreased at highest traffic volumes. Individual species showed different degrees of tolerance toward traffic, from higher abundance in areas with high traffic values to avoidance of it. Medium-sized opportunistic raptors increased their abundance near the traffic infrastructures, large scavenger raptors avoided areas with higher traffic values, and other species showed no direct response to traffic but to the presence of prey. Finally, our cross-scale analysis revealed that the effect of transport infrastructures on the behavior of some species might be detectable only at a broad scale. Also, food availability may attract raptor species to risky areas such as motorways.

  15. A psychology of the human brain-gut-microbiome axis.

    Science.gov (United States)

    Allen, Andrew P; Dinan, Timothy G; Clarke, Gerard; Cryan, John F

    2017-04-01

    In recent years, we have seen increasing research within neuroscience and biopsychology on the interactions between the brain, the gastrointestinal tract, the bacteria within the gastrointestinal tract, and the bidirectional relationship between these systems: the brain-gut-microbiome axis. Although research has demonstrated that the gut microbiota can impact upon cognition and a variety of stress-related behaviours, including those relevant to anxiety and depression, we still do not know how this occurs. A deeper understanding of how psychological development as well as social and cultural factors impact upon the brain-gut-microbiome axis will contextualise the role of the axis in humans and inform psychological interventions that improve health within the brain-gut-microbiome axis. Interventions ostensibly aimed at ameliorating disorders in one part of the brain-gut-microbiome axis (e.g., psychotherapy for depression) may nonetheless impact upon other parts of the axis (e.g., microbiome composition and function), and functional gastrointestinal disorders such as irritable bowel syndrome represent a disorder of the axis, rather than an isolated problem either of psychology or of gastrointestinal function. The discipline of psychology needs to be cognisant of these interactions and can help to inform the future research agenda in this emerging field of research. In this review, we outline the role psychology has to play in understanding the brain-gut-microbiome axis, with a focus on human psychology and the use of research in laboratory animals to model human psychology.

  16. Targeting gut microbiome: A novel and potential therapy for autism.

    Science.gov (United States)

    Yang, Yongshou; Tian, Jinhu; Yang, Bo

    2018-02-01

    Autism spectrum disorder (ASD) is a severely neurodevelopmental disorder that impairs a child's ability to communicate and interact with others. Children with neurodevelopmental disorder, including ASD, are regularly affected by gastrointestinal problems and dysbiosis of gut microbiota. On the other hand, humans live in a co-evolutionary association with plenty of microorganisms that resident on the exposed and internal surfaces of our bodies. The microbiome, refers to the collection of microbes and their genetic material, confers a variety of physiologic benefits to the host in many key aspects of life as well as being responsible for some diseases. A large body of preclinical literature indicates that gut microbiome plays an important role in the bidirectional gut-brain axis that communicates between the gut and central nervous system. Moreover, accumulating evidences suggest that the gut microbiome is involved in the pathogenesis of ASD. The present review introduces the increasing evidence suggesting the reciprocal interaction network among microbiome, gut and brain. It also discusses the possible mechanisms by which gut microbiome influences the etiology of ASD via altering gut-brain axis. Most importantly, it highlights the new findings of targeting gut microbiome, including probiotic treatment and fecal microbiota transplant, as novel and potential therapeutics for ASD diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. A psychology of the human brain–gut–microbiome axis

    Science.gov (United States)

    Allen, Andrew P.; Dinan, Timothy G.; Clarke, Gerard

    2017-01-01

    Abstract In recent years, we have seen increasing research within neuroscience and biopsychology on the interactions between the brain, the gastrointestinal tract, the bacteria within the gastrointestinal tract, and the bidirectional relationship between these systems: the brain–gut–microbiome axis. Although research has demonstrated that the gut microbiota can impact upon cognition and a variety of stress‐related behaviours, including those relevant to anxiety and depression, we still do not know how this occurs. A deeper understanding of how psychological development as well as social and cultural factors impact upon the brain–gut–microbiome axis will contextualise the role of the axis in humans and inform psychological interventions that improve health within the brain–gut–microbiome axis. Interventions ostensibly aimed at ameliorating disorders in one part of the brain–gut–microbiome axis (e.g., psychotherapy for depression) may nonetheless impact upon other parts of the axis (e.g., microbiome composition and function), and functional gastrointestinal disorders such as irritable bowel syndrome represent a disorder of the axis, rather than an isolated problem either of psychology or of gastrointestinal function. The discipline of psychology needs to be cognisant of these interactions and can help to inform the future research agenda in this emerging field of research. In this review, we outline the role psychology has to play in understanding the brain–gut–microbiome axis, with a focus on human psychology and the use of research in laboratory animals to model human psychology. PMID:28804508

  18. Protists are an integral part of the Arabidopsis thaliana microbiome.

    Science.gov (United States)

    Sapp, Melanie; Ploch, Sebastian; Fiore-Donno, Anna M; Bonkowski, Michael; Rose, Laura E

    2018-01-01

    Although protists occupy a vast range of habitats and are known to interact with plants among other things via disease suppression, competition or growth stimulation, their contributions to the 'phytobiome' are not well described. To contribute to a more comprehensive picture of the plant holobiont, we examined cercozoan and oomycete taxa living in association with the model plant Arabidopsis thaliana grown in two different soils. Soil, roots, leaves and wooden toothpicks were analysed before and after surface sterilization. Cercozoa were identified using 18S rRNA gene metabarcoding, whereas the Internal Transcribed Spacer 1 was used to determine oomycetes. Subsequent analyses revealed strong spatial structuring of protist communities between compartments, although oomycetes appeared more specialized than Cercozoa. With regards to oomycetes, only members of the Peronosporales and taxa belonging to the genus Globisporangium were identified as shared members of the A. thaliana microbiome. This also applied to cercozoan taxa belonging to the Glissomonadida and Cercomonadida. We identified a strong influence by edaphic factors on the rhizosphere, but not for the phyllosphere. Distinct differences of Cercozoa found preferably in wood or fresh plant material imply specific niche adaptations. Our results highlight the importance of micro-eukaryotes for the plant holobiont. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  19. Saccharide breakdown and fermentation by the honey bee gut microbiome.

    Science.gov (United States)

    Lee, Fredrick J; Rusch, Douglas B; Stewart, Frank J; Mattila, Heather R; Newton, Irene L G

    2015-03-01

    The honey bee, the world's most important agricultural pollinator, relies exclusively on plant-derived foods for nutrition. Nectar and pollen collected by honey bees are processed and matured within the nest through the activities of honey bee-derived microbes and enzymes. In order to better understand the contribution of the microbial community to food processing in the honey bee, we generated a metatranscriptome of the honey bee gut microbiome. The function of the microbial community in the honey bee, as revealed by metatranscriptome sequencing, resembles that of other animal guts and food-processing environments. We identified three major bacterial classes that are active in the gut (γ-Proteobacteria, Bacilli and Actinobacteria), all of which are predicted to participate in the breakdown of complex macromolecules (e.g. polysaccharides and polypeptides), the fermentation of component parts of these macromolecules, and the generation of various fermentation products, such as short-chain fatty acids and alcohol. The ability of the microbial community to metabolize these carbon-rich food sources was confirmed through the use of community-level physiological profiling. Collectively, these findings suggest that the gut microflora of the honey bee harbours bacterial members with unique roles, which ultimately can contribute to the processing of plant-derived food for colonies. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  20. [The importance of maternal microbiome in pregnancy].

    Science.gov (United States)

    Záhumenský, J; Hederlingová, J; Pšenková, P

    2017-01-01

    To bring the most actual published findings of the influence of maternal microbiome on the development of pregnancy and possibilities of its adjusting. Review. 2nd Department of Gyneacology and Obstetrics of the Faculty of Medicine and the University Hospital, Bratislava. Review of the literature. The appearance of microbes on various body surface areas determines the overall health status of the individual in significant manner. The change in composition of microbioma in pregnant woman is well known. It was believed that the placenta and the body of the newborn is sterile environment. Modern diagnostic methods proved the presence of microorganisms inside the fetoplacentar unit without the signs of inflammation. Mutual interaction between the immune system of the mother, microbioma and immune system of the newborn can decrease the risk of serious obstetrical syndromes as well as define the lifelong health status of the newborn. The risk can be decreased by the administration of probiotics during the pregnancy.

  1. Nutrition, the Gut and the Microbiome

    DEFF Research Database (Denmark)

    Kjølbæk, Louise

    , but an optimal diet to improve the success of weight loss maintenance has not reached consensus among worldwide expects. During the last decade, it has been observed that the gut microbiota composition is associated with obesity and obesity-associated diseases. However, a deeper understanding of how the host...... the gut and the microbiome in relation to obesity and obesity-associated diseases. The objective was investigated by the conduct of three studies (KIFU, PROKA, MNG). In KIFU, the effect of habitual calcium intake on faecal fat and energy excretions was investigated by an observational study. The 189...... (PUFA) intakes on the gut microbiota composition was investigated by a randomised cross-over study with two 4-week diets periods and a 4-week washout period. Faecal samples and metabolic markers were collected from 30 subjects before and after each diet period. Results showed that habitual dietary...

  2. Foraging Behavior of Odontomachus bauri on Barro Colorado Island, Panama

    Directory of Open Access Journals (Sweden)

    Birgit Ehmer

    1995-01-01

    Full Text Available Foraging behavior and partitioning of foraging areas of Odonomachus bauri were investigated on Barro Colorado Island in Panama. The activity of the ants did not show any daily pattern; foragers were active day and night. The type of prey captured by O. bauri supports the idea that in higher Odontomachus and Anochetus species, the high speed of mandible closure serves more for generating power than capturing elusive prey. Polydomous nests may enable O. bauri colonies to enlarge their foraging areas.

  3. Power law analysis of the human microbiome.

    Science.gov (United States)

    Ma, Zhanshan Sam

    2015-11-01

    Taylor's (1961, Nature, 189:732) power law, a power function (V = am(b) ) describing the scaling relationship between the mean and variance of population abundances of organisms, has been found to govern the population abundance distributions of single species in both space and time in macroecology. It is regarded as one of few generalities in ecology, and its parameter b has been widely applied to characterize spatial aggregation (i.e. heterogeneity) and temporal stability of single-species populations. Here, we test its applicability to bacterial populations in the human microbiome using extensive data sets generated by the US-NIH Human Microbiome Project (HMP). We further propose extending Taylor's power law from the population to the community level, and accordingly introduce four types of power-law extensions (PLEs): type I PLE for community spatial aggregation (heterogeneity), type II PLE for community temporal aggregation (stability), type III PLE for mixed-species population spatial aggregation (heterogeneity) and type IV PLE for mixed-species population temporal aggregation (stability). Our results show that fittings to the four PLEs with HMP data were statistically extremely significant and their parameters are ecologically sound, hence confirming the validity of the power law at both the population and community levels. These findings not only provide a powerful tool to characterize the aggregations of population and community in both time and space, offering important insights into community heterogeneity in space and/or stability in time, but also underscore the three general properties of power laws (scale invariance, no average and universality) and their specific manifestations in our four PLEs. © 2015 John Wiley & Sons Ltd.

  4. Analysis of Inter- and Intra-individual Variation in Foraging Habits of the Endangered Hawaiian Petrel Using Stables Isotopes

    Science.gov (United States)

    Morra, K. E.; Ostrom, P. H.; Wiley, A. E.; James, H. F.; Stricker, C. A.; Gandhi, H.

    2014-12-01

    Stable isotope analysis of the endangered Hawaiian petrel's (Pterodroma sandwichensis, HAPE) feathers provides otherwise intractable information regarding non-breeding season foraging habits. Adult HAPE spend 3.5-6 months at sea during the non-breeding season, at which time they sequentially molt their flight feathers. Because feathers are metabolically inert once synthesized, they capture isotopic signals while they are grown, providing an opportunity to study foraging habits over time. Here we use stable hydrogen (δD), carbon (δ13C) and nitrogen (δ15N) isotopes to assess variation in foraging habits within and between individuals, and among four breeding colonies. δD is an indicator of prevalence of fish vs. invertebrates in the diet. In one analysis, we observed large variation in feather δD (125‰), with adults from Maui and Kauai having significantly higher δD values than corresponding hatch-year birds, indicating significant dietary differences between age groups. In a second analysis, we utilized δ13C and δ15N of Hawaii, Maui and Lanai adults, values which vary with trophic level and also at the base of the food web across HAPE's foraging range, potentially revealing information about feeding location, as well as diet. Furthermore, because the sequence of molt is known, we are able to determine whether individual foraging specialization (continued use of the same foraging behavior over time) exists in this species. To do this, we analyzed two primary feathers, P1 and P6, which reflect the beginning and the middle of the non-breeding season, respectively. We did not find significant differences in δ13C or δ15N between P1 and P6, suggesting consistent foraging habits within individuals over time. This provides evidence that individual foraging specialization exists within these populations. Analysis of a secondary feather grown late in the molt sequence would further illuminate the extent of foraging specialization. Finally, δ15N differs

  5. Nocturnal Foraging by Red-Legged Kittiwakes, a Surface Feeding Seabird That Relies on Deep Water Prey During Reproduction.

    Science.gov (United States)

    Kokubun, Nobuo; Yamamoto, Takashi; Kikuchi, Dale M; Kitaysky, Alexander; Takahashi, Akinori

    2015-01-01

    Narrow foraging specialization may increase the vulnerability of marine predators to climate change. The red-legged kittiwake (Rissa brevirostris) is endemic to the Bering Sea and has experienced drastic population fluctuations in recent decades, presumably due to climate-driven changes in food resources. Red-legged kittiwakes are presumed to be a nocturnal surface-foraging seabird that feed almost entirely on deep water Myctophidae fishes. However, there is little empirical evidence confirming their nocturnal foraging activity during the breeding season. This study investigated the foraging behavior of red-legged kittiwakes by combining GPS tracking, accelerometry, and dietary analyses at the world's largest breeding colony of red-legged kittiwakes on St. George I. GPS tracking of 5 individuals revealed that 82.5% of non-flight behavior (including foraging and resting) occurred over the ocean basin (bottom depth >1,000 m). Acceleration data from 4 birds showed three types of behaviors during foraging trips: (1) flight, characterized by regular wing flapping, (2) resting on water, characterized by non-active behavior, and (3) foraging, when wing flapping was irregular. The proportions of both foraging and resting behaviors were higher at night (14.1 ± 7.1% and 20.8 ± 14.3%) compared to those during the day (6.5 ± 3.0% and 1.7 ± 2.7%). The mean duration of foraging (2.4 ± 2.9 min) was shorter than that of flight between prey patches (24.2 ± 53.1 min). Dietary analyses confirmed myctophids as the dominant prey (100% by occurrence and 98.4 ± 2.4% by wet-weight). Although the sample size was limited, these results suggest that breeding red-legged kittiwakes concentrated their foraging on myctophids available at the surface during nighttime in deep water regions. We propose that the diel patterns and ephemeral nature of their foraging activity reflected the availability of myctophids. Such foraging specialization may exacerbate the vulnerability of red

  6. Nocturnal Foraging by Red-Legged Kittiwakes, a Surface Feeding Seabird That Relies on Deep Water Prey During Reproduction.

