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Sample records for earthworm gut metagenome

  1. A catalog of the mouse gut metagenome

    DEFF Research Database (Denmark)

    Xiao, Liang; Feng, Qiang; Liang, Suisha

    2015-01-01

    We established a catalog of the mouse gut metagenome comprising ∼2.6 million nonredundant genes by sequencing DNA from fecal samples of 184 mice. To secure high microbiome diversity, we used mouse strains of diverse genetic backgrounds, from different providers, kept in different housing...... laboratories and fed either a low-fat or high-fat diet. Similar to the human gut microbiome, >99% of the cataloged genes are bacterial. We identified 541 metagenomic species and defined a core set of 26 metagenomic species found in 95% of the mice. The mouse gut microbiome is functionally similar to its human...... counterpart, with 95.2% of its Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups in common. However, only 4.0% of the mouse gut microbial genes were shared (95% identity, 90% coverage) with those of the human gut microbiome. This catalog provides a useful reference for future studies....

  2. A catalog of the mouse gut metagenome.

    Science.gov (United States)

    Xiao, Liang; Feng, Qiang; Liang, Suisha; Sonne, Si Brask; Xia, Zhongkui; Qiu, Xinmin; Li, Xiaoping; Long, Hua; Zhang, Jianfeng; Zhang, Dongya; Liu, Chuan; Fang, Zhiwei; Chou, Joyce; Glanville, Jacob; Hao, Qin; Kotowska, Dorota; Colding, Camilla; Licht, Tine Rask; Wu, Donghai; Yu, Jun; Sung, Joseph Jao Yiu; Liang, Qiaoyi; Li, Junhua; Jia, Huijue; Lan, Zhou; Tremaroli, Valentina; Dworzynski, Piotr; Nielsen, H Bjørn; Bäckhed, Fredrik; Doré, Joël; Le Chatelier, Emmanuelle; Ehrlich, S Dusko; Lin, John C; Arumugam, Manimozhiyan; Wang, Jun; Madsen, Lise; Kristiansen, Karsten

    2015-10-01

    We established a catalog of the mouse gut metagenome comprising ∼2.6 million nonredundant genes by sequencing DNA from fecal samples of 184 mice. To secure high microbiome diversity, we used mouse strains of diverse genetic backgrounds, from different providers, kept in different housing laboratories and fed either a low-fat or high-fat diet. Similar to the human gut microbiome, >99% of the cataloged genes are bacterial. We identified 541 metagenomic species and defined a core set of 26 metagenomic species found in 95% of the mice. The mouse gut microbiome is functionally similar to its human counterpart, with 95.2% of its Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups in common. However, only 4.0% of the mouse gut microbial genes were shared (95% identity, 90% coverage) with those of the human gut microbiome. This catalog provides a useful reference for future studies.

  3. A human gut microbial gene catalogue established by metagenomic sequencing

    DEFF Research Database (Denmark)

    dos Santos, Marcelo Bertalan Quintanilha; Sicheritz-Pontén, Thomas; Nielsen, Henrik Bjørn

    2010-01-01

    To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence...... gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively....

  4. Gut wall bacteria of earthworms: a natural selection process.

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    Thakuria, Dwipendra; Schmidt, Olaf; Finan, Dillon; Egan, Damian; Doohan, Fiona M

    2010-03-01

    Earthworms and microorganisms are interdependent and their interactions regulate the biogeochemistry of terrestrial soils. Investigating earthworm-microorganism interactions, we tested the hypothesis that differences in burrowing and feeding habits of anecic and endogeic earthworms are reflected by the existence of ecological group-specific gut wall bacterial communities. Bacterial community was detected using automated ribosomal intergenic spacer analysis of 16S and 23S genes and ribotype data was used to assess diversity and community composition. Using soil and earthworm samples collected from adjacent wheat-barley and grass-clover fields, we found that the anecic Lumbricus terrestris and L. friendi, the endogeic Aporrectodea caliginosa and A. longa (classically defined as anecic, but now known to possess endogeic characteristics) contain ecological group-specific gut wall-associated bacterial communities. The abundance of specific gut wall-associated bacteria (identified by sequence analysis of ribotype bands), including Proteobacteria, Firmicutes and an actinobacterium, was ecological group dependent. A microcosm study, conducted using A. caliginosa and L. terrestris and five different feeding regimes, indicated that food resource can cause shifts in gut wall-associated bacterial community, but the magnitude of these shifts did not obscure the delineation between ecological group specificity. Using A. caliginosa and A. longa samples collected in six different arable fields, we deduced that, within an ecological group, habitat was a more important determinant of gut wall-associated bacterial community composition than was host species. Hence, we conclude that the selection of bacteria associated with the gut wall of earthworms is a natural selection process and the strongest determinant of this process is in the order ecological group>habitat>species.

  5. Application of metagenomics in the human gut microbiome.

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    Wang, Wei-Lin; Xu, Shao-Yan; Ren, Zhi-Gang; Tao, Liang; Jiang, Jian-Wen; Zheng, Shu-Sen

    2015-01-21

    There are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against pathogenic microbes, modulating immunity, regulating metabolic processes, and is even regarded as an endocrine organ. However, traditional culture methods are very limited for identifying microbes. With the application of molecular biologic technology in the field of the intestinal microbiome, especially metagenomic sequencing of the next-generation sequencing technology, progress has been made in the study of the human intestinal microbiome. Metagenomics can be used to study intestinal microbiome diversity and dysbiosis, as well as its relationship to health and disease. Moreover, functional metagenomics can identify novel functional genes, microbial pathways, antibiotic resistance genes, functional dysbiosis of the intestinal microbiome, and determine interactions and co-evolution between microbiota and host, though there are still some limitations. Metatranscriptomics, metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome. This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects. The limitations of metagenomics to be overcome are also discussed. Metatranscriptomics, metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.

  6. A human gut microbial gene catalogue established by metagenomic sequencing

    NARCIS (Netherlands)

    Qin, J.; Li, R.; Raes, J.; Arumugam, M.; Tims, S.; Vos, de W.M.; Zoetendal, E.G.; Kleerebezem, M.

    2010-01-01

    To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence,

  7. Metagenomic Analysis of the Human Gut Microbiome

    DEFF Research Database (Denmark)

    dos Santos, Marcelo Bertalan Quintanilha

    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......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...

  8. 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.

  9. Metagenome of the gut of a malnourished child

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    Gupta Sourav

    2011-05-01

    Full Text Available Abstract Background Malnutrition, a major health problem, affects a significant proportion of preschool children in developing countries. The devastating consequences of malnutrition include diarrhoea, malabsorption, increased intestinal permeability, suboptimal immune response, etc. Nutritional interventions and dietary solutions have not been effective for treatment of malnutrition till date. Metagenomic procedures allow one to access the complex cross-talk between the gut and its microbial flora and understand how a different community composition affects various states of human health. In this study, a metagenomic approach was employed for analysing the differences between gut microbial communities obtained from a malnourished and an apparently healthy child. Results Our results indicate that the malnourished child gut has an abundance of enteric pathogens which are known to cause intestinal inflammation resulting in malabsorption of nutrients. We also identified a few functional sub-systems from these pathogens, which probably impact the overall metabolic capabilities of the malnourished child gut. Conclusion The present study comprehensively characterizes the microbial community resident in the gut of a malnourished child. This study has attempted to extend the understanding of the basis of malnutrition beyond nutrition deprivation.

  10. New insight into the gut microbiome through metagenomics

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    Ji B

    2015-01-01

    Full Text Available Boyang Ji, Jens Nielsen Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden Abstract: The human gut is colonized by different types of microorganisms, which are known to play important roles in the human host by maintaining physiological homeostasis. The human host provides a nutrient-rich environment, and the microbiota provides some necessary functions that humans cannot perform. A comprehensive analysis of the human gut microbiome is thus important for revealing the mechanisms of these host–microbe interactions. The development of high-throughput sequencing technology and related computational frameworks enables exploration of the metabolic interactions and their roles in human health and diseases. Herein, we describe the metagenomic methods used in human gut microbiome studies and review the roles of gut microbiota as well as the integrative analyses of metagenomic data with other omics data. Finally, we discuss the application of constraint-based modeling to elucidate the microbe–microbe interaction and host–microbe interaction in the human gut microbiota. Keywords: dysbiosis, host–microbe interaction, metabolic modeling 

  11. Application of metagenomics in the human gut microbiome

    OpenAIRE

    Wang, Wei-Lin; Xu, Shao-Yan; Ren, Zhi-Gang; Tao, Liang; Jiang, Jian-Wen; Zheng, Shu-Sen

    2015-01-01

    There are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against pathogenic microbes, modulating immunity, regulating metabolic processes, and is even regarded as an endocrine organ. However, traditional culture methods are very limited for identifying microbes. With the application of molecular biologic technology in the field of the intestinal microbiome, especially metagenomic sequencing of ...

  12. 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...

  13. Metagenomic Analysis of the Medicinal Leech Gut Microbiota

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    Michele A Maltz

    2014-04-01

    Full Text Available There are trillions of microbes found throughout the human body and they exceed the number of eukaryotic cells by ten-fold. Metagenomic studies have revealed that the majority of these microbes are found within the gut, playing an important role in the host’s digestion and nutrition. The complexity of the animal digestive tract, unculturable microbes and the lack of genetic tools for most culturable microbes make it challenging to explore the nature of theses microbial interactions within this niche. The medicinal leech, Hirudo verbana, has been shown to be a useful tool in overcoming these challenges, due to the simplicity of the microbiome and the availability of genetic tools for one of the two dominant gut symbionts, Aeromonas veronii. In this study, we utilize 16S rRNA gene pyrosequencing to further explore the microbial composition of the leech digestive tract, confirming the dominance of two taxa, the Rikenella-like bacterium and A. veronii. The deep sequencing approach revealed the presence of additional members of the microbial community that suggests the presence of a moderately complex microbial community with a richness of 36 taxa. The presence of a Proteus strain as a newly identified resident in the leech crop was confirmed using fluorescence in situ hybridization (FISH. The metagenome of this community was also pyrosequenced and the contigs were binned into the following taxonomic groups: Rikenella-like (3.1 MB, Aeromonas (4.5 MB, Proteus (2.9 MB, Clostridium (1.8 MB, Eryspelothrix (0.96 MB, Desulfovibrio (0.14 MB and Fusobacterium (0.27 MB. Functional analyses on the leech gut symbionts were explored using the metagenomic data and MG-RAST. A comparison of the COG and KEGG categories of the leech gut metagenome to that of other animal digestive-tract microbiomes revealed that the leech digestive-tract had a similar metabolic potential to the human digestive-tract, supporting the usefulness of this system as a model for studying

  14. Metagenomic analysis of the medicinal leech gut microbiota.

    Science.gov (United States)

    Maltz, Michele A; Bomar, Lindsey; Lapierre, Pascal; Morrison, Hilary G; McClure, Emily Ann; Sogin, Mitchell L; Graf, Joerg

    2014-01-01

    There are trillions of microbes found throughout the human body and they exceed the number of eukaryotic cells by 10-fold. Metagenomic studies have revealed that the majority of these microbes are found within the gut, playing an important role in the host's digestion and nutrition. The complexity of the animal digestive tract, unculturable microbes, and the lack of genetic tools for most culturable microbes make it challenging to explore the nature of these microbial interactions within this niche. The medicinal leech, Hirudo verbana, has been shown to be a useful tool in overcoming these challenges, due to the simplicity of the microbiome and the availability of genetic tools for one of the two dominant gut symbionts, Aeromonas veronii. In this study, we utilize 16S rRNA gene pyrosequencing to further explore the microbial composition of the leech digestive tract, confirming the dominance of two taxa, the Rikenella-like bacterium and A. veronii. The deep sequencing approach revealed the presence of additional members of the microbial community that suggests the presence of a moderately complex microbial community with a richness of 36 taxa. The presence of a Proteus strain as a newly identified resident in the leech crop was confirmed using fluorescence in situ hybridization (FISH). The metagenome of this community was also pyrosequenced and the contigs were binned into the following taxonomic groups: Rikenella-like (3.1 MB), Aeromonas (4.5 MB), Proteus (2.9 MB), Clostridium (1.8 MB), Eryspelothrix (0.96 MB), Desulfovibrio (0.14 MB), and Fusobacterium (0.27 MB). Functional analyses on the leech gut symbionts were explored using the metagenomic data and MG-RAST. A comparison of the COG and KEGG categories of the leech gut metagenome to that of other animal digestive-tract microbiomes revealed that the leech digestive tract had a similar metabolic potential to the human digestive tract, supporting the usefulness of this system as a model for studying digestive

  15. THE ROLE OF RED PIGMENT PRODIGIOSIN FROM BACTERIA OF EARTHWORM GUT AS AN ANTICANCER AGENT

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    Sruthy P.B.

    2014-12-01

    Full Text Available Earthworms are the most ancient invertebrate animals on earth which can be used as a good source of pharmaceutical compounds. A study was carried out to find out the distribution of microorganisms in the gut of earthworm, Eudrilus eugeniae. Significant number of microbial populations in the gut of earthworm was observed and it was gradually increased from the initial day to final day of composting. Pigmented colonies of bacteria from earthworm gut were selectively isolated, the pigment was extracted from the culture broth and a presumptive test was carried out for the confirmation of prodigiosin. The pigment component was separated using thin layer chromatography and the structural elucidation of the compound was performed using U.V. spectroscopy. The inhibitory effect of prodigiosin on bacterial pathogens was studied and the results confirmed the antibacterial activity against gram positive bacteria. The anticancer activity of the prodigiosin pigment was evaluated under in vitro conditions against the breast cancer cell lines and it was observed that prodigiosin induced the apoptosis in MCF-7 cell lines in a dose dependent manner. Then the potential isolate was subjected to morphological and biochemical analysis and it was confirmed that the colonies were of Serratia marcescens. The results obtained from the present study indicated that earthworm gut is promising and could be a vital source of habitat possessing antimicrobial and anticancer activity.

  16. Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

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    María Gómez-Brandón

    Full Text Available BACKGROUND: Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. METHODOLOGY: To address these questions we determined the microbial community structure (phospholipid fatty acid profiles and microbial activity (fluorescein diacetate hydrolysis in the earthworm casts derived from three types of animal manure (cow, horse and pig manure, which differed in microbial composition. PRINCIPAL FINDINGS: The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. CONCLUSIONS/SIGNIFICANCE: Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions

  17. Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes

    DEFF Research Database (Denmark)

    Verma, Manoj Kumar; Ahmed, Vasim; Gupta, Shashank

    2018-01-01

    is an important aspect of gut microbes for their survival and colonization. Identification of these survival mechanisms is a pivotal step towards understanding genomic suitability of a symbiont for successful human gut colonization. Here we highlight our recent work applying functional metagenomics to study human...... gut microbiome to identify candidate genes responsible for the salt stress tolerance. A plasmid borne metagenomic library of Bacteroidetes enriched human fecal metagenomic DNA led to identification of unique salt osmotolerance clones SR6 and SR7. Subsequent gene analysis combined with functional...

  18. Decay of low-density polyethylene by bacteria extracted from earthworm's guts

    NARCIS (Netherlands)

    Huerta Lwanga, Esperanza; Thapa, Binita; Yang, Xiaomei; Gertsen, Henny; Salánki, Tamás; Geissen, Violette; Garbeva, Paolina

    2018-01-01

    Low-density polyethylene (LDPE) is the most abundant source of microplastic pollution worldwide. A recent study found that LDPE decay was increased and the size of the plastic was decreased after passing through the gut of the earthworm Lumbricus terrestris (Oligochaeta). Here, we investigated the

  19. Metagenomic analysis of the turkey gut RNA virus community

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    Scheffler Brian E

    2010-11-01

    Full Text Available Abstract Viral enteric disease is an ongoing economic burden to poultry producers worldwide, and despite considerable research, no single virus has emerged as a likely causative agent and target for prevention and control efforts. Historically, electron microscopy has been used to identify suspect viruses, with many small, round viruses eluding classification based solely on morphology. National and regional surveys using molecular diagnostics have revealed that suspect viruses continuously circulate in United States poultry, with many viruses appearing concomitantly and in healthy birds. High-throughput nucleic acid pyrosequencing is a powerful diagnostic technology capable of determining the full genomic repertoire present in a complex environmental sample. We utilized the Roche/454 Life Sciences GS-FLX platform to compile an RNA virus metagenome from turkey flocks experiencing enteric disease. This approach yielded numerous sequences homologous to viruses in the BLAST nr protein database, many of which have not been described in turkeys. Our analysis of this turkey gut RNA metagenome focuses in particular on the turkey-origin members of the Picornavirales, the Caliciviridae, and the turkey Picobirnaviruses.

  20. Sensing microorganisms in the gut triggers the immune response in Eisenia andrei earthworms.

    Science.gov (United States)

    Dvořák, Jiří; Roubalová, Radka; Procházková, Petra; Rossmann, Pavel; Škanta, František; Bilej, Martin

    2016-04-01

    The tube-within-tube body plan of earthworms is appropriate for studying the interactions of microorganisms with the immune system of body cavities such as the digestive tract and coelom. This study aims to describe the immune response on the molecular and cellular level in the coelomic cavity and the gut of the earthworm Eisenia andrei after experimental microbial challenge by administering two bacterial strains (Escherichia coli and Bacillus subtilis) or yeast Saccharomyces cerevisiae to the environment. The changes in mRNA levels of defense molecules (pattern recognition receptor CCF, lysozyme, fetidin/lysenins) in the coelomocytes and gut tissue were determined by quantitative PCR. The immune response at a cellular level was captured in histological sections, and the expression of CCF was localized using in situ hybridization. Coelomocytes respond to the presence of bacteria in the coelomic cavity by increasing the mRNA levels of defense molecules, especially CCF. The immune response in gut tissue is less affected by microbial stimulation because the epithelial cells of gut exhibit basically strong mRNA synthesis of ccf as a defense against the continuous microbial load in the gut lumen. The cellular immune response is mediated by coelomocytes released from the mesenchymal lining of the coelomic cavity. These combined immune mechanisms are necessary for the survival of earthworms in the microbially rich environment of soil. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Metagenomics Study on the Polymorphism of Gut Microbiota and Their Function on Human Health

    DEFF Research Database (Denmark)

    Feng, Qiang

    diversity and functional complexity of the gut microbiome. Facilitated by the Next Generation Sequencing (NGS) technologies and the progress of bioinformatics in the past decade, we have acquired substantial achievements in metagenomic studies on human gut microbiome and established the fundamentals of our...... the gut microbiome of atherosclerosis CHD patients and healthy controls showed significant differences between the two groups. Further more, by integratively analyzing the urine metabolites and fecal microbiota, we demonstrated that gut microbiome dysbiosis was closely correlated with the metabolic...... understanding of the interactions between gut microbes and human body, and also the importance of this interaction on human health. As one of the milestones, the first integrated gene catalog in the human gut microbiome was constructed in 2010 in the scheme of the Metagenomics of Human Intestinal Tract (Meta...

  2. MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads.

    Science.gov (United States)

    Tyakht, Alexander V; Popenko, Anna S; Belenikin, Maxim S; Altukhov, Ilya A; Pavlenko, Alexander V; Kostryukova, Elena S; Selezneva, Oksana V; Larin, Andrei K; Karpova, Irina Y; Alexeev, Dmitry G

    2012-12-07

    MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies, including long reads (such as Sanger and 454 sequencing) and next-generation (including SOLiD and Illumina). It is the first metagenomic web service that is capable of processing SOLiD color-space reads, to authors' knowledge. The web service allows phylogenetic and functional profiling of metagenomic samples using coverage depth resulting from the alignment of the reads to the catalogue of reference sequences which are built into the pipeline and contain prevalent microbial genomes and genes of human gut microbiota. The obtained metagenomic composition vectors are processed by the statistical analysis and visualization module containing methods for clustering, dimension reduction and group comparison. Additionally, the MALINA database includes vectors of bacterial and functional composition for human gut microbiota samples from a large number of existing studies allowing their comparative analysis together with user samples, namely datasets from Russian Metagenome project, MetaHIT and Human Microbiome Project (downloaded from http://hmpdacc.org). MALINA is made freely available on the web at http://malina.metagenome.ru. The website is implemented in JavaScript (using Ext JS), Microsoft .NET Framework, MS SQL, Python, with all major browsers supported.

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

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    Martinson John

    2011-05-01

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

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

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    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

  5. Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes

    OpenAIRE

    Kurokawa, Ken; Itoh, Takehiko; Kuwahara, Tomomi; Oshima, Kenshiro; Toh, Hidehiro; Toyoda, Atsushi; Takami, Hideto; Morita, Hidetoshi; Vineet K. Sharma; Tulika P. Srivastava; Todd D. Taylor; Noguchi, Hideki; Mori, Hiroshi; Ogura, Yoshitoshi; Dusko S. Ehrlich

    2007-01-01

    Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants we...

  6. Microbial diversity and digestive enzyme activities in the gut of earthworms found in sawmill industries in Abeokuta, Nigeria

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    Bamidele Julius A.

    2014-09-01

    Full Text Available The growing demand for wood has resulted in large volumes of wood wastes that are daily released to the soil from the activities of sawmills in South-Western Nigeria. In an attempt to setup a bioremediation model for sawdust, this study therefore aimed at evaluating microbial diversity, and the level of digestive enzymes in the gut of earthworms (Eudrilus eugeniae, Libyodrilus violaceous and Hyperiodrilus africanus of sawmill origin. Four major sawmills located in Abeokuta (7o9’12” N - 3o19’35” E, namely Lafenwa, Sapon, Isale-Ake and Kotopo sawmills were used for this study. The arboretum of the Federal University of Agriculture, Abeokuta was used as control. Gut microbial analysis was carried out using the pour-plate method while digestive enzyme activities in the earthworm guts were done by the spectrophotometric method. Higher microbial counts (28.5±0.1x10³-97.0±0.1x10³cfu for bacteria and 7.0±0.1x10³-96.0±0.1x10³cfu for fungi and microbial diversity were recorded in the gut of earthworms of the sawmill locations than those of the control site (17.5±0.1x10³cfu for bacteria and 4.5±0.1x10³cfu for fungi. Streptococcus mutans and Proteus spp.were common in the gut of E. eugeniae, and L. violaceous from the study sawmills, while Streptococcus mutans were also identified in H. africanus, but absent in the gut of E. eugeniae from the control site. Cellulase (48.67±0.02mg/g and lipase (1.81±0.01mg/g activities were significantly higher (p<0.05 in the gut of earthworms from the control site than those of the study sawmills. Furthermore, amylase (α and β activity was highest in the gut of earthworms from the sawmills. Variations observed in the gut microbial and digestive enzyme activities of earthworms from the study sawmills as compared to the control site suggests that earthworms, especially E. eugeniae, could be a better organism for use as bioremediator of wood wastes. Rev. Biol. Trop. 62 (3: 1241-1249. Epub 2014 September

  7. Degradation of potassium rock by earthworms and responses of bacterial communities in its gut and surrounding substrates after being fed with mineral.

    Directory of Open Access Journals (Sweden)

    Dianfeng Liu

    Full Text Available BACKGROUND: Earthworms are an ecosystem's engineers, contributing to a wide range of nutrient cycling and geochemical processes in the ecosystem. Their activities can increase rates of silicate mineral weathering. Their intestinal microbes usually are thought to be one of the key drivers of mineral degradation mediated by earthworms,but the diversities of the intestinal microorganisms which were relevant with mineral weathering are unclear. METHODOLOGY/PRINCIPAL FINDINGS: In this report, we show earthworms' effect on silicate mineral weathering and the responses of bacterial communities in their gut and surrounding substrates after being fed with potassium-bearing rock powder (PBRP. Determination of water-soluble and HNO(3-extractable elements indicated some elements such as Al, Fe and Ca were significantly released from mineral upon the digestion of earthworms. The microbial communities in earthworms' gut and the surrounding substrates were investigated by amplified ribosomal DNA restriction analysis (ARDRA and the results showed a higher bacterial diversity in the guts of the earthworms fed with PBRP and the PBRP after being fed to earthworms. UPGMA dendrogram with unweighted UniFrac analysis, considering only taxa that are present, revealed that earthworms' gut and their surrounding substrate shared similar microbiota. UPGMA dendrogram with weighted UniFrac, considering the relative abundance of microbial lineages, showed the two samples from surrounding substrate and the two samples from earthworms' gut had similarity in microbial community, respectively. CONCLUSIONS/SIGNIFICANCE: Our results indicated earthworms can accelerate degradation of silicate mineral. Earthworms play an important role in ecosystem processe since they not only have some positive effects on soil structure, but also promote nutrient cycling of ecosystem by enhancing the weathering of minerals.

  8. Metagenomic Sequencing of Diamondback Moth Gut Microbiome Unveils Key Holobiont Adaptations for Herbivory

    Directory of Open Access Journals (Sweden)

    Minsheng You

    2017-04-01

    Full Text Available Herbivore specialists adapt to feed on a specific group of host plants by evolving various mechanisms to respond to plant defenses. Insects also possess complex gut microbiotas but their potential role in adaptation is poorly understood. Our previous study of the genome of diamondback moth, Plutella xylostella, revealed an intrinsic capacity to detoxify plant defense compounds, which is an important factor in its success as a pest. Here we expand on that work with a complete taxonomic and functional profile of the P. xylostella gut microbiota obtained by metagenomic sequencing. Gene enrichment in the metagenome, accompanied by functional identification, revealed an important role of specific gut bacteria in the breakdown of plant cell walls, detoxification of plant phenolics, and synthesis of amino acids. Microbes participating in these pathways mainly belonged to three highly abundant bacteria: Enterobacter cloacae, Enterobacter asburiae, and Carnobacterium maltaromaticum. Results show that while the gut microbial community may be complex, a small number of functionally active species can be disproportionally important. The presence of specific enzymes in the microbiota community, such as supporting amino acid synthesis, digestion and detoxification functions, demonstrates the beneficial interactions between P. xylostella and its gut microbiota. These interactions can be potential targets for manipulation to provide novel pest management approaches.

  9. Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies

    OpenAIRE

    Emmanouil Angelakis; Dipankar Bachar; Bernard Henrissat; Fabrice Armougom; Gilles Audoly; Jean-Christophe Lagier; Catherine Robert; Didier Raoult

    2016-01-01

    Exopolysaccharides produced by bacterial species and present in feces are extremely inhibitory to DNA restriction and can cause discrepancies in metagenomic studies. We determined the effects of different DNA extraction methods on the apparent composition of the gut microbiota using Illumina MiSeq deep sequencing technology. DNA was extracted from the stool from an obese female using 10 different methods and the choice of DNA extraction method affected the proportional abundance at the phylum...

  10. Metagenomics and development of the gut microbiota in infants

    DEFF Research Database (Denmark)

    Vallès, Y.; Gosalbes, M. J.; de Vries, Lisbeth Elvira

    2012-01-01

    , the gastrointestinal tract microbiota is often exposed to antibiotics, and may be an important reservoir of resistant strains and of transferable resistance genes from early infancy. We are investigating by means of diverse metagenomic approaches several areas of microbiota development in infants, including......Clin Microbiol Infect 2012; 18 (Suppl. 4): 21–26 The establishment of a balanced intestinal microbiota is essential for numerous aspects of human health, yet the microbial colonization of the gastrointestinal tract of infants is both complex and highly variable among individuals. In addition...

  11. Bisphenol A alters gut microbiome: Comparative metagenomics analysis.

    Science.gov (United States)

    Lai, Keng-Po; Chung, Yan-Tung; Li, Rong; Wan, Hin-Ting; Wong, Chris Kong-Chu

    2016-11-01

    Mounting evidence has shown that an alteration of the gut microbiota is associated with diet, and plays an important role in animal health and metabolic diseases. However, little is known about the influence of environmental contaminants on the gut microbial community. Bisphenol A (BPA), which is widely used for manufacturing plastic products, has recently been classified as an environmental obesogen. Although many studies have demonstrated the metabolic-disrupting effects of BPA on liver and pancreatic functions, the possible effects of this synthetic compound on the metabolic diversity of the intestinal microbiota is unknown. Using 16S rRNA gene sequencing analysis on caecum samples of CD-1 mice, the present study aimed to test the hypothesis that dietary BPA intake may influence the gut microbiota composition and functions, an important attributing factor to development of the metabolic syndrome. A high-fat diet (HFD) and high-sucrose diet (HSD) were included as the positive controls for comparing the changes in the intestinal microbial profiles. Our results demonstrated a significant reduction of species diversity in the gut microbiota of BPA-fed mice. Alpha and beta diversity analyses showed that dietary BPA intake led to a similar gut microbial community structure as that induced by HFD and HSD in mice. In addition, comparative analysis of the microbial communities revealed that both BPA and a HFD favored the growth of Proteobacteria, a microbial marker of dysbiosis. Consistently, growth induction of the family Helicobacteraceae and reduction of the Firmicutes and Clostridia populations were observed in the mice fed BPA or a HFD. Collectively, our study highlighted that the effects of dietary BPA intake on the shift of microbial community structure were similar to those of a HFD and HSD, and revealed microbial markers for the development of diseases associated with an unstable microbiota. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Functional and evolutionary insights into the simple yet specific gut microbiota of the honey bee from metagenomic analysis

    OpenAIRE

    Engel, Philipp; Moran, Nancy A

    2013-01-01

    The honey bee, Apis mellifera, harbors a characteristic gut microbiota composed of only a few species which seem to be specific to social bees. The maintenance of this stable and distinct microbial community depends on the social lifestyle of these insects. As in other animals, the bacteria in the gut of honey bees probably govern important functions critical to host health. We recently sequenced a metagenome of the gut microbiota of A. mellifera, assigned gene contents to bins corresponding ...

  13. Decay of low-density polyethylene by bacteria extracted from earthworm's guts: A potential for soil restoration.

    Science.gov (United States)

    Huerta Lwanga, Esperanza; Thapa, Binita; Yang, Xiaomei; Gertsen, Henny; Salánki, Tamás; Geissen, Violette; Garbeva, Paolina

    2017-12-19

    Low-density polyethylene (LDPE) is the most abundant source of microplastic pollution worldwide. A recent study found that LDPE decay was increased and the size of the plastic was decreased after passing through the gut of the earthworm Lumbricus terrestris (Oligochaeta). Here, we investigated the involvement of earthworm gut bacteria in the microplastic decay. The bacteria isolated from the earthworm's gut were Gram-positive, belonging to phylum Actinobacteria and Firmicutes. These bacteria were used in a short-term microcosm experiment performed with gamma-sterilized soil with or without LDPE microplastics (MP). We observed that the LDPE-MP particle size was significantly reduced in the presence of bacteria. In addition, the volatile profiles of the treatments were compared and clear differences were detected. Several volatile compounds such as octadecane, eicosane, docosane and tricosane were measured only in the treatments containing both bacteria and LDPE-MP, indicating that these long-chain alkanes are byproducts of bacterial LDPE-MP decay. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  14. Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome.

    Science.gov (United States)

    Beghini, Francesco; Pasolli, Edoardo; Truong, Tin Duy; Putignani, Lorenza; Cacciò, Simone M; Segata, Nicola

    2017-12-01

    The influence of unicellular eukaryotic microorganisms on human gut health and disease is still largely unexplored. Blastocystis spp. commonly colonize the gut, but its clinical significance and ecological role are currently unsettled. We have developed a high-sensitivity bioinformatic pipeline to detect Blastocystis subtypes (STs) from shotgun metagenomics, and applied it to 12 large data sets, comprising 1689 subjects of different geographic origin, disease status and lifestyle. We confirmed and extended previous observations on the high prevalence the microrganism in the population (14.9%), its non-random and ST-specific distribution, and its ability to cause persistent (asymptomatic) colonization. These findings, along with the higher prevalence observed in non-westernized individuals, the lack of positive association with any of the disease considered, and decreased presence in individuals with dysbiosis associated with colorectal cancer and Crohn's disease, strongly suggest that Blastocystis is a component of the healthy gut microbiome. Further, we found an inverse association between body mass index and Blastocystis, and strong co-occurrence with archaeal organisms (Methanobrevibacter smithii) and several bacterial species. The association of specific microbial community structures with Blastocystis was confirmed by the high predictability (up to 0.91 area under the curve) of the microorganism colonization based on the species-level composition of the microbiome. Finally, we reconstructed and functionally profiled 43 new draft Blastocystis genomes and discovered a higher intra subtype variability of ST1 and ST2 compared with ST3 and ST4. Altogether, we provide an in-depth epidemiologic, ecological, and genomic analysis of Blastocystis, and show how metagenomics can be crucial to advance population genomics of human parasites.

  15. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression.