    Directory of Open Access Journals (Sweden)

    Nobuo Kokubun

    Full Text Available Narrow foraging specialization may increase the vulnerability of marine predators to climate change. The red-legged kittiwake (Rissa brevirostris is endemic to the Bering Sea and has experienced drastic population fluctuations in recent decades, presumably due to climate-driven changes in food resources. Red-legged kittiwakes are presumed to be a nocturnal surface-foraging seabird that feed almost entirely on deep water Myctophidae fishes. However, there is little empirical evidence confirming their nocturnal foraging activity during the breeding season. This study investigated the foraging behavior of red-legged kittiwakes by combining GPS tracking, accelerometry, and dietary analyses at the world's largest breeding colony of red-legged kittiwakes on St. George I. GPS tracking of 5 individuals revealed that 82.5% of non-flight behavior (including foraging and resting occurred over the ocean basin (bottom depth >1,000 m. Acceleration data from 4 birds showed three types of behaviors during foraging trips: (1 flight, characterized by regular wing flapping, (2 resting on water, characterized by non-active behavior, and (3 foraging, when wing flapping was irregular. The proportions of both foraging and resting behaviors were higher at night (14.1 ± 7.1% and 20.8 ± 14.3% compared to those during the day (6.5 ± 3.0% and 1.7 ± 2.7%. The mean duration of foraging (2.4 ± 2.9 min was shorter than that of flight between prey patches (24.2 ± 53.1 min. Dietary analyses confirmed myctophids as the dominant prey (100% by occurrence and 98.4 ± 2.4% by wet-weight. Although the sample size was limited, these results suggest that breeding red-legged kittiwakes concentrated their foraging on myctophids available at the surface during nighttime in deep water regions. We propose that the diel patterns and ephemeral nature of their foraging activity reflected the availability of myctophids. Such foraging specialization may exacerbate the vulnerability of red

  7. Personal microbiome analysis improves student engagement and interest in Immunology, Molecular Biology, and Genomics undergraduate courses

    Science.gov (United States)

    Bridgewater, Laura C.; Jensen, Jamie L.; Breakwell, Donald P.; Nielsen, Brent L.; Johnson, Steven M.

    2018-01-01

    A critical area of emphasis for science educators is the identification of effective means of teaching and engaging undergraduate students. Personal microbiome analysis is a means of identifying the microbial communities found on or in our body. We hypothesized the use of personal microbiome analysis in the classroom could improve science education by making courses more applied and engaging for undergraduate students. We determined to test this prediction in three Brigham Young University undergraduate courses: Immunology, Advanced Molecular Biology Laboratory, and Genomics. These three courses have a two-week microbiome unit and students during the 2016 semester students could submit their own personal microbiome kit or use the demo data, whereas during the 2017 semester students were given access to microbiome data from an anonymous individual. The students were surveyed before, during, and after the human microbiome unit to determine whether analyzing their own personal microbiome data, compared to analyzing demo microbiome data, impacted student engagement and interest. We found that personal microbiome analysis significantly enhanced the engagement and interest of students while completing microbiome assignments, the self-reported time students spent researching the microbiome during the two week microbiome unit, and the attitudes of students regarding the course overall. Thus, we found that integrating personal microbiome analysis in the classroom was a powerful means of improving student engagement and interest in undergraduate science courses. PMID:29641525

  8. Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griffithsii.

    Directory of Open Access Journals (Sweden)

    Mary E Lucero

    2011-03-01

    Full Text Available Microbial diversity associated with micropropagated Atriplex species was assessed using microscopy, isolate culturing, and sequencing. Light, electron, and confocal microscopy revealed microbial cells in aseptically regenerated leaves and roots. Clone libraries and tag-encoded FLX amplicon pyrosequencing (TEFAP analysis amplified sequences from callus homologous to diverse fungal and bacterial taxa. Culturing isolated some seed borne endophyte taxa which could be readily propagated apart from the host. Microbial cells were observed within biofilm-like residues associated with plant cell surfaces and intercellular spaces. Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity. Bacterial and fungal TEFAP followed by alignment with sequences from curated databases revealed 7 bacterial and 17 ascomycete taxa in A. canescens, and 5 bacterial taxa in A. torreyi. Additional diversity was observed among isolates and clone libraries. Micropropagated Atriplex retains a complex, intimately associated microbiome which includes diverse strains well poised to interact in manners that influence host physiology. Microbiome analysis was facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities.

  9. Scheduling and development support in the Scavenger cyber foraging system

    DEFF Research Database (Denmark)

    Kristensen, Mads Darø; Bouvin, Niels Olof

    2010-01-01

    Cyber foraging is a pervasive computing technique where small mobile devices offload resource intensive tasks to stronger computing machinery in the vicinity. One of the main challenges within cyber foraging is that it is very difficult to develop cyber foraging enabled applications. An applicati...

  10. Evaluation of nutritional value some forage species available in Iran ...

    African Journals Online (AJOL)

    Novin

    2012-07-17

    Jul 17, 2012 ... and chemical composition of forage species was estimated. MATERIALS AND METHODS ... head per day at 8.00 a.m. and 6.00 p.m. Forage samples (2 g DM with 2 mm screen ) were weighed into nylon bags ..... methods to study the kinetics of degradation of forage species, instead of the in situ technique, ...

  11. 7 CFR 407.13 - Group risk plan for forage.

    Science.gov (United States)

    2010-01-01

    ... acres of hay in the county, as specified in the actuarial documents. The actuarial documents will... a period for forage regrowth. 2. Crop Insured The insured crop will be the forage types shown on the... the Group Risk Plan Common Policy, acreage seeded to forage after July 1 of the previous crop year...

  12. 7 CFR 457.117 - Forage production crop insurance provisions.

    Science.gov (United States)

    2010-01-01

    ... INSURANCE CORPORATION, DEPARTMENT OF AGRICULTURE COMMON CROP INSURANCE REGULATIONS § 457.117 Forage..., or a mixture thereof, or other species as shown in the Actuarial Documents. Harvest—Removal of forage... different price elections by type, in which case you may select one price election for each forage type...

  13. Blue Oak Canopy Effect on Seasonal Forage Production and Quality

    Science.gov (United States)

    William E. Frost; Neil K. McDougald; Montague W. Demment

    1991-01-01

    Forage production and forage quality were measured seasonally beneath the canopy of blue oak (Quercus douglasii) and in open grassland at the San Joaquin Experimental Range. At the March and peak standing crop sampling dates forage production was significantly greater (p=.05) beneath blue oak compared to open grassland. At most sampling dates, the...

  14. No apparent correlation between honey bee forager gut microbiota and honey production.

    Science.gov (United States)

    Horton, Melissa A; Oliver, Randy; Newton, Irene L

    2015-01-01

    One of the best indicators of colony health for the European honey bee (Apis mellifera) is its performance in the production of honey. Recent research into the microbial communities naturally populating the bee gut raise the question as to whether there is a correlation between microbial community structure and colony productivity. In this work, we used 16S rRNA amplicon sequencing to explore the microbial composition associated with forager bees from honey bee colonies producing large amounts of surplus honey (productive) and compared them to colonies producing less (unproductive). As supported by previous work, the honey bee microbiome was found to be dominated by three major phyla: the Proteobacteria, Bacilli and Actinobacteria, within which we found a total of 23 different bacterial genera, including known "core" honey bee microbiome members. Using discriminant function analysis and correlation-based network analysis, we identified highly abundant members (such as Frischella and Gilliamella) as important in shaping the bacterial community; libraries from colonies with high quantities of these Orbaceae members were also likely to contain fewer Bifidobacteria and Lactobacillus species (such as Firm-4). However, co-culture assays, using isolates from these major clades, were unable to confirm any antagonistic interaction between Gilliamella and honey bee gut bacteria. Our results suggest that honey bee colony productivity is associated with increased bacterial diversity, although this mechanism behind this correlation has yet to be determined. Our results also suggest researchers should not base inferences of bacterial interactions solely on correlations found using sequencing. Instead, we suggest that depth of sequencing and library size can dramatically influence statistically significant results from sequence analysis of amplicons and should be cautiously interpreted.

  15. The fecal microbiome in dogs with acute diarrhea and idiopathic inflammatory bowel disease.

    Directory of Open Access Journals (Sweden)

    Jan S Suchodolski

    Full Text Available BACKGROUND: Recent molecular studies have revealed a highly complex bacterial assembly in the canine intestinal tract. There is mounting evidence that microbes play an important role in the pathogenesis of acute and chronic enteropathies of dogs, including idiopathic inflammatory bowel disease (IBD. The aim of this study was to characterize the bacterial microbiota in dogs with various gastrointestinal disorders. METHODOLOGY/PRINCIPAL FINDINGS: Fecal samples from healthy dogs (n = 32, dogs with acute non-hemorrhagic diarrhea (NHD; n = 12, dogs with acute hemorrhagic diarrhea (AHD; n = 13, and dogs with active (n = 9 and therapeutically controlled idiopathic IBD (n = 10 were analyzed by 454-pyrosequencing of the 16S rRNA gene and qPCR assays. Dogs with acute diarrhea, especially those with AHD, had the most profound alterations in their microbiome, as significant separations were observed on PCoA plots of unweighted Unifrac distances. Dogs with AHD had significant decreases in Blautia, Ruminococcaceae including Faecalibacterium, and Turicibacter spp., and significant increases in genus Sutterella and Clostridium perfringens when compared to healthy dogs. No significant separation on PCoA plots was observed for the dogs with IBD. Faecalibacterium spp. and Fusobacteria were, however, decreased in the dogs with clinically active IBD, but increased during time periods of clinically insignificant IBD, as defined by a clinical IBD activity index (CIBDAI. CONCLUSIONS: Results of this study revealed a bacterial dysbiosis in fecal samples of dogs with various GI disorders. The observed changes in the microbiome differed between acute and chronic disease states. The bacterial groups that were commonly decreased during diarrhea are considered to be important short-chain fatty acid producers and may be important for canine intestinal health. Future studies should correlate these observed phylogenetic differences with functional changes in the intestinal

  16. Variability in the Foraging Distribution and Diet of Cape Gannets between the Guard and Post-guard Phases of the Breeding Cycle

    Directory of Open Access Journals (Sweden)

    Jonathan A. Botha

    2018-02-01

    Full Text Available During breeding, seabirds are central place foragers and are sensitive to changes in local prey availability. As the breeding season progresses, foraging behavior and distribution is expected to change in response to possible changes in local prey availability. In addition, adult gender, and the increasing nutritional demands of a growing chick may also influence the foraging behavior of individuals. At present, relatively few studies have assessed the foraging behavior of adult birds during the late post-guard stages of chick rearing. Through a combination of GPS tracking and diet sampling we investigated the foraging distances, spatial distribution, and prey composition of adult Cape gannets (Morus capensis during the guard and post-guard stages of chick rearing. We found no clear evidence for consistent sex-specific differences in foraging distances and spatial distribution during the guard stage, although marginal differences in the location of core foraging areas during the post-guard stage were apparent. Results, however, revealed a clear increase in foraging range from the early guard to the late post-guard stage of chick rearing. During December the diet was comprised almost exclusively of anchovy (Engraulis encrasicolus, the proportion of which had decreased significantly in the diet by January. This was mirrored by a substantial increase in the proportion of saury (Scomberesox saurus. These results suggest that Cape gannets show flexibility in the foraging behavior and diet, which may be related to changes in the abundance and distribution of prey or may reflect changes in the energetic requirements of the growing offspring. This study provides the first assessment of Cape gannet foraging behavior and spatial distribution during the post-guard stage of chick rearing. The importance of considering intra-annual variability in foraging distribution when using seabird tracking data in trophic and marine spatial planning studies are

  17. Adaptive foraging and flexible food web topology

    Czech Academy of Sciences Publication Activity Database

    Křivan, Vlastimil; Schmitz, O.

    2003-01-01

    Roč. 5, - (2003), s. 623-652 ISSN 1522-0613 R&D Projects: GA ČR GA201/03/0091 Institutional research plan: CEZ:AV0Z5007907 Keywords : adaptive foraging * food chain * food web structure Subject RIV: EH - Ecology, Behaviour Impact factor: 1.587, year: 2003

  18. Skill ontogeny among Tsimane forager-horticulturalists.

    Science.gov (United States)

    Schniter, Eric; Gurven, Michael; Kaplan, Hillard S; Wilcox, Nathaniel T; Hooper, Paul L

    2015-09-01

    We investigate whether age profiles of Tsimane forager-horticulturalists' reported skill development are consistent with predictions derived from life history theory about the timing of productivity and reproduction. Previous studies of forager skill development have often focused on a few abilities (e.g. hunting), and neglected the broad range of skills and services typical of forager economies (e.g. childcare, craft production, music performance, story-telling). By systematically examining age patterns in reported acquisition, proficiency, and expertise across a broad range of activities including food production, childcare, and other services, we provide the most complete skill development study of a traditional subsistence society to date. Our results show that: (1) most essential skills are acquired prior to first reproduction, then developed further so that their productive returns meet the increasing demands of dependent offspring during adulthood; (2) as postreproductive adults age beyond earlier years of peak performance, they report developing additional conceptual and procedural proficiency, and despite greater physical frailty than younger adults, are consensually regarded as the most expert (especially in music and storytelling), consistent with their roles as providers and educators. We find that adults have accurate understandings of their skillsets and skill levels -an important awareness for social exchange, comparison, learning, and pedagogy. These findings extend our understanding of the evolved human life history by illustrating how changes in embodied capital and the needs of dependent offspring predict the development of complementary skills and services in a forager-horticulturalist economy. © 2015 Wiley Periodicals, Inc.

  19. Improving tree establishment with forage crops

    Science.gov (United States)

    Eric J. Holzmueller; Carl W. Mize

    2003-01-01

    Tree establishment in Iowa can be difficult without adequate weed control. Although herbicides are effective at controlling weeds, they may not be desirable in riparian settings and some landowners are opposed to using them. An alternative to herbicides is the use of forage crops to control weeds. A research project was established in 1998 to evaluate the influence of...

  20. Information Foraging in E-Voting

    DEFF Research Database (Denmark)

    Vatrapu, Ravi; Robertson, Scott

    2009-01-01

    with others. Interaction analysis of the case study data consisted of applying Information Foraging Theory to understand participant specific behaviors in searching and browsing. Case study results show skewed time allocation to activities, a tradeoff between enrichment vs. exploitation of search results...

  1. Foraging strategies of Antarctic Fulmarine petrels

    NARCIS (Netherlands)

    Creuwels, J.C.S.; Engelhard, G.A.; Franeker, van J.A.; Veer, van der W.; Hasperhoven, J.G.; Ruiterman, W.

    2010-01-01

    During breeding, procellariiform seabirds are typical central-place foragers, depending on distant pelagic resources. Especially in polar environments, where there is only a short time window to complete the breeding season, high chick provisioning rates are needed to allow chicks to fledge

  2. Optimal search behavior and classic foraging theory

    International Nuclear Information System (INIS)

    Bartumeus, F; Catalan, J

    2009-01-01

    Random walk methods and diffusion theory pervaded ecological sciences as methods to analyze and describe animal movement. Consequently, statistical physics was mostly seen as a toolbox rather than as a conceptual framework that could contribute to theory on evolutionary biology and ecology. However, the existence of mechanistic relationships and feedbacks between behavioral processes and statistical patterns of movement suggests that, beyond movement quantification, statistical physics may prove to be an adequate framework to understand animal behavior across scales from an ecological and evolutionary perspective. Recently developed random search theory has served to critically re-evaluate classic ecological questions on animal foraging. For instance, during the last few years, there has been a growing debate on whether search behavior can include traits that improve success by optimizing random (stochastic) searches. Here, we stress the need to bring together the general encounter problem within foraging theory, as a mean for making progress in the biological understanding of random searching. By sketching the assumptions of optimal foraging theory (OFT) and by summarizing recent results on random search strategies, we pinpoint ways to extend classic OFT, and integrate the study of search strategies and its main results into the more general theory of optimal foraging.

  3. Field and Forage Crop Pests. MEP 310.

    Science.gov (United States)

    Morgan, Omar, D.; And Others

    As part of a cooperative extension service series by the University of Maryland, this publication introduces the identification and control of common agricultural pests that can be found in field and forage crops. The first of the five sections defines "pest" and "weed" and generally introduces different kinds of pests in the…

  4. Alternatives for forage evaluation in ruminants

    NARCIS (Netherlands)

    Gosselink, J.M.J.

    2004-01-01

    The objective of this thesis was to validate and to compare in situ and in vitro techniques with in vivo data. These techniques were also evaluated for future and practical use in feed evaluation for ruminants. The techniques were compared using the digestion data of 98 forages and the energy

  5. Foraging behavior analysis of swarm robotics system

    Directory of Open Access Journals (Sweden)

    Sakthivelmurugan E.

    2018-01-01

    Full Text Available Swarm robotics is a number of small robots that are synchronically works together to accomplish a given task. Swarm robotics faces many problems in performing a given task. The problems are pattern formation, aggregation, Chain formation, self-assembly, coordinated movement, hole avoidance, foraging and self-deployment. Foraging is most essential part in swarm robotics. Foraging is the task to discover the item and get back into the shell. The researchers conducted foraging experiments with random-movement of robots and they have end up with unique solutions. Most of the researchers have conducted experiments using the circular arena. The shell is placed at the centre of the arena and environment boundary is well known. In this study, an attempt is made to different strategic movements like straight line approach, parallel line approach, divider approach, expanding square approach, and parallel sweep approach. All these approaches are to be simulated by using player/stage open-source simulation software based on C and C++ programming language in Linux operating system. Finally statistical comparison will be done with task completion time of all these strategies using ANOVA to identify the significant searching strategy.

  6. Trapline foraging by bumble bees: VII. Adjustments for foraging success following competitor removal

    OpenAIRE

    Kazuharu Ohashi; Alison Leslie; James D. Thomson

    2013-01-01

    Animals collecting food from renewable resource patches scattered in space often establish small foraging areas to which they return faithfully. Such area fidelity offers foraging advantages through selection of profitable patches, route minimization, and regular circuit visits to these patches (“trapline foraging”). Resource distribution under field conditions may often vary in time, however, especially when competitors suddenly vanish and a number of patches become available for their neigh...

  7. Is there an endogenous tidal foraging rhythm in marine iguanas?

    Science.gov (United States)

    Wikelski, M; Hau, M

    1995-12-01

    As strictly herbivorous reptiles, Galápagos marine iguanas graze on algae in the intertidal areas during low tide. Daily foraging rhythms were observed on two islands during 3 years to determine the proximate factors underlying behavioral synchrony with the tides. Marine iguanas walked to their intertidal foraging grounds from far-off resting areas in anticipation of the time of low tide. Foraging activity was restricted to daytime, resulting in a complex bitidal rhythm including conspicuous switches from afternoon foraging to foraging during the subsequent morning when low tide occurred after dusk. The animals anticipated the daily low tide by a maximum of 4 h. The degree of anticipation depended on environmental parameters such as wave action and food supply. "Early foragers" survived in greater numbers than did animals arriving later at foraging sites, a result indicating selection pressure on the timing of anticipation. The timing of foraging trips was better predicted by the daily changes in tabulated low tide than it was by the daily changes in actual exposure of the intertidal foraging flats, suggesting an endogenous nature of the foraging rhythms. Endogenous rhythmicity would also explain why iguanas that had spontaneously fasted for several days nevertheless went foraging at the "right" time of day. A potential lunar component of the foraging rhythmicity of marine iguanas showed up in their assemblage on intertidal rocks during neap tide nights. This may indicate that iguanas possessed information on the semi-monthly rhythms in tide heights. Enclosure experiments showed that bitidal foraging rhythms of iguanas may free run in the absence of direct cues from the intertidal areas and operate independent of the light:dark cycle and social stimuli. Therefore, the existence of a circatidal oscillator in marine iguanas is proposed. The bitidal foraging pattern may result from an interaction of a circadian system with a circatidal system. Food intake or related

  8. Differential Ecological Specificity of Protist and Bacterial Microbiomes across a Set of Termite Species

    KAUST Repository

    Waidele, Lena; Korb, Judith; Voolstra, Christian R.; Kü nzel, Sven; Dedeine, Franck; Staubach, Fabian

    2017-01-01

    The gut microbiome of lower termites comprises protists and bacteria that help these insects to digest cellulose and to thrive on wood. The composition of the termite gut microbiome correlates with phylogenetic distance of the animal host and host

  9. Deciphering composition and function of the root microbiome of a legume plant

    NARCIS (Netherlands)

    Hartman, Kyle; van der Heijden, Marcel G A|info:eu-repo/dai/nl/240923901; Roussely-Provent, Valexia; Walser, Jean-Claude; Schlaeppi, Klaus

    2017-01-01

    BACKGROUND: Diverse assemblages of microbes colonize plant roots and collectively function as a microbiome. Earlier work has characterized the root microbiomes of numerous plant species, but little information is available for legumes despite their key role in numerous ecosystems including

  10. Turbidity interferes with foraging success of visual but not chemosensory predators.

    Science.gov (United States)

    Lunt, Jessica; Smee, Delbert L

    2015-01-01

    Predation can significantly affect prey populations and communities, but predator effects can be attenuated when abiotic conditions interfere with foraging activities. In estuarine communities, turbidity can affect species richness and abundance and is changing in many areas because of coastal development. Many fish species are less efficient foragers in turbid waters, and previous research revealed that in elevated turbidity, fish are less abundant whereas crabs and shrimp are more abundant. We hypothesized that turbidity altered predatory interactions in estuaries by interfering with visually-foraging predators and prey but not with organisms relying on chemoreception. We measured the effects of turbidity on the predation rates of two model predators: a visual predator (pinfish, Lagodon rhomboides) and a chemosensory predator (blue crabs, Callinectes sapidus) in clear and turbid water (0 and ∼100 nephelometric turbidity units). Feeding assays were conducted with two prey items, mud crabs (Panopeus spp.) that rely heavily on chemoreception to detect predators, and brown shrimp (Farfantepenaus aztecus) that use both chemical and visual cues for predator detection. Because turbidity reduced pinfish foraging on both mud crabs and shrimp, the changes in predation rates are likely driven by turbidity attenuating fish foraging ability and not by affecting prey vulnerability to fish consumers. Blue crab foraging was unaffected by turbidity, and blue crabs were able to successfully consume nearly all mud crab and shrimp prey. Turbidity can influence predator-prey interactions by reducing the feeding efficiency of visual predators, providing a competitive advantage to chemosensory predators, and altering top-down control in food webs.

  11. Project CONVERGE: Impacts of local oceanographic processes on Adélie penguin foraging ecology

    Science.gov (United States)

    Kohut, J. T.; Bernard, K. S.; Fraser, W.; Oliver, M. J.; Statscewich, H.; Patterson-Fraser, D.; Winsor, P.; Cimino, M. A.; Miles, T. N.

    2016-02-01

    During the austral summer of 2014-2015, project CONVERGE deployed a multi-platform network to sample the Adélie penguin foraging hotspot associated with Palmer Deep Canyon along the Western Antarctic Peninsula. The focus of CONVERGE was to assess the impact of prey-concentrating ocean circulation dynamics on Adélie penguin foraging behavior. Food web links between phytoplankton and zooplankton abundance and penguin behavior were examined to better understand the within-season variability in Adélie foraging ecology. Since the High Frequency Radar (HFR) network installation in November 2014, the radial component current data from each of the three sites were combined to provide a high resolution (0.5 km) surface velocity maps. These hourly maps have revealed an incredibly dynamic system with strong fronts and frequent eddies extending across the Palmer Deep foraging area. A coordinated fleet of underwater gliders were used in concert with the HFR fields to sample the hydrography and phytoplankton distributions associated with convergent and divergent features. Three gliders mapped the along and across canyon variability of the hydrography, chlorophyll fluorescence and acoustic backscatter in the context of the observed surface currents and simultaneous penguin tracks. This presentation will highlight these synchronized measures of the food web in the context of the observed HFR fronts and eddies. The location and persistence of these features coupled with ecological sampling through the food web offer an unprecedented view of the Palmer Deep ecosystem. Specific examples will highlight how the vertical structure of the water column beneath the surface features stack the primary and secondary producers relative to observed penguin foraging behavior. The coupling from the physics through the food web as observed by our multi-platform network gives strong evidence for the critical role that distribution patterns of lower trophic levels have on Adélie foraging.

  12. The human gut microbiome: current knowledge, challenges, and future directions.

    Science.gov (United States)

    Dave, Maneesh; Higgins, Peter D; Middha, Sumit; Rioux, Kevin P

    2012-10-01

    The Human Genome Project was completed a decade ago, leaving a legacy of process, tools, and infrastructure now being turned to the study of the microbes that reside in and on the human body as determinants of health and disease, and has been branded "The Human Microbiome Project." Of the various niches under investigation, the human gut houses the most complex and abundant microbial community and is an arena for important host-microbial interactions that have both local and systemic impact. Initial studies of the human microbiome have been largely descriptive, a testing ground for innovative molecular techniques and new hypotheses. Methods for studying the microbiome have quickly evolved from low-resolution surveys of microbial community structure to high-definition description of composition, function, and ecology. Next-generation sequencing technologies combined with advanced bioinformatics place us at the doorstep of revolutionary insight into the composition, capability, and activity of the human intestinal microbiome. Renewed efforts to cultivate previously "uncultivable" microbes will be important to the overall understanding of gut ecology. There remain numerous methodological challenges to the effective study and understanding of the gut microbiome, largely relating to study design, sample collection, and the number of predictor variables. Strategic collaboration of clinicians, microbiologists, molecular biologists, computational scientists, and bioinformaticians is the ideal paradigm for success in this field. Meaningful interpretation of the gut microbiome requires that host genetic and environmental influences be controlled or accounted for. Understanding the gut microbiome in healthy humans is a foundation for discovering its influence in various important gastrointestinal and nutritional diseases (eg, inflammatory bowel disease, diabetes, and obesity), and for rational translation to human health gains. Copyright © 2012 Mosby, Inc. All rights

  13. Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle.

    Science.gov (United States)

    Zhang, Jiachao; Xu, Chuanbiao; Huo, Dongxue; Hu, Qisong; Peng, Qiannan

    2017-02-08

    Previous studies suggested a close relationship between ruminant gut microbes and the mammary gland. In this study, shotgun metagenomic sequencing was used to reveal the differences in the intestinal microbiome potentially related to milk components in Murrah buffaloes and Chinese Holstein cattle. A PCoA based on the weighted Unifrac distances showed an apparent clustering pattern in the structure of intestinal microbiota between buffalo and cattle. We could attribute the structural difference to the genera of Sutterella, Coprococcus and Dorea. A further analysis of microbial functional features revealed that the biosynthesis of amino acids (including lysine, valine, leucine and isoleucine), lipopolysaccharide biosynthesis and cofactor/vitamin biosynthesis were enriched in the buffalo. In contrast, dairy cattle had higher levels of pyruvate metabolism and carbon fixation in photosynthetic organisms. A further correlation analysis based on different milk components and the typical microbiome uncovered a significant positive correlation between milk protein and the microbial biosynthesis of amino acids, which was also positively correlated in the genera of Parabacteroides, Dorea and Sutterella. This study will expand our understanding of the intestinal microbiome of buffalo and cattle as representative ruminants, as well as provide new views about how to improve the production and nutritional qualities of animal milk.

  14. Characterization of the oral fungal microbiome (mycobiome in healthy individuals.

    Directory of Open Access Journals (Sweden)

    Mahmoud A Ghannoum

    2010-01-01

    Full Text Available The oral microbiome-organisms residing in the oral cavity and their collective genome-are critical components of health and disease. The fungal component of the oral microbiota has not been characterized. In this study, we used a novel multitag pyrosequencing approach to characterize fungi present in the oral cavity of 20 healthy individuals, using the pan-fungal internal transcribed spacer (ITS primers. Our results revealed the "basal" oral mycobiome profile of the enrolled individuals, and showed that across all the samples studied, the oral cavity contained 74 culturable and 11 non-culturable fungal genera. Among these genera, 39 were present in only one person, 16 genera were present in two participants, and 5 genera were present in three people, while 15 genera (including non-culturable organisms were present in >/=4 (20% participants. Candida species were the most frequent (isolated from 75% of participants, followed by Cladosporium (65%, Aureobasidium, Saccharomycetales (50% for both, Aspergillus (35%, Fusarium (30%, and Cryptococcus (20%. Four of these predominant genera are known to be pathogenic in humans. The low-abundance genera may represent environmental fungi present in the oral cavity and could simply be spores inhaled from the air or material ingested with food. Among the culturable genera, 61 were represented by one species each, while 13 genera comprised between 2 and 6 different species; the total number of species identified were 101. The number of species in the oral cavity of each individual ranged between 9 and 23. Principal component (PCO analysis of the obtained data set followed by sample clustering and UniFrac analysis revealed that White males and Asian males clustered differently from each other, whereas both Asian and White females clustered together. This is the first study that identified the "basal mycobiome" of healthy individuals, and provides the basis for a detailed characterization of the oral mycobiome in

  15. Heat, sight and scent: multiple cues influence foraging site selection by an ambush-foraging snake Hoplocephalus bungaroides (Elapidae

    Directory of Open Access Journals (Sweden)

    Weiguo DU, Jonathan K. WEBB, Richard SHINE

    2009-08-01

    Full Text Available Most mobile organisms respond to multiple cues when selecting habitat types, and laboratory experiments that manipulate only single cues may fail to reveal the true complexity of habitat-selection behaviour. In south-eastern Australia, broad-headed snakes Hoplocephalus bungaroides (Elapidae lie in wait under sun-warmed rocks to ambush velvet geckos Oedura leseuerii (Gekkonidae. Previous laboratory work has shown that both the geckos and the snakes actively select hotter rather than colder rocks, and that the snakes actively select rocks scented by geckos. We manipulated rock temperature and the presence of two types of cues from geckos (chemical and visual information to clarify the causal basis for foraging site selection by the juveniles of this snake. When given a choice between cold lizard-scented rocks and hot unscented rocks, our captive snakes gave a higher priority to lizard scent than to temperature. The snakes also selected shelter-sites that provided visual as well as scent cues from lizards, rather than shelter-sites with scent cues alone. Thus, although broad-headed snakes show a direct preference for hotter rather than colder rocks in the laboratory, their choice of foraging site in the field may also be influenced by the presence of scent cues from prey. Our laboratory results suggest that habitat selection by broad-headed snakes may be more complex than has been suggested by previous single-factor laboratory trials[Current Zoology 55(4: 266–271, 2009].