    Directory of Open Access Journals (Sweden)

    Charles K Fisher

    Full Text Available Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is now possible to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the ecological interactions between species directly from sequence data. Any algorithm for inferring ecological interactions must overcome three major obstacles: 1 a correlation between the abundances of two species does not imply that those species are interacting, 2 the sum constraint on the relative abundances obtained from metagenomic studies makes it difficult to infer the parameters in timeseries models, and 3 errors due to experimental uncertainty, or mis-assignment of sequencing reads into operational taxonomic units, bias inferences of species interactions due to a statistical problem called "errors-in-variables". Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS, that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. We tested LIMITS on synthetic data and showed that it could reliably infer the topology of the inter-species ecological interactions. We then used LIMITS to characterize the species interactions in the gut microbiomes of two individuals and found that the interaction networks varied significantly between individuals. Furthermore, we found that the interaction networks of the two individuals are dominated by distinct "keystone species", Bacteroides fragilis and Bacteroided stercosis, that have a disproportionate influence on the structure of the gut microbiome even though they are only found in moderate abundance. Based on our results, we hypothesize that the abundances of certain keystone species may be responsible for individuality in

  16. Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome

    Science.gov (United States)

    Beghini, Francesco; Pasolli, Edoardo; Truong, Tin Duy; Putignani, Lorenza; Cacciò, Simone M; Segata, Nicola

    2017-01-01

    The influence of unicellular eukaryotic microorganisms on human gut health and disease is still largely unexplored. Blastocystis spp. commonly colonize the gut, but its clinical significance and ecological role are currently unsettled. We have developed a high-sensitivity bioinformatic pipeline to detect Blastocystis subtypes (STs) from shotgun metagenomics, and applied it to 12 large data sets, comprising 1689 subjects of different geographic origin, disease status and lifestyle. We confirmed and extended previous observations on the high prevalence the microrganism in the population (14.9%), its non-random and ST-specific distribution, and its ability to cause persistent (asymptomatic) colonization. These findings, along with the higher prevalence observed in non-westernized individuals, the lack of positive association with any of the disease considered, and decreased presence in individuals with dysbiosis associated with colorectal cancer and Crohn’s disease, strongly suggest that Blastocystis is a component of the healthy gut microbiome. Further, we found an inverse association between body mass index and Blastocystis, and strong co-occurrence with archaeal organisms (Methanobrevibacter smithii) and several bacterial species. The association of specific microbial community structures with Blastocystis was confirmed by the high predictability (up to 0.91 area under the curve) of the microorganism colonization based on the species-level composition of the microbiome. Finally, we reconstructed and functionally profiled 43 new draft Blastocystis genomes and discovered a higher intra subtype variability of ST1 and ST2 compared with ST3 and ST4. Altogether, we provide an in-depth epidemiologic, ecological, and genomic analysis of Blastocystis, and show how metagenomics can be crucial to advance population genomics of human parasites. PMID:28837129

  17. Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies.

    Science.gov (United States)

    Angelakis, Emmanouil; Bachar, Dipankar; Henrissat, Bernard; Armougom, Fabrice; Audoly, Gilles; Lagier, Jean-Christophe; Robert, Catherine; Raoult, Didier

    2016-05-18

    Exopolysaccharides produced by bacterial species and present in feces are extremely inhibitory to DNA restriction and can cause discrepancies in metagenomic studies. We determined the effects of different DNA extraction methods on the apparent composition of the gut microbiota using Illumina MiSeq deep sequencing technology. DNA was extracted from the stool from an obese female using 10 different methods and the choice of DNA extraction method affected the proportional abundance at the phylum level, species richness (Chao index, 227 to 2,714) and diversity (non parametric Shannon, 1.37 to 4.4). Moreover DNA was extracted from stools obtained from 83 different individuals by the fastest extraction assay and by an extraction assay that degradated exopolysaccharides. The fastest extraction method was able to detect 68% to 100% genera and 42% to 95% species whereas the glycan degradation extraction method was able to detect 56% to 93% genera and 25% to 87% species. To allow a good liberation of DNA from exopolysaccharides commonly presented in stools, we recommend the mechanical lysis of stools plus glycan degradation, used here for the first time. Caution must be taken in the interpretation of current metagenomic studies, as the efficiency of DNA extraction varies widely among stool samples.

  18. Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome

    Science.gov (United States)

    Culligan, Eamonn P.; Marchesi, Julian R.; Hill, Colin; Sleator, Roy D.

    2014-01-01

    In the current study, a number of salt-tolerant clones previously isolated from a human gut metagenomic library were screened using Phenotype MicroArray (PM) technology to assess their functional capacity. PM's can be used to study gene function, pathogenicity, metabolic capacity and identify drug targets using a series of specialized microtitre plate assays, where each well of the microtitre plate contains a different set of conditions and tests a different phenotype. Cellular respiration is monitored colorimetrically by the reduction of a tetrazolium dye. One clone, SMG 9, was found to be positive for utilization/transport of L-carnitine (a well-characterized osmoprotectant) in the presence of 6% w/v sodium chloride (NaCl). Subsequent experiments revealed a significant growth advantage in minimal media containing NaCl and L-carnitine. Fosmid sequencing revealed putative candidate genes responsible for the phenotype. Subsequent cloning of two genes did not replicate the L-carnitine-associated phenotype, although one of the genes, a σ54-dependent transcriptional regulator, did confer salt tolerance to Escherichia coli when expressed in isolation. The original clone, SMG 9, was subsequently found to have lost the original observed phenotype upon further investigation. Nevertheless, this study demonstrates the usefulness of a phenomic approach to assign a functional role to metagenome-derived clones. PMID:24808895

  19. Functional and evolutionary insights into the simple yet specific gut microbiota of the honey bee from metagenomic analysis.

    Science.gov (United States)

    Engel, Philipp; Moran, Nancy A

    2013-01-01

    The honey bee, Apis mellifera, harbors a characteristic gut microbiota composed of only a few species which seem to be specific to social bees. The maintenance of this stable and distinct microbial community depends on the social lifestyle of these insects. As in other animals, the bacteria in the gut of honey bees probably govern important functions critical to host health. We recently sequenced a metagenome of the gut microbiota of A. mellifera, assigned gene contents to bins corresponding to the major species present in the honey bee gut, and compared functional gene categories between these species, and between the complete metagenome and those of other animals. Gene contents could be linked to different symbiotic functions with the host. Further, we found a high degree of genetic diversity within each of these species. In the case of the gammaproteobacterial species Gilliamella apicola, we experimentally showed a link between genetic variation of isolates and functional differences suggesting that niche partitioning within this species has emerged during evolution with its bee hosts. The consistent presence of only a few species, combined with strain variation within each of these species, makes the gut microbiota of social bees an ideal model for studying functional, structural, and evolutionary aspects of host-associated microbial communities: many characteristics resemble the gut microbiota of humans and other mammals, but the complexity is considerably reduced. In this addendum, we summarize and discuss our major findings and provide a detailed perspective on future research.

  20. Variations in the Post-weaning Human Gut Metagenome Profile As Result of Bifidobacterium Acquisition in the Western Microbiome

    Science.gov (United States)

    Soverini, Matteo; Rampelli, Simone; Turroni, Silvia; Schnorr, Stephanie L.; Quercia, Sara; Castagnetti, Andrea; Biagi, Elena; Brigidi, Patrizia; Candela, Marco

    2016-01-01

    Studies of the gut microbiome variation among human populations revealed the existence of robust compositional and functional layouts matching the three subsistence strategies that describe a trajectory of changes across our recent evolutionary history: hunting and gathering, rural agriculture, and urban post-industrialized agriculture. In particular, beside the overall reduction of ecosystem diversity, the gut microbiome of Western industrial populations is typically characterized by the loss of Treponema and the acquisition of Bifidobacterium as an abundant inhabitant of the post-weaning gut microbial ecosystem. In order to advance the hypothesis about the possible adaptive nature of this exchange, here we explore specific functional attributes that correspond to the mutually exclusive presence of Treponema and Bifidobacterium using publically available gut metagenomic data from Hadza hunter-gatherers and urban industrial Italians. According to our findings, Bifidobacterium provides the enteric ecosystem with a diverse panel of saccharolytic functions, well suited to the array of gluco- and galacto-based saccharides that abound in the Western diet. On the other hand, the metagenomic functions assigned to Treponema are more predictive of a capacity to incorporate complex polysaccharides, such as those found in unrefined plant foods, which are consistently incorporated in the Hadza diet. Finally, unlike Treponema, the Bifidobacterium metagenome functions include genes that permit the establishment of microbe–host immunological cross-talk, suggesting recent co-evolutionary events between the human immune system and Bifidobacterium that are adaptive in the context of agricultural subsistence and sedentary societies. PMID:27462302

  1. Variations in the post-weaning human gut metagenome profile as result of Bifidobacterium acquisition in the Western microbiome

    Directory of Open Access Journals (Sweden)

    Matteo Soverini

    2016-07-01

    Full Text Available Studies of the gut microbiome variation among human populations revealed the existence of robust compositional and functional layouts matching the three subsistence strategies that describe a trajectory of changes across our recent evolutionary history: hunting and gathering, rural agriculture, and urban post-industrialized agriculture. In particular, beside the overall reduction of ecosystem diversity, the gut microbiome of Western industrial populations is typically characterized by the loss of Treponema and the acquisition of Bifidobacterium as an abundant inhabitant of the post-weaning gut microbial ecosystem. In order to advance the hypothesis about the possible adaptive nature of this exchange, here we explore specific functional attributes that correspond to the mutually exclusive presence of Treponema and Bifidobacterium using publically available gut metagenomic data from Hadza hunter-gatherers and urban industrial Italians. According to our findings, Bifidobacterium provides the enteric ecosystem with a diverse panel of saccharolytic functions, well suited to the array of gluco- and galacto-based saccharides that abound in the Western diet. On the other hand, the metagenomic functions assigned to Treponema are more predictive of a capacity to incorporate complex polysaccharides, such as those found in unrefined plant foods, which are consistently incorporated in the Hadza diet. Finally, unlike Treponema, the Bifidobacterium metagenome functions include genes that permit the establishment of microbe-host immunological cross-talk, suggesting recent co-evolutionary events between the human immune system and Bifidobacterium that are adaptive in the context of agricultural subsistence and sedentary societies.

  2. Combination of metagenomics and culture-based methods to study the interaction between ochratoxin a and gut microbiota.

    Science.gov (United States)

    Guo, Mingzhang; Huang, Kunlun; Chen, Siyuan; Qi, Xiaozhe; He, Xiaoyun; Cheng, Wen-Hsing; Luo, Yunbo; Xia, Kai; Xu, Wentao

    2014-09-01

    Gut microbiota represent an important bridge between environmental substances and host metabolism. Here we reported a comprehensive study of gut microbiota interaction with ochratoxin A (OTA), a major food-contaminating mycotoxin, using the combination of metagenomics and culture-based methods. Rats were given OTA (0, 70, or 210 μg/kg body weight) by gavage and fecal samples were collected at day 0 and day 28. Bacterial genomic DNA was extracted from the fecal samples and both 16S rRNA and shotgun sequencing (two main methods of metagenomics) were performed. The results indicated OTA treatment decreased the within-subject diversity of the gut microbiota, and the relative abundance of Lactobacillus increased considerably. Changes in functional genes of gut microbiota including signal transduction, carbohydrate transport, transposase, amino acid transport system, and mismatch repair were observed. To further understand the biological sense of increased Lactobacillus, Lactobacillus selective medium was used to isolate Lactobacillus species from fecal samples, and a strain with 99.8% 16S rRNA similarity with Lactobacillus plantarum strain PFK2 was obtained. Thin-layer chromatography showed that this strain could absorb but not degrade OTA, which was in agreement with the result in metagenomics that no genes related to OTA degradation increased. In conclusion, combination of metagenomics and culture-based methods can be a new strategy to study intestinal toxicity of toxins and find applicable bacterial strains for detoxification. When it comes to OTA, this kind of mycotoxin can cause compositional and functional changes of gut microbiota, and Lactobacillus are key genus to detoxify OTA in vivo. © The Author 2014. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  3. Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice.

    Science.gov (United States)

    Sharpton, Thomas; Lyalina, Svetlana; Luong, Julie; Pham, Joey; Deal, Emily M; Armour, Courtney; Gaulke, Christopher; Sanjabi, Shomyseh; Pollard, Katherine S

    2017-01-01

    The gut microbiome is linked to inflammatory bowel disease (IBD) severity and altered in late-stage disease. However, it is unclear how gut microbial communities change over the course of IBD development, especially in regard to function. To investigate microbiome-mediated disease mechanisms and discover early biomarkers of IBD, we conducted a longitudinal metagenomic investigation in an established mouse model of IBD, where damped transforming growth factor β (TGF-β) signaling in T cells leads to peripheral immune activation, weight loss, and severe colitis. IBD development is associated with abnormal gut microbiome temporal dynamics, including damped acquisition of functional diversity and significant differences in abundance trajectories for KEGG modules such as glycosaminoglycan degradation, cellular chemotaxis, and type III and IV secretion systems. Most differences between sick and control mice emerge when mice begin to lose weight and heightened T cell activation is detected in peripheral blood. However, levels of lipooligosaccharide transporter abundance diverge prior to immune activation, indicating that it could be a predisease indicator or microbiome-mediated disease mechanism. Taxonomic structure of the gut microbiome also significantly changes in association with IBD development, and the abundances of particular taxa, including several species of Bacteroides, correlate with immune activation. These discoveries were enabled by our use of generalized linear mixed-effects models to test for differences in longitudinal profiles between healthy and diseased mice while accounting for the distributions of taxon and gene counts in metagenomic data. These findings demonstrate that longitudinal metagenomics is useful for discovering the potential mechanisms through which the gut microbiome becomes altered in IBD. IMPORTANCE IBD patients harbor distinct microbial communities with functional capabilities different from those seen with healthy people. But is this

  4. Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls.

    Science.gov (United States)

    Mangericao, Tatiana C; Peng, Zhanhao; Zhang, Xuegong

    2016-01-11

    CRISPR has been becoming a hot topic as a powerful technique for genome editing for human and other higher organisms. The original CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats coupled with CRISPR-associated proteins) is an important adaptive defence system for prokaryotes that provides resistance against invading elements such as viruses and plasmids. A CRISPR cassette contains short nucleotide sequences called spacers. These unique regions retain a history of the interactions between prokaryotes and their invaders in individual strains and ecosystems. One important ecosystem in the human body is the human gut, a rich habitat populated by a great diversity of microorganisms. Gut microbiomes are important for human physiology and health. Metagenome sequencing has been widely applied for studying the gut microbiomes. Most efforts in metagenome study has been focused on profiling taxa compositions and gene catalogues and identifying their associations with human health. Less attention has been paid to the analysis of the ecosystems of microbiomes themselves especially their CRISPR composition. We conducted a preliminary analysis of CRISPR sequences in a human gut metagenomic data set of Chinese individuals of type-2 diabetes patients and healthy controls. Applying an available CRISPR-identification algorithm, PILER-CR, we identified 3169 CRISPR cassettes in the data, from which we constructed a set of 1302 unique repeat sequences and 36,709 spacers. A more extensive analysis was made for the CRISPR repeats: these repeats were submitted to a more comprehensive clustering and classification using the web server tool CRISPRmap. All repeats were compared with known CRISPRs in the database CRISPRdb. A total of 784 repeats had matches in the database, and the remaining 518 repeats from our set are potentially novel ones. The computational analysis of CRISPR composition based contigs of metagenome sequencing data is feasible. It provides an efficient

  5. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis.

    Science.gov (United States)

    Lu, Kun; Abo, Ryan Phillip; Schlieper, Katherine Ann; Graffam, Michelle E; Levine, Stuart; Wishnok, John S; Swenberg, James A; Tannenbaum, Steven R; Fox, James G

    2014-03-01

    The human intestine is host to an enormously complex, diverse, and vast microbial community-the gut microbiota. The gut microbiome plays a profound role in metabolic processing, energy production, immune and cognitive development, epithelial homeostasis, and so forth. However, the composition and diversity of the gut microbiome can be readily affected by external factors, which raises the possibility that exposure to toxic environmental chemicals leads to gut microbiome alteration, or dysbiosis. Arsenic exposure affects large human populations worldwide and has been linked to a number of diseases, including cancer, diabetes, and cardiovascular disorders. We investigated the impact of arsenic exposure on the gut microbiome composition and its metabolic profiles. We used an integrated approach combining 16S rRNA gene sequencing and mass spectrometry-based metabolomics profiling to examine the functional impact of arsenic exposure on the gut microbiome. 16S rRNA gene sequencing revealed that arsenic significantly perturbed the gut microbiome composition in C57BL/6 mice after exposure to 10 ppm arsenic for 4 weeks in drinking water. Moreover, metabolomics profiling revealed a concurrent effect, with a number of gut microflora-related metabolites being perturbed in multiple biological matrices. Arsenic exposure not only alters the gut microbiome community at the abundance level but also substantially disturbs its metabolic profiles at the function level. These findings may provide novel insights regarding perturbations of the gut microbiome and its functions as a potential new mechanism by which arsenic exposure leads to or exacerbates human diseases. Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG. 2014. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ Health Perspect 122:284-291; http://dx.doi.org/10.1289/ehp.1307429.

  6. Identification of a novel alkaline amylopullulanase from a gut metagenome of Hermetia illucens.

    Science.gov (United States)

    Lee, Young-Seok; Seo, So-Hyeon; Yoon, Sang-Hong; Kim, Su-Yeon; Hahn, Bum-Soo; Sim, Joon-Soo; Koo, Bon-Sung; Lee, Chang-Muk

    2016-01-01

    A novel pullulanase gene, PulSS4, was identified from the gut microflora of Hermetia illucens by a function-based metagenome screening. The PulSS4 gene had an open reading frame of 4455 base pairs, and encoded a mature protein of 1484 amino acids, with a signal peptide sequence of 44 amino acids. The deduced amino acid sequence of PulSS4 gene showed 51% identity with that of the amylopullulanase of Amphibacillus xylanus, exhibiting no significant sequence homology to already known pullulanases. A conserved domain analysis revealed it to be a pullulanase type II with respective active sites at the N-terminal pullulanase and C-terminal amylase domain. PulSS4 was active in the temperature range of 10-50°C, with an optimum activity at 40°C. It was active in the pH range of 6.5-10.5, with optimum pH at 9.0, and retained more than 80% of its original activity in a broad pH range of 5-11 for 24h at 30°C. Also, PulSS4 was highly stable against many different chemical reagents, including 10% polar organic solvents and 1% non-ionic detergents. Overall, PulSS4 is expected to have the strong potential for application in biotechnological industries that require high activity at moderate temperature and alkaline conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Swine Fecal Metagenomics

    Science.gov (United States)

    Metagenomic approaches are providing rapid and more robust means to investigate the composition and functional genetic potential of complex microbial communities. In this study, we utilized a metagenomic approach to further understand the functional diversity of the swine gut. To...

  8. Excellent N-fixing and P-solubilizing traits in earthworm gut-isolated bacteria: A vermicompost based assessment with vegetable market waste and rice straw feed mixtures.

    Science.gov (United States)

    Hussain, Nazneen; Singh, Archana; Saha, Sougata; Venkata Satish Kumar, Mattaparthi; Bhattacharyya, Pradip; Bhattacharya, Satya Sundar

    2016-12-01

    Vermicomposting is a dependable waste recycling technology which greatly augments N and P levels mainly through microbial action. This paper aims to identify efficient N-fixing (NFB) and P-solubilizing (PSB) bacteria from earthworm intestines. Various combinations of vegetable market waste, rice straw, and cowdung were fed to two earthworm species (Eisenia fetida and Perionyx excavatus). Total organic C decreased, pH shifted towards neutrality, and NPK availability, and microbial (NFB, PSB, and total bacteria) population increased remarkably during vermicomposting with E. fetida. Therefore, 45 NFB and 34 PSB strains isolated from Eisenia gut were initially screened, their inter-dominance assessed, and 8 prolific strains were identified through 16SrRNA sequencing. Interestingly, two novel N-fixing strains of Kluyvera ascorbata emerged as an efficient biofertilizer candidate. Moreover, both N-fixing and P-solubilizing strains of Serratia and Bacillus were isolated from earthworm gut. All the isolated strains significantly improved soil health and facilitated crop growth as compared to commercial biofertilizers. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda (Ailuropoda melanoleuca May Not Be Specialized for Fiber Fermentation

    Directory of Open Access Journals (Sweden)

    Wei Guo

    2018-02-01

    Full Text Available Bamboo-eating giant panda (Ailuropoda melanoleuca is an enigmatic species, which possesses a carnivore-like short and simple gastrointestinal tract (GIT. Despite the remarkable studies on giant panda, its diet adaptability status continues to be a matter of debate. To resolve this puzzle, we investigated the functional potential of the giant panda gut microbiome using shotgun metagenomic sequencing of fecal samples. We also compared our data with similar data from other animal species representing herbivores, carnivores, and omnivores from current and earlier studies. We found that the giant panda hosts a bear-like gut microbiota distinct from those of herbivores indicated by the metabolic potential of the microbiome in the gut of giant pandas and other mammals. Furthermore, the relative abundance of genes involved in cellulose- and hemicellulose-digestion, and enrichment of enzymes associated with pathways of amino acid degradation and biosynthetic reactions in giant pandas echoed a carnivore-like microbiome. Most significantly, the enzyme assay of the giant panda's feces indicated the lowest cellulase and xylanase activity among major herbivores, shown by an in-vitro experimental assay of enzyme activity for cellulose and hemicellulose-degradation. All of our results consistently indicate that the giant panda is not specialized to digest cellulose and hemicellulose from its bamboo diet, making the giant panda a good mammalian model to study the unusual link between the gut microbiome and diet. The increased food intake of the giant pandas might be a strategy to compensate for the gut microbiome functions, highlighting a strong need of conservation of the native bamboo forest both in high- and low-altitude ranges to meet the great demand of bamboo diet of giant pandas.

  10. Diversity of microflora in the gut and casts of tropical composting earthworms reared on different substrates.

    Science.gov (United States)

    Parthasarathi, K; Ranganathan, L S; Anandi, V; Zeyer, Josef

    2007-01-01

    The diversity of fungi, bacteria, yeast, actinomycetes and protozoa were analysed in the gut and casts of Eudrilus eugeniae, Lampito mauritii, Eisenia fetida and Perionyx excavatus, both qualitatively and quantitatively as influenced by different feed substrates like clay loam soil, cowdung and pressmud. While actinomycetes (Streptomyces albus, S. somaliensis, Nocardia asteroides, N. caviae and Saccharomonosporia) were not digested by any of these species of worms, protozoa (Amoeba proteus, A. terricola, Paramecium trichium, Euglena viridis, E. orientalis, Vorticella picta and Trichomonas hominis) and yeast (Candida tropicalis, C. krusei C. albicans and Cryptococcus neoformans) were totally digested. Certain species of fungi (Saksenae vasiformis, Mucor plumbeus, Cladosporium carrionii, C. herbacium, Alternaria sp., Cunninghamella echinulata, Mycetia sterila, Syncephalostrum racemosum, Curvalaria lunata, C. geniculata and Geotrichum candidum) and bacteria (Pseudomonas aeruginosa, Bacterium antitratum, Mima polymorpha, Enterobacter aerogenes, E. cloacae, Proteus vulgaris, P. mirabilis, P. rettgeri, Escherichia coli, Staphylococus citreus, Bacillus subtilis, B. cereus, Enterococci and Micrococci) were completely digested. Certain other species were not digested fungi like Aspergillus fumigatus, A. flavus, A. ochraceous, Trichoderma koningii (except by Eeugeniae), Fusarium moniliforme (except by E. eugeniae) and Rhizopus sp., and bacteria like Klebsiella pneumoniae and Morganella morganii) and these were multiplied during the transit of the organic residues through the gut of worms. The microbial proliferation was more in the casts, due to the environment prevailing--rich in nutrient supply and large surface area available for growth and reproduction of the microbes that lead to enhanced microbial activity and humic acid contents in the casts.

  11. Microbial and nutrient stabilization of two animal manures after the transit through the gut of the earthworm Eisenia fetida (Savigny, 1826).

    Science.gov (United States)

    Aira, Manuel; Domínguez, Jorge

    2009-01-30

    Here we studied how the transit through the gut of the earthworm Eisenia fetida affects the microbial and nutrient stabilization of pig and cow manure, by analyzing fresh casts. Earthworms reduced the pools of dissolved organic C and N in casts from both types of manure, as wells as mineral N. Microbial biomass was enhanced only in casts from pig manure and did not change in casts from cow manure, and fungal populations only raised in casts from cow manure. Earthworms reduced microbial activity in casts from cow manure and did not modify in casts from pig slurry. Enzyme activities in casts also depended on the manure ingested; there were no changes in dehydrogenase and beta-glucosidase activities, whereas acid and alkaline phosphatases increased. The results indicate that the first stage in vermicomposting of pig and cow manure by E. fetida, i.e. casting, produced a microbial stabilization decreasing the activity of microorganisms; this stabilization occurred despite of the increase in microbial biomass. The strong reduction in nutrient pools of manures may be the responsible of this contradiction. These changes will influence the dynamics of the organic matter degradation by reducing forms of C and N available to microorganisms and hence restricting their growth and multiplication. Nevertheless, casts were also characterized by an increased enzyme potential that might lead to a further thorough degradation of pig and cow manure.

  12. 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.

  13. Adapting functional genomic tools to metagenomic analyses: investigating the role of gut bacteria in relation to obesity.

    Science.gov (United States)

    Liu, Yuanhua; Zhang, Chenhong; Zhao, Liping; Nardini, Christine

    2010-12-01

    With the expanding availability of sequencing technologies, research previously centered on the human genome can now afford to include the study of humans' internal ecosystem (human microbiome). Given the scale of the data involved in this metagenomic research (two orders of magnitude larger than the human genome) and their importance in relation to human health, it is crucial to guarantee (along with the appropriate data collection and taxonomy) proper tools for data analysis. We propose to adapt the approaches defined for the analysis of gene-expression microarray in order to infer information in metagenomics. In particular, we applied SAM, a broadly used tool for the identification of differentially expressed genes among different samples classes, to a reported dataset on a research model with mice of two genotypes (a high density lipoprotein knockout mouse and its wild-type counterpart). The data contain two different diets (high-fat or normal-chow) to ensure the onset of obesity, prodrome of metabolic syndromes (MS). By using 16S rRNA gene as a genomic diversity marker, we illustrate how this approach can identify bacterial populations differentially enriched among different genetic and dietary conditions of the host. This approach faithfully reproduces highly-relevant results from phylogenetic and standard statistical analyses, used to explain the role of the gut microbiome in relation to obesity. This represents a promising proof-of-principle for using functional genomic approaches in the fast growing area of metagenomics, and warrants the availability of a large body of thoroughly tested and theoretically sound methodologies to this exciting new field.

  14. Metagenomic profiles and antibiotic resistance genes in gut microbiota of mice exposed to arsenic and iron.

    Science.gov (United States)

    Guo, Xuechao; Liu, Su; Wang, Zhu; Zhang, Xu-xiang; Li, Mei; Wu, Bing

    2014-10-01

    Iron (Fe) has been widely applied to treat arsenic (As)-contaminated water, and Fe could influence bioavailability and toxicity of As. However, little is known about the impact of As and/or Fe on gut microbiota, which plays important roles in host health. In this study, high-throughput sequencing and quantitative real time PCR were applied to analyze the impact of As and Fe on mouse gut microbiota. Co-exposure of As and Fe mitigated effects on microbial community to a certain extent. Correlation analysis showed the shifts in gut microbiota caused by As and/or Fe exposure might be important reason of changes in metabolic profiles of mouse. For antibiotic resistance genes (ARGs), co-exposure of As and Fe increased types and abundance of ARGs. But for high abundance ARGs, such as tetQ, tetO and tetM, co-exposure of As and Fe mitigated effects on their abundances compared to exposure to As and Fe alone. No obvious relationship between ARGs and mobile genetic elements were found. The changes in ARGs caused by metal exposure might be due to the alteration of gut microbial diversity. Our results show that changes of gut microbial community caused by As and/or Fe can influence host metabolisms and abundances of ARGs in gut, indicating that changes of gut microbiota should be considered during the risk assessment of As and/or Fe. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. [Impact of newly developed metagenomic tools on our knowledge of the gut microbiota and its role in human health: diagnostic and therapeutic issues].

    Science.gov (United States)

    Blottière, Hervé M; Doré, Joël

    2016-11-01

    Over the last years, our vision of the intestinal microbiota and its contribution to human physiology has been fully revisited, thanks to metagenomics. Next generation sequencing allowed a full characterization of the microbiome. Quantitative metagenomic permitted a deep understanding of the intestinal ecosystem, its structure, and potential dysbiosis in several human pathologies. The microbiome may be used as biomarker of disease or of risk to progress toward a disease. A good understanding of the mechanisms of interaction between gut microbiota and its host is needed; functional metagenomic is a useful tool to identify genes and metabolites able to interact with host's cells. Overall, the microbiome science that is developing opens new avenue for diagnosis, discovery of new drugs and potential therapeutic approaches. It is also a target for modulation by food, with potential impact on health. © 2016 médecine/sciences – Inserm.

  16. Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens — A Review

    Directory of Open Access Journals (Sweden)

    Ki Young Choi

    2015-09-01

    Full Text Available Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT, the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future.

  17. Taxonomic and functional annotation of gut bacterial communities of Eisenia foetida and Perionyx excavatus.

    Science.gov (United States)

    Singh, Arjun; Singh, Dushyant P; Tiwari, Rameshwar; Kumar, Kanika; Singh, Ran Vir; Singh, Surender; Prasanna, Radha; Saxena, Anil K; Nain, Lata

    2015-06-01

    Epigeic earthworms can significantly hasten the decomposition of organic matter, which is known to be mediated by gut associated microflora. However, there is scanty information on the abundance and diversity of the gut bacterial flora in different earthworm genera fed with a similar diet, particularly Eisenia foetida and Perionyx excavatus. In this context, 16S rDNA based clonal survey of gut metagenomic DNA was assessed after growth of these two earthworms on lignocellulosic biomass. A set of 67 clonal sequences belonging to E. foetida and 75 to P. excavatus were taxonomically annotated using MG-RAST and RDP pipeline servers. Highest number of sequences were annotated to Proteobacteria (38-44%), followed by unclassified bacteria (14-18%) and Firmicutes (9.3-11%). Comparative analyses revealed significantly higher abundance of Actinobacteria and Firmicutes in the gut of P. excavatus. The functional annotation for the 16S rDNA clonal libraries of both the metagenomes revealed a high abundance of xylan degraders (12.1-24.1%). However, chitin degraders (16.7%), ammonia oxidizers (24.1%) and nitrogen fixers (7.4%) were relatively higher in E. foetida, while in P. excavatus; sulphate reducers and sulphate oxidizers (12.1-29.6%) were more abundant. Lignin degradation was detected in 3.7% clones of E. foetida, while cellulose degraders represented 1.7%. The gut microbiomes showed relative abundance of dehalogenators (17.2-22.2%) and aromatic hydrocarbon degraders (1.7-5.6%), illustrating their role in bioremediation. This study highlights the significance of differences in the inherent microbiome of these two earthworms in shaping the metagenome for effective degradation of different types of biomass under tropical conditions. Copyright © 2015 Elsevier GmbH. All rights reserved.

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

    NARCIS (Netherlands)

    Zhernakova, A.; Kurilshikov, A.; Bonder, M.J.; Tigchelaar, E.F.; Schirmer, M.; Vatanen, T.; Mujagic, Z.; Vila, A.V.; Falony, G.; Vieira-Silva, S.; Wang, J; Imhann, F.; Brandsma, E.; Jankipersadsing, S.A.; Joossens, M.; Cenit, M.C.; Deelen, P.; Swertz, M.A.; Weersma, R.K.; Feskens, E.J.M.; Netea, M.G.; Gevers, D.; Jonkers, D.; Franke, L.; Aulchenko, Y.S.; Huttenhower, C.; Raes, J.; Hofker, M.H.; Xavier, R.J.; Wijmenga, C.; Fu, J.

    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

  19. 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 sev...

  20. Comparative Fecal Metagenomics Unveils Unique Functional Capacity of the Swine Gut

    Science.gov (United States)

    Uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health and to food and water safety due to the presence of human pathogens in pig feces. Limited information on the physiological...

  1. Comparative Metagenomic Analysis of Human Gut Microbiome Composition Using Two Different Bioinformatic Pipelines

    Directory of Open Access Journals (Sweden)

    Valeria D’Argenio

    2014-01-01

    Full Text Available Technological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial community composition. In particular, 16S rRNA-based methods have been widely used to analyze the whole set of bacteria present in a target environment. As a consequence, several specific bioinformatic pipelines have been developed to manage these data. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST and Quantitative Insights Into Microbial Ecology (QIIME are two freely available tools for metagenomic analyses that have been used in a wide range of studies. Here, we report the comparative analysis of the same dataset with both QIIME and MG-RAST in order to evaluate their accuracy in taxonomic assignment and in diversity analysis. We found that taxonomic assignment was more accurate with QIIME which, at family level, assigned a significantly higher number of reads. Thus, QIIME generated a more accurate BIOM file, which in turn improved the diversity analysis output. Finally, although informatics skills are needed to install QIIME, it offers a wide range of metrics that are useful for downstream applications and, not less important, it is not dependent on server times.