  16. Foraging strategies of the ant Ectatomma vizottoi (Hymenoptera, Formicidae

    Directory of Open Access Journals (Sweden)

    Luan D. Lima

    2013-12-01

    Full Text Available Foraging strategies of the ant Ectatomma vizottoi (Hymenoptera, Formicidae. Foraging activity may be limited by temperature, humidity, radiation, wind, and other abiotic factors, all of which can affect energy costs during foraging. Ectatomma vizottoi's biology has only recently been studied, and no detailed information is available on its foraging patterns or diet in the field. For this reason, and because foraging activity is an important part of the ecological success of social insects, the present study aimed to investigate E. vizottoi's foraging strategies and dietary habits. First, we determined how abiotic factors constrained E. vizottoi's foraging patterns in the field by monitoring the foraging activity of 16 colonies on eight different days across two seasons. Second, we characterized E. vizottoi's diet by monitoring another set of 26 colonies during peak foraging activity. Our results show that E. vizottoi has foraging strategies that are similar to those of congeneric species. In spite of having a low efficiency index, colonies adopted strategies that allowed them to successfully obtain food resources while avoiding adverse conditions. These strategies included preying on other ant species, a foraging tactic that could arise if a wide variety of food items are not available in the environment or if E. vizottoi simply prefers, regardless of resource availability, to prey on other invertebrates and especially on other ant species.

  17. Forage and sugar in dairy calves' starter diet and their interaction on performance, weaning age and rumen fermentation.

    Science.gov (United States)

    Beiranvand, H; Ghorbani, G R; Khorvash, M; Kazemi-Bonchenari, M

    2014-06-01

    The effects of sugar and forage inclusion in calves' starter and their interaction on animal performance and rumen fermentation parameters were investigated. Twenty-eight neonatal Holstein male calves 3 days of age with average body weights of 42 ± 4 kg were allocated to four different treatments. All calves were fed a similar basal diet consisting of milk and concentrate. The experimental treatments were: (i) basal diet with no supplementation (Control, hereafter designated by C), (ii) basal diet plus 5% granular sugar cane (Sugar, designated by S), (iii) basal diet plus 5% forage (Forage, designated by F) and (iv) basal diet plus 5% forage with 5% granular sugar cane (F × S). Supplement ingredients were used on a dry matter (DM) basis. Rumen fluid parameters were measured twice on days 35 and 70 of the study period. The calves were weaned when they could consume 1 kg of starter for three consecutive days. The results show that starter intake was not affected by treatment; however, the lowest ADG was observed with calves in the sugar treatment. Weaning age was affected by treatments, and forage showed to reduce milk consumption period down to its shortest. Forage-sugar interaction was found to have no effects on animal performance. The structural body indices as well as the health status of the calves were similar in different treatments. Rumen pH did not differ among the treatment groups. Among the rumen parameters, total VFA concentration and molar proportions of butyrate and propionate did not exhibit any significant differences among the treatments. However, ruminal acetate concentration decreased in calves that fed sugar cane during the early weeks of the study period. Comparison of forage and sugar included in the starter diets revealed that forage reduced weaning age, while sugar cane had a negative effect on calves' performance. Journal of Animal Physiology and Animal Nutrition © 2013 Blackwell Verlag GmbH.

  18. Additional file 6: Figure S1. of Pancreatic cyst fluid harbors a unique microbiome

    OpenAIRE

    Li, Shan; Fuhler, Gwenny; BN, Nahush; Jose, Tony; Bruno, Marco; Peppelenbosch, Maikel; Konstantinov, Sergey

    2017-01-01

    PCA of pancreatic cyst fluid (PCF) and 13 body site microbiome comparisons. PCA showing the difference between pancreatic cyst fluid and 13 different body site microbiome selected from Human Microbiome Project database. When compared 136 bacterial genus with p 

  19. The regulation of ant colony foraging activity without spatial information.

    Directory of Open Access Journals (Sweden)

    Balaji Prabhakar

    Full Text Available Many dynamical networks, such as the ones that produce the collective behavior of social insects, operate without any central control, instead arising from local interactions among individuals. A well-studied example is the formation of recruitment trails in ant colonies, but many ant species do not use pheromone trails. We present a model of the regulation of foraging by harvester ant (Pogonomyrmex barbatus colonies. This species forages for scattered seeds that one ant can retrieve on its own, so there is no need for spatial information such as pheromone trails that lead ants to specific locations. Previous work shows that colony foraging activity, the rate at which ants go out to search individually for seeds, is regulated in response to current food availability throughout the colony's foraging area. Ants use the rate of brief antennal contacts inside the nest between foragers returning with food and outgoing foragers available to leave the nest on the next foraging trip. Here we present a feedback-based algorithm that captures the main features of data from field experiments in which the rate of returning foragers was manipulated. The algorithm draws on our finding that the distribution of intervals between successive ants returning to the nest is a Poisson process. We fitted the parameter that estimates the effect of each returning forager on the rate at which outgoing foragers leave the nest. We found that correlations between observed rates of returning foragers and simulated rates of outgoing foragers, using our model, were similar to those in the data. Our simple stochastic model shows how the regulation of ant colony foraging can operate without spatial information, describing a process at the level of individual ants that predicts the overall foraging activity of the colony.

  20. Microbiome change by symbiotic invasion in lichens

    Science.gov (United States)

    Maier, Stefanie; Wedin, Mats; Fernandez-Brime, Samantha; Cronholm, Bodil; Westberg, Martin; Weber, Bettina; Grube, Martin

    2016-04-01

    Biological soil crusts (BSC) seal the soil surface from erosive forces in many habitats where plants cannot compete. Lichens symbioses of fungi and algae often form significant fraction of these microbial assemblages. In addition to the fungal symbiont, many species of other fungi can inhabit the lichenic structures and interact with their hosts in different ways, ranging from commensalism to parasitism. More than 1800 species of lichenicolous (lichen-inhabiting) fungi are known to science. One example is Diploschistes muscorum, a common species in lichen-dominated BSC that infects lichens of the genus Cladonia. D. muscorum starts as a lichenicolous fungus, invading the lichen Cladonia symphycarpa and gradually develops an independent Diploschistes lichen thallus. Furthermore, bacterial groups, such as Alphaproteobacteria and Acidobacteria, have been consistently recovered from lichen thalli and evidence is rapidly accumulating that these microbes may generally play integral roles in the lichen symbiosis. Here we describe lichen microbiome dynamics as the parasitic lichen D. muscorum takes over C. symphycarpa. We used high-throughput 16S rRNA gene and photobiont-specific ITS rDNA sequencing to track bacterial and algal transitions during the infection process, and employed fluorescence in situ hybridization to localize bacteria in the Cladonia and Diploschistes lichen thalli. We sampled four transitional stages, at sites in Sweden and Germany: A) Cladonia with no visible infection, B) early infection stage defined by the first visible Diploschistes thallus, C) late-stage infection with parts of the Cladonia thallus still identifiable, and D) final stage with a fully developed Diploschistes thallus, A gradual microbiome shift occurred during the transition, but fractions of Cladonia-associated bacteria were retained during the process of symbiotic reorganization. Consistent changes observed across sites included a notable decrease in the relative abundance of

  1. Impacts of the Human Gut Microbiome on Therapeutics.

    Science.gov (United States)

    Vázquez-Baeza, Yoshiki; Callewaert, Chris; Debelius, Justine; Hyde, Embriette; Marotz, Clarisse; Morton, James T; Swafford, Austin; Vrbanac, Alison; Dorrestein, Pieter C; Knight, Rob

    2018-01-06

    The human microbiome contains a vast source of genetic and biochemical variation, and its impacts on therapeutic responses are just beginning to be understood. This expanded understanding is especially important because the human microbiome differs far more among different people than does the human genome, and it is also dramatically easier to change. Here, we describe some of the major factors driving differences in the human microbiome among individuals and populations. We then describe some of the many ways in which gut microbes modify the action of specific chemotherapeutic agents, including nonsteroidal anti-inflammatory drugs and cardiac glycosides, and outline the potential of fecal microbiota transplant as a therapeutic. Intriguingly, microbes also alter how hosts respond to therapeutic agents through various pathways acting at distal sites. Finally, we discuss some of the computational and practical issues surrounding use of the microbiome to stratify individuals for drug response, and we envision a future where the microbiome will be modified to increase everyone's potential to benefit from therapy.

  2. Early Postnatal Diets Affect the Bioregional Small Intestine Microbiome and Ileal Metabolome in Neonatal Pigs.

    Science.gov (United States)

    Piccolo, Brian D; Mercer, Kelly E; Bhattacharyya, Sudeepa; Bowlin, Anne K; Saraf, Manish K; Pack, Lindsay; Chintapalli, Sree V; Shankar, Kartik; Adams, Sean H; Badger, Thomas M; Yeruva, Laxmi

    2017-08-01

    Background: Breastfeeding is known to be protective against gastrointestinal disorders and may modify gut development. Although the gut microbiome has been implicated, little is known about how early diet affects the small intestine microbiome. Objective: We hypothesized that disparate early diets would promote unique microbial profiles in the small intestines of neonatal pigs. Methods: Male and female 2-d-old White Dutch Landrace pigs were either sow fed or provided dairy (Similac Advance powder; Ross Products Abbott Laboratories) or soy (Enfamil Prosobee Lipil powder; Mead Johnson Nutritionals) infant formulas until day 21. Bacterial ecology was assessed in the contents of the small intestine through the use of 16S ribosomal RNA sequencing. α-Diversity, β-diversity, and differential abundances of operational taxonomic units were assessed by ANOVA, permutational ANOVA, and negative binomial regression, respectively. Ileum tissue metabolomics were measured by LC-mass spectrometry and assessed by weighted correlation network analysis. Results: Greater α-diversity was observed in the duodena of sow-fed compared with formula-fed neonatal pigs ( P 60% relative abundance in all of the groups. In the duodenum, 77 genera were altered by diet, followed by 48 in the jejunum and 19 in the ileum. Metabolomics analyses revealed associations between ileum tissue metabolites (e.g., acylcarnitines, 3-aminoisobutyric acid) and diet-responsive microbial genera. Conclusions: These results indicate that the neonatal diet has regional effects on the small intestine microbiome in pigs, with the most pronounced effects occurring in the duodena. Regional effects may be important factors when considering gut tissue metabolism and development in the postnatal period. © 2017 American Society for Nutrition.

  3. The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations

    Science.gov (United States)

    Oakley, Brian B.; Morales, Cesar A.; Line, J.; Berrang, Mark E.; Meinersmann, Richard J.; Tillman, Glenn E.; Wise, Mark G.; Siragusa, Gregory R.; Hiett, Kelli L.; Seal, Bruce S.

    2013-01-01

    Microbial communities associated with agricultural animals are important for animal health, food safety, and public health. Here we combine high-throughput sequencing (HTS), quantitative-PCR assays, and network analysis to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including Campylobacter, Clostridium, and Shigella. After the final stage of commercial poultry processing, taxonomic richness was ca. 2–4 times lower than the richness of fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples), significantly more than expected by chance. Among these were anaerobes such as Prevotella, Veillonella, Leptrotrichia, and multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were potentially metabolically active and encountered in on-farm samples. Network analysis was focused on the foodborne pathogen Campylobacter and revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. These data represent the first use of HTS to characterize the poultry microbiome across a series of farm-to-fork samples and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities. PMID:23468931

  4. Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants

    Directory of Open Access Journals (Sweden)

    Ruth eSchmidt

    2014-02-01

    Full Text Available Plant-associated bacteria fulfil important functions for plant growth and health of their host. However, our knowledge about the impact of bacterial treatments on the host’s microbiome and physiology is limited. The present study was conducted to assess the impact of bacterial inoculants on the microbiome of chamomile plants Chamomilla recutita (L. Rauschert grown in a field under organic management in Egypt. Chamomile seedlings were inoculated with three indigenous Gram-positive strains (Streptomyces subrutilus Wbn2-11, Bacillus subtilis Co1-6, Paenibacillus polymyxa Mc5Re-14 from Egypt and three European Gram-negative strains (Pseudomonas fluorescens L13-6-12, Stenotrophomonas rhizophila P69, Serratia plymuthica 3Re4-18 already known for their beneficial plant-microbe interaction. Molecular fingerprints of 16S rRNA gene as well as real-time PCR analyses did not show statistically significant differences for all applied bacterial antagonists compared to the control. In contrast, a pyrosequencing analysis of the 16S rRNA gene libraries revealed significant differences in the community structure of bacteria between the treatments. These differences could be clearly shown by a shift within the community structure and corresponding beta-diversity indices. Moreover, B. subtilis Co1-6 and P. polymyxa Mc5Re-14 showed an enhancement of the bioactive secondary metabolite apigenin-7-O-glucoside. This indicates a possible new function of bacterial inoculants: to interact with the plant microbiome as well as with the plant metabolome.

  5. The Influence of Land Use Intensity on the Plant-Associated Microbiome of Dactylis glomerata L.

    Directory of Open Access Journals (Sweden)

    Jennifer Estendorfer

    2017-06-01

    Full Text Available In this study, we investigated the impact of different land use intensities (LUI on the root-associated microbiome of Dactylis glomerata (orchardgrass. For this purpose, eight sampling sites with different land use intensity levels but comparable soil properties were selected in the southwest of Germany. Experimental plots covered land use levels from natural grassland up to intensively managed meadows. We used 16S rRNA gene based barcoding to assess the plant-associated community structure in the endosphere, rhizosphere and bulk soil of D. glomerata. Samples were taken at the reproductive stage of the plant in early summer. Our data indicated that roots harbor a distinct bacterial community, which clearly differed from the microbiome of the rhizosphere and bulk soil. Our results revealed Pseudomonadaceae, Enterobacteriaceae and Comamonadaceae as the most abundant endophytes independently of land use intensity. Rhizosphere and bulk soil were dominated also by Proteobacteria, but the most abundant families differed from those obtained from root samples. In the soil, the effect of land use intensity was more pronounced compared to root endophytes leading to a clearly distinct pattern of bacterial communities under different LUI from rhizosphere and bulk soil vs. endophytes. Overall, a change of community structure on the plant–soil interface was observed, as the number of shared OTUs between all three compartments investigated increased with decreasing land use intensity. Thus, our findings suggest a stronger interaction of the plant with its surrounding soil under low land use intensity. Furthermore, the amount and quality of available nitrogen was identified as a major driver for shifts in the microbiome structure in all compartments.

  6. The poultry-associated microbiome: network analysis and farm-to-fork characterizations.

    Directory of Open Access Journals (Sweden)

    Brian B Oakley

    Full Text Available Microbial communities associated with agricultural animals are important for animal health, food safety, and public health. Here we combine high-throughput sequencing (HTS, quantitative-PCR assays, and network analysis to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including Campylobacter, Clostridium, and Shigella. After the final stage of commercial poultry processing, taxonomic richness was ca. 2-4 times lower than the richness of fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples, significantly more than expected by chance. Among these were anaerobes such as Prevotella, Veillonella, Leptrotrichia, and multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were potentially metabolically active and encountered in on-farm samples. Network analysis was focused on the foodborne pathogen Campylobacter and revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. These data represent the first use of HTS to characterize the poultry microbiome across a series of farm-to-fork samples and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities.

  7. The microbiome of the lung and its extracellular vesicles in nonsmokers, healthy smokers and COPD patients

    Science.gov (United States)

    Kim, Hyun Jung; Kim, You-Sun; Kim, Kang-Hyun; Choi, Jun-Pyo; Kim, Yoon-Keun; Yun, Sunmi; Sharma, Lokesh; Dela Cruz, Charles S; Lee, Jae Seung; Oh, Yeon-Mok; Lee, Sang-Do; Lee, Sei Won

    2017-01-01

    Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disease, and bacterial infection plays a role in its pathogenesis. Bacteria secrete nanometer-sized extracellular vesicles (EVs), which may induce more immune dysfunction and inflammation than the bacteria themselves. We hypothesized that the microbiome of lung EVs might have distinct characteristics depending on the presence of COPD and smoking status. We analyzed and compared the microbiomes of 13 nonsmokers with normal spirometry, 13 smokers with normal spirometry (healthy smokers) and 13 patients with COPD by using 16S ribosomal RNA gene sequencing of surgical lung tissue and lung EVs. Subjects were matched for age and sex in all groups and for smoking levels in the COPD and healthy smoker groups. Each group included 12 men and 1 woman with the same mean age of 65.5 years. In all groups, EVs consistently showed more operational taxonomic units (OTUs) than lung tissue. In the healthy smoker and COPD groups, EVs had a higher Shannon index and a lower Simpson index than lung tissue and this trend was more prominent in the COPD group. Principal component analysis (PCA) showed clusters based on sample type rather than participants' clinical characteristics. Stenotrophomonas, Propionibacterium and Alicyclobacillus were the most commonly found genera. Firmicutes were highly present in the EVs of the COPD group compared with other samples or groups. Our analysis of the lung microbiome revealed that the bacterial communities present in the EVs and in the COPD group possessed distinct characteristics with differences in the OTUs, diversity indexes and PCA clustering. PMID:28408748

  8. Advancements toward a Systems Level Understanding of the Human Oral Microbiome

    Directory of Open Access Journals (Sweden)

    Jeffrey Scott Mclean

    2014-07-01

    Full Text Available Oral microbes represent one of the most well studied microbial communities owing to the fact that they are a fundamental part of human development influencing health and disease, an easily accessible human microbiome, a highly structured and remarkably resilient biofilm as well as a model of bacteria-bacteria and bacteria-host interactions. In the last eighty years since oral plaque was first characterized for its functionally stable physiological properties such as the highly repeatable rapid pH decrease upon carbohydrate addition and subsequent recovery phase, the fundamental approaches to study the oral microbiome have cycled back and forth between community level investigations and characterizing individual model isolates. Since that time, many individual species have been well characterized and the development of the early plaque community, which involves many cell–cell binding interactions, has been carefully described. With high throughput sequencing enabling the enormous diversity of the oral cavity to be realized, a number of new challenges to progress were revealed. The large number of uncultivated oral species, the high interpersonal variability of taxonomic carriage and the possibility of multiple pathways to dysbiosis pose as major hurdles to obtain a systems level understanding from the community to the gene level. It is now possible however to start connecting the insights gained from single species with community wide approaches. This review will discuss some of the recent insights into the oral microbiome at a fundamental level, existing knowledge gaps, as well as challenges that have surfaced and the approaches to address them.

  9. Oral Microbiome of Deep and Shallow Dental Pockets In Chronic Periodontitis

    Science.gov (United States)

    Ge, Xiuchun; Rodriguez, Rafael; Trinh, My; Gunsolley, John; Xu, Ping

    2013-01-01

    We examined the subgingival bacterial biodiversity in untreated chronic periodontitis patients by sequencing 16S rRNA genes. The primary purpose of the study was to compare the oral microbiome in deep (diseased) and shallow (healthy) sites. A secondary purpose was to evaluate the influences of smoking, race and dental caries on this relationship. A total of 88 subjects from two clinics were recruited. Paired subgingival plaque samples were taken from each subject, one from a probing site depth >5 mm (deep site) and the other from a probing site depth ≤3mm (shallow site). A universal primer set was designed to amplify the V4–V6 region for oral microbial 16S rRNA sequences. Differences in genera and species attributable to deep and shallow sites were determined by statistical analysis using a two-part model and false discovery rate. Fifty-one of 170 genera and 200 of 746 species were found significantly different in abundances between shallow and deep sites. Besides previously identified periodontal disease-associated bacterial species, additional species were found markedly changed in diseased sites. Cluster analysis revealed that the microbiome difference between deep and shallow sites was influenced by patient-level effects such as clinic location, race and smoking. The differences between clinic locations may be influenced by racial distribution, in that all of the African Americans subjects were seen at the same clinic. Our results suggested that there were influences from the microbiome for caries and periodontal disease and these influences are independent. PMID:23762384

  10. Boldness predicts an individual's position along an exploration-exploitation foraging trade-off.

    Science.gov (United States)

    Patrick, Samantha C; Pinaud, David; Weimerskirch, Henri

    2017-09-01

    -off itself. These results demonstrate a clear trade-off between information gathering and exploitation of prey patches, and reveals for the first time that boldness may drive these differences. This provides a mechanism through which widely reported links between personality and foraging may emerge. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

  11. Forage Quality Determined by Botanic Species’ Contribution on Permanent Pastures

    Directory of Open Access Journals (Sweden)

    Neculai Dragomir

    2011-10-01

    Full Text Available The chemical composition of the forage obtained from permanent pastures is determined, in its turn, by the floristic structure consisted of species belonging to various botanic families. Each botanic species presents a specific chemical content and a certain contribution to the balancing of forage’s nutritional value. The chemical analyses performed, at species level, revealed the importance of the “diverse” species, which, with their content in mineral elements, may influence animals’ capacity of production and reproduction. Some of the species, considered to be weeds within the permanent pastures’ floristic composition, presented high crude protein content values: Achillea millefolium with 24.22%, Taraxacum officinale 24.06%, Urtica dioica with 32.46%, Plantago major with 17.04%, etc.

  12. Visual perception and social foraging in birds.

    Science.gov (United States)

    Fernández-Juricic, Esteban; Erichsen, Jonathan T; Kacelnik, Alex

    2004-01-01

    Birds gather information about their environment mainly through vision by scanning their surroundings. Many prevalent models of social foraging assume that foraging and scanning are mutually exclusive. Although this assumption is valid for birds with narrow visual fields, these models have also been applied to species with wide fields. In fact, available models do not make precise predictions for birds with large visual fields, in which the head-up, head-down dichotomy is not accurate and, moreover, do not consider the effects of detection distance and limited attention. Studies of how different types of visual information are acquired as a function of body posture and of how information flows within flocks offer new insights into the costs and benefits of living in groups.

  13. Role of the Lung Microbiome in the Pathogenesis of Chronic Obstructive Pulmonary Disease.

    Science.gov (United States)

    Wang, Lei; Hao, Ke; Yang, Ting; Wang, Chen

    2017-09-05

    The development of culture-independent techniques for microbiological analysis shows that bronchial tree is not sterile in either healthy or chronic obstructive pulmonary disease (COPD) individuals. With the advance of sequencing technologies, lung microbiome has become a new frontier for pulmonary disease research, and such advance has led to better understanding of the lung microbiome in COPD. This review aimed to summarize the recent advances in lung microbiome, its relationships with COPD, and the possible mechanisms that microbiome contributed to COPD pathogenesis. Literature search was conducted using PubMed to collect all available studies concerning lung microbiome in COPD. The search terms were "microbiome" and "chronic obstructive pulmonary disease", or "microbiome" and "lung/pulmonary". The papers in English about lung microbiome or lung microbiome in COPD were selected, and the type of articles was not limited. The lung is a complex microbial ecosystem; the microbiome in lung is a collection of viable and nonviable microbiota (bacteria, viruses, and fungi) residing in the bronchial tree and parenchymal tissues, which is important for health. The following types of respiratory samples are often used to detect the lung microbiome: sputum, bronchial aspirate, bronchoalveolar lavage, and bronchial mucosa. Disordered bacterial microbiome is participated in pathogenesis of COPD; there are also dynamic changes in microbiota during COPD exacerbations. Lung microbiome may contribute to the pathogenesis of COPD by manipulating inflammatory and/or immune process. Normal lung microbiome could be useful for prophylactic or therapeutic management in COPD, and the changes of lung microbiome could also serve as biomarkers for the evaluation of COPD.

  14. The human gut microbiome, a taxonomic conundrum.

    Science.gov (United States)

    Sankar, Senthil Alias; Lagier, Jean-Christophe; Pontarotti, Pierre; Raoult, Didier; Fournier, Pierre-Edouard

    2015-06-01

    From culture to metagenomics, within only 130 years, our knowledge of the human microbiome has considerably improved. With >1000 microbial species identified to date, the gastro-intestinal microbiota is the most complex of human biotas. It is composed of a majority of Bacteroidetes and Firmicutes and, although exhibiting great inter-individual variations according to age, geographic origin, disease or antibiotic uptake, it is stable over time. Metagenomic studies have suggested associations between specific gut microbiota compositions and a variety of diseases, including irritable bowel syndrome, Crohn's disease, colon cancer, type 2 diabetes and obesity. However, these data remain method-dependent, as no consensus strategy has been defined to decipher the complexity of the gut microbiota. High-throughput culture-independent techniques have highlighted the limitations of culture by showing the importance of uncultured species, whereas modern culture methods have demonstrated that metagenomics underestimates the microbial diversity by ignoring minor populations. In this review, we highlight the progress and challenges that pave the way to a complete understanding of the human gastrointestinal microbiota and its influence on human health. Copyright © 2015 Elsevier GmbH. All rights reserved.

  15. Utilization of 15N in the sequence of mineral fertilizer - forage - animal - slurry - forage

    International Nuclear Information System (INIS)

    Peschke, H.

    1981-01-01

    After systematic application of 15 N-ammonium nitrate, the change of the dinuclidic composition and 15 N quantity was studied by isotope analysis of several open systems in the sequence mineral fertilizer - (soil) - forage - (animal) - slurry - (soil) - forage. The relative 15 N isotope frequency of 50 atom% in the mineral fertilizer declined to 12.2 to 21.4 atom% in the forage (beet, oats, hay) and went down to 3.15 atom% in the slurry of a dairy cow fed on this forage. Silage maize manured with the slurry of the dairy cow only showed 1.98 atom %, green oats grown after the silage maize on the same area was found to have 0.45 atom%. The 15 N quantity of 104.5 g N in the fertilizer gradually decreased to 41.6 g N in the forage, 30.5 g N in the slurry and 22.6 g N in the silage maize. The causes discussed are 15 N isotope dilution as qualitative factor and productive and unproductive N losses as quantitative factors. (author)

  16. Hybrid value foraging: How the value of targets shapes human foraging behavior.

    Science.gov (United States)

    Wolfe, Jeremy M; Cain, Matthew S; Alaoui-Soce, Abla

    2018-04-01

    In hybrid foraging, observers search visual displays for multiple instances of multiple target types. In previous hybrid foraging experiments, although there were multiple types of target, all instances of all targets had the same value. Under such conditions, behavior was well described by the marginal value theorem (MVT). Foragers left the current "patch" for the next patch when the instantaneous rate of collection dropped below their average rate of collection. An observer's specific target selections were shaped by previous target selections. Observers were biased toward picking another instance of the same target. In the present work, observers forage for instances of four target types whose value and prevalence can vary. If value is kept constant and prevalence manipulated, participants consistently show a preference for the most common targets. Patch-leaving behavior follows MVT. When value is manipulated, observers favor more valuable targets, though individual foraging strategies become more diverse, with some observers favoring the most valuable target types very strongly, sometimes moving to the next patch without collecting any of the less valuable targets.

  17. Utilization of /sup 15/N in the sequence of mineral fertilizer - forage - animal - slurry - forage

    Energy Technology Data Exchange (ETDEWEB)

    Peschke, H [Humboldt-Universitaet, Berlin (German Democratic Republic). Sektion Pflanzenproduktion

    1981-12-01

    After systematic application of /sup 15/N-ammonium nitrate, the change of the dinuclidic composition and /sup 15/N quantity was studied by isotope analysis of several open systems in the sequence mineral fertilizer - (soil) - forage - (animal) - slurry - (soil) - forage. The relative /sup 15/N isotope frequency of 50 atom% in the mineral fertilizer declined to 12.2 to 21.4 atom% in the forage (beet, oats, hay) and went down to 3.15 atom% in the slurry of a dairy cow fed on this forage. Silage maize manured with the slurry of the dairy cow only showed 1.98 atom %, green oats grown after the silage maize on the same area was found to have 0.45 atom%. The /sup 15/N quantity of 104.5 g N in the fertilizer gradually decreased to 41.6 g N in the forage, 30.5 g N in the slurry and 22.6 g N in the silage maize. The causes discussed are /sup 15/N isotope dilution as qualitative factor and productive and unproductive N losses as quantitative factors.

  18. Protein Binding Capacity of Different Forages Tannin

    Science.gov (United States)

    Yusiati, L. M.; Kurniawati, A.; Hanim, C.; Anas, M. A.