  2. Metagenomic analysis of the gut microbiota of the Timber Rattlesnake, Crotalus horridus.

    Science.gov (United States)

    McLaughlin, Richard William; Cochran, Philip A; Dowd, Scot E

    2015-07-01

    Snakes are capable of surviving long periods without food. In this study we characterized the microbiota of a Timber Rattlesnake (Crotalus horridus), devoid of digesta, living in the wild. Pyrosequencing-based metagenomics were used to analyze phylogenetic and metabolic profiles with the aid of the MG-RAST server. Pyrosequencing of samples taken from the stomach, small intestine and colon yielded 691696, 957756 and 700419 high quality sequence reads. Taxonomic analysis of metagenomic reads indicated Eukarya was the most predominant domain, followed by bacteria and then viruses, for all three tissues. The most predominant phylum in the domain Bacteria was Proteobacteria for the tissues examined. Functional classifications by the subsystem database showed cluster-based subsystems were most predominant (10-15 %). Almost equally predominant (10-13 %) was carbohydrate metabolism. To identify bacteria in the colon at a finer taxonomic resolution, a 16S rRNA gene clone library was created. Proteobacteria was again found to be the most predominant phylum. The present study provides a baseline for understanding the microbial ecology of snakes living in the wild.

  3. Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet.

    Science.gov (United States)

    Koo, Hyunmin; Hakim, Joseph A; Powell, Mickie L; Kumar, Ranjit; Eipers, Peter G; Morrow, Casey D; Crowley, Michael; Lefkowitz, Elliot J; Watts, Stephen A; Bej, Asim K

    2017-04-01

    In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using a metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine. The CFD-fed D. rerio exhibited KEGG functional categories of bacteria-mediated cobalamin biosynthesis, which was supported by the presence of cobalamin synthesizers such as Bacteroides and Lactobacillus. Though these bacteria were absent in GFD-fed D. rerio, a comparable level of the cobalamin biosynthesis KEGG functional category was observed, which could be contributed by the compensatory enrichment of Cetobacterium. Based on these results, we conclude D. rerio to be a suitable alternative animal model for the use of a targeted metagenomics approach along with bioinformatics tools to further investigate the relationship between the gluten diet and microbiome profile in the gut ecosystem leading to gastrointestinal diseases and other undesired adverse health effects. Copyright © 2017. Published by Elsevier B.V.

  4. Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome.

    Directory of Open Access Journals (Sweden)

    Eamonn P Culligan

    Full Text Available Functional environmental screening of metagenomic libraries is a powerful means to identify and assign function to novel genes and their encoded proteins without any prior sequence knowledge. In the current study we describe the identification and subsequent analysis of a salt-tolerant clone from a human gut metagenomic library. Following transposon mutagenesis we identified an unknown gene (stlA, for "salt tolerance locus A" with no current known homologues in the databases. Subsequent cloning and expression in Escherichia coli MKH13 revealed that stlA confers a salt tolerance phenotype in its surrogate host. Furthermore, a detailed in silico analysis was also conducted to gain additional information on the properties of the encoded StlA protein. The stlA gene is rare when searched against human metagenome datasets such as MetaHit and the Human Microbiome Project and represents a novel and unique salt tolerance determinant which appears to be found exclusively in the human gut environment.

  5. [Taxonomic composition of metagenomic community in the larval gut of mosquito Anopheles sinensis (Diptera: Culicidae)].

    Science.gov (United States)

    Nan, Chun-Yan; Ma, Ya-Jun; Xu, Jian-Nong; Liang, Jian

    2013-04-01

    To investigate the bacteria diversity in larval gut of field-collected Anopheles sinensis. The 16S rDNA V4 region of An. sinensis larvae collected from paddy on Jiading District of Shanghai (L1/L2) and small seeping water on Wenchang City of Hainan (AS) was sequenced by high-throughput pyrosequencing. Using Qiime and Mothur softwares, the number of sequences and operational taxonomic units (OTUs) for each sample was sorted and calculated, the species abundance and distribution, Alpha diversity index and difference times of species abundance among samples were analyzed. The number of sequences and OTUs for each sample were 253 724/3 930 (L1), 225 203/4 312 (L2) and 73 990/2 380 (AS). The rarefaction curves showed that adequate sampling was achieved. The number of OTUs was close to actual situation. The value of richness index was 5 942.61/6 534.88 (L1), 6 328.17/7 235.89 (L2) and 4228.66/5 651.20 (AS); diversity index was 4.63/0.03 (L1), 5.10/0.02 (L2) and 0.14/3.94 (AS). The dominant species of An. sinensis larvae gut microbiota all belonged to the phylum Proteobacteria, with a percentage of 87% (AS) and 90% (L). In addition, the dominant phyla among them were Firmicutes, Bacteroidetes and Actinobacteria. The comparison of bacterial abundance between L and AS showed that there were 18 phyla with significant difference, except the Proteobacteria and Deinococcus-Thermus; only 9 phyla were different significantly between L1 and L2. Evenness and richness of bacteria flora in the An. sinensis larvae gut collected from paddy and small seeping waters were obtained.

  6. Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency.

    Science.gov (United States)

    Yan, Wei; Sun, Congjiao; Yuan, Jingwei; Yang, Ning

    2017-03-28

    Interactions between the host and gut microbiota can affect gut metabolism. In this study, the individual performances of 252 hens were recorded to evaluate feed efficiency. Hens with contrasting feed efficiencies (14 birds per group) were selected to investigate their duodenal, cecal and fecal microbial composition by sequencing the 16S rRNA gene V4 region. The results showed that the microbial community in the cecum was quite different from those in the duodenum and feces. The highest biodiversity and all differentially abundant taxa between the different efficiency groups were observed in the cecal microbial community with false discovery rate (FDR) feed efficiency (BFE) group. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis revealed that the functions relating to glycometabolism and amino acid metabolism were enriched in the cecal microbiota of the BFE group. These results indicated the prominent role of cecal microbiota in the feed efficiency of chickens and suggested plausible uses of Lactobacillus to improve the feed efficiency of host.

  7. The Effect of Helicobacter pylori Eradication on Human Microbiota: Metagenome Analysis of the Human Gut Microbiome

    Directory of Open Access Journals (Sweden)

    D.R. Khusnutdinova

    2017-06-01

    Full Text Available A total of 152 stool samples from 76 patients with symptoms of gastrointestinal diseases have been analyzed using metagenomic shotgun sequencing technology to assess the effect of Helicobacter pylori eradication therapy on Bifidobacterium, Lactobacillus, Escherichia, and Clostridium genera. The relative abundance of bacteria representing these genera in the intestinal microflora of patients before and after antibiotic therapy has been evaluated. It has been shown that the therapy did not have any critical effect in the majority of cases on the number of Lactobacillus, Escherichia and Clostridium genera in the microbial community. Their abundance varied within 0.5% in 76.5%, 51.3%, and 55.2% of patients, respectively. The Bifidobacterium genus has been found to be more susceptible to antibiotics (their number decreased significantly in 60.5% of cases. However, 9.2% of patients have shown the opposite effect. Thus, the obtained data demonstrate that Helicobacter pylori eradication therapy does not have uniform effects on the key members of human intestinal microbiota. This fact should be taken into account when predicting the risks of side effects of antibiotics.

  8. Screening and characterization of a novel cellulase gene from the gut microflora of Hermetia illucens using metagenomic library.

    Science.gov (United States)

    Lee, Chang-Muk; Lee, Young-Seok; Seo, So-Hyeon; Yoon, Sang-Hong; Kim, Soo-Jin; Hahn, Bum-Soo; Sim, Joon-Soo; Koo, Bon-Sung

    2014-09-01

    A metagenomic fosmid library was constructed using genomic DNA isolated from the gut microflora of Hermetia illucens, a black soldier fly. A cellulase-positive clone, with the CS10 gene, was identified by extensive Congo-red overlay screenings for cellulase activity from the fosmid library of 92,000 clones. The CS10 gene was composed of a 996 bp DNA sequence encoding the mature protein of 331 amino acids. The deduced amino acids of CS10 showed 72% sequence identity with the glycosyl hydrolase family 5 gene of Dysgonomonas mossii, displaying no significant sequence homology to already known cellulases. The purified CS10 protein presented a single band of cellulase activity with a molecular mass of approximately 40 kDa on the SDS-PAGE gel and zymogram. The purified CS10 protein exhibited optimal activity at 50°C and pH 7.0, and the thermostability and pH stability of CS10 were preserved at the ranges of 20~50°C and pH 4.0~10.0. CS10 exhibited little loss of cellulase activity against various chemical reagents such as 10% polar organic solvents, 1% non-ionic detergents, and 0.5 M denaturing agents. Moreover, the substrate specificity and the product patterns by thinlayer chromatography suggested that CS10 is an endo-β-1,4-glucanase. From these biochemical properties of CS10, it is expected that the enzyme has the potential for application in industrial processes.

  9. Nanomaterials: Earthworms lit with quantum dots

    Science.gov (United States)

    Tilley, Richard D.; Cheong, Soshan

    2013-01-01

    Yeast, bacteria and fungi have been used to synthesize a variety of nanocrystals. Now, the metal detoxification process in the gut of an earthworm is exploited to produce biocompatible cadmium telluride quantum dots.

  10. Gut

    DEFF Research Database (Denmark)

    Muscogiuri, Giovanna; Balercia, Giancarlo; Barrea, Luigi

    2017-01-01

    which may be related to both the intestinal microbiological profile and patterns of gut hormones secretion. Intestinal microbiota includes trillions of microorganisms but its composition and function may be adversely affected in type 2 diabetes. The intestinal microbiota may be responsible......The gut regulates glucose and energy homeostasis; thus, the presence of ingested nutrients into the gut activates sensing mechanisms that affect both glucose homeostasis and regulate food intake. Increasing evidence suggest that gut may also play a key role in the pathogenesis of type 2 diabetes...... metabolism. Thus, the aim of this manuscript is to review the current evidence on the role of the gut in the pathogenesis of type 2 diabetes, taking into account both hormonal and microbiological aspects....

  11. Earthworm eco-physiological characteristics and quantification of earthworm feeding in vermifiltration system for sewage sludge stabilization using stable isotopic natural abundance

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xiaowei; Xing, Meiyan, E-mail: lixiaowei419@163.com; Yang, Jian; Dai, Xiaohu

    2014-07-15

    Highlights: • Earthworm growth biomass and activity decreased with the VF depth. • Earthworm gut microbial communities were dominated by Gammaproteobacteria. • δ{sup 15}N and δ{sup 13}C in earthworms decreased with time, and increased with the VF depth. • Effect of earthworm feeding in enhanced VSS reduction was analyzed quantitatively. • Earthworm feeding had low contribution to the enhanced VSS reduction. - Abstract: Previous studies showed that the presence of earthworm improves treatment performance of vermifilter (VF) for sewage sludge stabilization, but earthworm eco-physiological characteristics and effects in VF were not fully investigated. In this study, earthworm population, enzymatic activity, gut microbial community and stable isotopic abundance were investigated in the VF. Results showed that biomass, average weight, number and alkaline phosphatase activity of the earthworms tended to decrease, while protein content and activities of peroxidase and catalase had an increasing tendency as the VF depth. Earthworm gut microbial communities were dominated by Gammaproteobacteria, and the percentages arrived to 76–92% of the microbial species detected. {sup 15}N and {sup 13}C natural abundance of the earthworms decreased with operation time, and increased as the VF depth. Quantitative analysis using δ{sup 15}N showed that earthworm feeding and earthworm–microorganism interaction were responsible for approximately 21% and 79%, respectively, of the enhanced volatile suspended solid reduction due to the presence of earthworm. The finding provides a quantitative insight into how earthworms influence on sewage sludge stabilization in vermifiltration system.

  12. Metagenomic identification of a novel salt tolerance gene from the human gut microbiome which encodes a membrane protein with homology to a brp/blh-family β-carotene 15,15'-monooxygenase.

    Directory of Open Access Journals (Sweden)

    Eamonn P Culligan

    Full Text Available The human gut microbiome consists of at least 3 million non-redundant genes, 150 times that of the core human genome. Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. Cloning and heterologous expression of brpA in Escherichia coli confers a significant salt tolerance phenotype. Furthermore, when cultured in the presence of exogenous β-carotene, cell pellets adopt a red/orange pigmentation indicating the incorporation of carotenoids in the cell membrane.

  13. Metagenomic Analysis of the Dynamic Changes in the Gut Microbiome of the Participants of the MARS-500 Experiment, Simulating Long Term Space Flight.

    Science.gov (United States)

    Mardanov, A V; Babykin, M M; Beletsky, A V; Grigoriev, A I; Zinchenko, V V; Kadnikov, V V; Kirpichnikov, M P; Mazur, A M; Nedoluzhko, A V; Novikova, N D; Prokhortchouk, E B; Ravin, N V; Skryabin, K G; Shestakov, S V

    2013-07-01

    A metagenomic analysis of the dynamic changes of the composition of the intestinal microbiome of five participants of the MARS-500 experiment was performed. DNA samples were isolated from the feces of the participants taken just before the experiment, upon 14, 30, 210, 363 and 510 days of isolation in the experimental module, and two weeks upon completion of the experiment. The taxonomic composition of the microbiome was analyzed by pyrosequencing of 16S rRNA gene fragments. Both the taxonomic and functional gene content of the microbiome of one participant were analyzed by whole metagenome sequencing using the SOLiD technique. Each participant had a specific microbiome that could be assigned to one of three recognized enterotypes. Two participants had enterotype I microbiomes characterized by the prevalence of Bacteroides, while the microbiomes of two others, assigned to type II, were dominated by Prevotella. One participant had a microbiome of mixed type. It was found that (1) changes in the taxonimic composition of the microbiomes occurred in the course of the experiment, but the enterotypes remained the same; (2) significant changes in the compositions of the microbiomes occurred just 14-30 days after the beginning of the experiment, presumably indicating the influence of stress factors in the first stage of the experiment; (3) a tendency toward a reversion of the microbiomes to their initial composition was observed two weeks after the end of the experiment, but complete recovery was not achieved. The metagenomic analysis of the microbiome of one of the participants showed that in spite of variations in the taxonomic compositions of microbiomes, the "functional" genetic composition was much more stable for most of the functional gene categories. Probably in the course of the experiment the taxonomic composition of the gut microbiome was adaptively changed to reflect the individual response to the experimental conditions. A new, balanced taxonomic composition

  14. The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics.

    Science.gov (United States)

    Dubourg, G; Lagier, J C; Armougom, F; Robert, C; Hamad, I; Brouqui, P; Raoult, D

    2013-05-01

    Gut microbiota consists of 10(10) bacteria per gram of stool. Many antibiotic regimens induce a reduction in both the diversity and the abundance of the gut flora. We analyzed one stool sample collected from a patient treated for drug-resistant Mycobacterium tuberculosis and who ultimately died from pneumonia due to a Streptococcus pneumoniae 10 months later. We performed microscopic observation, used 70 culture conditions (microbial culturomics) with identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and 16S rRNA amplification and sequencing, pyrosequencing, and 18S rRNA amplification and clone sequencing. Electron and optical microscopic observations revealed the presence of yeast, but no bacterial species were observed. By culture, only 39 bacterial species were identified, including one new species, as well as three species that have not been previously observed in the human gut. The pyrosequencing showed only 18 phylotypes, detecting a lower number of bacterial species than the culture techniques. Only two phylotypes overlapped with culturomics. In contrast, an amount of chloroplasts was found. Additionally, specific molecular eukaryote detection found three fungal species. We recovered, for the first time, more cultivable than non-cultivable bacterial species in a patient with a low bacterial load in the gut, demonstrating the depth bias of pyrosequencing. We propose that the desertification of gut microbiota in this patient is a reflection of the total body microbiota and may have contributed to the invasive infection of S. pneumoniae. This finding suggests that caution should be applied when treating patients with broad-spectrum antibiotics, and preventive measures should be taken in order to avoid invasive infection.

  15. Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota.

    Directory of Open Access Journals (Sweden)

    Sébastien Raguideau

    2016-12-01

    Full Text Available Whole Genome Shotgun (WGS metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems, both from the taxonomic and functional point of view. Gene inventories of otherwise uncultured microbial communities make the direct functional profiling of microbial communities possible. The concept of community aggregated trait has been adapted from environmental and plant functional ecology to the framework of microbial ecology. Community aggregated traits are quantified from WGS data by computing the abundance of relevant marker genes. They can be used to study key processes at the ecosystem level and correlate environmental factors and ecosystem functions. In this paper we propose a novel model based approach to infer combinations of aggregated traits characterizing specific ecosystemic metabolic processes. We formulate a model of these Combined Aggregated Functional Traits (CAFTs accounting for a hierarchical structure of genes, which are associated on microbial genomes, further linked at the ecosystem level by complex co-occurrences or interactions. The model is completed with constraints specifically designed to exploit available genomic information, in order to favor biologically relevant CAFTs. The CAFTs structure, as well as their intensity in the ecosystem, is obtained by solving a constrained Non-negative Matrix Factorization (NMF problem. We developed a multicriteria selection procedure for the number of CAFTs. We illustrated our method on the modelling of ecosystemic functional traits of fiber degradation by the human gut microbiota. We used 1408 samples of gene abundances from several high-throughput sequencing projects and found that four CAFTs only were needed to represent the fiber degradation potential. This data reduction highlighted biologically consistent functional patterns while providing a high quality preservation of the original data. Our method is generic and can be applied to other

  16. Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes.

    Science.gov (United States)

    Wang, Mingjie; Doak, Thomas G; Ye, Yuzhen

    2015-11-02

    Comparative metagenomics remains challenging due to the size and complexity of metagenomic datasets. Here we introduce subtractive assembly, a de novo assembly approach for comparative metagenomics that directly assembles only the differential reads that distinguish between two groups of metagenomes. Using simulated datasets, we show it improves both the efficiency of the assembly and the assembly quality of the differential genomes and genes. Further, its application to type 2 diabetes (T2D) metagenomic datasets reveals clear signatures of the T2D gut microbiome, revealing new phylogenetic and functional features of the gut microbial communities associated with T2D.

  17. Snapshot on a Pilot Metagenomic Study for the Appraisal of Gut Microbial Diversity in Mice, Cat, and Man

    Directory of Open Access Journals (Sweden)

    Coline Plé

    2016-01-01

    Full Text Available Gut microbiota plays a key role in the maintenance of homeostasis and host physiology, comprising development, metabolism, and immunity. Profiling the composition and the gastrointestinal microbiome with a reliable methodology is of substantial interest to yield new insights into the pathogenesis of many diseases as well as defining new prophylactic and therapeutic interventions. Here, we briefly present our methodology applied to fecal samples from mice and then further extended to the samples from a cat and a single human subject at 4 different time points as examples to illustrate the methodological strengths. Both interindividual and time-related variations are demonstrated and discussed.

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

    Directory of Open Access Journals (Sweden)

    Sandrine Louis

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

  19. Nitrous oxide reductase genes (nosZ) of denitrifying populations in soil and the earthworm gut are phylogenetically similar

    DEFF Research Database (Denmark)

    Horn, Marcus A.; Drake, Harold L.; Schramm, Andreas

    2006-01-01

    -derived sequences, or were related to N2O reductases of the genera Bradyrhizobium, Brucella, Dechloromonas, Flavobacterium, Pseudomonas, Ralstonia, and Sinorhizobium. Although the numbers of estimators for genotype richness of sequence data from the gut were higher than those of soil, only one gut-derived nos...

  20. Novel Strategies for Applied Metagenomics.

    Science.gov (United States)

    Moore-Connors, Jessica M; Dunn, Katherine A; Bielawski, Joseph P; Van Limbergen, Johan

    2016-03-01

    Detailed analyses of the gut microbiome and its effect on human physiology and disease are emerging, thanks to advances in high-throughput DNA-sequencing technology and the burgeoning field of metagenomics. Metagenomics examines the structure and functional potential of microbial communities in their native habitats through the direct isolation and analysis of community DNA. In inflammatory bowel disease, gut microbiome studies have shown an association with perturbations in community composition and, especially, function. In this review, we discuss the application of next-generation sequencing to microbiome research and highlight the importance of modeling microbiome structure and function to the future of inflammatory bowel disease research and treatment.

  1. Investigating the chicken and turkey enteric microbiomes: metagenomics as a tool for virus discovery and community analysis in the poultry gut

    Science.gov (United States)

    Gut health and the management of the gut microflora in poultry are complicated and overarching concepts that are influenced through management approaches (including the administration of antibiotic growth promoters), feed nutrient composition and utilization, early gut damage by pathogens such as en...

  2. A retrospective metagenomics approach to studying Blastocystis

    DEFF Research Database (Denmark)

    Andersen, Lee O'Brien; Bonde, Ida; Nielsen, Henrik Bjørn

    2015-01-01

    Blastocystis is a common single-celled intestinal parasitic genus, comprising several subtypes. Here, we screened data obtained by metagenomic analysis of faecal DNA for Blastocystis by searching for subtype-specific genes in coabundance gene groups, which are groups of genes that covary across......- and Prevotella-driven enterotypes. This is the first study to investigate the relationship between Blastocystis and communities of gut bacteria using a metagenomics approach. The study serves as an example of how it is possible to retrospectively investigate microbial eukaryotic communities in the gut using...... metagenomic datasets targeting the bacterial component of the intestinal microbiome and the interplay between these microbial communities....

  3. Earthworm eco-physiological characteristics and quantification of earthworm feeding in vermifiltration system for sewage sludge stabilization using stable isotopic natural abundance.

    Science.gov (United States)

    Li, Xiaowei; Xing, Meiyan; Yang, Jian; Dai, Xiaohu

    2014-07-15

    Previous studies showed that the presence of earthworm improves treatment performance of vermifilter (VF) for sewage sludge stabilization, but earthworm eco-physiological characteristics and effects in VF were not fully investigated. In this study, earthworm population, enzymatic activity, gut microbial community and stable isotopic abundance were investigated in the VF. Results showed that biomass, average weight, number and alkaline phosphatase activity of the earthworms tended to decrease, while protein content and activities of peroxidase and catalase had an increasing tendency as the VF depth. Earthworm gut microbial communities were dominated by Gammaproteobacteria, and the percentages arrived to 76-92% of the microbial species detected. (15)N and (13)C natural abundance of the earthworms decreased with operation time, and increased as the VF depth. Quantitative analysis using δ(15)N showed that earthworm feeding and earthworm-microorganism interaction were responsible for approximately 21% and 79%, respectively, of the enhanced volatile suspended solid reduction due to the presence of earthworm. The finding provides a quantitative insight into how earthworms influence on sewage sludge stabilization in vermifiltration system. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Assembling large, complex environmental metagenomes

    Energy Technology Data Exchange (ETDEWEB)

    Howe, A. C. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Plant Soil and Microbial Sciences; Jansson, J. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division; Malfatti, S. A. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Tringe, S. G. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Tiedje, J. M. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Plant Soil and Microbial Sciences; Brown, C. T. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Computer Science and Engineering

    2012-12-28

    The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more computationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.

  5. Identification and characterization of RNA viruses in the turkey gut using metagenomics: an abundance of picornaviruses and other “small, round viruses”

    Science.gov (United States)

    Poultry enteric disease is marked by diarrhea, stunting, immune dysfunction and mortality. Numerous viruses have been detected in the poultry gut, and have subsequently been implicated in enteric disease.Knowledge of the complete viral flora present in the poultry gut would facilitate the developmen...

  6. Teacher's Guide for Earthworms.

    Science.gov (United States)

    Bruno, Merle S.; And Others

    This teacher's guide on earthworms includes four major sections: (1) introduction, (2) caring for earthworms in the classroom, (3) classroom activities, and (4) the appendix. The introduction includes information concerning grade level, scheduling, materials, obtaining earthworms, field study, classroom clean-up, and records. Caring for earthworms…

  7. Gut microbiomes of Indian children of varying nutritional status

    National Research Council Canada - National Science Library

    Ghosh, Tarini Shankar; Gupta, Sourav Sen; Bhattacharya, Tanudeep; Yadav, Deepak; Barik, Anamitra; Chowdhury, Abhijit; Das, Bhabatosh; Mande, Sharmila S; Nair, G Balakrish

    2014-01-01

    .... Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition. Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status...

  8. Earthworms and Soil Pollutants

    Directory of Open Access Journals (Sweden)

    Kazuyoshi Tamae

    2011-11-01

    Full Text Available Although the toxicity of metal contaminated soils has been assessed with various bioassays, more information is needed about the biochemical responses, which may help to elucidate the mechanisms involved in metal toxicity. We previously reported that the earthworm, Eisenia fetida, accumulates cadmium in its seminal vesicles. The bio-accumulative ability of earthworms is well known, and thus the earthworm could be a useful living organism for the bio-monitoring of soil pollution. In this short review, we describe recent studies concerning the relationship between earthworms and soil pollutants, and discuss the possibility of using the earthworm as a bio-monitoring organism for soil pollution.

  9. Enhanced bioremoval of lead by earthworm-Lumbricus terrestris co-cultivated with bacteria-Klebsiella variicola.

    Science.gov (United States)

    Das, Anamika; Osborne, Jabez W

    2017-10-01

    Lead is a toxic heavy metal having devastating effects on the environment. The current study was focussed on bioremoval of lead using earthworm and lead resistant bacteria. Earthworms were subjected to various concentrations of lead in the soil bioaugmented with lead resistant bacteria (VITMVCJ1) to enhance the uptake of lead from the contaminated soil. Significant increase was observed in the length and body weight of the earthworms supplemented with lead resistant bacteria. Similarly, there was a substantial increase in the locomotion rate of the earthworms treated with lead resistant bacteria in comparison with the control. The gut micro flora of bacterial treated earthworms had increased number of bacterial cells than the untreated earthworms. The histopathological studies revealed the toxic effects of lead on the gut of earthworms indicating severe damage in lead resistant bacteria untreated worms, whereas the cells were intact in lead resistant bacteria treated worms. COMET assay showed increased DNA damage with higher tail DNA percent in the untreated earthworms. Further, the colonisation of the bacteria supplemented, onto the gut region of earthworms was observed by scanning electron microscopy. Atomic absorption spectrophotometry indicated a fair 50% uptake of lead within the biomass of earthworm treated with lead resistant bacteria. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Gut Microbiota-brain Axis.

    Science.gov (United States)

    Wang, Hong-Xing; Wang, Yu-Ping

    2016-10-05

    To systematically review the updated information about the gut microbiota-brain axis. All articles about gut microbiota-brain axis published up to July 18, 2016, were identified through a literature search on PubMed, ScienceDirect, and Web of Science, with the keywords of "gut microbiota", "gut-brain axis", and "neuroscience". All relevant articles on gut microbiota and gut-brain axis were included and carefully reviewed, with no limitation of study design. It is well-recognized that gut microbiota affects the brain's physiological, behavioral, and cognitive functions although its precise mechanism has not yet been fully understood. Gut microbiota-brain axis may include gut microbiota and their metabolic products, enteric nervous system, sympathetic and parasympathetic branches within the autonomic nervous system, neural-immune system, neuroendocrine system, and central nervous system. Moreover, there may be five communication routes between gut microbiota and brain, including the gut-brain's neural network, neuroendocrine-hypothalamic-pituitary-adrenal axis, gut immune system, some neurotransmitters and neural regulators synthesized by gut bacteria, and barrier paths including intestinal mucosal barrier and blood-brain barrier. The microbiome is used to define the composition and functional characteristics of gut microbiota, and metagenomics is an appropriate technique to characterize gut microbiota. Gut microbiota-brain axis refers to a bidirectional information network between the gut microbiota and the brain, which may provide a new way to protect the brain in the near future.

  11. Earthworm Collections of the World

    OpenAIRE

    Sherlock, Emma; Livermore, Laurence; Scott, Ben

    2013-01-01

    A poster presenting "Earthworm Collections of the World" This site provides a central hub for researchers and students to locate earthworm collections and specimens, along with useful information on the various earthworm families and species.

  12. Development and utility of the FDA 'GutProbe' DNA microarray for identification, genotyping and metagenomic analysis of commercially available probiotics.

    Science.gov (United States)

    Patro, J N; Ramachandran, P; Lewis, J L; Mammel, M K; Barnaba, T; Pfeiler, E A; Elkins, C A

    2015-06-01

    Lactic acid bacteria are beneficial microbes added to many food products and dietary supplements for their purported health benefits. Proper identification of bacteria is important to assess safety as well as proper product labelling. A custom microarray (FDA GutProbe) was developed to verify accurate labelling in commercial dietary supplements. Strain-specific attribution was achieved with GutProbe array which contains genes from the most commonly found species in probiotic supplements and food ingredients. Applied utility of the array was assessed with direct from product DNA hybridization to determine (i) if identification of multiple strains in one sample can be conducted and (ii) if any lot-to-lot variations exist with eight probiotics found on the US market. GutProbe is a useful tool in identifying a mixture of microbials in probiotics and did reveal some product variations. In addition, the array is able to identify lot-to-lot differences in these products. These strain level attribution may be useful for routine monitoring of batch variation as part of a 'Good Manufacturing Practices' process. The FDA GutProbe is an efficient and reliable platform to identify the presence of microbial ingredients and determining microbe differences in dietary supplements. The GutProbe is a fast, rapid method for direct community profiling or food matrix sampling. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

  13. Metagenomics and novel gene discovery

    Science.gov (United States)

    Culligan, Eamonn P; Sleator, Roy D; Marchesi, Julian R; Hill, Colin

    2014-01-01

    Metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. Herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of each type of approach, as well as potential solutions. Furthermore, we discuss the potential for metagenomic biotherapeutic discovery, with a particular focus on the human gut microbiome and finally, we outline how the discovery of novel genes may be used to create bioengineered probiotics. PMID:24317337

  14. The effect of anthropogenic arsenic contamination on the earthworm microbiome.

    Science.gov (United States)

    Pass, Daniel Antony; Morgan, Andrew John; Read, Daniel S; Field, Dawn; Weightman, Andrew J; Kille, Peter

    2015-06-01

    Earthworms are globally distributed and perform essential roles for soil health and microbial structure. We have investigated the effect of an anthropogenic contamination gradient on the bacterial community of the keystone ecological species Lumbricus rubellus through utilizing 16S rRNA pyrosequencing for the first time to establish the microbiome of the host and surrounding soil. The earthworm-associated microbiome differs from the surrounding environment which appears to be a result of both filtering and stimulation likely linked to the altered environment associated with the gut micro-habitat (neutral pH, anoxia and increased carbon substrates). We identified a core earthworm community comprising Proteobacteria (∼50%) and Actinobacteria (∼30%), with lower abundances of Bacteroidetes (∼6%) and Acidobacteria (∼3%). In addition to the known earthworm symbiont (Verminephrobacter sp.), we identified a potential host-associated Gammaproteobacteria species (Serratia sp.) that was absent from soil yet observed in most earthworms. Although a distinct bacterial community defines these earthworms, clear family- and species-level modification were observed along an arsenic and iron contamination gradient. Several taxa observed in uncontaminated control microbiomes are suppressed by metal/metalloid field exposure, including eradication of the hereto ubiquitously associated Verminephrobacter symbiont, which raises implications to its functional role in the earthworm microbiome. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  15. Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

    Science.gov (United States)

    Bedarf, J R; Hildebrand, F; Coelho, L P; Sunagawa, S; Bahram, M; Goeser, F; Bork, P; Wüllner, U

    2017-04-28

    Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naïve PD patients might also serve as a biomarker. We performed metagenomic shotgun analyses and compared the fecal microbiomes of 31 early stage, L-DOPA-naïve PD patients to 28 age-matched controls. We found increased Verrucomicrobiaceae (Akkermansia muciniphila) and unclassified Firmicutes, whereas Prevotellaceae (Prevotella copri) and Erysipelotrichaceae (Eubacterium biforme) were markedly lowered in PD samples. The observed differences could reliably separate PD from control with a ROC-AUC of 0.84. Functional analyses of the metagenomes revealed differences in microbiota metabolism in PD involving the ẞ-glucuronate and tryptophan metabolism. While the abundances of prophages and plasmids did not differ between PD and controls, total virus abundance was decreased in PD participants. Based on our analyses, the intake of either a MAO inhibitor, amantadine, or a dopamine agonist (which in summary relates to 90% of PD patients) had no overall influence on taxa abundance or microbial functions. Our data revealed differences of colonic microbiota and of microbiota metabolism between PD patients and controls at an unprecedented detail not achievable through 16S sequencing. The findings point to a yet unappreciated aspect of PD, possibly involving the intestinal barrier function and immune function in PD patients. The influence of the parkinsonian medication should be further investigated in the future in larger cohorts.