    2018-02-01

    Eight forages of tannin sources(Leucaena leucocephala, Arachis hypogaea, Mimosa pudica, Morus alba L, Swietenia mahagoni, Manihot esculenta, Gliricidia sepium, and Bauhinia purpurea)were evaluated their tannin content and protein binding capacity. The protein binding capacity of tannin were determined using precipitation of bovine serum albumin (BSA). Swietenia mahagonihas higest total tannin level and condensed tannin (CT) compared with other forages (P<0.01). The Leucaena leucocephala has highest hydrolysable tannin (HT) level (P<0.01). The total and condensed tannin content of Swietenia mahagoni were 11.928±0.04 mg/100 mg and 9.241±0.02mg/100mg dry matter (DM) of leaves. The hydrolysable tannin content of Leucaena leucocephala was 5.338±0.03 mg/100 mg DM of leaves. Binding capacity was highest in Swietenia mahagoni and Leucaena leucocephala compared to the other forages (P<0.01). The optimum binding of BSA to tannin in Leucaena leucocephala and Swietenia mahagoniwere1.181±0.44 and 1.217±0.60mg/mg dry matter of leaves. The present study reports that Swietenia mahagoni has highest of tannin content and Leucaena leucocephala and Swietenia mahagoni capacity of protein binding.

  19. Mercury in San Francisco Bay forage fish

    Energy Technology Data Exchange (ETDEWEB)

    Greenfield, Ben K., E-mail: ben@sfei.or [San Francisco Estuary Institute, 7770 Pardee Lane, Oakland, CA 94621 (United States); Jahn, Andrew, E-mail: andyjahn@mac.co [1000 Riverside Drive, Ukiah, CA 95482 (United States)

    2010-08-15

    In the San Francisco Estuary, management actions including tidal marsh restoration could change fish mercury (Hg) concentrations. From 2005 to 2007, small forage fish were collected and analyzed to identify spatial and interannual variation in biotic methylmercury (MeHg) exposure. The average whole body total Hg concentration was 0.052 {mu}g g{sup -1} (wet-weight) for 457 composite samples representing 13 fish species. MeHg constituted 94% of total Hg. At a given length, Hg concentrations were higher in nearshore mudflat and wetland species (Clevelandia ios, Menidia audens, and Ilypnus gilberti), compared to species that move offshore (e.g., Atherinops affinis and Lepidogobius lepidus). Gut content analysis indicated similar diets between Atherinops affinis and Menidia audens, when sampled at the same locations. Hg concentrations were higher in sites closest to the Guadalupe River, which drains a watershed impacted by historic Hg mining. Results demonstrate that despite differences among years and fish species, nearshore forage fish exhibit consistent Hg spatial gradients. - Total mercury in estuarine forage fish varies with species, habitat, and proximity to a historic mercury mine.

  20. Nutritional characteristics of forages from Niger

    Directory of Open Access Journals (Sweden)

    F. Infascelli

    2010-04-01

    Full Text Available In the production systems of the semi-arid areas low quality forages are commonly used as the basal diet (Wilkins, 2000 and, as a consequence, the nutritional status of ruminants depends mainly on the ability of rumen fermentation to yield nutrients such as the short chain fatty acids and microbial biomass (Preston and Leng, 1987. The forages browsed by the livestock can be classified into two main groups: ephemeral annual plants, which germinate and remain green for only a few weeks after rain, perennial shrubs and tree fodders. Despite their potential as feeds, little research has determined their nutritive value. In vivo evaluation is the best estimation method of feed’s nutritional value, however it is very laborious and difficult to standardize with browsing animals. O the contrary, in vitro methods are less expensive, less time consuming and allow a better control of experimental conditions than in vivo experiments. The in vitro gas production technique (IVGPT appears to be the most suitable method for use in developing countries where resources may be limited (Makkar, 2004. Increased interest in use of non-conventional feed resources has led to an increase in use of this technique, since IVGPT can provide useful data on digestion kinetics of both the soluble and insoluble fractions of feedstuffs. The aim of the present research was to evaluate twelve forages from the arid zone of Niger using the IVGPT.

  1. Mercury in San Francisco Bay forage fish

    International Nuclear Information System (INIS)

    Greenfield, Ben K.; Jahn, Andrew

    2010-01-01

    In the San Francisco Estuary, management actions including tidal marsh restoration could change fish mercury (Hg) concentrations. From 2005 to 2007, small forage fish were collected and analyzed to identify spatial and interannual variation in biotic methylmercury (MeHg) exposure. The average whole body total Hg concentration was 0.052 μg g -1 (wet-weight) for 457 composite samples representing 13 fish species. MeHg constituted 94% of total Hg. At a given length, Hg concentrations were higher in nearshore mudflat and wetland species (Clevelandia ios, Menidia audens, and Ilypnus gilberti), compared to species that move offshore (e.g., Atherinops affinis and Lepidogobius lepidus). Gut content analysis indicated similar diets between Atherinops affinis and Menidia audens, when sampled at the same locations. Hg concentrations were higher in sites closest to the Guadalupe River, which drains a watershed impacted by historic Hg mining. Results demonstrate that despite differences among years and fish species, nearshore forage fish exhibit consistent Hg spatial gradients. - Total mercury in estuarine forage fish varies with species, habitat, and proximity to a historic mercury mine.

  2. The Effects of Forage Policy on Feed Costs in Korea

    Directory of Open Access Journals (Sweden)

    Jae Bong Chang

    2018-05-01

    Full Text Available Feeding operations are substantial on livestock farms, besides being potentially expensive. Feeding efficiency has been considered a major influence on profits in the livestock industry. Indeed, feed costs are shown to be the largest single item of production cost in Korea. To promote production and use of domestic forage, the Korean government has enforced the forage base expansion program that strengthens the competitiveness of the livestock industry by reducing the production cost. The forage base expansion program includes three main policies: subsidized forage production, support for processing and distribution, and expanding land for forage production. This paper investigates the influence of the government’s policies often conjectured to have pronounced effects on forage production. To evaluate the forage policies, this paper uses a path-analysis approach linking government spending on forage base expansion programs and feed costs. Results indicate that the Korean government’s spending on supporting domestic forage production results in a decrease in the ratio of forage expenses to total feed cost.

  3. Diversity, structure and convergent evolution of the global sponge microbiome

    Science.gov (United States)

    Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel; Björk, Johannes R.; Easson, Cole; Astudillo-García, Carmen; Olson, Julie B.; Erwin, Patrick M.; López-Legentil, Susanna; Luter, Heidi; Chaves-Fonnegra, Andia; Costa, Rodrigo; Schupp, Peter J.; Steindler, Laura; Erpenbeck, Dirk; Gilbert, Jack; Knight, Rob; Ackermann, Gail; Victor Lopez, Jose; Taylor, Michael W.; Thacker, Robert W.; Montoya, Jose M.; Hentschel, Ute; Webster, Nicole S.

    2016-01-01

    Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host–microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions. PMID:27306690

  4. A hundred-year-old insight into the gut microbiome!

    Science.gov (United States)

    Aziz, Ramy Karam

    2009-12-07

    As the National Institutes of Health-funded Human Microbiome Project enters its second phase, and as a major part of this project focuses on the human gut microbiome and its effects on human health, it might help us to travel a century back in time and examine how microbiologists dealt with microbiome-related challenges similar to those of the 21st century using the tools of their time. An article by Arthur I. Kendall, published in The Journal of Biological Chemistry in November 1909 (Some observations on the study of the intestinal bacteria J Biol Chem 1909, 6:499-507), offers a visionary insight into many of today's hot research questions.

  5. Microbiome and mental health in the modern environment.

    Science.gov (United States)

    Deans, Emily

    2016-06-27

    A revolution in the understanding of the pathophysiology of mental illness combined with new knowledge about host/microbiome interactions and psychoneuroimmunology has opened an entirely new field of study, the "psychobiotics". The modern microbiome is quite changed compared to our ancestral one due to diet, antibiotic exposure, and other environmental factors, and these differences may well impact our brain health. The sheer complexity and scope of how diet, probiotics, prebiotics, and intertwined environmental variables could influence mental health are profound obstacles to an organized and useful study of the microbiome and psychiatric disease. However, the potential for positive anti-inflammatory effects and symptom amelioration with perhaps few side effects makes the goal of clarifying the role of the microbiota in mental health a vital one.

  6. Understanding the holobiont: the interdependence of plants and their microbiome.

    Science.gov (United States)

    Sánchez-Cañizares, Carmen; Jorrín, Beatriz; Poole, Philip S; Tkacz, Andrzej

    2017-08-01

    The holobiont is composed by the plant and its microbiome. In a similar way to ecological systems of higher organisms, the holobiont shows interdependent and complex dynamics [1,2]. While plants originate from seeds, the microbiome has a multitude of sources. The assemblage of these communities depends on the interaction between the emerging seedling and its surrounding environment, with soil being the main source. These microbial communities are controlled by the plant through different strategies, such as the specific profile of root exudates and its immune system. Despite this control, the microbiome is still able to adapt and thrive. The molecular knowledge behind these interactions and microbial '-omic' technologies are developing to the point of enabling holobiont engineering. For a long time microorganisms were in the background of plant biology but new multidisciplinary approaches have led to an appreciation of the importance of the holobiont, where plants and microbes are interdependent. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

  7. Regulation of host metabolism and immunity by the gut microbiome

    DEFF Research Database (Denmark)

    Laursen, Janne Marie

    During recent years, central roles of the gut microbiome in metabolic and immunological diseases have been uncovered, and multiple studies have shown that bacterial-derived components shape host physiology and immune responses via direct cellular interactions. The intestinal immune system...... developed a computational framework for identifying bacteria that produce specific endotoxin variants with opposing immunological effects in metagenomic fecal samples. This framework was used to identify the endotoxin variant distribution amongst bacteria in the gut microbiome of Danes and Chinese...... with obesity and type 2 diabetes. We show for the first time that species producing pro-inflammatory endotoxin variants are vastly underrepresented in the gut microbiome compared to species producing non-inflammatory endotoxin and we identify country-specific gram-negative bacterial modules associated...

  8. Clinical implications of the microbiome in urinary tract diseases.

    Science.gov (United States)

    Hiergeist, Andreas; Gessner, André

    2017-03-01

    The purpose of this review is to outline and evaluate the most recent literature on the role of the microbiome in urinary tract diseases. High throughput molecular DNA sequencing of bacterial 16S rRNA genes enabled the analysis of complex microbial communities inhabiting the human urinary tract. Several recent studies have identified bacterial taxa of the urinary microbiome to impact urinary tract diseases including interstitial cystitis, urgency urinary incontinence or calcium oxalate stone formation. Furthermore, treatment of urinary tract infections by antibiotics globally impacts community profiles of the intestinal microbiota and might indirectly influence human health. Alternative treatment options like application of probiotics for the treatment of urinary tract infections are currently under investigation. The urinary microbiome and its relationship to urinary tract diseases is currently under comprehensive investigation. Further studies are needed to shed light on the role of commensal microbiota for urinary tract infections.

  9. A hundred-year-old insight into the gut microbiome!

    Directory of Open Access Journals (Sweden)

    Aziz Ramy

    2009-12-01

    Full Text Available Abstract As the National Institutes of Health-funded Human Microbiome Project enters its second phase, and as a major part of this project focuses on the human gut microbiome and its effects on human health, it might help us to travel a century back in time and examine how microbiologists dealt with microbiome-related challenges similar to those of the 21st century using the tools of their time. An article by Arthur I. Kendall, published in The Journal of Biological Chemistry in November 1909 (Some observations on the study of the intestinal bacteria J Biol Chem 1909, 6:499-507, offers a visionary insight into many of today's hot research questions.

  10. Microbiome-wide association studies link dynamic microbial consortia to disease

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, Jack A.; Quinn, Robert A.; Debelius, Justine; Xu, Zhenjiang Z.; Morton, James; Garg, Neha; Jansson, Janet K.; Dorrestein, Pieter C.; Knight, Rob

    2016-07-06

    Rapid advances in DNA sequencing, metabolomics, proteomics and computation dramatically increase accessibility of microbiome studies and identify links between the microbiome and disease. Microbial time-series and multiple molecular perspectives enable Microbiome-Wide Association Studies (MWAS), analogous to Genome-Wide Association Studies (GWAS). Rapid research advances point towards actionable results, although approved clinical tests based on MWAS are still in the future. Appreciating the complexity of interactions between diet, chemistry, health and the microbiome, and determining the frequency of observations needed to capture and integrate this dynamic interface, is paramount for addressing the need for personalized and precision microbiome-based diagnostics and therapies.

  11. Early Visual Foraging in Relationship to Familial Risk for Autism and Hyperactivity/Inattention.

    Science.gov (United States)

    Gliga, Teodora; Smith, Tim J; Likely, Noreen; Charman, Tony; Johnson, Mark H

    2015-12-04

    Information foraging is atypical in both autism spectrum disorders (ASDs) and ADHD; however, while ASD is associated with restricted exploration and preference for sameness, ADHD is characterized by hyperactivity and increased novelty seeking. Here, we ask whether similar biases are present in visual foraging in younger siblings of children with a diagnosis of ASD with or without additional high levels of hyperactivity and inattention. Fifty-four low-risk controls (LR) and 50 high-risk siblings (HR) took part in an eye-tracking study at 8 and 14 months and at 3 years of age. At 8 months, siblings of children with ASD and low levels of hyperactivity/inattention (HR/ASD-HI) were more likely to return to previously visited areas in the visual scene than were LR and siblings of children with ASD and high levels of hyperactivity/inattention (HR/ASD+HI). We show that visual foraging is atypical in infants at-risk for ASD. We also reveal a paradoxical effect, in that additional family risk for ADHD core symptoms mitigates the effect of ASD risk on visual information foraging. © The Author(s) 2015.

  12. Migrations of green turtles (Chelonia mydas between nesting and foraging grounds across the Coral Sea.

    Directory of Open Access Journals (Sweden)

    Tyffen C Read

    Full Text Available Marine megafauna tend to migrate vast distances, often crossing national borders and pose a significant challenge to managers. This challenge is particularly acute in the Pacific, which contains numerous small island nations and thousands of kilometers of continental margins. The green sea turtle, Chelonia mydas, is one such megafauna that is endangered in Pacific waters due to the overexploitation of eggs and adults for human consumption. Data from long-term tagging programs in Queensland (Australia and New Caledonia were analysed to investigate the migrations by C. mydas across the Coral Sea between their nesting site and their feeding grounds. A review of data collected over the last 50 years by different projects identified multiple migrations of C. mydas to and from New Caledonia (n = 97 and indicate that turtles foraging in New Caledonia nest in the Great Barrier Reef (Australia and vice versa. Several explanations exist for turtles exhibiting this energetically costly movement pattern from breeding to distant foraging grounds (1200-2680 km away despite viable foraging habitat being available in the local vicinity. These include hatchling drift, oceanic movements and food abundance predictability. Most of the tag recoveries in New Caledonia belonged to females from the south Great Barrier Reef genetic stock. Some females (n = 2 even showed fidelity to foraging sites located 1200 km away from the nesting site located in New Caledonia. This study also reveals previously unknown migrations pathways of turtles within the Coral Sea.

  13. The microbiome of the built environment and mental health.

    Science.gov (United States)

    Hoisington, Andrew J; Brenner, Lisa A; Kinney, Kerry A; Postolache, Teodor T; Lowry, Christopher A

    2015-12-17

    The microbiome of the built environment (MoBE) is a relatively new area of study. While some knowledge has been gained regarding impacts of the MoBE on the human microbiome and disease vulnerability, there is little knowledge of the impacts of the MoBE on mental health. Depending on the specific microbial species involved, the transfer of microorganisms from the built environment to occupant's cutaneous or mucosal membranes has the potential to increase or disrupt immunoregulation and/or exaggerate or suppress inflammation. Preclinical evidence highlighting the influence of the microbiota on systemic inflammation supports the assertion that microorganisms, including those originating from the built environment, have the potential to either increase or decrease the risk of inflammation-induced psychiatric conditions and their symptom severity. With advanced understanding of both the ecology of the built environment, and its influence on the human microbiome, it may be possible to develop bioinformed strategies for management of the built environment to promote mental health. Here we present a brief summary of microbiome research in both areas and highlight two interdependencies including the following: (1) effects of the MoBE on the human microbiome and (2) potential opportunities for manipulation of the MoBE in order to improve mental health. In addition, we propose future research directions including strategies for assessment of changes in the microbiome of common areas of built environments shared by multiple human occupants, and associated cohort-level changes in the mental health of those who spend time in the buildings. Overall, our understanding of the fields of both the MoBE and influence of host-associated microorganisms on mental health are advancing at a rapid pace and, if linked, could offer considerable benefit to health and wellness.

  14. The early infant gut microbiome varies in association with a maternal high-fat diet.

    Science.gov (United States)

    Chu, Derrick M; Antony, Kathleen M; Ma, Jun; Prince, Amanda L; Showalter, Lori; Moller, Michelle; Aagaard, Kjersti M

    2016-08-09

    Emerging evidence suggests that the in utero environment is not sterile as once presumed. Work in the mouse demonstrated transmission of commensal bacteria from mother to fetus during gestation, though it is unclear what modulates this process. We have previously shown in the nonhuman primate that, independent of obesity, a maternal high-fat diet during gestation and lactation persistently shapes the juvenile gut microbiome. We therefore sought to interrogate in a population-based human longitudinal cohort whether a maternal high-fat diet similarly alters the neonatal and infant gut microbiome in early life. A representative cohort was prospectively enrolled either in the early third trimester or intrapartum (n = 163), with a subset consented to longitudinal sampling through the postpartum interval (n = 81). Multiple body site samples, including stool and meconium, were collected from neonates at delivery and by 6 weeks of age. A rapid dietary questionnaire was administered to estimate intake of fat, added sugars, and fiber over the past month (National Health and Examination Survey). DNA was extracted from each infant meconium/stool sample (MoBio) and subjected to 16S rRNA gene sequencing and analysis. On average, the maternal dietary intake of fat ranged from 14.0 to 55.2 %, with an average intake of 33.1 % (σ = 6.1 %). Mothers whose diets significantly differed from the mean (±1 standard deviation) were separated into two distinct groups, a control group (n = 13, μ = 24.4 %) and a high-fat group (n = 13, μ = 43.1 %). Principal coordinate analysis revealed that the microbiome of the neonatal stool at birth (meconium) clustered differently by virtue of maternal gestational diet (PERMANOVA p = 0.001). LEfSe feature selection identified several taxa that discriminated the groups, with a notable relative depletion of Bacteroides in the neonates exposed to a maternal high-fat gestational diet (Student's t-test, p < 0

  15. Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality.

    Science.gov (United States)

    Marasco, Ramona; Rolli, Eleonora; Fusi, Marco; Michoud, Grégoire; Daffonchio, Daniele

    2018-01-03

    The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The majority of phyllosphere endophytes originate from the soil and migrate up to the aerial compartments through the root endosphere. Thus, the soil and root endosphere partially define the aerial endosphere in the leaves and berries, contributing to the terroir of the fruit. However, V. vinifera cultivars are invariably grafted onto the rootstocks of other Vitis species and hybrids. It has been hypothesized that the plant species determines the microbiome of the root endosphere and, as a consequence, the aerial endosphere. In this work, we test the first part of this hypothesis. We investigate whether different rootstocks influence the bacteria selected from the surrounding soil, affecting the bacterial diversity and potential functionality of the rhizosphere and root endosphere. Bacterial microbiomes from both the root tissues and the rhizosphere of Barbera cultivars, both ungrafted and grafted on four different rootstocks, cultivated in the same soil from the same vineyard, were characterized by 16S rRNA high-throughput sequencing. To assess the influence of the root genotype on the bacterial communities' recruitment in the root system, (i) the phylogenetic diversity coupled with the predicted functional profiles and (ii) the co-occurrence bacterial networks were determined. Cultivation-dependent approaches were used to reveal the plant-growth promoting (PGP) potential associated with the grafted and ungrafted root systems. Richness, diversity and bacterial community networking in the root compartments were significantly influenced by the rootstocks. Complementary to a shared bacterial microbiome, different subsets of soil bacteria, including those endowed with PGP traits, were selected by the root system compartments of different rootstocks. The interaction

  16. Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality

    KAUST Repository

    Marasco, Ramona; Rolli, Eleonora; Fusi, Marco; Michoud, Gregoire; Daffonchio, Daniele

    2018-01-01

    The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The majority of phyllosphere endophytes originate from the soil and migrate up to the aerial compartments through the root endosphere. Thus, the soil and root endosphere partially define the aerial endosphere in the leaves and berries, contributing to the terroir of the fruit. However, V. vinifera cultivars are invariably grafted onto the rootstocks of other Vitis species and hybrids. It has been hypothesized that the plant species determines the microbiome of the root endosphere and, as a consequence, the aerial endosphere. In this work, we test the first part of this hypothesis. We investigate whether different rootstocks influence the bacteria selected from the surrounding soil, affecting the bacterial diversity and potential functionality of the rhizosphere and root endosphere.Bacterial microbiomes from both the root tissues and the rhizosphere of Barbera cultivars, both ungrafted and grafted on four different rootstocks, cultivated in the same soil from the same vineyard, were characterized by 16S rRNA high-throughput sequencing. To assess the influence of the root genotype on the bacterial communities' recruitment in the root system, (i) the phylogenetic diversity coupled with the predicted functional profiles and (ii) the co-occurrence bacterial networks were determined. Cultivation-dependent approaches were used to reveal the plant-growth promoting (PGP) potential associated with the grafted and ungrafted root systems.Richness, diversity and bacterial community networking in the root compartments were significantly influenced by the rootstocks. Complementary to a shared bacterial microbiome, different subsets of soil bacteria, including those endowed with PGP traits, were selected by the root system compartments of different rootstocks. The interaction

  17. Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality

    KAUST Repository

    Marasco, Ramona

    2018-01-03

    The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The majority of phyllosphere endophytes originate from the soil and migrate up to the aerial compartments through the root endosphere. Thus, the soil and root endosphere partially define the aerial endosphere in the leaves and berries, contributing to the terroir of the fruit. However, V. vinifera cultivars are invariably grafted onto the rootstocks of other Vitis species and hybrids. It has been hypothesized that the plant species determines the microbiome of the root endosphere and, as a consequence, the aerial endosphere. In this work, we test the first part of this hypothesis. We investigate whether different rootstocks influence the bacteria selected from the surrounding soil, affecting the bacterial diversity and potential functionality of the rhizosphere and root endosphere.Bacterial microbiomes from both the root tissues and the rhizosphere of Barbera cultivars, both ungrafted and grafted on four different rootstocks, cultivated in the same soil from the same vineyard, were characterized by 16S rRNA high-throughput sequencing. To assess the influence of the root genotype on the bacterial communities\\' recruitment in the root system, (i) the phylogenetic diversity coupled with the predicted functional profiles and (ii) the co-occurrence bacterial networks were determined. Cultivation-dependent approaches were used to reveal the plant-growth promoting (PGP) potential associated with the grafted and ungrafted root systems.Richness, diversity and bacterial community networking in the root compartments were significantly influenced by the rootstocks. Complementary to a shared bacterial microbiome, different subsets of soil bacteria, including those endowed with PGP traits, were selected by the root system compartments of different rootstocks. The interaction

  18. The human gut microbiome of Latin America populations: a landscape to be discovered.

    Science.gov (United States)

    Magne, Fabien; O'Ryan, Miguel L; Vidal, Roberto; Farfan, Mauricio

    2016-10-01

    The gut microbiome is critical for human health, and its alteration is associated with intestinal, autoimmune and metabolic diseases. Numerous studies have focused on prevention or treatment of dysbiotic microbiome to reduce the risk or effect of these diseases. A key issue is to define the microbiome associated with the state of good health. The purpose of this review is to describe factors influencing the gut microbiome with special emphasis on contributions from Latin America. In addition, we will highlight opportunities for future studies on gut microbiome in Latin America. A relevant factor influencing gut microbiome composition is geographical location associated with specific genetic, dietary and lifestyle factors. Geographical specificities suggest that a universal 'healthy microbiome' is unlikely. Several research programs, mostly from Europe and North America, are extensively sequencing gut microbiome of healthy people, whereas data from Latin America remain scarce yet slowly increasing. Few studies have shown difference in the composition of gut microbiome between their local populations with that of other industrialized countries (North American populations). Latin America is composed of countries with a myriad of lifestyles, traditions, genetic backgrounds and socioeconomic conditions, which may determine differences in gut microbiome of individuals from different countries. This represents an opportunity to better understand the relationship between these factors and gut microbiome.

  19. Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics.

    Science.gov (United States)

    ElRakaiby, Marwa; Dutilh, Bas E; Rizkallah, Mariam R; Boleij, Annemarie; Cole, Jason N; Aziz, Ramy K

    2014-07-01

    The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome influence human health, immunity, and different disease states. In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics. We propose a microbiome cloud model, reflecting the temporal and spatial uncertainty of defining an individual's microbiome composition, with examples of how intra-individual variations (such as age and mode of delivery) shape the microbiome structure. Additionally, we discuss how this microbiome cloud concept explains the difficulty to define a core human microbiome and to classify individuals according to their biome types. Detailed examples are presented on microbiome changes related to colorectal cancer, antibiotic administration, and pharmacomicrobiomics, or drug-microbiome interactions, highlighting how an improved understanding of the human microbiome, and alterations thereof, may lead to the development of novel therapeutic agents, the modification of antibiotic policies and implementation, and improved health outcomes. Finally, the prospects of a collaborative computational microbiome research initiative in Africa are discussed.

  20. Effect of postnatal low-dose exposure to environmental chemicals on the gut microbiome in a rodent model.

    Science.gov (United States)

    Hu, Jianzhong; Raikhel, Vincent; Gopalakrishnan, Kalpana; Fernandez-Hernandez, Heriberto; Lambertini, Luca; Manservisi, Fabiana; Falcioni, Laura; Bua, Luciano; Belpoggi, Fiorella; L Teitelbaum, Susan; Chen, Jia

    2016-06-14

    This proof-of-principle study examines whether postnatal, low-dose exposure to environmental chemicals modifies the composition of gut microbiome. Three chemicals that are widely used in personal care products-diethyl phthalate (DEP), methylparaben (MPB), triclosan (TCS)-and their mixture (MIX) were administered at doses comparable to human exposure to Sprague-Dawley rats from birth through adulthood. Fecal samples were collected at two time points: postnatal day (PND) 62 (adolescence) and PND 181 (adulthood). The gut microbiome was profiled by 16S ribosomal RNA gene sequencing, taxonomically assigned and assessed for diversity. Metagenomic profiling revealed that the low-dose chemical exposure resulted in significant changes in the overall bacterial composition, but in adolescent rats only. Specifically, the individual taxon relative abundance for Bacteroidetes (Prevotella) was increased while the relative abundance of Firmicutes (Bacilli) was reduced in all treated rats compared to controls. Increased abundance was observed for Elusimicrobia in DEP and MPB groups, Betaproteobacteria in MPB and MIX groups, and Deltaproteobacteria in TCS group. Surprisingly, these differences diminished by adulthood (PND 181) despite continuous exposure, suggesting that exposure to the environmental chemicals produced a more profound effect on the gut microbiome in adolescents. We also observed a small but consistent reduction in the bodyweight of exposed rats in adolescence, especially with DEP and MPB treatment (p gut microbiota in adolescent rats; whether these changes lead to downstream health effects requires further investigation.

  1. Assessment of Chicken Carcass Microbiome Responses During Processing in the Presence of Commercial Antimicrobials Using a Next Generation Sequencing Approach

    Science.gov (United States)

    Ae Kim, Sun; Hong Park, Si; In Lee, Sang; Owens, Casey M.; Ricke, Steven C.

    2017-01-01

    The purpose of this study was to 1) identify microbial compositional changes on chicken carcasses during processing, 2) determine the antimicrobial efficacy of peracetic acid (PAA) and Amplon (blend of sulfuric acid and sodium sulfate) at a poultry processing pilot plant scale, and 3) compare microbial communities between chicken carcass rinsates and recovered bacteria from media. Birds were collected from each processing step and rinsates were applied to estimate aerobic plate count (APC) and Campylobacter as well as Salmonella prevalence. Microbiome sequencing was utilized to identify microbial population changes over processing and antimicrobial treatments. Only the PAA treatment exhibited significant reduction of APC at the post chilling step while both Amplon and PAA yielded detectable Campylobacter reductions at all steps. Based on microbiome sequencing, Firmicutes were the predominant bacterial group at the phyla level with over 50% frequency in all steps while the relative abundance of Proteobacteria decreased as processing progressed. Overall microbiota between rinsate and APC plate microbial populations revealed generally similar patterns at the phyla level but they were different at the genus level. Both antimicrobials appeared to be effective on reducing problematic bacteria and microbiome can be utilized to identify optimal indicator microorganisms for enhancing product quality. PMID:28230180

  2. Does the change on gastrointestinal tract microbiome affects host?

    Directory of Open Access Journals (Sweden)

    Elisa M. Beirão

    2014-11-01

    Full Text Available During the past decade, studies on the composition of human microbiota and its relation to the host became one of the most explored subjects of the medical literature. The development of high-throughput molecular technologies allowed a deeper characterization of human microbiota and a better understanding of its relationship with health and disease. Changes in human habits including wide use of antimicrobials can result in dysregulation of host–microbiome homeostasis, with multiple consequences. The purpose of this review is to highlight the most important evidence in the literature of host–microbiome interactions and illustrate how these intriguing relations may lead to new treatment and prevention strategies.

  3. Capturing One of the Human Gut Microbiome's Most Wanted

    DEFF Research Database (Denmark)

    Jeraldo, Patricio; Hernandez, Alvaro; Nielsen, Henrik Bjørn

    2016-01-01

    The role of the microbiome in health and disease is attracting great attention, yet we still know little about some of the most prevalent microorganisms inside our bodies. Several years ago, Human Microbiome Project (HMP) researchers generated a list of "most wanted" taxa: bacteria both prevalent...... the environment, and to lack virulence genes. Thus, the evidence is consistent with a secondary degrader that occupies a host-dependent, nutrient scavenging niche within the gut; its ability to produce butyrate, which is thought to play an anti-inflammatory role, makes it intriguing for the study of diseases...