  16. Comparison of heavy-metal uptake by Eisenia foetida with that of other common earthworms. Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    Stafford, E.A.; Edwards, C.A.

    1986-01-01

    Earthworms have been used in the field to indicate levels of soil pollution and in the laboratory for the ecotoxicological testing of industrial chemicals. An earthworm bioassay procedure developed at the Waterways Experiment Station (Vicksburg, Mississippi) was modified and evaluated as a method of providing information on heavy-metal bioavailability in contaminated soils and sediments from Europe. Eight soils/sediments containing elevated levels of a least one of the elements Zn, Cu, Cd and Pb were selected as well as a control and a reference soil. Six species of earthworm, including the WES bioassay earthworm E. foetida, and five field species were grown in the soils/sediments for periods of 15, 28 or 56 days. Concentrations of the elements Zn, Cu, Cd, Ni, Cr and Pb present in the earthworm samples (corrected for the presence of soil-derived metals within the earthworm gut) were compared between earthworm species from the same soil and for each earthworm species from a range of metal contaminated soils/sediments. A close linear relationship between metal uptake by E.foetida and the field species of earthworm emerged and good correlation between total (HNO3/HC104) soil Pb and Cd levels and earthworm tissue concentrations and between DTPA extractable soil Cu and Cc levels and earthworm tissue concentrations was observed.

  17. Effects of biochar and the geophagous earthworm Metaphire guillelmi on fate of (14)C-catechol in an agricultural soil.

    Science.gov (United States)

    Shan, Jun; Wang, Yongfeng; Gu, Jianqiang; Zhou, Wenqiang; Ji, Rong; Yan, Xiaoyuan

    2014-07-01

    Both biochar and earthworms can exert influence on behaviors of soil-borne monomeric phenols in soil; however, little was known about the combined effects of biochar and earthworm activities on fate of these chemicals in soil. Using (14)C-catechol as a representative, the mineralization, transformation and residue distribution of phenolic humus monomer in soil amended with different amounts of biochar (0%, 0.05%, 0.5%, and 5%) without/with the geophagous earthworm Metaphire guillelmi were investigated. The results showed biochar at amendment rate Earthworms did not affect the mineralization of (14)C-catechol in soil amended with earthworms were removed from the soil, the mineralization of (14)C-catechol was significantly lower than that of in earthworm-free soil indicating that (14)C-catecholic residues were stabilized during their passage through earthworm gut. The assimilation of (14)C by earthworms was low (1.2%), and was significantly enhanced by biochar amendment, which was attributed to the release of biochar-associated (14)C-catecholic residues during gut passage of earthworm. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Gut Microbiomes of Indian Children of Varying Nutritional Status: e95547

    National Research Council Canada - National Science Library

    Tarini Shankar Ghosh; Sourav Sen Gupta; Tanudeep Bhattacharya; Deepak Yadav; Anamitra Barik; Abhijit Chowdhury; Bhabatosh Das; Sharmila S Mande; G Balakrish Nair

    2014-01-01

    .... Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition. Methodology/Principal Findings Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status...

  19. Quality control of microbiota metagenomics by k-mer analysis.

    Science.gov (United States)

    Plaza Onate, Florian; Batto, Jean-Michel; Juste, Catherine; Fadlallah, Jehane; Fougeroux, Cyrielle; Gouas, Doriane; Pons, Nicolas; Kennedy, Sean; Levenez, Florence; Dore, Joel; Ehrlich, S Dusko; Gorochov, Guy; Larsen, Martin

    2015-03-14

    The biological and clinical consequences of the tight interactions between host and microbiota are rapidly being unraveled by next generation sequencing technologies and sophisticated bioinformatics, also referred to as microbiota metagenomics. The recent success of metagenomics has created a demand to rapidly apply the technology to large case-control cohort studies and to studies of microbiota from various habitats, including habitats relatively poor in microbes. It is therefore of foremost importance to enable a robust and rapid quality assessment of metagenomic data from samples that challenge present technological limits (sample numbers and size). Here we demonstrate that the distribution of overlapping k-mers of metagenome sequence data predicts sequence quality as defined by gene distribution and efficiency of sequence mapping to a reference gene catalogue. We used serial dilutions of gut microbiota metagenomic datasets to generate well-defined high to low quality metagenomes. We also analyzed a collection of 52 microbiota-derived metagenomes. We demonstrate that k-mer distributions of metagenomic sequence data identify sequence contaminations, such as sequences derived from "empty" ligation products. Of note, k-mer distributions were also able to predict the frequency of sequences mapping to a reference gene catalogue not only for the well-defined serial dilution datasets, but also for 52 human gut microbiota derived metagenomic datasets. We propose that k-mer analysis of raw metagenome sequence reads should be implemented as a first quality assessment prior to more extensive bioinformatics analysis, such as sequence filtering and gene mapping. With the rising demand for metagenomic analysis of microbiota it is crucial to provide tools for rapid and efficient decision making. This will eventually lead to a faster turn-around time, improved analytical quality including sample quality metrics and a significant cost reduction. Finally, improved quality

  20. Gut Microbiota-brain Axis

    Science.gov (United States)

    Wang, Hong-Xing; Wang, Yu-Ping

    2016-01-01

    Objective: To systematically review the updated information about the gut microbiota-brain axis. Data Sources: All articles about gut microbiota-brain axis published up to July 18, 2016, were identified through a literature search on PubMed, ScienceDirect, and Web of Science, with the keywords of “gut microbiota”, “gut-brain axis”, and “neuroscience”. Study Selection: All relevant articles on gut microbiota and gut-brain axis were included and carefully reviewed, with no limitation of study design. Results: It is well-recognized that gut microbiota affects the brain's physiological, behavioral, and cognitive functions although its precise mechanism has not yet been fully understood. Gut microbiota-brain axis may include gut microbiota and their metabolic products, enteric nervous system, sympathetic and parasympathetic branches within the autonomic nervous system, neural-immune system, neuroendocrine system, and central nervous system. Moreover, there may be five communication routes between gut microbiota and brain, including the gut-brain's neural network, neuroendocrine-hypothalamic-pituitary-adrenal axis, gut immune system, some neurotransmitters and neural regulators synthesized by gut bacteria, and barrier paths including intestinal mucosal barrier and blood-brain barrier. The microbiome is used to define the composition and functional characteristics of gut microbiota, and metagenomics is an appropriate technique to characterize gut microbiota. Conclusions: Gut microbiota-brain axis refers to a bidirectional information network between the gut microbiota and the brain, which may provide a new way to protect the brain in the near future. PMID:27647198

  1. Distribution of bacteria and fungi in the earthworm Libyodrillus violaceous (Annelida: Oligochaeta, a native earthworm from Nigeria

    Directory of Open Access Journals (Sweden)

    A. B Idowu

    2006-03-01

    Full Text Available Earthworms are soil invertebrates that play a key role in recycling organic matter in soils.In Nigeria, earthworms include Libyodrillus violaceous. Aerobic and anaerobic bacterial counts, as well as fungal counts of viable microorganisms in soils and gut sections, were made on twenty L. violaceous collected from different sites on the campus of the University of Agriculture, Abeokuta, Nigeria. The samples were collected between April and November, 2002. Numbers of microorganisms were higher in castings and gut sections than in uningested soil samples. The guts and their contents also had higher moisture and total nitrogen contents than the uningested soils. Bacteria and fungi isolated from the samples were identified by standard microbiological procedures on the bases of their morphological and biochemical characteristics. Isolated bacteria were identified as Staphylococcus, Bacillus spp., Pseudomonas aeruginosa, Streptococcus mutans, Clostridium, Spirocheata spp., Azotobacter spp., Micrococcus lylae, Acinetobacter spp., Halobacterium for bacteria. Yeast isolates were identified as Candida spp., Zygosaccharomyces spp., Pichia spp., and Saccharomyces spp while molds were identified as, Aspergillus spp., Pytium spp., Penicillium spp., Fusarium spp and Rhizopus spp. Of the five locations examined, the refuse dump area had the highest numbers of both aerobic and anaerobic organisms, followed by the arboretum while the cultivated land area recorded the lowest counts. The higher numbers of microorganisms observed in the gut sections and casts of the earthworms examined in this work reinforce the general concept that the gut and casts of earthworms show higher microbial diversity and activity than the surrounding soil. Rev. Biol. Trop. 54 (1: 49-58. Epub 2006 Mar 31.

  2. Mapping earthworm communities in Europe

    NARCIS (Netherlands)

    Rutgers, M.; Orgiazzi, A.; Gardi, C.; Römbke, J.; Jansch, S.; Keith, A.; Neilson, R.; Boag, B.; Schmidt, O.; Murchie, A.K.; Blackshaw, R.P.; Pérès, G.; Cluzeau, D.; Guernion, M.; Briones, M.J.I.; Rodeiro, J.; Pineiro, R.; Diaz Cosin, D.J.; Sousa, J.P.; Suhadolc, M.; Kos, I.; Krogh, P.H.; Faber, J.H.; Mulder, C.; Bogte, J.J.; Wijnen, van H.J.; Schouten, A.J.; Zwart, de D.

    2016-01-01

    Existing data sets on earthworm communities in Europe were collected, harmonized, collated, modelled and depicted on a soil biodiversity map. Digital Soil Mapping was applied using multiple regressions relating relatively low density earthworm community data to soil characteristics, land use,

  3. Human milk metagenome: a functional capacity analysis

    Science.gov (United States)

    2013-01-01

    Background Human milk contains a diverse population of bacteria that likely influences colonization of the infant gastrointestinal tract. Recent studies, however, have been limited to characterization of this microbial community by 16S rRNA analysis. In the present study, a metagenomic approach using Illumina sequencing of a pooled milk sample (ten donors) was employed to determine the genera of bacteria and the types of bacterial open reading frames in human milk that may influence bacterial establishment and stability in this primal food matrix. The human milk metagenome was also compared to that of breast-fed and formula-fed infants’ feces (n = 5, each) and mothers’ feces (n = 3) at the phylum level and at a functional level using open reading frame abundance. Additionally, immune-modulatory bacterial-DNA motifs were also searched for within human milk. Results The bacterial community in human milk contained over 360 prokaryotic genera, with sequences aligning predominantly to the phyla of Proteobacteria (65%) and Firmicutes (34%), and the genera of Pseudomonas (61.1%), Staphylococcus (33.4%) and Streptococcus (0.5%). From assembled human milk-derived contigs, 30,128 open reading frames were annotated and assigned to functional categories. When compared to the metagenome of infants’ and mothers’ feces, the human milk metagenome was less diverse at the phylum level, and contained more open reading frames associated with nitrogen metabolism, membrane transport and stress response (P milk metagenome also contained a similar occurrence of immune-modulatory DNA motifs to that of infants’ and mothers’ fecal metagenomes. Conclusions Our results further expand the complexity of the human milk metagenome and enforce the benefits of human milk ingestion on the microbial colonization of the infant gut and immunity. Discovery of immune-modulatory motifs in the metagenome of human milk indicates more exhaustive analyses of the functionality of the human

  4. 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 advances in next generation sequencing, which has allowed for large-scale metagenomics studies of different niches of the human microbiota. Especially the gut microbiota has been studied intensively. However, most studies have been purely descriptive, thus there is still a lot to learn regarding...... the interplay between species in the microbiota and also between the host and the inhabiting microorganisms. Additionally, the non-bacterial part of the microbiota, which includes bacteriophages, plasmids and micro-eukaryotes, is not very well described. In this thesis, metagenomics data from the human gut...

  5. Structure and earthworms

    Science.gov (United States)

    Earthworms are an important part of the soil ecosystem and an indicator of soil quality. Sometimes referred to as ecosystem engineers, they play a pivotal role in maintaining soil productivity. Their burrowing, feeding, and casting activities alter the physical, chemical, and biological properties o...

  6. Bioremediation and detoxification of industrial wastes by earthworms: Vermicompost as powerful crop nutrient in sustainable agriculture.

    Science.gov (United States)

    Bhat, Sartaj Ahmad; Singh, Sharanpreet; Singh, Jaswinder; Kumar, Sunil; Bhawana; Vig, Adarsh Pal

    2018-03-01

    Vermicompost is the final product of the vermicomposting process involving the collective action of earthworms and microbes. During this process, the waste is converted into useful manure by reducing the harmful effects of waste. Toxicity of industrial wastes is evaluated by plant bioassays viz. Allium cepa and Vicia faba test. These bioassays are sensitive and cost-effective for the monitoring of environmental contamination. The valorization potential of earthworms and their ability to detoxify heavy metals in industrial wastes is because of their strong metabolic system and involvement of earthworm gut microbes and chloragocyte cells. Most of the studies reported that the vermicompost produced from organic wastes contains higher amounts of humic substances, which plays a major role in growth of plants. The present article discusses the detoxification of industrial wastes by earthworms and the role of final vermicompost in plant growth and development. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. Field preservation and DNA extraction methods for intestinal microbial diversity analysis in earthworms.

    Science.gov (United States)

    Thakuria, Dwipendra; Schmidt, Olaf; Liliensiek, Ann-Kathrin; Egan, Damian; Doohan, Fiona M

    2009-03-01

    We assessed the effect of DNA extraction and sample preservation methods on the DNA yield and quality obtained from earthworm (Aporrectodea caliginosa Savigny) gut samples and on the results obtained by bacterial and fungal automated ribosomal intergenic spacer analysis (ARISA) of DNA extracts. Methods based on a hexadecyltrimethylammonium bromide dithiotreitol (CTAB-DTT) extraction buffer yielded more favourable results than those based on a sodium dodecyl sulphate (SDS) buffer. For both of these buffers, incorporation of a bead-beating during the lysis step increased the ARISA-derived bacterial ribotype numbers and diversity estimates, as determined for gut wall samples (PDNA extracted by the CTAB-DTT and SDS-based methods were of comparable quality (P> or =0.05), the former method yielded >1.5 times more DNA from both gut contents and gut walls of earthworms than the latter method (both incorporating the bead beating step) (PDNA extracted by the CTAB-DTT- as compared to the SDS-based method (PDNA extracted by the CTAB-DTT (but not by the SDS-based) method (Global R=0.76, PCTAB-DTT-based method, we showed that earthworm preservation in ethanol yielded higher quality DNA from gut contents than preservation in either chloroform or liquid N, as determined by spectrophotometry, PCR inhibition analysis and bacterial and fungal ARISA (PCTAB-DTT-based DNA extraction method described herein are also suitable for the analysis of gut-associated microbiota in other soil and sediment feeding invertebrates.

  8. [A review on the bioinformatics pipelines for metagenomic research].

    Science.gov (United States)

    Ye, Dan-Dan; Fan, Meng-Meng; Guan, Qiong; Chen, Hong-Ju; Ma, Zhan-Shan

    2012-12-01

    Metagenome, a term first dubbed by Handelsman in 1998 as "the genomes of the total microbiota found in nature", refers to sequence data directly sampled from the environment (which may be any habitat in which microbes live, such as the guts of humans and animals, milk, soil, lakes, glaciers, and oceans). Metagenomic technologies originated from environmental microbiology studies and their wide application has been greatly facilitated by next-generation high throughput sequencing technologies. Like genomics studies, the bottle neck of metagenomic research is how to effectively and efficiently analyze the gigantic amount of metagenomic sequence data using the bioinformatics pipelines to obtain meaningful biological insights. In this article, we briefly review the state-of-the-art bioinformatics software tools in metagenomic research. Due to the differences between the metagenomic data obtained from whole genome sequencing (i.e., shotgun metagenomics) and amplicon sequencing (i.e., 16S-rRNA and gene-targeted metagenomics) methods, there are significant differences between the corresponding bioinformatics tools for these data; accordingly, we review the computational pipelines separately for these two types of data.

  9. Metagenomic Analysis of the Human Gut Microbiome

    OpenAIRE

    dos Santos, Marcelo Bertalan Quintanilha; Nielsen, Henrik Bjørn; Sicheritz-Pontén, Thomas

    2013-01-01

    At forstå betydningen af den mikrobielle flora i menneskets tarmsystem i sammenhæng med vores sundhed, er et af de største videnskabelige udfordringer i vores årti. Da 90% af vores celler er bakterier, og det mikrobielle genom indeholder 200 gange flere gener end det humane genom, kan en undersøgelse af den humane mikrobiom have potentiale til at påvirke mange områder vedrørende vores helbredet. I dette PhD forløb har vi genereret en stor mængde eksperimentelle data baseret på DNA og RNA af d...

  10. Comparison of metagenomic samples using sequence signatures

    Directory of Open Access Journals (Sweden)

    Jiang Bai

    2012-12-01

    are obtained through the analyses. Our results show that sequence signatures of the mammalian gut are closely associated with diet and gut physiology of the mammals, and that sequence signatures of marine communities are closely related to location and temperature. Conclusions Sequence signatures can successfully reveal major group and gradient relationships among metagenomic samples from NGS reads without alignment to reference databases. The d2S dissimilarity measure is a good choice in all application scenarios. The optimal choice of tuple size depends on sequencing depth, but it is quite robust within a range of choices for moderate sequencing depths.

  11. Invasion of exotic earthworms into ecosystems inhabited by native earthworms

    Science.gov (United States)

    P. F. Hendrix; G. H. Baker; M. A. Callaham Jr; G. A. Damoff; Fragoso C.; G. Gonzalez; S. W. James; S. L. Lachnicht; T. Winsome; X. Zou

    2006-01-01

    The most conspicuous biological invasions in terrestrial ecosystems have been by exotic plants, insects and vertebrates. Invasions by exotic earthworms, although not as well studied, may be increasing with global commerce in agriculture, waste management and bioremediation. A number of cases has documented where invasive earthworms have caused significant changes in...

  12. Insect gut microbiome - An unexploited reserve for biotechnological application.

    Science.gov (United States)

    Krishnan, Muthukalingan; Bharathiraja, Chinnapandi; Pandiarajan, Jeyaraj; Prasanna, Vimalanathan Arun; Rajendhran, Jeyaprakash; Gunasekaran, Paramasamy

    2014-05-01

    Metagenomics research has been developed over the past decade to elucidate the genomes of the uncultured microorganisms with an aim of understanding microbial ecology. On the other hand, it has also been provoked by the increasing biotechnological demands for novel enzymes, antibiotic and signal mimics. The gut microbiota of insects plays crucial roles in the growth, development and environmental adaptation to the host insects. Very recently, the insect microbiota and their genomes (microbiome), isolated from insects were recognized as a major genetic resources for bio-processing industry. Consequently, the exploitation of insect gut microbiome using metagenomic approaches will enable us to find novel biocatalysts and to develop innovative strategies for identifying smart molecules for biotechnological applications. In this review, we discuss the critical footstep in extraction and purification of metagenomic DNA from insect gut, construction of metagenomic libraries and screening procedure for novel gene identification. Recent innovations and potential applications in bioprocess industries are highlighted.

  13. Oscillospira and related bacteria - from metagenomics species to metabolic features

    DEFF Research Database (Denmark)

    Gophna, Uri; Konikoff, Tom; Nielsen, Henrik Bjørn

    2017-01-01

    with interesting traits, especially leanness. However, very little is known about its metabolism or physiology. Here we used nearly complete genomes derived from shot-gun metagenomic data from the human gut to analyze Oscillospira and related bacteria. We used sequence similarity, gene neighbourhood information...

  14. Amino Acid Profile of Earthworm and Earthworm Meal (Lumbricus Rubellus) for Animal Feedstuff

    OpenAIRE

    L. Istiqomah; A. Sofyan; E. Damayanti; H. Julendra

    2009-01-01

    Earthworm meal (Lumbricus rubellus) has become one of natural material that could be used asfeed additive. Powdering method of earthworm was done by using formic acid addition. The study wascarried out (1) to evaluate the essential amino acid profile of earthworm and earthworm meal, (2) tocalculate the value of essential amino acid index (EAAI) of both materials. A modified EAAI equationwas developed from the essential amino acid profile of earthworm and earthworm meal. The resultshowed that ...

  15. AMINO ACID PROFILE OF EARTHWORM AND EARTHWORM MEAL (Lumbricus rubellus) FOR ANIMAL FEEDSTUFF

    OpenAIRE

    L. Istiqomah; A. Sofyan; E. Damayanti; H. Julendra

    2014-01-01

    Earthworm meal (Lumbricus rubellus) has become one of natural material that could be used asfeed additive. Powdering method of earthworm was done by using formic acid addition. The study wascarried out (1) to evaluate the essential amino acid profile of earthworm and earthworm meal, (2) tocalculate the value of essential amino acid index (EAAI) of both materials. A modified EAAI equationwas developed from the essential amino acid profile of earthworm and earthworm meal. The resultshowed that ...

  16. The future of skin metagenomics.

    Science.gov (United States)

    Mathieu, Alban; Vogel, Timothy M; Simonet, Pascal

    2014-01-01

    Metagenomics, the direct exploitation of environmental microbial DNA, is complementary to traditional culture-based approaches for deciphering taxonomic and functional microbial diversity in a plethora of ecosystems, including those related to the human body such as the mouth, saliva, teeth, gut or skin. DNA extracted from human skin analyzed by sequencing the PCR-amplified rrs gene has already revealed the taxonomic diversity of microbial communities colonizing the human skin ("skin microbiome"). Each individual possesses his/her own skin microbial community structure, with marked taxonomic differences between different parts of the body and temporal evolution depending on physical and chemical conditions (sweat, washing etc.). However, technical limitations due to the low bacterial density at the surface of the human skin or contamination by human DNA still has inhibited extended use of the metagenomic approach for investigating the skin microbiome at a functional level. These difficulties have been overcome in part by the new generation of sequencing platforms that now provide sequences describing the genes and functions carried out by skin bacteria. These methodological advances should help us understand the mechanisms by which these microorganisms adapt to the specific chemical composition of each skin and thereby lead to a better understanding of bacteria/human host interdependence. This knowledge will pave the way for more systemic and individualized pharmaceutical and cosmetic applications. Copyright © 2013 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  17. FY11 Report on Metagenome Analysis using Pathogen Marker Libraries

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, Shea N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Allen, Jonathan E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); McLoughlin, Kevin S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Slezak, Tom [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2011-06-02

    detection probability appears to be a function of both coverages. Multiple species could be detected simultaneously in a simulated low-coverage, complex metagenome, and the largest PML gave no false negative species and no false positive genera. The presence of multiple species was predicted in a complex metagenome from a human gut microbiome with 1.9 GB of short reads (75 nt); the species predicted were reasonable gut flora and no biothreat agents were detected, showing the feasibility of PML analysis of empirical complex metagenomes.

  18. Mapping earthworm communities in Europe

    DEFF Research Database (Denmark)

    Rutgers, Michiel; Orgiazzi, Alberto; Gardi, Ciro

    Existing data sets on earthworm communities in Europe were collected, harmonized, modelled and depicted on a soil biodiversity map of Europe. Digital Soil Mapping was applied using multiple regressions relating relatively low density earthworm community data to soil characteristics, land use......, vegetation and climate factors (covariables) with a greater spatial resolution. Statistically significant relationships were used to build habitat-response models for constructing earthworm maps with abundance, species richness, and diversity data. While a good number of environmental predictors were...... significant in our multiple regressions, geographical factors alone seem to be less relevant than climatic factors. Despite differing sampling protocols, land use and geological history were the most relevant factors determining the demography and diversity of the earthworms across Europe. Case studies from...

  19. Metagenomics at Grass Roots

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 22; Issue 3. Metagenomics at Grass Roots. Sudeshna ... benefit human health, agriculture, and ecosystemfunctions. This article provides a brief history of technicaladvances in metagenomics, including DNA sequencing methods,and some case studies.

  20. Bioinformatics Approaches for Human Gut Microbiome Research

    Directory of Open Access Journals (Sweden)

    Zhijun Zheng

    2016-07-01

    Full Text Available The human microbiome has received much attention because many studies have reported that the human gut microbiome is associated with several diseases. The very large datasets that are produced by these kinds of studies means that bioinformatics approaches are crucial for their analysis. Here, we systematically reviewed bioinformatics tools that are commonly used in microbiome research, including a typical pipeline and software for sequence alignment, abundance profiling, enterotype determination, taxonomic diversity, identifying differentially abundant species/genes, gene cataloging, and functional analyses. We also summarized the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our understanding of unclassified and poorly understood gut microbes that are undocumented in the current genome databases. Additionally, we examined the methods used to identify metagenomic biomarkers based on the gut microbiome, which might help to expand the knowledge and approaches for disease detection and monitoring.

  1. The human gut microbiota and virome: Potential therapeutic implications.

    Science.gov (United States)

    Scarpellini, Emidio; Ianiro, Gianluca; Attili, Fabia; Bassanelli, Chiara; De Santis, Adriano; Gasbarrini, Antonio

    2015-12-01

    Human gut microbiota is a complex ecosystem with several functions integrated in the host organism (metabolic, immune, nutrients absorption, etc.). Human microbiota is composed by bacteria, yeasts, fungi and, last but not least, viruses, whose composition has not been completely described. According to previous evidence on pathogenic viruses, the human gut harbours plant-derived viruses, giant viruses and, only recently, abundant bacteriophages. New metagenomic methods have allowed to reconstitute entire viral genomes from the genetic material spread in the human gut, opening new perspectives on the understanding of the gut virome composition, the importance of gut microbiome, and potential clinical applications. This review reports the latest evidence on human gut "virome" composition and its function, possible future therapeutic applications in human health in the context of the gut microbiota, and attempts to clarify the role of the gut "virome" in the larger microbial ecosystem. Copyright © 2015 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

  2. Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis and North American Moose (Alces americanus after Long-Term Enrichment

    Directory of Open Access Journals (Sweden)

    Mabel T. Wong

    2017-12-01

    Full Text Available To identify carbohydrate-active enzymes (CAZymes that might be particularly relevant for wood fiber processing, we performed a comparative metagenomic analysis of digestive systems from Canadian beaver (Castor canadensis and North American moose (Alces americanus following 3 years of enrichment on either microcrystalline cellulose or poplar hydrolysate. In total, 9,386 genes encoding CAZymes and carbohydrate-binding modules (CBMs were identified, with up to half predicted to originate from Firmicutes, Bacteroidetes, Chloroflexi, and Proteobacteria phyla, and up to 17% from unknown phyla. Both PCA and hierarchical cluster analysis distinguished the annotated glycoside hydrolase (GH distributions identified herein, from those previously reported for grass-feeding mammals and herbivorous foragers. The CAZyme profile of moose rumen enrichments also differed from a recently reported moose rumen metagenome, most notably by the absence of GH13-appended dockerins. Consistent with substrate-driven convergence, CAZyme profiles from both poplar hydrolysate-fed cultures differed from cellulose-fed cultures, most notably by increased numbers of unique sequences belonging to families GH3, GH5, GH43, GH53, and CE1. Moreover, pairwise comparisons of moose rumen enrichments further revealed higher counts of GH127 and CE15 families in cultures fed with poplar hydrolysate. To expand our scope to lesser known carbohydrate-active proteins, we identified and compared multi-domain proteins comprising both a CBM and domain of unknown function (DUF as well as proteins with unknown function within the 416 predicted polysaccharide utilization loci (PULs. Interestingly, DUF362, identified in iron–sulfur proteins, was consistently appended to CBM9; on the other hand, proteins with unknown function from PULs shared little identity unless from identical PULs. Overall, this study sheds new light on the lignocellulose degrading capabilities of microbes originating from

  3. 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...

  4. 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...... 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......), 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...

  5. Ecological functions of earthworms in soil

    NARCIS (Netherlands)

    Andriuzzi, W.S.

    2015-01-01

    Ecological functions of earthworms in soil Walter S. Andriuzzi Abstract Earthworms are known to play an important role in soil structure and fertility, but there are still big knowledge gaps on the functional ecology of distinct earthworm species, on their own and in interaction

  6. The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline

    OpenAIRE

    Lluch, J?r?me; Servant, Florence; Pa?ss?, Sandrine; Valle, Carine; Vali?re, Sophie; Kuchly, Claire; Vilchez, Ga?lle; Donnadieu, C?cile; Courtney, Michael; Burcelin, R?my; Amar, Jacques; Bouchez, Olivier; Lelouvier, Benjamin

    2015-01-01

    Background Substantial progress in high-throughput metagenomic sequencing methodologies has enabled the characterisation of bacteria from various origins (for example gut and skin). However, the recently-discovered bacterial microbiota present within animal internal tissues has remained unexplored due to technical difficulties associated with these challenging samples. Results We have optimized a specific 16S rDNA-targeted metagenomics sequencing (16S metabarcoding) pipeline based on the Illu...

  7. GUTs without guts

    Energy Technology Data Exchange (ETDEWEB)

    Gato-Rivera, B. [NIKHEF Theory Group, Science Park 105, 1098 XG Amsterdam (Netherlands); Instituto de Física Fundamental, IFF-CSIC, Serrano 123, Madrid 28006 (Spain); Schellekens, A.N., E-mail: t58@nikhef.nl [NIKHEF Theory Group, Science Park 105, 1098 XG Amsterdam (Netherlands); Instituto de Física Fundamental, IFF-CSIC, Serrano 123, Madrid 28006 (Spain); IMAPP, Radboud Universiteit, Nijmegen (Netherlands)

    2014-06-15

    The structure of a Standard Model family is derived in a class of brane models with a U(M)×U(N) factor, from two mildly anthropic requirements: a massless photon and a universe that does not turn into a plasma of massless charged particles. If we choose M=3 and N=2, the only option is shown to be the Standard Model with an undetermined number of families. We do not assume the U(1) embedding, charge quantization, family repetition, nor the fermion representations; all of these features are derived, assuming a doublet Higgs. With a slightly stronger assumption even the Higgs representation is determined. We also consider a more general class, requiring an asymptotically free strong SU(M) (with M⩾3) interaction from the first factor and an electromagnetic U(1) embedded in both factors. We allow Higgs symmetry breaking of the U(N)×U(1) flavor group by at most one Higgs boson in any representation, combined with any allowed chiral symmetry breaking by SU(M). For M=3 there is a large number of solutions with an unbroken U(1). In all of these, “quarks” have third-integral charges and color singlets have integer charges in comparison to leptons. Hence Standard Model charge quantization holds for any N. Only for N=2 these models allow an SU(5) GUT extension, but this extension offers no advantages whatsoever for understanding the Standard Model; it only causes complications, such as the doublet–triplet splitting problem. Although all these models have a massless photon, all except the Standard Model are ruled out by the second anthropic requirement. In this class of brane models the Standard Model is realized as a GUT with its intestines removed, to keep only the good parts: a GUT without guts.

  8. Metagenomic Analysis of Silage

    OpenAIRE

    Tennant, Richard K.; Sambles, Christine M; Diffey, Georgina E.; Moore, Karen A.; Love, John

    2017-01-01

    Metagenomics is defined as the direct analysis of deoxyribonucleic acid (DNA) purified from environmental samples and enables taxonomic identification of the microbial communities present within them. Two main metagenomic approaches exist; sequencing the 16S rRNA gene coding region, which exhibits sufficient variation between taxa for identification, and shotgun sequencing, in which genomes of the organisms that are present in the sample are analyzed and ascribed to "operational taxonomic uni...

  9. Tree Species Identity Shapes Earthworm Communities

    DEFF Research Database (Denmark)

    Schelfhout, Stephanie; Mertens, Jan; Verheyen, Kris

    2017-01-01

    of soil and foliar litter, and determined the forest floor turnover rate and the density and biomass of the earthworm species occurring in the stands. Tree species significantly affected earthworm communities via leaf litter and/or soil characteristics. Anecic earthworms were abundant under Fraxinus, Acer...... and Tilia, which is related to calcium-rich litter and low soil acidification. Epigeic earthworms were indifferent to calcium content in leaf litter and were shown to be mainly related to soil moisture content and litter C:P ratios. Almost no earthworms were found in Picea stands, likely because......Earthworms are key organisms in forest ecosystems because they incorporate organic material into the soil and affect the activity of other soil organisms. Here, we investigated how tree species affect earthworm communities via litter and soil characteristics. In a 36-year old common garden...

  10. Earthworm species, a searchable database

    Directory of Open Access Journals (Sweden)

    Csuzdi, Cs.

    2012-07-01

    Full Text Available The first earthworm species named was Lumbricus terrestris Linnaeus, 1758. Since then, there were some 6000earthworm (Oligochaeta: Megadrili species names described, from which ca. 3000–3500 are valid. In order to help the orientation in such a huge amount of data a web-based database was created. Each record contains the basic data of the species names described; i.e. family, genus, specific epithet, author, year, reference to the original description and optionally the valid combination of the species name and deposition of type specimens. The database is searchable by every field mentioned and the resulted list can be arranged alphabetically.

  11. Critical Assessment of Metagenome Interpretation

    DEFF Research Database (Denmark)

    Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter

    2017-01-01

    Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark...

  12. Earthworm invasions in the tropics

    Science.gov (United States)

    Grizelle Gonzalez; Ching Yu Huang; Xiaoming Zou; Carlos Rodriguez

    2006-01-01

    The effects and implications of invasive species in belowground terrestrial ecosystems are not well known in comparison with aboveground terrestrial and marine environments. The study of earthworm invasions in the tropics is limited by a lack of taxonomic knowledge and the potential for loss of species in native habitats due to anthropogenic land use change. Alteration...

  13. Gut Microbiomes of Indian Children of Varying Nutritional Status

    OpenAIRE

    Tarini Shankar Ghosh; Sourav Sen Gupta; Tanudeep Bhattacharya; Deepak Yadav; Anamitra Barik; Abhijit Chowdhury; Bhabatosh Das; Mande, Sharmila S; Balakrish Nair, G.

    2014-01-01

    BACKGROUND: Malnutrition is a global health problem affecting more than 300 million pre-school children worldwide. It is one of the major health concerns in India since around 50% of children below the age of two suffer from various forms of malnutrition. The gut microbiome plays an important role in nutrient pre-processing, assimilation and energy harvest from food. Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition. METHODOLOGY/PRINCIPAL FINDINGS: Metagenomics...

  14. Taxonomic and functional diversity of the culturable microbiomes of epigeic earthworms and their prospects in agriculture.

    Science.gov (United States)

    Singh, Arjun; Tiwari, Rameshwar; Sharma, Anamika; Adak, Anurup; Singh, Surender; Prasanna, Radha; Saxena, Anil K; Nain, Lata; Singh, Ran Vir

    2016-09-01

    Eisenia foetida and Perionyx excavatus are potent vermicomposting earthworms having immense importance in organic matter recycling under tropical conditions, particularly in India. Comparative assessment of the cultivable gut microbiome of these two epigeic earthworms after growth on lignocellulosic biomass, revealed populations of 3.2-8.3 × 10(9) CFU. Diversity analyses using 16S rDNA sequences revealed that the major dominating classes were Firmicutes (50-60%), followed by Actinobacteria (26.7-33%), and Alphaproteobacteria (5.6-6.7%). Despite exhibiting similar diversity indices and species richness, Betaproteobacteria (6.7%) and Gammaproteobacteria (11.1%) were solely present in E. foetida and P. excavatus, respectively. A set of 33 distinct morphotypes, including 18 from E. foetida and 15 from P. excavatus were selected. Carbohydrate utilization profiles generated using Hi-Carbo™ kits revealed that the isolates from the gut of P. excavatus - Arthrobacter pascens IARI-L13 and Bacillus subtilis IARIC were able to utilize 54 and 51.4% of the carbohydrates tested. Sorbose was not utilized, while unusual carbohydrates - adonitol and methyl-d-mannoside were utilized only by members from the gut of P. excavatus, while melizitose was utilized by those uniquely by E. foetida microbiome. Functional characterization revealed that β-glucosidase activity was most prevalent in the culturable microbial community. Alkaline and acid phosphatase activity was more widespread in the E. foetida gut microbiome. All the culturable gut bacterial isolates produced ammonia, but IAA was detected only in five cultures. The unique functional attributes of the two culturable microbiomes, grown on a similar diet, reveals the significance of proper selection of earthworm substrate combinations for effective vermicomposting. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. 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......, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties...

  16. Metagenomics and Applications

    Directory of Open Access Journals (Sweden)

    L Rafati

    2016-11-01

    Full Text Available Introduction: Bacteria are a group of microorganisms which in contrast to their diversity in nature, only very few of them can be grown and isolated in the current standard laboratories. Metagenomics as a new field of research, during the last decade has worked on clarification of the genomes of the non-cultured microbes and researchers around the world with serious study of this group of bacteria, looking for new compounds such as new antibiotics, anti-cancer agents, new enzymes and biomolecules. Methods: This article is reviews study which with study of Texts and Internet and handy browsing of key words from reliable scientific resources and sites amongst: Google Scholar, Pub med, Science direct, Sid and Scopus in the years 2000 to 2013 were collected and studied. Results: The data collection instrument in the study includes all printed metagenomics related texts. Although, nowadays metagenomics is used to screen samples but now as a perfect technique beside the medium application and other traditional techniques will have better position. The highest usage of metagenomics is in clinical cases where with conventional techniques can't be discovered microbial reasons. So for tests and analyze information need to skilled scientists. Conclusion: This paper focuses on some of the latest achievements of Metagenomics and its application in new drugs, detection of enzymes, potential of biotechnology and environment.

  17. AMINO ACID PROFILE OF EARTHWORM AND EARTHWORM MEAL (Lumbricus rubellus FOR ANIMAL FEEDSTUFF

    Directory of Open Access Journals (Sweden)

    L. Istiqomah

    2014-10-01

    Full Text Available Earthworm meal (Lumbricus rubellus has become one of natural material that could be used asfeed additive. Powdering method of earthworm was done by using formic acid addition. The study wascarried out (1 to evaluate the essential amino acid profile of earthworm and earthworm meal, (2 tocalculate the value of essential amino acid index (EAAI of both materials. A modified EAAI equationwas developed from the essential amino acid profile of earthworm and earthworm meal. The resultshowed that essential amino acid of earthworm was dominated by histidine (0.63% of dry matter basis,meanwhile the earthworm meal was dominated by isoleucine (1.98% of dry matter basis. The nonessential amino acid of earthworm and earthworm meal was dominated by glutamic acid (1.52% and3.60% of dry matter basis respectively. The value of essential amino acid index obtained fromearthworm meal was higher (58.67% than those from earthworm (21.23%. It is concluded thatpowdering method of earthworm by using formic acid addition had higher amino acid balance thanearthworm.

  18. Evolution of earthworm burrow systems after inoculation of lumbricid earthworms in a pasture in the Netherlands.

    NARCIS (Netherlands)

    Ligthart, T.N.; Peek, G.J.C.W.

    1997-01-01

    In 1983, an earthworm-free pasture was inoculated with four earthworm species. The earthworms dispersed with an average velocity of 6.3 my-1. In 1991, four burrow systems, ranging in age from 0.6 to 7.3 y, were mapped three-dimensionally to establish the development of these systems. Aporrectodea

  19. Uptake routes and toxicokinetics of silver nanoparticles and silver ions in the earthworm Lumbricus rubellus.

    Science.gov (United States)

    Diez-Ortiz, Maria; Lahive, Elma; Kille, Peter; Powell, Kate; Morgan, A John; Jurkschat, Kerstin; Van Gestel, Cornelis A M; Mosselmans, J Fred W; Svendsen, Claus; Spurgeon, David J

    2015-10-01

    Current bioavailability models, such as the free ion activity model and biotic ligand model, explicitly consider that metal exposure will be mainly to the dissolved metal in ionic form. With the rise of nanotechnology products and the increasing release of metal-based nanoparticles (NPs) to the environment, such models may increasingly be applied to support risk assessment. It is not immediately clear, however, whether the assumption of metal ion exposure will be relevant for NPs. Using an established approach of oral gluing, a toxicokinetics study was conducted to investigate the routes of silver nanoparticles (AgNPs) and Ag(+) ion uptake in the soil-dwelling earthworm Lumbricus rubellus. The results indicated that a significant part of the Ag uptake in the earthworms is through oral/gut uptake for both Ag(+) ions and NPs. Thus, sealing the mouth reduced Ag uptake by between 40% and 75%. An X-ray analysis of the internal distribution of Ag in transverse sections confirmed the presence of increased Ag concentrations in exposed earthworm tissues. For the AgNPs but not the Ag(+) ions, high concentrations were associated with the gut wall, liver-like chloragogenous tissue, and nephridia, which suggest a pathway for AgNP uptake, detoxification, and excretion via these organs. Overall, the results indicate that Ag in the ionic and NP forms is assimilated and internally distributed in earthworms and that this uptake occurs predominantly via the gut epithelium and less so via the body wall. The importance of oral exposure questions the application of current metal bioavailability models, which implicitly consider that the dominant route of exposure is via the soil solution, for bioavailability assessment and modeling of metal-based NPs. © 2015 SETAC.

  20. Specific gut microbiota features and metabolic markers in postmenopausal women with obesity

    DEFF Research Database (Denmark)

    Brahe, Lena Kirchner; Le Chatelier, E; Prifti, E

    2015-01-01

    BACKGROUND: Gut microbial gene richness and specific bacterial species are associated with metabolic risk markers in humans, but the impact of host physiology and dietary habits on the link between the gut microbiota and metabolic markers remain unclear. The objective of this study was to identify...... adjustment for potential confounders, such as long-term diet composition. The study supports the use of gut metagenomic markers for metabolic disease prediction and warrants further investigation of causality....... gut metagenomic markers associated with estimates of insulin resistance, lipid metabolism and inflammation in obesity, and to explore whether the associations between metagenomic and metabolic markers persisted after adjustment for body fat, age and habitual dietary intake. METHODS: Faecal DNA from 53...

  1. New records of earthworms (Oligochaeta from Madagascar

    Directory of Open Access Journals (Sweden)

    Razafindrakoto, M.

    2010-10-01

    Full Text Available New records of earthworms from Madagascar are presented. This is the first taxonomic report on the earthwormfauna of Madagascar since the last paper of Michaelsen (1931. Altogether data on 14 peregrine earthworm species belonging tofive families are summarized. Together with the native taxa, 33 valid earthworm species have so far been recorded fromMadagascar of which 18 (55% are endemic in the Island and 15 (45% introduced.

  2. Legacy of earthworms' engineering effects enlarges the actual effects of earthworms on plants

    Science.gov (United States)

    Mudrák, Obdřej; Frouz, Jan

    2015-04-01

    Earthworms were recognized as key factor responsible for changes from early to late successional plant communities. They incorporate organic matter into the soil and creates there persistent structures, which improves conditions for plant growth. Earthworm activity might be therefore expected to be more important in early stages of the succession, when earthworm colonization of previously earthworm free soil starts, than in the late stages of the succession, where the soil was previously modified by earthworms. However, earthworms affect plants also via other effects such as increase of nutrient availability. The relative importance of soil structure modification and other earthworm effects on plants is poorly known, despite it is important for both theoretical and applied ecology. To test the effect of earthworms (Lumbricus rubellus and Aporrectodea caliginosa) on plants we performed microcosm laboratory experiment, where earthworms were affecting early successional (Poa compressa, Medicago lupulina, and Daucus carota) and late successional (Arrhenatherum elatius, Lotus corniculatus, and Plantago laceolata) plat species in soil previously unaffected by earthworms and in soil with previous long term effect of earthworms. These soils were taken from the early and late successional monitoring sites of the Sokolov coal mining district with known history. Earthworms increased plant biomass proportionally more in late successional soil. It was mainly because they increased availability of nutrients (nitrate and potassium) and plants get higher advantage out of this in late successional soil. Earthworms increased plant biomass of both early and late successional species, but late successional species suppressed early successional species in competition. This suppression was more intensive in presence of earthworms and in late successional soil. We therefore found multiplicative effect between earthworm soil engineering activity and their other effects, which might be

  3. The effect of host genetics on the gut microbiome

    NARCIS (Netherlands)

    Bonder, Marc Jan; Kurilshchikov, Aleksandr; Tigchelaar-Feenstra, Ettje; Mujagic, Zlatan; Imhann, Floris; Vila, Arnau Vich; Deelen, Patrick; Vatanen, Tommi; Schirmer, Melanie; Smeekens, Sanne P; Zhernakova, Daria V; Jankipersadsing, Soesma A; Jaeger, Martin; Oosting, Marije; Cenit, Maria Carmen; Masclee, Ad A M; Swertz, Morris A; Li, Yang; Kumar, Vinod; Joosten, Leo; Harmsen, Hermie; Weersma, Rinse K; Franke, Lude; Hofker, Marten H; Xavier, Ramnik J; Jonkers, Daisy; Netea, Mihai G; Wijmenga, Cisca; Fu, Jingyuan; Zhernakova, Alexandra

    2016-01-01

    The gut microbiome is affected by multiple factors, including genetics. In this study, we assessed the influence of host genetics on microbial species, pathways and gene ontology categories, on the basis of metagenomic sequencing in 1,514 subjects. In a genome-wide analysis, we identified

  4. Comparative metagenomic analyses of the poultry enteric virome: implications for diagnostics

    Science.gov (United States)

    Previous comparative metagenomic analyses of the viral communities present in the poultry gut have revealed novel enteric viruses that may affect the overall performance of birds or that may play roles in disease syndromes such as Runting-Stunting Syndrome (RSS) or Poult Enteritis Complex (PEC). Ou...

  5. 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.

  6. Gut indigenous microbiota and epigenetics

    Directory of Open Access Journals (Sweden)

    Boris Arkadievich Shenderov

    2012-03-01

    Full Text Available This review introduces and discusses data regarding fundamental and applied investigations in mammalian epigenomics and gut microbiota received over the last 10 years. Analysis of these data enabled the author first to come to the conclusion that the multiple low molecular weight substances of indigenous gut microbiota origin should be considered one of the main endogenous factors actively participating in epigenomic mechanisms that responsible for the mammalian genome reprogramming and post-translated modifications. Gut microecological imbalance coursed by various biogenic and abiogenic agents and factors can produce the different epigenetic abnormalities and the onset and progression of metabolic diseases associated. The author substantiates the necessity to create an international project ‘Human Gut Microbiota and Epigenomics’ that facilitates interdisciplinary collaborations among scientists and clinicians engaged in host microbial ecology, nutrition, metagenomics, epigenomics and metabolomics investigations as well as in diseases prevention and treatment. Some priority scientific and applied directions in the current omic technologies coupled with gnotobiological approaches are suggested that can open a new era in characterizing the role of the symbiotic microbiota small metabolic and signal molecules in the host epigenomics. Although discussed subject is only at an early stage its validation can open novel approaches in drug discovery studies.

  7. [Current view on gut microbiota].

    Science.gov (United States)

    Bourlioux, P

    2014-01-01

    Gut microbiota is more and more important since metagenomic research have brought new knowledge on this topic especially for human health. Firstly, gut microbiota is a key element for our organism he lives in symbiosis with. Secondly, it interacts favorably with many physiological functions of our organism. Thirdly, at the opposite, it can be an active participant in intestinal pathologies linked to a dysbiosis mainly in chronic inflammatory bowel diseases like Crohn disease or ulcerative colitis but also in obesity, metabolic syndrome, and more prudently in autism and behavioral disorders. In order to keep a good health, it is essential to protect our gut microbiota as soon as our young age and maintain it healthy. Face to a more and more important number of publications for treating certain digestive diseases with fecal microbial transplantation, it needs to be very careful and recommend further studies in order to assess risks and define standardized protocols. Gut microbiota metabolic capacities towards xenobiotics need to be developed, and we must take an interest in the modifications they induce on medicinal molecules. On the other hand, it is essential to study the potent effects of pesticides and other pollutants on microbiota functions. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  8. Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil

    Science.gov (United States)

    Bernard, Laetitia; Chapuis-Lardy, Lydie; Razafimbelo, Tantely; Razafindrakoto, Malalatiana; Pablo, Anne-Laure; Legname, Elvire; Poulain, Julie; Brüls, Thomas; O'Donohue, Michael; Brauman, Alain; Chotte, Jean-Luc; Blanchart, Eric

    2012-01-01

    Priming effect (PE) is defined as a stimulation of the mineralization of soil organic matter (SOM) following a supply of fresh organic matter. This process can have important consequences on the fate of SOM and on the management of residues in agricultural soils, especially in tropical regions where soil fertility is essentially based on the management of organic matter. Earthworms are ecosystem engineers known to affect the dynamics of SOM. Endogeic earthworms ingest large amounts of soil and assimilate a part of organic matter it contains. During gut transit, microorganisms are transported to new substrates and their activity is stimulated by (i) the production of readily assimilable organic matter (mucus) and (ii) the possible presence of fresh organic residues in the ingested soil. The objective of our study was to see (i) whether earthworms impact the PE intensity when a fresh residue is added to a tropical soil and (ii) whether this impact is linked to a stimulation/inhibition of bacterial taxa, and which taxa are affected. A tropical soil from Madagascar was incubated in the laboratory, with a 13C wheat straw residue, in the presence or absence of a peregrine endogeic tropical earthworm, Pontoscolex corethrurus. Emissions of 12CO2 and 13CO2 were followed during 16 days. The coupling between DNA-SIP (stable isotope probing) and pyrosequencing showed that stimulation of both the mineralization of wheat residues and the PE can be linked to the stimulation of several groups especially belonging to the Bacteroidetes phylum. PMID:21753801

  9. Recent progresses in metagenomics

    Science.gov (United States)

    Metagenomics addresses the collective genetic structure and functional composition of a microbial community at its native habitat. This approach has emerged as a powerful tool to study the structure and function of the microbiota for the past few years and is revolutionizing studies of microbial ec...

  10. Dynamics of gut microbiota in autoimmune lupus.

    Science.gov (United States)

    Zhang, Husen; Liao, Xiaofeng; Sparks, Joshua B; Luo, Xin M

    2014-12-01

    Gut microbiota has been recognized as an important environmental factor in health, as well as in metabolic and immunological diseases, in which perturbation of the host gut microbiota is often observed in the diseased state. However, little is known on the role of gut microbiota in systemic lupus erythematosus. We investigated the effects of host genetics, sex, age, and dietary intervention on the gut microbiome in a murine lupus model. In young, female lupus-prone mice resembling women at childbearing age, a population with the highest risk for lupus, we found marked depletion of lactobacilli, and increases in Lachnospiraceae and overall diversity compared to age-matched healthy controls. The predicted metagenomic profile in lupus-prone mice showed a significant enrichment of bacterial motility- and sporulation-related pathways. Retinoic acid as a dietary intervention restored lactobacilli that were downregulated in lupus-prone mice, and this correlated with improved symptoms. The predicted metagenomes also showed that retinoic acid reversed many lupus-associated changes in microbial functions that deviated from the control. In addition, gut microbiota of lupus-prone mice were different between sexes, and an overrepresentation of Lachnospiraceae in females was associated with an earlier onset of and/or more severe lupus symptoms. Clostridiaceae and Lachnospiraceae, both harboring butyrate-producing genera, were more abundant in the gut of lupus-prone mice at specific time points during lupus progression. Together, our results demonstrate the dynamics of gut microbiota in murine lupus and provide evidence to suggest the use of probiotic lactobacilli and retinoic acid as dietary supplements to relieve inflammatory flares in lupus patients. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  11. Potential applications of metagenomics to assess the biological effects of food structure and function.

    Science.gov (United States)

    Santiago-Rodriguez, Tasha M; Cano, Raul; Jiménez-Flores, Rafael

    2016-10-12

    Metagenomics, or the collective study of genomes is an important emerging area in microbiology and related fields, and is increasingly being recognized as a tool to characterize the microbial community structure and function of diverse sample types. Metagenomics compares sequences to existing databases to enable the identification of potential microbial reservoirs and predict specific functions; yet, metagenomics has not been widely applied to understand how changes in the food structure and composition affect microbial communities and their function in the human gut. Studies are needed to understand the digestion of food products, and to measure their effectiveness in preserving a healthy microbiome, as well as intestinal function. We suggest the use of metagenomics with validation techniques such as Polymerase Chain Reaction (PCR), cloning and functional assays to assess the biological effects of food structure and function.

  12. The metagenomic telescope.

    Directory of Open Access Journals (Sweden)

    Balázs Szalkai

    Full Text Available Next generation sequencing technologies led to the discovery of numerous new microbe species in diverse environmental samples. Some of the new species contain genes never encountered before. Some of these genes encode proteins with novel functions, and some of these genes encode proteins that perform some well-known function in a novel way. A tool, named the Metagenomic Telescope, is described here that applies artificial intelligence methods, and seems to be capable of identifying new protein functions even in the well-studied model organisms. As a proof-of-principle demonstration of the Metagenomic Telescope, we considered DNA repair enzymes in the present work. First we identified proteins in DNA repair in well-known organisms (i.e., proteins in base excision repair, nucleotide excision repair, mismatch repair and DNA break repair; next we applied multiple alignments and then built hidden Markov profiles for each protein separately, across well-researched organisms; next, using public depositories of metagenomes, originating from extreme environments, we identified DNA repair genes in the samples. While the phylogenetic classification of the metagenomic samples are not typically available, we hypothesized that some very special DNA repair strategies need to be applied in bacteria and Archaea living in those extreme circumstances. It is a difficult task to evaluate the results obtained from mostly unknown species; therefore we applied again the hidden Markov profiling: for the identified DNA repair genes in the extreme metagenomes, we prepared new hidden Markov profiles (for each genes separately, subsequent to a cluster analysis; and we searched for similarities to those profiles in model organisms. We have found well known DNA repair proteins, numerous proteins with unknown functions, and also proteins with known, but different functions in the model organisms.

  13. Beyond biodiversity: fish metagenomes.

    Directory of Open Access Journals (Sweden)

    Alba Ardura

    Full Text Available Biodiversity and intra-specific genetic diversity are interrelated and determine the potential of a community to survive and evolve. Both are considered together in Prokaryote communities treated as metagenomes or ensembles of functional variants beyond species limits.Many factors alter biodiversity in higher Eukaryote communities, and human exploitation can be one of the most important for some groups of plants and animals. For example, fisheries can modify both biodiversity and genetic diversity (intra specific. Intra-specific diversity can be drastically altered by overfishing. Intense fishing pressure on one stock may imply extinction of some genetic variants and subsequent loss of intra-specific diversity. The objective of this study was to apply a metagenome approach to fish communities and explore its value for rapid evaluation of biodiversity and genetic diversity at community level. Here we have applied the metagenome approach employing the barcoding target gene coi as a model sequence in catch from four very different fish assemblages exploited by fisheries: freshwater communities from the Amazon River and northern Spanish rivers, and marine communities from the Cantabric and Mediterranean seas.Treating all sequences obtained from each regional catch as a biological unit (exploited community we found that metagenomic diversity indices of the Amazonian catch sample here examined were lower than expected. Reduced diversity could be explained, at least partially, by overexploitation of the fish community that had been independently estimated by other methods.We propose using a metagenome approach for estimating diversity in Eukaryote communities and early evaluating genetic variation losses at multi-species level.

  14. Fate, Uptake and Distribution of Nanoencapsulated Pesticides in Soil-Earthworm Systems, Implications for Environmental Risk Assessment.

    Science.gov (United States)

    Firdaus, Mohd Anuar Mohd; Agatz, Annika; Hodson, Mark E; Al-Khazrajy, Omar S A; Boxall, Alistair B A

    2018-01-17

    Nanopesticides are novel plant protection products offering numerous benefits. As nanoparticles behave differently from dissolved chemicals, environmental risks of these materials could differ from conventional pesticides. Here we used soil-earthworm systems to compare the fate and uptake of analytical grade bifenthrin to that of bifenthrin in traditional and nano-encapsulated formulations. Apparent sorption coefficients for bifenthrin in the nano-treatments were up to 3.8 times lower than in the non-nano treatments whereas dissipation half-lives of the nano-treatments were up to two time longer. Earthworms in the nano-treatments accumulated around 50% more bifenthrin than those in the non-nano treatments. In the non-nano treatments, most of the accumulated material was found in the earthworm tissue while in the nano-treatments, the majority resided in the gut. Evaluation of toxicokinetic modelling approaches showed that models incorporating the release rate of bifenthrin from the nanocapsule and distribution within the earthworm provided the best estimations of uptake from the nanoformulations. Overall, our findings indicate that the risks of nanopesticides may be different from conventional formulations. The modelling presented here provides a starting point for assessing risks of these materials but needs to be further developed to better consider the behaviour of the nanoencapsulated pesticide within the gut system. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  15. Soil metagenomics and tropical soil productivity

    OpenAIRE

    Garrett, Karen A.

    2009-01-01

    This presentation summarizes research in the soil metagenomics cross cutting research activity. Soil metagenomics studies soil microbial communities as contributors to soil health.C CCRA-4 (Soil Metagenomics)

  16. Life on human surfaces: skin metagenomics.

    Directory of Open Access Journals (Sweden)

    Alban Mathieu

    Full Text Available The human skin microbiome could provide another example, after the gut, of the strong positive or negative impact that human colonizing bacteria can have on health. Deciphering functional diversity and dynamics within human skin microbial communities is critical for understanding their involvement and for developing the appropriate substances for improving or correcting their action. We present a direct PCR-free high throughput sequencing approach to unravel the human skin microbiota specificities through metagenomic dataset analysis and inter-environmental comparison. The approach provided access to the functions carried out by dominant skin colonizing taxa, including Corynebacterium, Staphylococcus and Propionibacterium, revealing their specific capabilities to interact with and exploit compounds from the human skin. These functions, which clearly illustrate the unique life style of the skin microbial communities, stand as invaluable investigation targets for understanding and potentially modifying bacterial interactions with the human host with the objective of increasing health and well being.

  17. Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome.

    Science.gov (United States)

    Manor, Ohad; Borenstein, Elhanan

    2017-02-08

    Recent metagenomic analyses of the human gut microbiome identified striking variability in its taxonomic composition across individuals. Notably, however, these studies often reported marked functional uniformity, with relatively little variation in the microbiome's gene composition or in its overall metabolic capacity. Here, we address this surprising discrepancy between taxonomic and functional variations and set out to track its origins. Specifically, we demonstrate that the functional uniformity observed in microbiome studies can be attributed, at least partly, to common computational metagenomic processing procedures that mask true functional variation across microbiome samples. We identify several such procedures, including commonly used practices for gene abundance normalization, mapping of gene families to functional pathways, and gene family aggregation. We show that accounting for these factors and using revised metagenomic processing procedures uncovers such hidden functional variation, significantly increasing observed variation in the abundance of functional elements across samples. Importantly, we find that this uncovered variation is biologically meaningful and that it is associated with both host identity and health. Accurate characterization of functional variation in the microbiome is essential for comparative metagenomic analyses in health and disease. Our finding that metagenomic processing procedures mask underlying and biologically meaningful functional variation therefore highlights an important challenge such studies may face. Alternative schemes for metagenomic processing that uncover this hidden functional variation can facilitate improved metagenomic analysis and help pinpoint disease- and host-associated shifts in the microbiome's functional capacity.

  18. Abundance of earthworms in Nigerian ecological zones ...

    African Journals Online (AJOL)

    Forests with SIINDEX less than 0.2 should be regarded as endangered, because their earthworm functions are too low to accomplish significant leaf-litter breakdown and recycling. We suggest that if the illegal annual bush burning is prevented, the soil surface will be naturally mulched, earthworms protected, and by their ...

  19. Does earthworms density really modify soil's hydrodynamic ...

    African Journals Online (AJOL)

    It was carried out on the meadows soils of the valley of Wadi Bousselam. Although the treated water has high organic and particulate filler, it improved the earthworm abundance, total porosity and hydraulic conductivity of the soil. Keywords: meadows soils; earthworm density; soil morphology; treated water; hydrodynamic ...

  20. EARTHWORMS AND THEIR IMPACT ON SLUG CONTROL

    Science.gov (United States)

    Increases in the anecic earthworm species, Lumbricus terrestris L., have occurred in western Oregon grass fields due to increases in surface residue since the phase-out of open field burning. The use of earthworm toxic chemicals has been reduced through concerns for other important vertebrate and in...

  1. Identifying personal microbiomes using metagenomic codes.

    Science.gov (United States)

    Franzosa, Eric A; Huang, Katherine; Meadow, James F; Gevers, Dirk; Lemon, Katherine P; Bohannan, Brendan J M; Huttenhower, Curtis

    2015-06-02

    Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30-300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed >80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability-a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability.

  2. Mining the human gut microbiome for novel stress resistance genes

    Science.gov (United States)

    Culligan, Eamonn P.; Marchesi, Julian R.; Hill, Colin; Sleator, Roy D.

    2012-01-01

    With the rapid advances in sequencing technologies in recent years, the human genome is now considered incomplete without the complementing microbiome, which outnumbers human genes by a factor of one hundred. The human microbiome, and more specifically the gut microbiome, has received considerable attention and research efforts over the past decade. Many studies have identified and quantified “who is there?,” while others have determined some of their functional capacity, or “what are they doing?” In a recent study, we identified novel salt-tolerance loci from the human gut microbiome using combined functional metagenomic and bioinformatics based approaches. Herein, we discuss the identified loci, their role in salt-tolerance and their importance in the context of the gut environment. We also consider the utility and power of functional metagenomics for mining such environments for novel genes and proteins, as well as the implications and possible applications for future research. PMID:22688726

  3. Vulnerable Earthworm Species Identified from Nilgiri Biosphere Reserve

    OpenAIRE

    E.V. Ramasamy; M.S. Shylesh Chandran; Mahesh Mohan

    2011-01-01

    Diversity of earthworms at Nilgiri Biosphere Reserve is less known even though it is one among the biodiversity hot spots. Unless an authentic record of available earthworm species is made, the consequences of human alternation or climate change on the earthworm species diversity cannot be assessed. In this regard, the present study is relevant. Earthworms were collected from twenty three sites of NBR. The findings of this study showed that out of the total earthworm species identified from s...

  4. 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...

  5. Metagenomics and CAZyme Discovery.

    Science.gov (United States)

    Kunath, Benoit J; Bremges, Andreas; Weimann, Aaron; McHardy, Alice C; Pope, Phillip B

    2017-01-01

    Microorganisms play a primary role in regulating biogeochemical cycles and are a valuable source of enzymes that have biotechnological applications, such as carbohydrate-active enzymes (CAZymes). However, the inability to culture the majority of microorganisms that exist in natural ecosystems using common culture-dependent techniques restricts access to potentially novel cellulolytic bacteria and beneficial enzymes. The development of molecular-based culture-independent methods such as metagenomics enables researchers to study microbial communities directly from environmental samples, and presents a platform from which enzymes of interest can be sourced. We outline key methodological stages that are required as well as describe specific protocols that are currently used for metagenomic projects dedicated to CAZyme discovery.

  6. The YNP metagenome project

    DEFF Research Database (Denmark)

    Inskeep, William P.; Jay, Zackary J.; Tringe, Susannah G.

    2013-01-01

    The Yellowstone geothermal complex contains over 10,000 diverse geothermal features that host numerous phylogenetically deeply rooted and poorly understood archaea, bacteria, and viruses. Microbial communities in high-temperature environments are generally less diverse than soil, marine, sediment......, and environmental variables. Twenty geochemically distinct geothermal ecosystems representing a broad spectrum of Yellowstone hot-spring environments were used for metagenomic and geochemical analysis and included approximately equal numbers of: (1) phototrophic mats, (2) “filamentous streamer” communities, and (3...

  7. Diets Alter the Gut Microbiome of Crocodile Lizards

    Directory of Open Access Journals (Sweden)

    Hai-Ying Jiang

    2017-10-01

    Full Text Available The crocodile lizard is a critically endangered reptile, and serious diseases have been found in this species in recent years, especially in captive lizards. Whether these diseases are caused by changes in the gut microbiota and the effect of captivity on disease remains to be determined. Here, we examined the relationship between the gut microbiota and diet and disease by comparing the fecal microbiota of wild lizards with those of sick and healthy lizards in captivity. The gut microbiota in wild crocodile lizards was consistently dominated by Proteobacteria (∼56.4% and Bacteroidetes (∼19.1%. However, the abundance of Firmicutes (∼2.6% in the intestine of the wild crocodile lizards was distinctly lower than that in other vertebrates. In addition, the wild samples from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve also had a high abundance of Deinococcus–Thermus while the wild samples from Guangxi Daguishan Crocodile Lizard National Nature Reserve had a high abundance of Tenericutes. The gut microbial community in loach-fed crocodile lizards was significantly different from the gut microbial community in the earthworm-fed and wild lizards. In addition, significant differences in specific bacteria were detected among groups. Notably, in the gut microbiota, the captive lizards fed earthworms resulted in enrichment of Fusobacterium, and the captive lizards fed loaches had higher abundances of Elizabethkingia, Halomonas, Morganella, and Salmonella, all of which are pathogens or opportunistic pathogens in human or other animals. However, there is no sufficient evidence that the gut microbiota contributes to either disease A or disease B. These results provide a reference for the conservation of endangered crocodile lizards and the first insight into the relationship between disease and the gut microbiota in lizards.