  4. Keystone taxa as drivers of microbiome structure and functioning.

    Science.gov (United States)

    Banerjee, Samiran; Schlaeppi, Klaus; van der Heijden, Marcel G A

    2018-05-22

    Microorganisms have a pivotal role in the functioning of ecosystems. Recent studies have shown that microbial communities harbour keystone taxa, which drive community composition and function irrespective of their abundance. In this Opinion article, we propose a definition of keystone taxa in microbial ecology and summarize over 200 microbial keystone taxa that have been identified in soil, plant and marine ecosystems, as well as in the human microbiome. We explore the importance of keystone taxa and keystone guilds for microbiome structure and functioning and discuss the factors that determine their distribution and activities.

  5. Association of disease severity with skin microbiome and filaggrin gene mutations in adult atopic dermatitis

    DEFF Research Database (Denmark)

    Clausen, Maja Lisa; Agner, Tove; Lilje, Berit

    2018-01-01

    IMPORTANCE Skin microbiome correlates with disease severity for lesional and nonlesional skin, indicating a global influence of atopic dermatitis (AD). A relation between skin microbiome and filaggrin gene (FLG) mutations proposes a possible association between skin microbiome and host genetics....... OBJECTIVES To assess skin and nasal microbiome diversity and composition in patients with AD and compare with healthy controls, and to investigate the microbiome in relation to disease severity and FLG mutations in patients with AD. DESIGN, SETTING, AND PARTICIPANTS An observational case-control study of 45...... analyses of the microbiome were analyzed using R statistical software (version 3.3.1, R Foundation Inc). MAIN OUTCOMES AND MEASURES Skin microbiomeswere investigated using next-generation sequencing targeting 16S ribosomal RNA. RESULTS Microbiome alpha diversity was lower in patients with AD compared...

  6. Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways

    Energy Technology Data Exchange (ETDEWEB)

    Denner, Darcy R.; Sangwan, Naseer; Becker, Julia B.; Hogarth, D. Kyle; Oldham, Justin; Castillo, Jamee; Sperling, Anne I.; Solway, Julian; Naureckas, Edward T.; Gilbert, Jack A.; White, Steven R.

    2016-05-01

    The lung has a diverse microbiome that is modest in biomass. This microbiome differs in asthmatic patients compared with control subjects, but the effects of clinical characteristics on the microbial community composition and structure are not clear. OBJECTIVES: We examined whether the composition and structure of the lower airway microbiome correlated with clinical characteristics of chronic persistent asthma, including airflow obstruction, use of corticosteroid medications, and presence of airway eosinophilia. METHODS: DNA was extracted from endobronchial brushings and bronchoalveolar lavage fluid collected from 39 asthmatic patients and 19 control subjects, along with negative control samples. 16S rRNA V4 amplicon sequencing was used to compare the relative abundance of bacterial genera with clinical characteristics. RESULTS: Differential feature selection analysis revealed significant differences in microbial diversity between brush and lavage samples from asthmatic patients and control subjects. Lactobacillus, Pseudomonas, and Rickettsia species were significantly enriched in samples from asthmatic patients, whereas Prevotella, Streptococcus, and Veillonella species were enriched in brush samples from control subjects. Generalized linear models on brush samples demonstrated oral corticosteroid use as an important factor affecting the relative abundance of the taxa that were significantly enriched in asthmatic patients. In addition, bacterial α-diversity in brush samples from asthmatic patients was correlated with FEV1 and the proportion of lavage eosinophils. CONCLUSION: The diversity and composition of the bronchial airway microbiome of asthmatic patients is distinct from that of nonasthmatic control subjects and influenced by worsening airflow obstruction and corticosteroid use. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  7. Work or sleep? : honeybee foragers opportunistically nap during the day when forage is not available

    OpenAIRE

    Klein, Barrett; Seeley, Thomas D.

    2011-01-01

    Shifts in work schedules test humans’ capacity to be flexible in the timing of both work and sleep. Honeybee, Apis mellifera, foragers also shift their work schedules, but how flexible they are in the timing of sleep as they shift the timing of work is unknown, despite the importance of colony-level plasticity in the face of a changing environment. We hypothesized that sleep schedules of foragers are not fixed and instead vary depending on the time when food is available. We trained bees to v...

  8. Migratory geese foraging on grassland:Case study in the region of Flanders (Belgium)

    OpenAIRE

    Van Gils, Bert; De Vliegher, Alex; Huysentruyt, Frank; Casaer, Jim; Devos, Koen

    2012-01-01

    Every winter nearly 100 000 migratory geese visit Northwestern Flanders (Belgium), including several protected species such as the pink-footed goose (Anser brachyrhynchus). The geese mainly forage on agricultural grassland, where they remove all the green parts and leave substantial amounts of droppings. In 2009 several farmers’ concerns about this phenomenon were thoroughly investigated. The main findings revealed that grass production on grazed parcels is reduced by 450 kg DM/ha on average ...

  9. Characterisation of the ruminal fermentation and microbiome in lambs supplemented with hydrolysable and condensed tannins.

    Science.gov (United States)

    Salami, Saheed A; Valenti, Bernardo; Bella, Marco; O'Grady, Michael N; Luciano, Giuseppe; Kerry, Joseph P; Jones, Eleanor; Priolo, Alessandro; Newbold, Charles J

    2018-05-01

    This study characterised the response of ruminal fermentation and the rumen microbiome in lambs fed commercial vegetal sources of hydrolysable tannins (HT) and condensed tannins (CT). Forty-four lambs (19.56 ± 2.06 kg) were randomly assigned to either a concentrate diet (CON, n = 8) or CON supplemented with 4% of two HT [chestnut (Castanea sativa, HT-c) and tara (Caesalpinia spinosa, HT-t)] and CT [mimosa (Acacia negra, CT-m) and gambier (Uncaria gambir, CT-g)] extracts (all, n = 9) for 75 days pre-slaughter. Tannin supplementation did not influence ruminal fermentation traits. Quantitative PCR demonstrated that tannins did not affect the absolute abundance of ruminal bacteria or fungi. However, CT-m (-12.8%) and CT-g (-11.5%) significantly reduced the abundance of methanogens, while HT-t (-20.7%) and CT-g (-20.8%) inhibited protozoal abundance. Ribosomal amplicon sequencing revealed that tannins caused changes in the phylogenetic structure of the bacterial and methanogen communities. Tannins inhibited the fibrolytic bacterium, Fibrobacter and tended to suppress the methanogen genus, Methanosphaera. Results demonstrated that both HT and CT sources could impact the ruminal microbiome when supplemented at 4% inclusion level. HT-t, CT-m and CT-g extracts displayed specific antimicrobial activity against methanogens and protozoa without compromising ruminal fermentation in a long-term feeding trial.

  10. Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria.

    Science.gov (United States)

    Sánchez-López, Ariadna S; Pintelon, Isabel; Stevens, Vincent; Imperato, Valeria; Timmermans, Jean-Pierre; González-Chávez, Carmen; Carrillo-González, Rogelio; Van Hamme, Jonathan; Vangronsveld, Jaco; Thijs, Sofie

    2018-01-19

    Metal contaminated soils are increasing worldwide. Metal-tolerant plants growing on metalliferous soils are fascinating genetic and microbial resources. Seeds can vertically transmit endophytic microorganisms that can assist next generations to cope with environmental stresses, through yet poorly understood mechanisms. The aims of this study were to identify the core seed endophyte microbiome of the pioneer metallophyte Crotalaria pumila throughout three generations, and to better understand the plant colonisation of the seed endophyte Methylobacterium sp. Cp3. Strain Cp3 was detected in C. pumila seeds across three successive generations and showed the most dominant community member. When inoculated in the soil at the time of flowering, strain Cp3 migrated from soil to seeds. Using confocal microscopy, Cp3-mCherry was demonstrated to colonise the root cortex cells and xylem vessels of the stem under metal stress. Moreover, strain Cp3 showed genetic and in planta potential to promote seed germination and seedling development. We revealed, for the first time, that the seed microbiome of a pioneer plant growing in its natural environment, and the colonisation behaviour of an important plant growth promoting systemic seed endophyte. Future characterization of seed microbiota will lead to a better understanding of their functional contribution and the potential use for seed-fortification applications.

  11. The human gut microbiome and its dysfunctions through the meta-omics prism.

    Science.gov (United States)

    Mondot, Stanislas; Lepage, Patricia

    2016-05-01

    The microorganisms inhabiting the human gut are abundant (10(14) cells) and diverse (approximately 500 species per individual). It is now acknowledged that the microbiota has coevolved with its host to achieve a symbiotic relationship, leading to physiological homeostasis. The gut microbiota ensures vital functions, such as food digestibility, maturation of the host immune system, and protection against pathogens. Over the last few decades, the gut microbiota has also been associated with numerous diseases, such as inflammatory bowel disease, irritable bowel syndrome, obesity, and metabolic diseases. In most of these pathologies, a microbial dysbiosis has been found, indicating shifts in the taxonomic composition of the gut microbiota and changes in its functionality. Our understanding of the influence of the gut microbiota on human health is still growing. Working with microorganisms residing in the gut is challenging since most of them are anaerobic and a vast majority (approximately 75%) are uncultivable to date. Recently, a wide range of new approaches (meta-omics) has been developed to bypass the uncultivability and reveal the intricate mechanisms that sustain gut microbial homeostasis. After a brief description of these approaches (metagenomics, metatranscriptomics, metaproteomics, and metabolomics), this review will discuss the importance of considering the gut microbiome as a structured ecosystem and the use of meta-omics to decipher dysfunctions of the gut microbiome in diseases. © 2016 New York Academy of Sciences.

  12. The microbiota and microbiome in aging: potential implications in health and age-related diseases.

    Science.gov (United States)

    Zapata, Heidi J; Quagliarello, Vincent J

    2015-04-01

    Advances in bacterial deoxyribonucleic acid sequencing allow for characterization of the human commensal bacterial community (microbiota) and its corresponding genome (microbiome). Surveys of healthy adults reveal that a signature composite of bacteria characterizes each unique body habitat (e.g., gut, skin, oral cavity, vagina). A myriad of clinical changes, including a basal proinflammatory state (inflamm-aging), that directly interface with the microbiota of older adults and enhance susceptibility to disease accompany aging. Studies in older adults demonstrate that the gut microbiota correlates with diet, location of residence (e.g., community dwelling, long-term care settings), and basal level of inflammation. Links exist between the microbiota and a variety of clinical problems plaguing older adults, including physical frailty, Clostridium difficile colitis, vulvovaginal atrophy, colorectal carcinoma, and atherosclerotic disease. Manipulation of the microbiota and microbiome of older adults holds promise as an innovative strategy to influence the development of comorbidities associated with aging. © 2015, Copyright the Authors Journal compilation © 2015, The American Geriatrics Society.

  13. Biochemical association of metabolic profile and microbiome in chronic pressure ulcer wounds.

    Directory of Open Access Journals (Sweden)

    Mary Cloud B Ammons

    Full Text Available Chronic, non-healing wounds contribute significantly to the suffering of patients with co-morbidities in the clinical population with mild to severely compromised immune systems. Normal wound healing proceeds through a well-described process. However, in chronic wounds this process seems to become dysregulated at the transition between resolution of inflammation and re-epithelialization. Bioburden in the form of colonizing bacteria is a major contributor to the delayed headlining in chronic wounds such as pressure ulcers. However how the microbiome influences the wound metabolic landscape is unknown. Here, we have used a Systems Biology approach to determine the biochemical associations between the taxonomic and metabolomic profiles of wounds colonized by bacteria. Pressure ulcer biopsies were harvested from primary chronic wounds and bisected into top and bottom sections prior to analysis of microbiome by pyrosequencing and analysis of metabolome using 1H nuclear magnetic resonance (NMR spectroscopy. Bacterial taxonomy revealed that wounds were colonized predominantly by three main phyla, but differed significantly at the genus level. While taxonomic profiles demonstrated significant variability between wounds, metabolic profiles shared significant similarity based on the depth of the wound biopsy. Biochemical association between taxonomy and metabolic landscape indicated significant wound-to-wound similarity in metabolite enrichment sets and metabolic pathway impacts, especially with regard to amino acid metabolism. To our knowledge, this is the first demonstration of a statistically robust correlation between bacterial colonization and metabolic landscape within the chronic wound environment.

  14. Influence of acidic pH on hydrogen and acetate production by an electrosynthetic microbiome.

    Directory of Open Access Journals (Sweden)

    Edward V LaBelle

    Full Text Available Production of hydrogen and organic compounds by an electrosynthetic microbiome using electrodes and carbon dioxide as sole electron donor and carbon source, respectively, was examined after exposure to acidic pH (∼ 5. Hydrogen production by biocathodes poised at -600 mV vs. SHE increased >100-fold and acetate production ceased at acidic pH, but ∼ 5-15 mM (catholyte volume/day acetate and >1,000 mM/day hydrogen were attained at pH ∼ 6.5 following repeated exposure to acidic pH. Cyclic voltammetry revealed a 250 mV decrease in hydrogen overpotential and a maximum current density of 12.2 mA/cm2 at -765 mV (0.065 mA/cm2 sterile control at -800 mV by the Acetobacterium-dominated community. Supplying -800 mV to the microbiome after repeated exposure to acidic pH resulted in up to 2.6 kg/m3/day hydrogen (≈ 2.6 gallons gasoline equivalent, 0.7 kg/m3/day formate, and 3.1 kg/m3/day acetate ( = 4.7 kg CO2 captured.

  15. Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria

    Directory of Open Access Journals (Sweden)

    Ariadna S. Sánchez-López

    2018-01-01

    Full Text Available Metal contaminated soils are increasing worldwide. Metal-tolerant plants growing on metalliferous soils are fascinating genetic and microbial resources. Seeds can vertically transmit endophytic microorganisms that can assist next generations to cope with environmental stresses, through yet poorly understood mechanisms. The aims of this study were to identify the core seed endophyte microbiome of the pioneer metallophyte Crotalaria pumila throughout three generations, and to better understand the plant colonisation of the seed endophyte Methylobacterium sp. Cp3. Strain Cp3 was detected in C. pumila seeds across three successive generations and showed the most dominant community member. When inoculated in the soil at the time of flowering, strain Cp3 migrated from soil to seeds. Using confocal microscopy, Cp3-mCherry was demonstrated to colonise the root cortex cells and xylem vessels of the stem under metal stress. Moreover, strain Cp3 showed genetic and in planta potential to promote seed germination and seedling development. We revealed, for the first time, that the seed microbiome of a pioneer plant growing in its natural environment, and the colonisation behaviour of an important plant growth promoting systemic seed endophyte. Future characterization of seed microbiota will lead to a better understanding of their functional con