  8. The Gut Microbiota in Host Metabolism and Pathogen Challenges

    DEFF Research Database (Denmark)

    Holm, Jacob Bak

    community where both composition and function can be affected by changes in the local environment. With the microbiota containing ~150 times more genes than the human host, the microbiota provides a large modifiable “secondary genome” (metagenome). Within the last decade, changes in the gut microbiota...... composition has indeed been established as a factor contributing to the health of the host. Therefore, being able to understand, control and modify the gut microbiota is a promising way of improving health. The following thesis is based on four different projects investigating the murine gut microbiota......, knowledge about the consequences of such pathogenic infections are valuable. We investigated which effects Trichuris muris infection has on the gut microbiota composition and immune response in mice. Chronic infection with T. muris resulted in major changes in the gut microbiota composition in parallel...

  9. Social networks predict gut microbiome composition in wild baboons.

    Science.gov (United States)

    Tung, Jenny; Barreiro, Luis B; Burns, Michael B; Grenier, Jean-Christophe; Lynch, Josh; Grieneisen, Laura E; Altmann, Jeanne; Alberts, Susan C; Blekhman, Ran; Archie, Elizabeth A

    2015-03-16

    Social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. Using shotgun metagenomic data from wild baboons, we found that social group membership and social network relationships predicted both the taxonomic structure of the gut microbiome and the structure of genes encoded by gut microbial species. Rates of interaction directly explained variation in the gut microbiome, even after controlling for diet, kinship, and shared environments. They therefore strongly implicate direct physical contact among social partners in the transmission of gut microbial species. We identified 51 socially structured taxa, which were significantly enriched for anaerobic and non-spore-forming lifestyles. Our results argue that social interactions are an important determinant of gut microbiome composition in natural animal populations-a relationship with important ramifications for understanding how social relationships influence health, as well as the evolution of group living.

  10. Probiotics, Prebiotics, and Synbiotics: Gut and Beyond

    Directory of Open Access Journals (Sweden)

    Usha Vyas

    2012-01-01

    Full Text Available The human intestinal tract has been colonized by thousands of species of bacteria during the coevolution of man and microbes. Gut-borne microbes outnumber the total number of body tissue cells by a factor of ten. Recent metagenomic analysis of the human gut microbiota has revealed the presence of some 3.3 million genes, as compared to the mere 23 thousand genes present in the cells of the tissues in the entire human body. Evidence for various beneficial roles of the intestinal microbiota in human health and disease is expanding rapidly. Perturbation of the intestinal microbiota may lead to chronic diseases such as autoimmune diseases, colon cancers, gastric ulcers, cardiovascular disease, functional bowel diseases, and obesity. Restoration of the gut microbiota may be difficult to accomplish, but the use of probiotics has led to promising results in a large number of well-designed (clinical studies. Microbiomics has spurred a dramatic increase in scientific, industrial, and public interest in probiotics and prebiotics as possible agents for gut microbiota management and control. Genomics and bioinformatics tools may allow us to establish mechanistic relationships among gut microbiota, health status, and the effects of drugs in the individual. This will hopefully provide perspectives for personalized gut microbiota management.

  11. Gut microbiome, gut function, and probiotics: Implications for health.

    Science.gov (United States)

    Hajela, Neerja; Ramakrishna, B S; Nair, G Balakrish; Abraham, Philip; Gopalan, Sarath; Ganguly, Nirmal K

    2015-03-01

    New insights from a rapidly developing field of research have ushered in a new era of understanding of the complexity of host-microbe interactions within the human body. The paradigm shift from culturing to metagenomics has provided an insight into the complex diversity of the microbial species that we harbor, revealing the fact that we are in fact more microbes than human cells. The largest consortium of these microbes resides in the gut and is called the gut microbiota. This new science has expanded the ability to document shifts in microbial populations to an unparalleled degree. It is now understood that signals from the microbiota provide trophic, nutritional, metabolic, and protective effects for the development and maintenance of the host digestive, immune, and neuroendocrine system. Evidence linking changes in the gut microbiota to gastrointestinal and extraintestinal disorders like irritable bowel syndrome, inflammatory bowel disease, obesity, diabetes, and celiac disease have begun to emerge recently. Probiotics act through diverse mechanisms positively affecting the composition and/or function of the commensal microbiota and alter host immunological responses. Well-controlled intervention trials, systematic reviews, and meta-analysis provide convincing evidence for the benefit of probiotics in prevention and treatment of gastrointestinal as well as extraintestinal disorders.

  12. Databases of the marine metagenomics.

    Science.gov (United States)

    Mineta, Katsuhiko; Gojobori, Takashi

    2016-02-01

    The metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Databases of the marine metagenomics

    KAUST Repository

    Mineta, Katsuhiko

    2015-10-28

    The metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database.

  14. Tree Species Identity Shapes Earthworm Communities

    Directory of Open Access Journals (Sweden)

    Stephanie Schelfhout

    2017-03-01

    Full Text Available Earthworms are key organisms in forest ecosystems because they incorporate organic material into the soil and affect the activity of other soil organisms. Here, we investigated how tree species affect earthworm communities via litter and soil characteristics. In a 36-year old common garden experiment, replicated six times over Denmark, six tree species were planted in blocks: sycamore maple (Acer pseudoplatanus, beech (Fagus sylvatica, ash (Fraxinus excelsior, Norway spruce (Picea abies, pedunculate oak (Quercus robur and lime (Tilia cordata. We studied the chemical characteristics of soil and foliar litter, and determined the forest floor turnover rate and the density and biomass of the earthworm species occurring in the stands. Tree species significantly affected earthworm communities via leaf litter and/or soil characteristics. Anecic earthworms were abundant under Fraxinus, Acer and Tilia, which is related to calcium-rich litter and low soil acidification. Epigeic earthworms were indifferent to calcium content in leaf litter and were shown to be mainly related to soil moisture content and litter C:P ratios. Almost no earthworms were found in Picea stands, likely because of the combined effects of recalcitrant litter, low pH and low soil moisture content.

  15. 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.

  16. Gut microbiota, the immune system, and diet influence the neonatal gut-brain axis.

    Science.gov (United States)

    Sherman, Michael P; Zaghouani, Habib; Niklas, Victoria

    2015-01-01

    The conceptual framework for a gut-brain axis has existed for decades. The Human Microbiome Project is responsible for establishing intestinal dysbiosis as a mediator of inflammatory bowel disease, obesity, and neurodevelopmental disorders in adults. Recent advances in metagenomics implicate gut microbiota and diet as key modulators of the bidirectional signaling pathways between the gut and brain that underlie neurodevelopmental and psychiatric disorders in adults. Evidence linking intestinal dysbiosis to neurodevelopmental disease outcomes in preterm infants is emerging. Recent clinical studies show that intestinal dysbiosis precedes late-onset neonatal sepsis and necrotizing enterocolitis in intensive care nurseries. Moreover, strong epidemiologic evidence links late-onset neonatal sepsis and necrotizing enterocolitis in long-term psychomotor disabilities of very-low-birth-weight infants. The notion of the gut-brain axis thereby supports that intestinal microbiota can indirectly harm the brain of preterm infants. In this review, we highlight the anatomy and physiology of the gut-brain axis and describe transmission of stress signals caused by immune-microbial dysfunction in the gut. These messengers initiate neurologic disease in preterm infants. Understanding neural and humoral signaling through the gut-brain axis will offer insight into therapeutic and dietary approaches that may improve the outcomes of very-low-birth-weight infants.

  17. Gut microbiome and liver diseases.

    Science.gov (United States)

    Tilg, Herbert; Cani, Patrice D; Mayer, Emeran A

    2016-12-01

    The gut microbiota has recently evolved as a new important player in the pathophysiology of many intestinal and extraintestinal diseases. The liver is the organ which is in closest contact with the intestinal tract, and is exposed to a substantial amount of bacterial components and metabolites. Various liver disorders such as alcoholic liver disease, non-alcoholic liver disease and primary sclerosing cholangitis have been associated with an altered microbiome. This dysbiosis may influence the degree of hepatic steatosis, inflammation and fibrosis through multiple interactions with the host's immune system and other cell types. Whereas few results from clinical metagenomic studies in liver disease are available, evidence is accumulating that in liver cirrhosis an oral microbiome is overrepresented in the lower intestinal tract, potentially contributing to disease process and severity. A major role for the gut microbiota in liver disorders is also supported by the accumulating evidence that several complications of severe liver disease such as hepatic encephalopathy are efficiently treated by various prebiotics, probiotics and antibiotics. A better understanding of the gut microbiota and its components in liver diseases might provide a more complete picture of these complex disorders and also form the basis for novel therapies. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  18. Microbial Metagenomics: Beyond the Genome

    Science.gov (United States)

    Gilbert, Jack A.; Dupont, Christopher L.

    2011-01-01

    Metagenomics literally means “beyond the genome.” Marine microbial metagenomic databases presently comprise ˜400 billion base pairs of DNA, only ˜3% of that found in 1 ml of seawater. Very soon a trillion-base-pair sequence run will be feasible, so it is time to reflect on what we have learned from metagenomics. We review the impact of metagenomics on our understanding of marine microbial communities. We consider the studies facilitated by data generated through the Global Ocean Sampling expedition, as well as the revolution wrought at the individual laboratory level through next generation sequencing technologies. We review recent studies and discoveries since 2008, provide a discussion of bioinformatic analyses, including conceptual pipelines and sequence annotation and predict the future of metagenomics, with suggestions of collaborative community studies tailored toward answering some of the fundamental questions in marine microbial ecology.

  19. Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle.

    Science.gov (United States)

    Scully, Erin D; Geib, Scott M; Hoover, Kelli; Tien, Ming; Tringe, Susannah G; Barry, Kerrie W; Glavina del Rio, Tijana; Chovatia, Mansi; Herr, Joshua R; Carlson, John E

    2013-01-01

    The Asian longhorned beetle (Anoplophoraglabripennis) is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. A large impediment faced by A. glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars and other nutrients locked in cellulose and hemicellulose. We previously demonstrated that lignin, cellulose, and hemicellulose are actively deconstructed in the beetle gut and that the gut harbors an assemblage of microbes hypothesized to make significant contributions to these processes. While lignin degrading mechanisms have been well characterized in pure cultures of white rot basidiomycetes, little is known about such processes in microbial communities associated with wood-feeding insects. The goals of this study were to develop a taxonomic and functional profile of a gut community derived from an invasive population of larval A. glabripennis collected from infested host trees and to identify genes that could be relevant for the digestion of woody tissue and nutrient acquisition. To accomplish this goal, we taxonomically and functionally characterized the A. glabripennis midgut microbiota through amplicon and shotgun metagenome sequencing and conducted a large-scale comparison with the metagenomes from a variety of other herbivore-associated communities. This analysis distinguished the A. glabripennis larval gut metagenome from the gut communities of other herbivores, including previously sequenced termite hindgut metagenomes. Genes encoding enzymes were identified in the A. glabripennis gut metagenome that could have key roles in woody tissue digestion including candidate lignin degrading genes (laccases, dye-decolorizing peroxidases, novel peroxidases and β-etherases), 36 families of glycoside hydrolases (such as cellulases and xylanases), and genes that could facilitate nutrient recovery, essential nutrient synthesis, and detoxification. This community could serve as a

  20. Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle.

    Directory of Open Access Journals (Sweden)

    Erin D Scully

    Full Text Available The Asian longhorned beetle (Anoplophoraglabripennis is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. A large impediment faced by A. glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars and other nutrients locked in cellulose and hemicellulose. We previously demonstrated that lignin, cellulose, and hemicellulose are actively deconstructed in the beetle gut and that the gut harbors an assemblage of microbes hypothesized to make significant contributions to these processes. While lignin degrading mechanisms have been well characterized in pure cultures of white rot basidiomycetes, little is known about such processes in microbial communities associated with wood-feeding insects. The goals of this study were to develop a taxonomic and functional profile of a gut community derived from an invasive population of larval A. glabripennis collected from infested host trees and to identify genes that could be relevant for the digestion of woody tissue and nutrient acquisition. To accomplish this goal, we taxonomically and functionally characterized the A. glabripennis midgut microbiota through amplicon and shotgun metagenome sequencing and conducted a large-scale comparison with the metagenomes from a variety of other herbivore-associated communities. This analysis distinguished the A. glabripennis larval gut metagenome from the gut communities of other herbivores, including previously sequenced termite hindgut metagenomes. Genes encoding enzymes were identified in the A. glabripennis gut metagenome that could have key roles in woody tissue digestion including candidate lignin degrading genes (laccases, dye-decolorizing peroxidases, novel peroxidases and β-etherases, 36 families of glycoside hydrolases (such as cellulases and xylanases, and genes that could facilitate nutrient recovery, essential nutrient synthesis, and detoxification. This community

  1. Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach.

    Science.gov (United States)

    Decuypere, Saskia; Meehan, Conor J; Van Puyvelde, Sandra; De Block, Tessa; Maltha, Jessica; Palpouguini, Lompo; Tahita, Marc; Tinto, Halidou; Jacobs, Jan; Deborggraeve, Stijn

    2016-02-01

    Bacterial bloodstream infection (bBSI) is one of the leading causes of death in critically ill patients and accurate diagnosis is therefore crucial. We here report a 16S metagenomics approach for diagnosing and understanding bBSI. The proof-of-concept was delivered in 75 children (median age 15 months) with severe febrile illness in Burkina Faso. Standard blood culture and malaria testing were conducted at the time of hospital admission. 16S metagenomics testing was done retrospectively and in duplicate on the blood of all patients. Total DNA was extracted from the blood and the V3-V4 regions of the bacterial 16S rRNA genes were amplified by PCR and deep sequenced on an Illumina MiSeq sequencer. Paired reads were curated, taxonomically labeled, and filtered. Blood culture diagnosed bBSI in 12 patients, but this number increased to 22 patients when combining blood culture and 16S metagenomics results. In addition to superior sensitivity compared to standard blood culture, 16S metagenomics revealed important novel insights into the nature of bBSI. Patients with acute malaria or recovering from malaria had a 7-fold higher risk of presenting polymicrobial bloodstream infections compared to patients with no recent malaria diagnosis (p-value = 0.046). Malaria is known to affect epithelial gut function and may thus facilitate bacterial translocation from the intestinal lumen to the blood. Importantly, patients with such polymicrobial blood infections showed a 9-fold higher risk factor for not surviving their febrile illness (p-value = 0.030). Our data demonstrate that 16S metagenomics is a powerful approach for the diagnosis and understanding of bBSI. This proof-of-concept study also showed that appropriate control samples are crucial to detect background signals due to environmental contamination.

  2. Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach.

    Directory of Open Access Journals (Sweden)

    Saskia Decuypere

    2016-02-01

    Full Text Available Bacterial bloodstream infection (bBSI is one of the leading causes of death in critically ill patients and accurate diagnosis is therefore crucial. We here report a 16S metagenomics approach for diagnosing and understanding bBSI.The proof-of-concept was delivered in 75 children (median age 15 months with severe febrile illness in Burkina Faso. Standard blood culture and malaria testing were conducted at the time of hospital admission. 16S metagenomics testing was done retrospectively and in duplicate on the blood of all patients. Total DNA was extracted from the blood and the V3-V4 regions of the bacterial 16S rRNA genes were amplified by PCR and deep sequenced on an Illumina MiSeq sequencer. Paired reads were curated, taxonomically labeled, and filtered. Blood culture diagnosed bBSI in 12 patients, but this number increased to 22 patients when combining blood culture and 16S metagenomics results. In addition to superior sensitivity compared to standard blood culture, 16S metagenomics revealed important novel insights into the nature of bBSI. Patients with acute malaria or recovering from malaria had a 7-fold higher risk of presenting polymicrobial bloodstream infections compared to patients with no recent malaria diagnosis (p-value = 0.046. Malaria is known to affect epithelial gut function and may thus facilitate bacterial translocation from the intestinal lumen to the blood. Importantly, patients with such polymicrobial blood infections showed a 9-fold higher risk factor for not surviving their febrile illness (p-value = 0.030.Our data demonstrate that 16S metagenomics is a powerful approach for the diagnosis and understanding of bBSI. This proof-of-concept study also showed that appropriate control samples are crucial to detect background signals due to environmental contamination.

  3. Shotgun Metaproteomics of the Human Distal Gut Microbiota

    Energy Technology Data Exchange (ETDEWEB)

    Verberkmoes, Nathan C [ORNL; Erickson, Alison L [ORNL; Shah, Manesh B [ORNL; Godzik, A [Burnham Institute for Medical Research, La Jolla, CA; Rosenquist, M [Swedish University of Agricultural Sciences, Upsalla, Sweden; Halfvarsson, J [Orebro University Hospital, Orebro, Sweden; Lefsrud, Mark G [McGill University, Montreal, Quebec; Apajalahti, J. [Alimetrics Ltd,; Hettich, Robert {Bob} L [ORNL; Jansson, J [Swedish University of Agricultural Sciences, Upsalla, Sweden

    2009-01-01

    The human gut contains a dense, complex, and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about what genes were expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production, and carbohydrate metabolism compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

  4. Shotgun metaproteomics of the human distal gut microbiota

    Energy Technology Data Exchange (ETDEWEB)

    VerBerkmoes, N.C.; Russell, A.L.; Shah, M.; Godzik, A.; Rosenquist, M.; Halfvarsson, J.; Lefsrud, M.G.; Apajalahti, J.; Tysk, C.; Hettich, R.L.; Jansson, Janet K.

    2008-10-15

    The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

  5. Impact of cadmium on the bacterial communities in the gut of Metaphire posthuma

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Shih-Hsiung; Chen, Mu-Hsuan; Chen, Chien-Cheng; Chen, Colin S. [Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan (China); Chen, Jiun-Hong [Department of Life Science, National Taiwan University, Taipei, Taiwan (China); Chen, Ssu Ching, E-mail: osycchna@ksts.seed.net.tw [Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan (China)

    2009-12-30

    The effects of cadmium (Cd) contamination in soil onto the bacterial communities of the guts pooled from ten Metaphire posthuma were addressed during 14 days' incubation. We found that about 50% of Cd (5 mg/kg, dry weight soil) in the contaminated soil was bio-accumulated into the earthworms. DNA was extracted from the guts of M. posthuma and their dwelling soil irrespective of Cd treatment for the analysis of the bacterial communities of guts in M. posthuma and in soil by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). A distinctive cluster of bacterial communities of the guts in the earthworm with and without Cd treatment using the analysis of unweighted pair-group method using arithmetic averages (UPGMA) was observed, indicating that the bacterial community of guts could be changed by Cd. However, no differences in the bacterial communities in soil irrespective of Cd treatment were observed, which could be resulted from the bioremediation of Cd by earthworms leading to insignificant effect of Cd on bacterial communities in soil. For the sequencing of some of the dominant bands in the DGGE profile, Bradyrhizobium japonicum, Stenotrophomonas sp. D2, and Labrys, sp. CC-BB4, whose sequences display an identity of more than 97% using blast program against a known sequence in the GeneBank database and Ribosomal database, were identified. Collectively, our results showed that earthworm treatment can decrease the concentrations of Cd in soil, and Cd cause a shift in the bacterial communities in the guts of M. posthuma. The application of M. posthuma for Cd bioremediation would be desired.

  6. Inter-individual differences in the gene content of human gut bacterial species.

    Science.gov (United States)

    Zhu, Ana; Sunagawa, Shinichi; Mende, Daniel R; Bork, Peer

    2015-04-21

    Gene content differences in human gut microbes can lead to inter-individual phenotypic variations such as digestive capacity. It is unclear whether gene content variation is caused by differences in microbial species composition or by the presence of different strains of the same species; the extent of gene content variation in the latter is unknown. Unlike pan-genome studies of cultivable strains, the use of metagenomic data can provide an unbiased view of structural variation of gut bacterial strains by measuring them in their natural habitats, the gut of each individual in this case, representing native boundaries between gut bacterial populations. We analyzed publicly available metagenomic data from fecal samples to characterize inter-individual variation in gut bacterial species. A comparison of 11 abundant gut bacterial species showed that the gene content of strains from the same species differed, on average, by 13% between individuals. This number is based on gene deletions only and represents a lower limit, yet the variation is already in a similar range as observed between completely sequenced strains of cultivable species. We show that accessory genes that differ considerably between individuals can encode important functions, such as polysaccharide utilization and capsular polysaccharide synthesis loci. Metagenomics can yield insights into gene content variation of strains in complex communities, which cannot be predicted by phylogenetic marker genes alone. The large degree of inter-individual variability in gene content implies that strain resolution must be considered in order to fully assess the functional potential of an individual's human gut microbiome.

  7. Herbicide Glyphosate Impact to Earthworm (E. fetida

    Directory of Open Access Journals (Sweden)

    Greta Dajoraitė

    2016-10-01

    Full Text Available Glyphosate is a broad spectrum weed resistant herbicide. Glyphosate may pose negative impact on land ecosystems because of wide broad usage and hydrofilic characteristic. The aim of this study was to investigate negative effects of glyphosate on soil invertebrate organisms (earthworm Eisenia fetida. The duration of experiment was 8 weeks. The range of the test concentrations of glyphosate were: 0,1, 1, 5, 10, 20 mg/kg. To investigate the glyphosate impact on earthworm Eisenia fetida the following endpoints were measured: survival, reproduction and weight. The exposure to 20 mg/kg glyphosate has led to the 100% mortality of earthworms. Glyphosate has led to decreased E. fetida reproduction, the cocoons were observed only in the lowest concentration (0,1 mg/kg. In general: long-term glyphosate toxicity to earthworms (E. fetida may be significant.

  8. 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...... 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...... that there is a division of labor between the bacterial species in the human gut microbiome....

  9. Microplastic transport in soil by earthworms

    OpenAIRE

    Rillig, Matthias C.; Lisa Ziersch; Stefan Hempel

    2017-01-01

    Despite great general benefits derived from plastic use, accumulation of plastic material in ecosystems, and especially microplastic, is becoming an increasing environmental concern. Microplastic has been extensively studied in aquatic environments, with very few studies focusing on soils. We here tested the idea that microplastic particles (polyethylene beads) could be transported from the soil surface down the soil profile via earthworms. We used Lumbricus terrestris L., an anecic earthworm...

  10. Autofluorescence in eleocytes of some earthworm species.

    OpenAIRE

    Barbara Płytycz; A John Morgan; Stephen R StĂźrzenbaum; Michael O' Reilly; Feeney, Graham P.; Justyna Cholewa

    2006-01-01

    Immunocompetent cells of earthworms, coelomocytes, comprise adherent amoebocytes and granular eleocytes (chloragocytes). Both cell populations can be expelled via dorsal pores of adult earthworms by exposure to an electric current (4.5 V) for 1 min. Analysis by phase contrast/fluorescence microscopy and flow cytometry demonstrated that eleocyte population of several species exhibits a strong autofluorescence. A high percentage (11-35%) of autofluorescent eleocytes was recorded in Allolobophor...

  11. Development of earthworm burrow systems and the influence of earthworms on soil hydrology

    NARCIS (Netherlands)

    Ligthart, T.N.

    1996-01-01


    Inoculation of earthworms can help to restore or ameliorate land qualities. Earthworms create burrows and alter the structure of the soil matrix, which influence the water infiltration, drainage, water retention and the aeration of the soil. The way and rate of the development of

  12. Decay of low-density polyethylene by bacteria extracted from earthworm’s guts: a potential for soil restoration

    NARCIS (Netherlands)

    Huerta Lwanga, E.; Thapa, B.; Yang, X.; Gertsen, H.; Salánki, T.; Geissen, V.; Garbeva, P.V.

    2018-01-01

    Low-density polyethylene (LDPE) is the most abundant source of microplastic pollution worldwide. A recent study found that LDPE decay was increased and the size of the plastic was decreased after passing through the gut of the earthworm Lumbricus terrestris (Oligochaeta). Here, we investigated the

  13. Effect of Soil Physical State on the Earthworms in Hungary

    OpenAIRE

    Marta Birkas; Laszlo Bottlik; Attila Stingli; Csaba Gyuricza; Márton Jolánkai

    2010-01-01

    Hungarian authors have long been discussing the role of earthworms in improving soil productivity. Earthworm counts in our higher quality soils are similar to those found in soils where more attention is paid to earthworm activity. Negative impacts that are independent of farming—such as sustained dry spells in the summer—also affect earthworm counts. Negative impacts that definitely depend on farming include land use causing soil moisture loss, deep stubble treatment leaving the soil without...

  14. First earthworm (Oligochaeta: Lumbricidae record from Sithonia Peninsula (Greece

    Directory of Open Access Journals (Sweden)

    HRISTO VALCHOVSKI

    2016-07-01

    Full Text Available The paper deals with the earthworm diversity of Chalkidiki Peninsula, Greece. Aporrectodea longa (Ude, 1885 proved to be new species for the fauna of Greece and also represents the first earthworm record from Sithonia Peninsula. According to the literature and authors data 14 earthworm taxa are registered from the explored region. The paper underlines lumbricid richness of Chalkidiki Peninsula and provides information about the zoogeographical position of the earthworm species present.

  15. First earthworm (Oligochaeta: Lumbricidae) record from Sithonia Peninsula (Greece)

    OpenAIRE

    HRISTO VALCHOVSKI

    2016-01-01

    The paper deals with the earthworm diversity of Chalkidiki Peninsula, Greece. Aporrectodea longa (Ude, 1885) proved to be new species for the fauna of Greece and also represents the first earthworm record from Sithonia Peninsula. According to the literature and authors data 14 earthworm taxa are registered from the explored region. The paper underlines lumbricid richness of Chalkidiki Peninsula and provides information about the zoogeographical position of the earthworm species...

  16. Potential applications of gut microbiota to control human physiology.

    Science.gov (United States)

    Umu, Ozgün Candan Onarman; Oostindjer, Marije; Pope, Phillip B; Svihus, Birger; Egelandsdal, Bjørg; Nes, Ingolf F; Diep, Dzung B

    2013-11-01

    The microorganisms living in our gut have been a black box to us for a long time. However, with the recent advances in high throughput DNA sequencing technologies, it is now possible to assess virtually all microorganisms in our gut including non-culturable ones. With the use of powerful bioinformatics tools to deal with multivariate analyses of huge amounts of data from metagenomics, metatranscriptomics, metabolomics, we now start to gain some important insights into these tiny gut inhabitants. Our knowledge is increasing about who they are, to some extent, what they do and how they affect our health. Gut microbiota have a broad spectrum of possible effects on health, from preventing serious diseases, improving immune system and gut health to stimulating the brain centers responsible for appetite and food intake control. Further, we may be on the verge of being capable of manipulating the gut microbiota by diet control to possibly improve our health. Diets consisting of different components that are fermentable by microbiota are substrates for different kinds of microbes in the gut. Thus, diet control can be used to favor the growth of some selected gut inhabitants. Nowadays, the gut microbiota is taken into account as a separate organ in human body and their activities and metabolites in gut have many physiological and neurological effects. In this mini-review, we discuss the diversity of gut microbiota, the technologies used to assess them, factors that affect microbial composition and metabolites that affect human physiology, and their potential applications in satiety control via the gut-brain axis.

  17. Enterotypes of the human gut microbiome

    DEFF Research Database (Denmark)

    Arumugam, M.; Raes, J.; Pelletier, E.

    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 previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous...

  18. MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequence

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Dongwan; Froula, Jeff; Egan, Rob; Wang, Zhong

    2014-03-21

    Grouping large fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Here we developed automated metagenome binning software, called MetaBAT, which integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. On synthetic datasets MetaBAT on average achieves 98percent precision and 90percent recall at the strain level with 281 near complete unique genomes. Applying MetaBAT to a human gut microbiome data set we recovered 176 genome bins with 92percent precision and 80percent recall. Further analyses suggest MetaBAT is able to recover genome fragments missed in reference genomes up to 19percent, while 53 genome bins are novel. In summary, we believe MetaBAT is a powerful tool to facilitate comprehensive understanding of complex microbial communities.

  19. Metagenomics and novel gene discovery: promise and potential for novel therapeutics.

    Science.gov (United States)

    Culligan, Eamonn P; Sleator, Roy D; Marchesi, Julian R; Hill, Colin

    2014-04-01

    Metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. Herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of each type of approach, as well as potential solutions. Furthermore, we discuss the potential for metagenomic biotherapeutic discovery, with a particular focus on the human gut microbiome and finally, we outline how the discovery of novel genes may be used to create bioengineered probiotics.

  20. Earthworms and post agricultural succession in the Neotropics

    Science.gov (United States)

    Grizelle Gonzalez; C.Y. Huang; S.C. Chang

    2008-01-01

    Earthworms are classified into endogeic, anecic, and epigeic species to represent soil, soil and litter, and litter feeders, respectively (Bouché 1977). Earthworms can alter soil physical properties and biogeochemical processes (e.g., Ewards and Bohlen 1996) according to their functionality. Endogeic earthworms alter soil properties primarily through changing soil...

  1. Predicting exotic earthworm distribution in the northern Great Lakes region

    Science.gov (United States)

    Lindsey M. Shartell; Erik A. Lilleskov; Andrew J. Storer

    2013-01-01

    Identifying influences of earthworm invasion and distribution in the northern Great Lakes is an important step in predicting the potential extent and impact of earthworms across the region. The occurrence of earthworm signs, indicating presence in general, and middens, indicating presence of Lumbricus terrestris exclusively, in the Huron Mountains...

  2. Effect of earthworm inoculation on the bioremediation of used ...

    African Journals Online (AJOL)

    ... in the without-earthworm but manually tilled and the without-earthworm and untilled samples where compared with samples inoculated with earthworm for bioremediation, both samples without worms recorded higher bioremediation rates. Keywords: Concentration, Time, Total petroleum hydrocarbon, vermicomposting, ...

  3. Challenges of metabolomics in human gut microbiota research.

    Science.gov (United States)

    Smirnov, Kirill S; Maier, Tanja V; Walker, Alesia; Heinzmann, Silke S; Forcisi, Sara; Martinez, Inés; Walter, Jens; Schmitt-Kopplin, Philippe

    2016-08-01

    The review highlights the role of metabolomics in studying human gut microbial metabolism. Microbial communities in our gut exert a multitude of functions with huge impact on human health and disease. Within the meta-omics discipline, gut microbiome is studied by (meta)genomics, (meta)transcriptomics, (meta)proteomics and metabolomics. The goal of metabolomics research applied to fecal samples is to perform their metabolic profiling, to quantify compounds and classes of interest, to characterize small molecules produced by gut microbes. Nuclear magnetic resonance spectroscopy and mass spectrometry are main technologies that are applied in fecal metabolomics. Metabolomics studies have been increasingly used in gut microbiota related research regarding health and disease with main focus on understanding inflammatory bowel diseases. The elucidated metabolites in this field are summarized in this review. We also addressed the main challenges of metabolomics in current and future gut microbiota research. The first challenge reflects the need of adequate analytical tools and pipelines, including sample handling, selection of appropriate equipment, and statistical evaluation to enable meaningful biological interpretation. The second challenge is related to the choice of the right animal model for studies on gut microbiota. We exemplified this using NMR spectroscopy for the investigation of cross-species comparison of fecal metabolite profiles. Finally, we present the problem of variability of human gut microbiota and metabolome that has important consequences on the concepts of personalized nutrition and medicine. Copyright © 2016 Elsevier GmbH. All rights reserved.

  4. Genomic variation landscape of the human gut microbiome

    DEFF Research Database (Denmark)

    Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi

    2013-01-01

    polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates......Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal...

  5. Early-life gut microbiome and egg allergy.

    Science.gov (United States)

    Fazlollahi, Mina; Chun, Yoojin; Grishin, Alexander; Wood, Robert A; Burks, A Wesley; Dawson, Peter; Jones, Stacie M; Leung, Donald Y M; Sampson, Hugh A; Sicherer, Scott H; Bunyavanich, Supinda

    2018-01-10

    Gut microbiota may play a role in egg allergy. We sought to examine the association between early-life gut microbiota and egg allergy. We studied 141 children with egg allergy and controls from the multi-center Consortium of Food Allergy Research study. At enrollment (age 3 to 16 months), fecal samples were collected and clinical evaluation, egg specific IgE measurement, and egg skin prick test were performed. Gut microbiome was profiled by 16S rRNA sequencing. Analyses for the primary outcome of egg allergy at enrollment, and the secondary outcomes of egg sensitization at enrollment and resolution of egg allergy by age 8 years, were performed using Quantitative Insights into Microbial Ecology (QIIME), Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), and Statistical Analysis of Metagenomic Profiles (STAMP). Compared to controls, increased alpha diversity and distinct taxa (PERMANOVA P=5.0x10 -4 ) characterized the early-life gut microbiome of children with egg allergy. Genera from the Lachnospiraceae, Streptococcaceae, and Leuconostocaceae families were differentially abundant in children with egg allergy. Predicted metagenome functional analyses showed differential purine metabolism by the gut microbiota of egg allergic subjects (Kruskal Wallis P adj =0.021). Greater gut microbiome diversity and genera from Lachnospiraceae and Ruminococcaceae were associated with egg sensitization (PERMANOVA P = 5.0x10 -4 ). Among those with egg allergy, there was no association between early-life gut microbiota and egg allergy resolution by age 8 years. The distinct early-life gut microbiota in egg allergic and egg-sensitized children identified by our study may point to targets for preventive or therapeutic intervention. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  6. Identification of RNA viruses in the turkey gut using metagenomics.

    Science.gov (United States)

    Poultry enteric disease is marked by diarrhea, stunting, increased time to market, immune dysfunction and increased mortality. Numerous viruses have been detected in the intestinal tract of poultry, and have subsequently been implicated in enteric disease. Knowledge of the complete viral flora prese...

  7. Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies.

    Science.gov (United States)

    Santiago-Rodriguez, Tasha M; Fornaciari, Gino; Luciani, Stefania; Dowd, Scot E; Toranzos, Gary A; Marota, Isolina; Cano, Raul J

    2016-11-01

    Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

    Directory of Open Access Journals (Sweden)

    Jitendra Kumar

    2016-12-01

    Full Text Available Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (>23 kb metagenomic DNA (260/280 ratio >1.8 with a good yield (55.8 ± 3.8 ng/mg of feces. We also confirm that there is very low human genomic DNA contamination (eubacterial: human genomic DNA marker genes = 227.9:1 in the human feces. The newly-developed method robustly performs for fresh as well as stored fecal samples as demonstrated by 16S rRNA gene sequencing using 454 FLX+. Moreover, 16S rRNA gene analysis indicated that compared to other DNA extraction methods tested, the fecal metagenomic DNA isolated with current methodology retains species richness and does not show microbial diversity biases, which is further confirmed by qPCR with a known quantity of spike-in genomes. Overall, our data highlight a protocol with a balance between quality, amount, user-friendliness, and cost effectiveness for its suitability toward usage for culture-independent analysis of the human gut microbiome, which provides a robust solution to overcome key issues associated with fecal metagenomic DNA isolation in human gut microbiome studies.

  9. Evaluation method for the potential functionome harbored in the genome and metagenome

    Science.gov (United States)

    2012-01-01

    Background One of the main goals of genomic analysis is to elucidate the comprehensive functions (functionome) in individual organisms or a whole community in various environments. However, a standard evaluation method for discerning the functional potentials harbored within the genome or metagenome has not yet been established. We have developed a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules. Results Distribution of the completion ratio of the KEGG functional modules in 768 prokaryotic species varied greatly with the kind of module, and all modules primarily fell into 4 patterns (universal, restricted, diversified and non-prokaryotic modules), indicating the universal and unique nature of each module, and also the versatility of the KEGG Orthology (KO) identifiers mapped to each one. The module completion ratio in 8 phenotypically different bacilli revealed that some modules were shared only in phenotypically similar species. Metagenomes of human gut microbiomes from 13 healthy individuals previously determined by the Sanger method were analyzed based on the module completion ratio. Results led to new discoveries in the nutritional preferences of gut microbes, believed to be one of the mutualistic representations of gut microbiomes to avoid nutritional competition with the host. Conclusions The method developed in this study could characterize the functionome harbored in genomes and metagenomes. As this method also provided taxonomical information from KEGG modules as well as the gene hosts constructing the modules, interpretation of completion profiles was simplified and we could identify the complementarity between biochemical functions in human hosts and the nutritional preferences in human gut microbiomes. Thus, our method has the potential to be a powerful tool for comparative functional analysis in genomics and metagenomics, able to target unknown

  10. An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction.

    Science.gov (United States)

    Kumar, Jitendra; Kumar, Manoj; Gupta, Shashank; Ahmed, Vasim; Bhambi, Manu; Pandey, Rajesh; Chauhan, Nar Singh

    2016-12-01

    Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (>23kb) metagenomic DNA (260/280 ratio >1.8) with a good yield (55.8±3.8ng/mg of feces). We also confirm that there is very low human genomic DNA contamination (eubacterial: human genomic DNA marker genes=227.9:1) in the human feces. The newly-developed method robustly performs for fresh as well as stored fecal samples as demonstrated by 16S rRNA gene sequencing using 454 FLX+. Moreover, 16S rRNA gene analysis indicated that compared to other DNA extraction methods tested, the fecal metagenomic DNA isolated with current methodology retains species richness and does not show microbial diversity biases, which is further confirmed by qPCR with a known quantity of spike-in genomes. Overall, our data highlight a protocol with a balance between quality, amount, user-friendliness, and cost effectiveness for its suitability toward usage for culture-independent analysis of the human gut microbiome, which provides a robust solution to overcome key issues associated with fecal metagenomic DNA isolation in human gut microbiome studies. Copyright © 2016 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  11. Open resource metagenomics: a model for sharing metagenomic libraries.

    Science.gov (United States)

    Neufeld, J D; Engel, K; Cheng, J; Moreno-Hagelsieb, G; Rose, D R; Charles, T C

    2011-11-30

    Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM(2)BL [1]). The CM(2)BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the

  12. Microplastic transport in soil by earthworms.

    Science.gov (United States)

    Rillig, Matthias C; Ziersch, Lisa; Hempel, Stefan

    2017-05-02

    Despite great general benefits derived from plastic use, accumulation of plastic material in ecosystems, and especially microplastic, is becoming an increasing environmental concern. Microplastic has been extensively studied in aquatic environments, with very few studies focusing on soils. We here tested the idea that microplastic particles (polyethylene beads) could be transported from the soil surface down the soil profile via earthworms. We used Lumbricus terrestris L., an anecic earthworm species, in a factorial greenhouse experiment with four different microplastic sizes. Presence of earthworms greatly increased the presence of microplastic particles at depth (we examined 3 soil layers, each 3.5 cm deep), with smaller PE microbeads having been transported downward to a greater extent. Our study clearly shows that earthworms can be significant transport agents of microplastics in soils, incorporating this material into soil, likely via casts, burrows (affecting soil hydraulics), egestion and adherence to the earthworm exterior. This movement has potential consequences for exposure of other soil biota to microplastics, for the residence times of microplastic at greater depth, and for the possible eventual arrival of microplastics in the groundwater.

  13. Microbial detoxification in the gut of a specialist avian herbivore, the Greater Sage-Grouse.

    Science.gov (United States)

    Kohl, Kevin D; Connelly, John W; Dearing, M Denise; Forbey, Jennifer Sorensen

    2016-07-01

    One function of the gut microbiota gaining recent attention, especially in herbivorous mammals and insects, is the metabolism of plant secondary metabolites (PSMs). We investigated whether this function exists within the gut communities of a specialist avian herbivore. We sequenced the cecal metagenome of the Greater Sage-Grouse (Centrocercus urophasianus), which specializes on chemically defended sagebrush (Artemisia spp.). We predicted that the cecal metagenome of the sage-grouse would be enriched in genes associated with the metabolism of PSMs when compared to the metagenome of the domestic chicken. We found that representation of microbial genes associated with 'xenobiotic degradation and metabolism' was 3-fold higher in the sage-grouse cecal metagenomes when compared to that of the domestic chicken. Further, we identified a complete metabolic pathway for the degradation of phenol to pyruvate, which was not detected in the metagenomes of the domestic chicken, bovine rumen or 14 species of mammalian herbivores. Evidence of monoterpene degradation (a major class of PSMs in sagebrush) was less definitive, although we did detect genes for several enzymes associated with this process. Overall, our results suggest that the gut microbiota of specialist avian herbivores plays a similar role to the microbiota of mammalian and insect herbivores in degrading PSMs. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Is the Gut Microbiota a New Factor Contributing to Obesity and Its Metabolic Disorders?

    Directory of Open Access Journals (Sweden)

    Kristina Harris

    2012-01-01

    Full Text Available The gut microbiota refers to the trillions of microorganisms residing in the intestine and is integral in multiple physiological processes of the host. Recent research has shown that gut bacteria play a role in metabolic disorders such as obesity, diabetes, and cardiovascular diseases. The mechanisms by which the gut microbiota affects metabolic diseases are by two major routes: (1 the innate immune response to the structural components of bacteria (e.g., lipopolysaccharide resulting in inflammation and (2 bacterial metabolites of dietary compounds (e.g., SCFA from fiber, which have biological activities that regulate host functions. Gut microbiota has evolved with humans as a mutualistic partner, but dysbiosis in a form of altered gut metagenome and collected microbial activities, in combination with classic genetic and environmental factors, may promote the development of metabolic disorders. This paper reviews the available literature about the gut microbiota and aforementioned metabolic disorders and reveals the gaps in knowledge for future study.

  15. Autofluorescence in eleocytes of some earthworm species.

    Directory of Open Access Journals (Sweden)

    Barbara Płytycz

    2006-04-01

    Full Text Available Immunocompetent cells of earthworms, coelomocytes, comprise adherent amoebocytes and granular eleocytes (chloragocytes. Both cell populations can be expelled via dorsal pores of adult earthworms by exposure to an electric current (4.5 V for 1 min. Analysis by phase contrast/fluorescence microscopy and flow cytometry demonstrated that eleocyte population of several species exhibits a strong autofluorescence. A high percentage (11-35% of autofluorescent eleocytes was recorded in Allolobophora chlorotica, Dendrodrilus rubidus, Eisenia fetida, and Octolasion sp. (O. cyaneum, O. tyrtaeum tyrtaeum and O. tyrtaeum lacteum. In contrast, autofluorescent coelomocytes were exceptionally scarce (less than 1% in representative Aporrectodea sp. (A. caliginosa and A. longa and Lumbricus sp. (L. castaneus, L. festivus, L. rubellus, L. terrestris. Thus, this paper for the first time describes profound intrinsic fluorescence of eleocytes in some--but not all--earthworm species. The function (if any and inter-species differences of the autofluorescent coelomocytes still remain elusive.

  16. Autofluorescence in eleocytes of some earthworm species.

    Science.gov (United States)

    Cholewa, Justyna; Feeney, Graham P; O'Reilly, Michael; Stürzenbaum, Stephen R; Morgan, A John; Płytycz, Barbara

    2006-01-01

    Immunocompetent cells of earthworms, coelomocytes, comprise adherent amoebocytes and granular eleocytes (chloragocytes). Both cell populations can be expelled via dorsal pores of adult earthworms by exposure to an electric current (4.5 V) for 1 min. Analysis by phase contrast/fluorescence microscopy and flow cytometry demonstrated that eleocyte population of several species exhibits a strong autofluorescence. A high percentage (11-35%) of autofluorescent eleocytes was recorded in Allolobophora chlorotica, Dendrodrilus rubidus, Eisenia fetida, and Octolasion sp. (O. cyaneum, O. tyrtaeum tyrtaeum and O. tyrtaeum lacteum). In contrast, autofluorescent coelomocytes were exceptionally scarce (less than 1%) in representative Aporrectodea sp. (A. caliginosa and A. longa) and Lumbricus sp. (L. castaneus, L. festivus, L. rubellus, L. terrestris). Thus, this paper for the first time describes profound intrinsic fluorescence of eleocytes in some--but not all--earthworm species. The function (if any) and inter-species differences of the autofluorescent coelomocytes still remain elusive.

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

    Directory of Open Access Journals (Sweden)

    Phillip B Pope

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

  18. Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis.

    Science.gov (United States)

    Xiao, Jinqiu; Tanca, Alessandro; Jia, Ben; Yang, Runqing; Wang, Bo; Zhang, Yu; Li, Jing

    2018-02-26

    Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.

  19. Gut bacterium of Dendrobaena veneta (Annelida: Oligochaeta) possesses antimycobacterial activity.

    Science.gov (United States)

    Fiołka, Marta J; Zagaja, Mirosław P; Piersiak, Tomasz D; Wróbel, Marek; Pawelec, Jarosław

    2010-09-01

    The new bacterial strain with antimycobacterial activity has been isolated from the midgut of Dendrobaena veneta (Annelida). Biochemical and molecular characterization of isolates from 18 individuals identified all as Raoultella ornithinolytica genus with 99% similarity. The bacterium is a possible symbiont of the earthworm D. veneta. The isolated microorganism has shown the activity against four strains of fast-growing mycobacteria: Mycobacterium butiricum, Mycobacterium jucho, Mycobacterium smegmatis and Mycobacterium phlei. The multiplication of the gut bacterium on plates with Sauton medium containing mycobacteria has caused a lytic effect. After the incubation of the cell free extract prepared from the gut bacterium with four strains of mycobacteria in liquid Sauton medium, the cells of all tested strains were deformed and divided to small oval forms and sometimes created long filaments. The effect was observed by the use of light, transmission and scanning microscopy. Viability of all examined species of mycobacteria was significantly decreased. The antimycobacterial effect was probably the result of the antibiotic action produced by the gut bacterium of the earthworm. The application of ultrafiltration procedure allowed to demonstrate that antimicrobial substance with strong antimycobacterial activity from bacterial culture supernatant, is a protein with the molecular mass above 100 kDa. Copyright 2010 Elsevier Inc. All rights reserved.

  20. Biochemical diversity of betaines in earthworms

    Energy Technology Data Exchange (ETDEWEB)

    Liebeke, Manuel [Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ (United Kingdom); Bundy, Jacob G., E-mail: j.bundy@imperial.ac.uk [Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ (United Kingdom)

    2013-01-25

    Highlights: ► We develop a method for rapid untargetted analysis of betaines. ► We profile betaines in a comparative study of ten earthworm species. ► Earthworms contain a surprisingly high number of different betaine metabolites. ► Earthworms contain betaines normally seen only in plants or marine animals. -- Abstract: The ability to accumulate osmoprotectant compounds, such as betaines, is an important evolutionary feature in many organisms. This is particularly the case for organisms that live in variable environments, which may have fluctuations in moisture and salinity levels. There is, surprisingly, very little known about betaines in soil invertebrates in general, and there is almost no information about earthworms – a group that are important ‘ecosystem engineers’ and key indicators of soil health. Here, we describe a fast and reliable {sup 1}H–{sup 13}C heteronuclear single quantum coherence (HSQC) 2D NMR approach for the metabolic profiling of a series of betaines and related metabolites in tissue extracts, and list {sup 1}H and {sup 13}C chemical shifts for the trimethylammonium signal for 23 such compounds. The analysis of ten different species from three different families (Lumbricidae, Megascolecidae and Glossoscolecidae) showed an unexpected diversity of betaines present in earthworms. In total ten betaines were identified, including hydroxyproline-betaine, proline-betaine, taurine-betaine, GABA-betaine and histidine-betaine, and a further eleven as-yet unassigned putative betaine metabolites detected. The findings clearly indicate a hitherto-unappreciated important role for betaine metabolism in earthworms.

  1. Earthworms and radionuclides, with experimental investigations on the uptake and exchangeability of radiocaesium.

    Science.gov (United States)

    Brown, S L; Bell, J N

    1995-01-01

    The potential influence of earthworm activity on the mobility of radionuclides in soils and their subsequent availability for uptake by plants and transfer to higher trophic levels is briefly reviewed. The accumulation of caesium by the earthworm Aporrectodea longa from soil and from plant litter was investigated in laboratory experiments, as was the effect of reworking (through burrowing and ingestion) soil and soil with added organic material, on the extractability of caesium (ammonium acetate extraction). Soil was spiked with (134)Cs, organic matter with (137)Cs. In soil-fed worms, most of the radioactivity measured was eliminated with the gut contents; 5-25% of the ingested radioactivity was retained or assimilated. Loss of caesium from soil-fed worms followed a two component curve, with an initial rapid loss due to gut clearance (half-life of loss (Tb1/2) of about 0.2-0.6 days) and a slower loss of assimilated caesium (Tb1/2 of 15-26 days). Loss rates of assimilated caesium from worms fed on fragmented apple leaves were found to have half-lives of 18-54 days. Assimilation of caesium from apple leaves was higher than from soil, ranging from 55-100% of the activity measured before gut clearance. Dry weight transfer factors (concentration in worm tissue/concentration in substrate) for worms cleared of their gut contents were similar for the two substrates 0.04 and 0.04 for two loss experiments with worms fed on radioactive soil, and 0.03 and 0.05 for worms fed on apple leaves. After three months of reworking soil and soil/organic mixtures, A. longa was found to have no measurable effect on the extractable fraction of caesium. If earthworms have any subtle effects they were masked by changes in availability that occurred when the spiked soil and organic substrates were mixed together. Only about half of the extractable fraction in soil was recovered when soil was mixed with organic material suggesting that some of the labile fraction in soil had become complexed

  2. Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks.

    Science.gov (United States)

    Walsh, Aaron M; Crispie, Fiona; Daari, Kareem; O'Sullivan, Orla; Martin, Jennifer C; Arthur, Cornelius T; Claesson, Marcus J; Scott, Karen P; Cotter, Paul D

    2017-08-15

    The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole-metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole-metagenome assembly, which is a computationally demanding process. Here we demonstrated that three short-read-alignment-based methods, i.e., MetaMLST, PanPhlAn, and StrainPhlAn, could accurately and rapidly identify pathogenic strains in spinach metagenomes that had been intentionally spiked with Shiga toxin-producing Escherichia coli in a previous study. Subsequently, we employed the methods, in combination with other metagenomics approaches, to assess the safety of nunu, a traditional Ghanaian fermented milk product that is produced by the spontaneous fermentation of raw cow milk. We showed that nunu samples were frequently contaminated with bacteria associated with the bovine gut and, worryingly, we detected putatively pathogenic E. coli and Klebsiella pneumoniae strains in a subset of nunu samples. Ultimately, our work establishes that short-read-alignment-based bioinformatics approaches are suitable food safety tools, and we describe a real-life example of their utilization. IMPORTANCE Foodborne pathogens are responsible for millions of illnesses each year. Here we demonstrate that short-read-alignment-based bioinformatics tools can accurately and rapidly detect pathogenic strains in food products by using shotgun metagenomics data. The methods used here are considerably faster than both traditional culturing methods and alternative bioinformatics approaches that rely on metagenome assembly; therefore, they can potentially be used for more high-throughput food safety testing. Overall, our results suggest that whole-metagenome sequencing can be used as a practical food safety tool to prevent diseases or to link outbreaks to specific food products. Copyright

  3. Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena)

    OpenAIRE

    Lu Hsiao-Pei; Wang Yu-bin; Huang Shiao-Wei; Lin Chung-Yen; Wu Martin; Hsieh Chih-hao; Yu Hon-Tsen

    2012-01-01

    Abstract Background Animals co-evolve with their gut microbiota; the latter can perform complex metabolic reactions that cannot be done independently by the host. Although the importance of gut microbiota has been well demonstrated, there is a paucity of research regarding its role in foliage-foraging mammals with a specialized digestive system. Results In this study, a 16S rRNA gene survey and metagenomic sequencing were used to characterize genetic diversity and functional capability of cec...

  4. Influence of feeding and earthworm density on compound bioaccumulation in earthworms Eisenia andrei.

    Science.gov (United States)

    Šmídová, Klára; Šerá, Jana; Bielská, Lucie; Hofman, Jakub

    2015-12-01

    Earthworm density and feeding during exposure to contaminated soil have been used inconsistently in bioaccumulation studies, which may lead to possible errors in risk assessment and modeling. Hydrophobic organic pollutants with a wide range of environmental properties (phenanthrene, pyrene, lindane, p,p'-DDT, and PCB 153) were used to study the effect of different earthworm densities in combination with the presence or absence of feeding on bioaccumulation factors (BAFs). Similar BAFs were found at various soil-to-worm ratios, with the exception of phenanthrene. We recommend using at least 15 gsoil dw per earthworm. The absence of feeding doubled the BAFs and, thus, using no food ration can be considered as "the worst case scenario". Whenever food is to be applied (i.e. to ensure the validity of the test in earthworm mass loss), we suggest feeding depending on the organic carbon content of the studied soil. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Web Resources for Metagenomics Studies.

    Science.gov (United States)

    Dudhagara, Pravin; Bhavsar, Sunil; Bhagat, Chintan; Ghelani, Anjana; Bhatt, Shreyas; Patel, Rajesh

    2015-10-01

    The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint. Copyright © 2015. Production and hosting by Elsevier Ltd.

  6. Metagenomics and the niche concept.

    Science.gov (United States)

    Marco, Diana

    2008-08-01

    The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept in metagenomic studies. In particular, I raise the necessity of including the microbial genetic background as another variable into the niche space.

  7. Metazen - metadata capture for metagenomes.

    Science.gov (United States)

    Bischof, Jared; Harrison, Travis; Paczian, Tobias; Glass, Elizabeth; Wilke, Andreas; Meyer, Folker

    2014-01-01

    As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. Unfortunately, these tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.

  8. Altered gut microbiota in Rett syndrome.

    Science.gov (United States)

    Strati, Francesco; Cavalieri, Duccio; Albanese, Davide; De Felice, Claudio; Donati, Claudio; Hayek, Joussef; Jousson, Olivier; Leoncini, Silvia; Pindo, Massimo; Renzi, Daniela; Rizzetto, Lisa; Stefanini, Irene; Calabrò, Antonio; De Filippo, Carlotta

    2016-07-30

    The human gut microbiota directly affects human health, and its alteration can lead to gastrointestinal abnormalities and inflammation. Rett syndrome (RTT), a progressive neurological disorder mainly caused by mutations in MeCP2 gene, is commonly associated with gastrointestinal dysfunctions and constipation, suggesting a link between RTT's gastrointestinal abnormalities and the gut microbiota. The aim of this study was to evaluate the bacterial and fungal gut microbiota in a cohort of RTT subjects integrating clinical, metabolomics and metagenomics data to understand if changes in the gut microbiota of RTT subjects could be associated with gastrointestinal abnormalities and inflammatory status. Our findings revealed the occurrence of an intestinal sub-inflammatory status in RTT subjects as measured by the elevated values of faecal calprotectin and erythrocyte sedimentation rate. We showed that, overall, RTT subjects harbour bacterial and fungal microbiota altered in terms of relative abundances from those of healthy controls, with a reduced microbial richness and dominated by microbial taxa belonging to Bifidobacterium, several Clostridia (among which Anaerostipes, Clostridium XIVa, Clostridium XIVb) as well as Erysipelotrichaceae, Actinomyces, Lactobacillus, Enterococcus, Eggerthella, Escherichia/Shigella and the fungal genus Candida. We further observed that alterations of the gut microbiota do not depend on the constipation status of RTT subjects and that this dysbiotic microbiota produced altered short chain fatty acids profiles. We demonstrated for the first time that RTT is associated with a dysbiosis of both the bacterial and fungal component of the gut microbiota, suggesting that impairments of MeCP2 functioning favour the establishment of a microbial community adapted to the costive gastrointestinal niche of RTT subjects. The altered production of short chain fatty acids associated with this microbiota might reinforce the constipation status of RTT

  9. Heavy metal concentrations in soil and earthworms in a floodplain grassland

    NARCIS (Netherlands)

    Vliet, van P.C.J.; Zee, van der S.E.A.T.M.; Ma, W.C.

    2005-01-01

    We determined accumulated heavy metal concentrations (Cd, Pb, Cu, Zn) of earthworms in moderately contaminated floodplain soils. Both soil and mature earthworms were sampled before and after flooding and earthworm species were identified to understand species specific differences in

  10. POPULATION DYNAMICS OF AMBIENT AND ALTERED EARTHWORM COMMUNITIES IN ROW-CROP AGROECOSYSTEMS IN OHIO, USA

    Science.gov (United States)

    Although earthworms are known to influence agroecosystem processes, there are relatively few long-term studies addressing population dynamics under cropping systems in which earthworm populations were intentionally altered. We assessed earthworm communities from fall 1994 to spr...

  11. Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations.

    Science.gov (United States)

    Lee, Aaron Y; Lee, Cecilia S; Van Gelder, Russell N

    2016-07-28

    Next generation sequencing technology has enabled characterization of metagenomics through massively parallel genomic DNA sequencing. The complexity and diversity of environmental samples such as the human gut microflora, combined with the sustained exponential growth in sequencing capacity, has led to the challenge of identifying microbial organisms by DNA sequence. We sought to validate a Scalable Metagenomics Alignment Research Tool (SMART), a novel searching heuristic for shotgun metagenomics sequencing results. After retrieving all genomic DNA sequences from the NCBI GenBank, over 1 × 10(11) base pairs of 3.3 × 10(6) sequences from 9.25 × 10(5) species were indexed using 4 base pair hashtable shards. A MapReduce searching strategy was used to distribute the search workload in a computing cluster environment. In addition, a one base pair permutation algorithm was used to account for single nucleotide polymorphisms and sequencing errors. Simulated datasets used to evaluate Kraken, a similar metagenomics classification tool, were used to measure and compare precision and accuracy. Finally using a same set of training sequences we compared Kraken, CLARK, and SMART within the same computing environment. Utilizing 12 computational nodes, we completed the classification of all datasets in under 10 min each using exact matching with an average throughput of over 1.95 × 10(6) reads classified per minute. With permutation matching, we achieved sensitivity greater than 83 % and precision greater than 94 % with simulated datasets at the species classification level. We demonstrated the application of this technique applied to conjunctival and gut microbiome metagenomics sequencing results. In our head to head comparison, SMART and CLARK had similar accuracy gains over Kraken at the species classification level, but SMART required approximately half the amount of RAM of CLARK. SMART is the first scalable, efficient, and rapid metagenomics classification algorithm

  12. Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema

    KAUST Repository

    Oh, Seungdae

    2017-10-19

    Gut microbiota play an important role in human immunological processes, potentially affecting allergic diseases such as eczema. The diversity and structure of gut microbiota in infants with eczema have been previously documented. This study aims to evaluate by comparative metagenomics differences in genetic content in gut microbiota of infants with eczema and their matched controls. Stools were collected at the age of one month old from twelve infants from an at risk birth cohort in a case control manner. Clinical follow up for atopic outcomes were carried out at the age of 12 and 24 months. Microbial genomic DNA were extracted from stool samples and used for shotgun sequencing. Comparative metagenomic analysis showed that immune-regulatory TCAAGCTTGA motifs were significantly enriched in the six healthy controls (C) communities compared to the six eczema subjects (E), with many encoded by Bifidobacterium (38% of the total motifs in the C communities). Draft genomes of five Bifidobacterium species populations (B. longum, B. bifidum, B. breve, B. dentium, and B. pseudocatenulatum) were recovered from metagenomic datasets. The B. longum BFN-121-2 genome encoded more TCAAGCTTGA motifs (4.2 copies per one million genome sequence) than other Bifidobacterium genomes. Additionally, the communities in the stool of controls (C) were also significantly enriched in functions associated with tetrapyrrole biosynthesis compared to those of eczema (E). Our results show distinct immune-modulatory genomic properties of gut microbiota in infants associated with eczema and provide new insights into potential role of gut microbiota in affecting human immune homeostasis.

  13. Earthworms increase plant production: a meta- analysis

    NARCIS (Netherlands)

    Groenigen, van J.W.; Lubbers, I.M.; Vos, H.M.J.; Brown, G.G.; Deyn, de G.B.; Groenigen, van K.J.

    2014-01-01

    To meet the challenge of feeding a growing world population with minimal environmental impact, we need comprehensive and quantitative knowledge of ecological factors affecting crop production. Earthworms are among the most important soil dwelling invertebrates. Their activity affects both biotic and

  14. Earthworms, pesticides and sustainable agriculture: a review.

    Science.gov (United States)

    Datta, Shivika; Singh, Joginder; Singh, Sharanpreet; Singh, Jaswinder

    2016-05-01

    The aim of this review is to generate awareness and understand the importance of earthworms in sustainable agriculture and effect of pesticides on their action. The natural resources are finite and highly prone to degradation by the misuse of land and mismanagement of soil. The world is in utter need of a healthy ecosystem that provides with fertile soil, clean water, food and other natural resources. Anthropogenic activities have led to an increased contamination of land. The intensification of industrial and agricultural practices chiefly the utilization of pesticides has in almost every way made our natural resources concave. Earthworms help in a number of tasks that support many ecosystem services that favor agrosystem sustainability but are degraded by exhaustive practices such as the use of pesticides. The present review assesses the response of earthworm toward the pesticides and also evaluates the relationship between earthworm activity and plant growth. We strictly need to refresh and rethink on the policies and norms devised by us on sustainable ecology. In an equivalent way, the natural resources should be utilized and further, essential ways for betterment of present and future livelihood should be sought.

  15. Basic Research Tools for Earthworm Ecology

    Directory of Open Access Journals (Sweden)

    Kevin R. Butt

    2010-01-01

    Full Text Available Earthworms are responsible for soil development, recycling organic matter and form a vital component within many food webs. For these and other reasons earthworms are worthy of investigation. Many technologically-enhanced approaches have been used within earthworm-focused research. These have their place, may be a development of existing practices or bring techniques from other fields. Nevertheless, let us not overlook the fact that much can still be learned through utilisation of more basic approaches which have been used for some time. New does not always equate to better. Information on community composition within an area and specific population densities can be learned using simple collection techniques, and burrowing behaviour can be determined from pits, resin-insertion or simple mesocosms. Life history studies can be achieved through maintenance of relatively simple cultures. Behavioural observations can be undertaken by direct observation or with low cost webcam usage. Applied aspects of earthworm research can also be achieved through use of simple techniques to enhance population development and even population dynamics can be directly addressed with use of relatively inexpensive, effective marking techniques. This paper seeks to demonstrate that good quality research in this sphere can result from appropriate application of relatively simple research tools.

  16. Soil fauna research in Poland: earthworms (Lumbricidae

    Directory of Open Access Journals (Sweden)

    Pączka Grzegorz

    2015-06-01

    Full Text Available Living organisms are the foundation of ecosystem services. Of particular notice is zooedaphone, often underestimated and basically unknown to the general public. The present review summarizes the current state of knowledge related to earthworms occurring in natural and anthropogenically altered habitats in Poland, in the context of the requirement for protection of soil biodiversity.

  17. Antimicrobial activity of earthworm (Eudrilus eugeniae) paste

    African Journals Online (AJOL)

    kavi pradeep

    2013-08-01

    Aug 1, 2013 ... Minimum inhibitory concentration (MIC) was determined using micro dilution broth method. Earthworm paste at a dose of 100 µl was able to inhibit the growth of bacteria of S. aureus at a maximum level as compared to other bacteria; the ..... peptide containing 62 amino acids including proline. (15%) with a ...

  18. Does earthworms density really modify soil's hydrodynamic ...

    African Journals Online (AJOL)

    Our study has the general objective to understand the impact of the valuation of treated water on earthworm abundance and total porosity of the soil and the effect of the interaction between these two physical-biological components of the hydrological functioning of soils. It was carried out on the meadows soils of the valley ...

  19. Easy Extraction of Roundworms from Earthworm Hosts.

    Science.gov (United States)

    Eyster, Linda S.; Fried, Bernard

    2000-01-01

    Describes the inexpensive and safe method of using roundworms in the classroom or laboratories. Because parasitic infections are so common, students should learn about worms. Provides statistics on just how many people have a worm infection in the world. Explains how to study living nematodes, and obtain and use earthworms. (Contains 13…

  20. Earthworm Cast Biomass Under Three Managed Ecosystems ...

    African Journals Online (AJOL)

    The study was conducted to determine earthworm cast biomass under three managed ecosystems, Gmelina, Cashew and Banana plantations at Federal University of Agriculture, Abeokuta and its impact on the soil physicochemical parameters. Seven, five and four plots of 3 m2 each were sampled in Gmelina, Cashew and ...

  1. Metagenomics of the Methane Ice Worm, Hesiocaeca methanicola

    Science.gov (United States)

    Goodwin, K. D.; Edsall, L.; Xin, W.; Head, S. R.; Gelbart, T.; Wood, A. M.; Gaasterland, T.

    2012-12-01

    The methane ice worm (Hesiocaeca methanicola) is a polychaete found on methane hydrate deposits for which there appears to be no publically available genomic or metagenomic data. Methane ice worms were collected in 2009 by the Johnson-Sea-Link submersible (543m depth; N 27:44.7526 W 91:13.3168). Next-generation sequencing (HiSeq2000) was applied to samples of tissue and gut contents. A subset of the assembled data (40M reads, randomly selected) was run through MG-RAST. Preliminary results for the gut content (1,269,153 sequences, average length 202 bp) indicated that 0.1% of the sequences contained ribosomal RNA genes with the majority (67%) classified as Bacteria, a relatively small per cent (1.4%) as Archae, and 31% as Eukaryota. Campylobacterales was the predominant order (14%), with unclassified (7.5%) and Desulfobacterales (4%) being the next dominant. Preliminary results for the worm tissue (2,716,461 sequences, average length 241 bp) indicated that the majority of sequences were Eukaryota (73%), with 256 sequences classified as phylum Annelida and 58% of those belonging to class Polychaeta. For the bacterial sequences obtained from the tissue samples, the predominant order was Actinomycetales (2.7%). For both the tissue and gut content samples, the majority of proteins were classified as clustering-based subsystems. This preliminary analysis will be compared to an assembly consisting of 40M of the highest quality reads.; methane ice worms on methane hydrate

  2. Metagenomic analysis of microbial communities and beyond

    DEFF Research Database (Denmark)

    Schreiber, Lars

    2014-01-01

    From small clone libraries to large next-generation sequencing datasets – the field of community genomics or metagenomics has developed tremendously within the last years. This chapter will summarize some of these developments and will also highlight pitfalls of current metagenomic analyses....... It will illustrate the general workflow of a metagenomic study and introduce the three different metagenomic approaches: (1) the random shotgun approach that focuses on the metagenome as a whole, (2) the targeted approach that focuses on metagenomic amplicon sequences, and (3) the function-driven approach that uses...... heterologous expression of metagenomic DNA fragments to discover novel metabolic functions. Lastly, the chapter will shortly discuss the meta-analysis of gene expression of microbial communities, more precisely metatranscriptomics and metaproteomics....

  3. The Gut as Reservoir of Antibiotic Resistance: Microbial Diversity of Tetracycline Resistance in Mother and Infant

    DEFF Research Database (Denmark)

    de Vries, Lisbeth Elvira; Valles, Yvonne; Agersø, Yvonne

    2011-01-01

    study using a metagenomic approach to determine the diversity of microorganisms conferring tetracycline resistance (Tc-r) in the guts of a healthy mother-infant pair one month after childbirth, and to investigate the potential for horizontal transfer and maternal transmission of Tc-r genes. Fecal fosmid...... the infant's gut. In addition, although not found in the infant metagenomic library, tet(O) and tet(W) could be detected in the uncloned DNA purified from the infant fecal sample. This is the first study to reveal the diversity of Tc-r bacteria in the human gut, to detect a likely transmission of antibiotic......The microbiota in the human gastrointestinal tract (GIT) is highly exposed to antibiotics, and may be an important reservoir of resistant strains and transferable resistance genes. Maternal GIT strains can be transmitted to the offspring, and resistances could be acquired from birth. This is a case...

  4. Multi-Omics Reveals that Lead Exposure Disturbs Gut Microbiome Development, Key Metabolites, and Metabolic Pathways.

    Science.gov (United States)

    Gao, Bei; Chi, Liang; Mahbub, Ridwan; Bian, Xiaoming; Tu, Pengcheng; Ru, Hongyu; Lu, Kun

    2017-04-17

    Lead exposure remains a global public health issue, and the recent Flint water crisis has renewed public concern about lead toxicity. The toxicity of lead has been well established in a variety of systems and organs. The gut microbiome has been shown to be highly involved in many critical physiological processes, including food digestion, immune system development, and metabolic homeostasis. However, despite the key role of the gut microbiome in human health, the functional impact of lead exposure on the gut microbiome has not been studied. The aim of this study is to define gut microbiome toxicity induced by lead exposure in C57BL/6 mice using multiomics approaches, including 16S rRNA sequencing, whole genome metagenomics sequencing, and gas chromatography-mass spectrometry (GC-MS) metabolomics. 16S rRNA sequencing revealed that lead exposure altered the gut microbiome trajectory and phylogenetic diversity. Metagenomics sequencing and metabolomics profiling showed that numerous metabolic pathways, including vitamin E, bile acids, nitrogen metabolism, energy metabolism, oxidative stress, and the defense/detoxification mechanism, were significantly disturbed by lead exposure. These perturbed molecules and pathways may have important implications for lead toxicity in the host. Taken together, these results demonstrated that lead exposure not only altered the gut microbiome community structures/diversity but also greatly affected metabolic functions, leading to gut microbiome toxicity.

  5. Diversity of Gut Microbiota Metabolic Pathways in 10 Pairs of Chinese Infant Twins.

    Science.gov (United States)

    Zhou, Shaoming; Xu, Ruihuan; He, Fusheng; Zhou, Jiaxiu; Wang, Yan; Zhou, Jianli; Wang, Mingbang; Zhou, Wenhao

    2016-01-01

    Early colonization of gut microbiota in human gut is a complex process. It remains unclear when gut microbiota colonization occurs and how it proceeds. In order to study gut microbiota composition in human early life, the present study recruited 10 healthy pairs of twins, including five monozygotic (MZ) and five dizygotic (DZ) twin pairs, whose age ranged from 0 to 6 years old. 20 fecal samples from these twins were processed by shotgun metagenomic sequencing, and their averaged data outputs were generated as 2G per sample. We used MEGAN5 to perform taxonomic and functional annotation of the metagenomic data, and systematically analyzed those 20 samples, including Jaccard index similarity, principle component, clustering, and correlation analyses. Our findings indicated that within our study group: 1) MZ-twins share more microbes than DZ twins or non-twin pairs, 2) gut microbiota distribution is relatively stable at metabolic pathways level, 3) age represents the strongest factor that can account for variation in gut microbiota, and 4) a clear metabolic pathway shift can be observed, which speculatively occurs around the age of 1 year old. This research will serve as a base for future studies of gut microbiota-related disease research.

  6. Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.

    Science.gov (United States)

    Lee, Sonny T M; Kahn, Stacy A; Delmont, Tom O; Shaiber, Alon; Esen, Özcan C; Hubert, Nathaniel A; Morrison, Hilary G; Antonopoulos, Dionysios A; Rubin, David T; Eren, A Murat

    2017-05-04

    Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits. We used shotgun metagenomics together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from fecal samples of a single FMT donor. We then used metagenomic mapping to track the occurrence and distribution patterns of donor MAGs in two FMT recipients. Our analyses revealed that 22% of the 92 highly complete bacterial MAGs that we identified from the donor successfully colonized and remained abundant in two recipients for at least 8 weeks. Most MAGs with a high colonization rate belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales, and colonization success was negatively correlated with the number of genes related to sporulation. Our analysis of 151 publicly available gut metagenomes showed that the donor MAGs that colonized both recipients were prevalent, and the ones that colonized neither were rare across the participants of the Human Microbiome Project. Although our dataset showed a link between taxonomy and the colonization ability of a given MAG, we also identified MAGs that belong to the same taxon with different colonization properties, highlighting the importance of an appropriate level of resolution to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems. The analytical strategy adopted in our study can provide genomic insights into bacterial

  7. From lifetime to evolution: timescales of human gut microbiota adaptation

    Directory of Open Access Journals (Sweden)

    Sara eQuercia

    2014-11-01

    Full Text Available Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The gut microbiota continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societies.

  8. Activity of earthworm in Latosol under simulated acid rain stress.

    Science.gov (United States)

    Zhang, Jia-En; Yu, Jiayu; Ouyang, Ying

    2015-01-01

    Acid rain is still an issue of environmental concerns. This study investigated the impacts of simulated acid rain (SAR) upon earthworm activity from the Latosol (acidic red soil). Laboratory experiment was performed by leaching the soil columns grown with earthworms (Eisenia fetida) at the SAR pH levels ranged from 2.0 to 6.5 over a 34-day period. Results showed that earthworms tended to escape from the soil and eventually died for the SAR at pH = 2.0 as a result of acid toxicity. The catalase activity in the earthworms decreased with the SAR pH levels, whereas the superoxide dismutases activity in the earthworms showed a fluctuate pattern: decreasing from pH 6.5 to 5.0 and increasing from pH 5.0 to 4.0. Results implied that the growth of earthworms was retarded at the SAR pH ≤ 3.0.

  9. Toxicity of a neonicotinoid insecticide, guadipyr, in earthworm (Eisenia fetida).

    Science.gov (United States)

    Wang, Kai; Mu, Xiyan; Qi, Suzhen; Chai, Tingting; Pang, Sen; Yang, Yang; Wang, Chengju; Jiang, Jiazhen

    2015-04-01

    Neonicotinoid insecticides are new class of pesticides and it is very meaningful to evaluate the toxicity of guadipyr to earthworm (Eisenia fetida). In the present study, effects of guadipyr on reproduction, growth, catalase(CAT), superoxide dismutase (SOD), acetylcholinesterase (AChE) and DNA damage in earthworm were assessed using an artificial soil medium. Guadipyr showed low toxicity to earthworms and did not elicit an effect on earthworm reproduction or growth in artificial soils at concentrations earthworm increased and then decreased to control level. AChE activity decreased at day 3 at 50 and 100mg/kg and then increased to control level. Our data indicate that guadipyr did not induce DNA damage in earthworms at concentration of <100mg/kg. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. Genotoxic effects of glyphosate or paraquat on earthworm coelomocytes.

    Science.gov (United States)

    Muangphra, Ptumporn; Kwankua, Wimon; Gooneratne, Ravi

    2014-06-01

    The potential genotoxicity (nuclear anomalies, damage to single-strand DNA) and pinocytic adherence activity of two (glyphosate-based and paraquat-based) commercial herbicides to earthworm coelomocytes (immune cells in the coelomic cavity) were assessed. Coelomocytes were extracted from earthworms (Pheretima peguana) exposed to concentrations earthworms exposed to glyphosate at 25 × 10(-1) (10(-3) LC50) and paraquat at 39 × 10(-5) (10(-4) LC50) μg cm(-2) filter paper. In earthworms exposed to glyphosate, no differences in tail DNA%, tail length, and tail moment of coelomocytes were detected. In contrast, for paraquat at 10(-1) LC50 concentration, there were significant (P earthworm coelomocytes whereas glyphosate causes only aneugenic effects and therefore does not pose a risk of gene mutation in this earthworm. Copyright © 2012 Wiley Periodicals, Inc.

  11. Functional Intestinal Metagenomics (Chapter 18)

    NARCIS (Netherlands)

    Bogert, van den B.; Leimena, M.M.; Vos, de W.M.; Zoetendal, E.G.; Kleerebezem, M.

    2011-01-01

    The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA

  12. Estimating richness from phage metagenomes

    Science.gov (United States)

    Bacteriophages are important drivers of ecosystem functions, yet little is known about the vast majority of phages. Phage metagenomics, or the study of the collective genome of an assemblage of phages, enables the investigation of broad ecological questions in phage communities. One ecological cha...

  13. Metagenomic Analysis of Dairy Bacteriophages

    DEFF Research Database (Denmark)

    Muhammed, Musemma K.; Kot, Witold; Neve, Horst

    2017-01-01

    Despite their huge potential for characterizing the biodiversity of phages, metagenomic studies are currently not available for dairy bacteriophages, partly due to the lack of a standard procedure for phage extraction. We optimized an extraction method that allows to remove the bulk protein from...

  14. Diversity of earthworms (Oligochaeta: Lumbricidae) in Sofia Plain, Bulgaria

    OpenAIRE

    Hristo; Valchovski

    2014-01-01

    A rich earthworm material from 47 different localities in Sofia Plain has been elaborated. During the investigations between the years 2010 and 2013, thirteen earthworm species and subspecies were collected altogether, belonging to seven genera. Among them, three new records are reported. Aporrectodea longa (Ude, 1885), Eisenia lucens (Waga, 1857) and Octodrilus transpadanus (Rosa, 1884) proved to be new to the earthworm fauna of Sofia plain.

  15. Diversity of earthworms (Oligochaeta: Lumbricidae in Sofia Plain, Bulgaria

    Directory of Open Access Journals (Sweden)

    Hristo

    2014-10-01

    Full Text Available A rich earthworm material from 47 different localities in Sofia Plain has been elaborated. During the investigations between the years 2010 and 2013, thirteen earthworm species and subspecies were collected altogether, belonging to seven genera. Among them, three new records are reported. Aporrectodea longa (Ude, 1885, Eisenia lucens (Waga, 1857 and Octodrilus transpadanus (Rosa, 1884 proved to be new to the earthworm fauna of Sofia plain.

  16. Accumulation of heavy metals in the earthworm eisenia foetida

    Energy Technology Data Exchange (ETDEWEB)

    Hartenstein, R.; Neuhauser, E.F.; Collier, J.

    Earthworms are often utilized in the management and treatment of sludges. A study was conducted to determine earthworm bioaccumulation of heavy metals present in some sludges. Experimental methods and materials used are described. Conversion of activated sludge into egesta by the earthworm Eisenia foetida resulted in neither an increase nor a decrease of extractable cadmium, copper, nickel, zinc, or lead. Bioaccumulations ranged from 8-250 ppm. (7 graphs, 18 references, 4 tables)

  17. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.

    Science.gov (United States)

    Meyer, F; Paarmann, D; D'Souza, M; Olson, R; Glass, E M; Kubal, M; Paczian, T; Rodriguez, A; Stevens, R; Wilke, A; Wilkening, J; Edwards, R A

    2008-09-19

    Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers. A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats. The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis - the availability of high-performance computing for annotating the data. http://metagenomics.nmpdr.org.

  18. 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...

  19. Gut microbiota dysbiosis contributes to the development of hypertension.

    Science.gov (United States)

    Li, Jing; Zhao, Fangqing; Wang, Yidan; Chen, Junru; Tao, Jie; Tian, Gang; Wu, Shouling; Liu, Wenbin; Cui, Qinghua; Geng, Bin; Zhang, Weili; Weldon, Ryan; Auguste, Kelda; Yang, Lei; Liu, Xiaoyan; Chen, Li; Yang, Xinchun; Zhu, Baoli; Cai, Jun

    2017-02-01

    Recently, the potential role of gut microbiome in metabolic diseases has been revealed, especially in cardiovascular diseases. Hypertension is one of the most prevalent cardiovascular diseases worldwide, yet whether gut microbiota dysbiosis participates in the development of hypertension remains largely unknown. To investigate this issue, we carried out comprehensive metagenomic and metabolomic analyses in a cohort of 41 healthy controls, 56 subjects with pre-hypertension, 99 individuals with primary hypertension, and performed fecal microbiota transplantation from patients to germ-free mice. Compared to the healthy controls, we found dramatically decreased microbial richness and diversity, Prevotella-dominated gut enterotype, distinct metagenomic composition with reduced bacteria associated with healthy status and overgrowth of bacteria such as Prevotella and Klebsiella, and disease-linked microbial function in both pre-hypertensive and hypertensive populations. Unexpectedly, the microbiome characteristic in pre-hypertension group was quite similar to that in hypertension. The metabolism changes of host with pre-hypertension or hypertension were identified to be closely linked to gut microbiome dysbiosis. And a disease classifier based on microbiota and metabolites was constructed to discriminate pre-hypertensive and hypertensive individuals from controls accurately. Furthermore, by fecal transplantation from hypertensive human donors to germ-free mice, elevated blood pressure was observed to be transferrable through microbiota, and the direct influence of gut microbiota on blood pressure of the host was demonstrated. Overall, our results describe a novel causal role of aberrant gut microbiota in contributing to the pathogenesis of hypertension. And the significance of early intervention for pre-hypertension was emphasized.

  20. Gut microbiomes of Indian children of varying nutritional status.

    Directory of Open Access Journals (Sweden)

    Tarini Shankar Ghosh

    Full Text Available BACKGROUND: Malnutrition is a global health problem affecting more than 300 million pre-school children worldwide. It is one of the major health concerns in India since around 50% of children below the age of two suffer from various forms of malnutrition. The gut microbiome plays an important role in nutrient pre-processing, assimilation and energy harvest from food. Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition. METHODOLOGY/PRINCIPAL FINDINGS: Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status. The changes in the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. A core set of 23 genera were observed across samples, with some showing differential abundances with varying nutritional status. One of the findings of the current study is the positive/negative associations of specific taxonomic and functional groups with the nutritional status of the children. Notable alterations in the architecture of the inter-microbial co-occurrence networks were also observed with changes in nutritional status. A key example is the clustering of potentially pathogenic groups into a distinct hub in severely malnourished gut. Our data does not demonstrate causality with the microbiome patterns that we observed, rather a description of some interesting patterns, whose underlying mechanism remains to be uncovered. CONCLUSIONS: The present study envisioned interrelationships between the pattern of gut microbiome and the nutritional status of children. The cause of this pattern needs to be explored. However, insights obtained from the present study form the basis for further metagenomic investigations on larger population of children. Results of such studies will be useful in identifying the key microbial groups that can be utilized for targeted therapeutic interventions for managing severe acute

  1. Gut microbiomes of Indian children of varying nutritional status.

    Science.gov (United States)

    Ghosh, Tarini Shankar; Gupta, Sourav Sen; Bhattacharya, Tanudeep; Yadav, Deepak; Barik, Anamitra; Chowdhury, Abhijit; Das, Bhabatosh; Mande, Sharmila S; Nair, G Balakrish

    2014-01-01

    Malnutrition is a global health problem affecting more than 300 million pre-school children worldwide. It is one of the major health concerns in India since around 50% of children below the age of two suffer from various forms of malnutrition. The gut microbiome plays an important role in nutrient pre-processing, assimilation and energy harvest from food. Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition. Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status. The changes in the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. A core set of 23 genera were observed across samples, with some showing differential abundances with varying nutritional status. One of the findings of the current study is the positive/negative associations of specific taxonomic and functional groups with the nutritional status of the children. Notable alterations in the architecture of the inter-microbial co-occurrence networks were also observed with changes in nutritional status. A key example is the clustering of potentially pathogenic groups into a distinct hub in severely malnourished gut. Our data does not demonstrate causality with the microbiome patterns that we observed, rather a description of some interesting patterns, whose underlying mechanism remains to be uncovered. The present study envisioned interrelationships between the pattern of gut microbiome and the nutritional status of children. The cause of this pattern needs to be explored. However, insights obtained from the present study form the basis for further metagenomic investigations on larger population of children. Results of such studies will be useful in identifying the key microbial groups that can be utilized for targeted therapeutic interventions for managing severe acute malnutrition.

  2. Measurement of earthworm radial pressures during peristaltic motion

    Science.gov (United States)

    Ruiz, Siul; Or, Dani

    2017-04-01

    Earthworm activity and formation of burrowing networks are important for soil structure formation and transport processes. We developed models for earthworm penetration cavity expansion that consider soil hydration and mechanical status. A key parameter is the maxima axial and radial pressure exerted by the earthworm hydroskeleton (presently estimated at 200 kPa). To test a range of pressures exerted by moving earthworms we developed a coaxial chamber consisting of Plexiglas tube fitted with a thin and inflatable silicon tubing that hosts the earthworm. We pressurize the gap between the Plexiglas and flexible tubing using an incompressible liquid linked to a pressure transducer. Earthworm motion and concurrent pressure were recorded by the transducer and a dedicated video camera. The instrument was calibrated using a cardiac catheter resulting in close agreement between the catheter and chamber pressures. Measurements using anecic earthworms passing across the cylinder show mean radial pressures of 70 kPa, consistent with earlier findings of anecic earthworm pressure measurements using different measurement techniques. Analyses are underway to resolve local pressures induced during peristaltic motion. The study delineates mechanical constraints to soil bioturbation by earthworms for different mechanical conditions including compaction. Tests are underway for direct measurement of plant root pressures during growth.

  3. Root foraging influences plant growth responses to earthworm foraging.

    Directory of Open Access Journals (Sweden)

    Erin K Cameron

    Full Text Available Interactions among the foraging behaviours of co-occurring animal species can impact population and community dynamics; the consequences of interactions between plant and animal foraging behaviours have received less attention. In North American forests, invasions by European earthworms have led to substantial changes in plant community composition. Changes in leaf litter have been identified as a critical indirect mechanism driving earthworm impacts on plants. However, there has been limited examination of the direct effects of earthworm burrowing on plant growth. Here we show a novel second pathway exists, whereby earthworms (Lumbricus terrestris L. impact plant root foraging. In a mini-rhizotron experiment, roots occurred more frequently in burrows and soil cracks than in the soil matrix. The roots of Achillea millefolium L. preferentially occupied earthworm burrows, where nutrient availability was presumably higher than in cracks due to earthworm excreta. In contrast, the roots of Campanula rotundifolia L. were less likely to occur in burrows. This shift in root behaviour was associated with a 30% decline in the overall biomass of C. rotundifolia when earthworms were present. Our results indicate earthworm impacts on plant foraging can occur indirectly via physical and chemical changes to the soil and directly via root consumption or abrasion and thus may be one factor influencing plant growth and community change following earthworm invasion. More generally, this work demonstrates the potential for interactions to occur between the foraging behaviours of plants and soil animals and emphasizes the importance of integrating behavioural understanding in foraging studies involving plants.

  4. Root foraging influences plant growth responses to earthworm foraging.

    Science.gov (United States)

    Cameron, Erin K; Cahill, James F; Bayne, Erin M

    2014-01-01

    Interactions among the foraging behaviours of co-occurring animal species can impact population and community dynamics; the consequences of interactions between plant and animal foraging behaviours have received less attention. In North American forests, invasions by European earthworms have led to substantial changes in plant community composition. Changes in leaf litter have been identified as a critical indirect mechanism driving earthworm impacts on plants. However, there has been limited examination of the direct effects of earthworm burrowing on plant growth. Here we show a novel second pathway exists, whereby earthworms (Lumbricus terrestris L.) impact plant root foraging. In a mini-rhizotron experiment, roots occurred more frequently in burrows and soil cracks than in the soil matrix. The roots of Achillea millefolium L. preferentially occupied earthworm burrows, where nutrient availability was presumably higher than in cracks due to earthworm excreta. In contrast, the roots of Campanula rotundifolia L. were less likely to occur in burrows. This shift in root behaviour was associated with a 30% decline in the overall biomass of C. rotundifolia when earthworms were present. Our results indicate earthworm impacts on plant foraging can occur indirectly via physical and chemical changes to the soil and directly via root consumption or abrasion and thus may be one factor influencing plant growth and community change following earthworm invasion. More generally, this work demonstrates the potential for interactions to occur between the foraging behaviours of plants and soil animals and emphasizes the importance of integrating behavioural understanding in foraging studies involving plants.

  5. Gut microbiota: an Indicator to Gastrointestinal Tract Diseases.

    Science.gov (United States)

    Patel, Trupti; Bhattacharya, Priyanjali; Das, Suvrajit

    2016-09-01

    Gut microbiota is predicted to play a key role in manifestation of gastrointestinal tract cancers. The human gastrointestinal tract is a complex and abundant network of microbial community. Gut microbiota depicts the microbe population living in our intestine. Humans harbour more than 10(14) microbes in the gut, and the diversity and densities of the microbiota increase from stomach to colon. The beneficial relationship between endogenous microbiota and the eukaryotic hosts helps in maintaining various metabolic activities of the body as well as temperature and pH balance. Studies using culturing methods have suggested that the oesophagus is either sterile or contains only a few transient microbes that originates from the oropharynx by swallowing or from the stomach by gastroesophageal reflux. However, metagenomics suggest that large numbers of uncultured organisms are harboured in the human gut. Observations suggest that research directed towards manipulation of the gut microbiota can be employed in prevention as well as treatment of these conditions. Well-designed, randomized, placebo-controlled human studies using probiotics and/or prebiotics are necessary to formulate the directions for prevention and therapy. Change in gut microbes in gastrointestinal (GI) tract may have major implication in gastric cancer, the fifth most occurring malignancy in the world. Affected population manifests multiple conditions and diseases, which majorly includes inflammatory bowel disease and colorectal malignancy.

  6. Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.

    Science.gov (United States)

    Fang, Chao; Zhong, Huanzi; Lin, Yuxiang; Chen, Bin; Han, Mo; Ren, Huahui; Lu, Haorong; Luber, Jacob Mayne; Xia, Min; Li, Wangsheng; Stein, Shayna; Xu, Xun; Zhang, Wenwei; Drmanac, Radoje; Wang, Jian; Yang, Huanming; Hammarström, Lennart; Kostic, Aleksandar David; Kristiansen, Karsten; Li, Junhua

    2017-12-23

    More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of two Illumina platforms. Using fecal samples from 20 healthy individuals we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency, was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform versus the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the two Illumina platforms against each other. By a newly developed overall accuracy quality control method, an average of 82.45 million high quality reads (96.06% of raw reads) per sample with 90.56% of bases scoring Q30 and above was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02% -3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias towards genes with higher GC content being enriched on the HiSeq platforms. Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.

  7. Metabolic reconstruction for metagenomic data and its application to the human microbiome.

    Directory of Open Access Journals (Sweden)

    Sahar Abubucker

    Full Text Available Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP. This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/humann. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high

  8. Distribution, isomerization and enantiomer selectivity of hexabromocyclododecane (HBCD) diastereoisomers in different tissue and subcellular fractions of earthworms.

    Science.gov (United States)

    Li, Bing; Chen, Hao; Sun, Hongwen; Lan, Zhonghui

    2017-05-01

    In this study, earthworms Eisenia fetida (E. fetida) were exposed to a soil artificially contaminated with individual hexabromocyclododecane (HBCD) diastereoisomers (α-, β- and γ-HBCDs) to investigate the distribution, isomerization and enantiomer selectivity of HBCDs at tissue and subcellular levels. At the tissue level, the concentrations of HBCDs all followed the order of gut>bodyfluid>body wall, which suggested that earthworms accumulated HBCDs mainly via ingesting soil particles. At the subcellular level, the concentrations of HBCDs in an extracellular fraction consisting of granules, tissue fragment, cell membrane and intact cells (fraction A) were higher than those in an intracellular fractions consisting of the microsomal and cytosol (fraction B+C). This confirmed the passive diffusion during the distribution of HBCDs into the intracellular compartment. The distribution proportions of HBCDs varied among different tissue and subcellular fractions, and all changed over time within 14 days. The variable distributions of HBCDs in different fractions were a result of the comprehensive effects of dynamics and thermodynamics processes. The β- and γ-HBCDs were isomerized to α-HBCD in all tissue and subcellular fractions except for fraction C, and the isomerization ratios varied a lot, which seemed to be related to HBCDs residence time. The selective enrichment of (-) α-, (-) β and (-) γ-HBCDs was found in all fractions and this is consistent with that in the whole earthworm. Besides, the extents of enantio-selectivity did not change significantly among different tissue and subcellular fractions. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Symbiosis insights through metagenomic analysis of a microbialconsortium

    Energy Technology Data Exchange (ETDEWEB)

    Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N.; Hunteman,Marcel; Richter, Michael; Gloeckner, Frank Oliver; Boffelli, Dario; Barry, Kerrie W.; Shapiro, Harris J.; Anderson, Iain J.; Szeto, Ernest; Kyrpides, Nikos C.; Mussmann, Marc; Amann, Rudolf; Bergin, Claudia; Ruehland, Caroline; Rubin, Edward M.; Dubilier, Nicole

    2006-09-01

    Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here, we used a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut, and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulfur-oxidizing and sulfate-reducing bacteria, all of which are capable of carbon fixation, providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model which describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments which it inhabits.

  10. Metagenomic Analysis of Microbial Symbionts in a Gutless Worm

    Energy Technology Data Exchange (ETDEWEB)

    Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N.; Hunteman, Marcel; Richter, Michael; Gloeckner, Frank Oliver; Boeffelli, Dario; Barry, Kerrie W.; Shapiro, Harris J.; Anderson, Iain J.; Szeto, Ernest; Kyrpides, Nikos C.; Mussmann, Marc; Amann, Rudolf; Bergin, Claudia; Ruehland, Caroline; Rubin, Edward M.; Dubilier, Nicole

    2006-05-01

    Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulphur-oxidizing and sulphate-reducing bacteria, all of which are capable of carbon fixation, thus providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits.

  11. Isolation, identification, and characterization of gut microflora of Perionyx excavatus collected from Midnapore, West Bengal.

    Science.gov (United States)

    Samanta, Tanushree Tulsian; Das, Ankita

    2016-03-01

    Agriculture is an important part of the economy of the undivided Midnapore district. Agricultural land is its asset and most importantly its means of sustenance as well as survival. Earthworms are invertebrates that play a key role in recycling organic matters in soils. Since the intestines of earthworms harbor wide ranges of microorganisms, enzymes, hormones etc., these half digested materials decompose rapidly and are transformed into a stabilized material called vermicompost which is very useful for increasing the soil fertility. One has to look for these characters before recommending any species for vermiculture. In the present study, Perionyx excavatus specimens were collected from the undivided Midnapore district and from the Earthworms gut, bacteria, fungus, actinobacteria, and yeast were isolated and identified using various morphological and biochemical tests. All the bacterial isolates were identified using morphological study, staining techniques, and different biochemical tests such as catalase test, KOH test, H2 SO4 test, Starch hydrolysis test, oxidase test, and sucrose hydrolysis test. All the fungal, actinobacteria, and yeast isolates were subjected to staining and morphological characterization (color and texture of fungal colony). Bacterial isolates of genus Bacillus sp., Staphylococcus sp., Enterococci, Micrococcus sp., Enterobacter sp., and Citrobacter sp. were identified. Among the fungal isolates Aspergilus sp., and P. boydii were identified. Streptomyces sp., Nocardia sp. among the actinobacteria and Candida sp. among yeast were also found to be present in earthworm gut and these might play an important role along with the earthworm to increase the quality and fertility of soil. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Combining gene prediction methods to improve metagenomic gene annotation

    Directory of Open Access Journals (Sweden)

    Rosen Gail L

    2011-01-01

    Full Text Available Abstract Background Traditional gene annotation methods rely on characteristics that may not be available in short reads generated from next generation technology, resulting in suboptimal performance for metagenomic (environmental samples. Therefore, in recent years, new programs have been developed that optimize performance on short reads. In this work, we benchmark three metagenomic gene prediction programs and combine their predictions to improve metagenomic read gene annotation. Results We not only analyze the programs' performance at different read-lengths like similar studies, but also separate different types of reads, including intra- and intergenic regions, for analysis. The main deficiencies are in the algorithms' ability to predict non-coding regions and gene edges, resulting in more false-positives and false-negatives than desired. In fact, the specificities of the algorithms are notably worse than the sensitivities. By combining the programs' predictions, we show significant improvement in specificity at minimal cost to sensitivity, resulting in 4% improvement in accuracy for 100 bp reads with ~1% improvement in accuracy for 200 bp reads and above. To correctly annotate the start and stop of the genes, we find that a consensus of all the predictors performs best for shorter read lengths while a unanimous agreement is better for longer read lengths, boosting annotation accuracy by 1-8%. We also demonstrate use of the classifier combinations on a real dataset. Conclusions To optimize the performance for both prediction and annotation accuracies, we conclude that the consensus of all methods (or a majority vote is the best for reads 400 bp and shorter, while using the intersection of GeneMark and Orphelia predictions is the best for reads 500 bp and longer. We demonstrate that most methods predict over 80% coding (including partially coding reads on a real human gut sample sequenced by Illumina technology.

  13. In silico analysis of antibiotic resistance genes in the gut microflora of individuals from diverse geographies and age-groups.

    Directory of Open Access Journals (Sweden)

    Tarini Shankar Ghosh

    Full Text Available The spread of antibiotic resistance, originating from the rampant and unrestrictive use of antibiotics in humans and livestock over the past few decades has emerged as a global health problem. This problem has been further compounded by recent reports implicating the gut microbial communities to act as reservoirs of antibiotic resistance. We have profiled the presence of probable antibiotic resistance genes in the gut flora of 275 individuals from eight different nationalities. For this purpose, available metagenomic data sets corresponding to 275 gut microbiomes were analyzed. Sequence similarity searches of the genomic fragments constituting each of these metagenomes were performed against genes conferring resistance to around 240 antibiotics. Potential antibiotic resistance genes conferring resistance against 53 different antibiotics were detected in the human gut microflora analysed in this study. In addition to several geography/country-specific patterns, four distinct clusters of gut microbiomes, referred to as 'Resistotypes', exhibiting similarities in their antibiotic resistance profiles, were identified. Groups of antibiotics having similarities in their resistance patterns within each of these clusters were also detected. Apart from this, mobile multi-drug resistance gene operons were detected in certain gut microbiomes. The study highlighted an alarmingly high abundance of antibiotic resistance genes in two infant gut microbiomes. The results obtained in the present study presents a holistic 'big picture' on the spectra of antibiotic resistance within our gut microbiota across different geographies. Such insights may help in implementation of new regulations and stringency on the existing ones.

  14. In Silico Analysis of Antibiotic Resistance Genes in the Gut Microflora of Individuals from Diverse Geographies and Age-Groups

    Science.gov (United States)

    Ghosh, Tarini Shankar; Gupta, Sourav Sen; Nair, Gopinath Balakrish; Mande, Sharmila S.

    2013-01-01

    The spread of antibiotic resistance, originating from the rampant and unrestrictive use of antibiotics in humans and livestock over the past few decades has emerged as a global health problem. This problem has been further compounded by recent reports implicating the gut microbial communities to act as reservoirs of antibiotic resistance. We have profiled the presence of probable antibiotic resistance genes in the gut flora of 275 individuals from eight different nationalities. For this purpose, available metagenomic data sets corresponding to 275 gut microbiomes were analyzed. Sequence similarity searches of the genomic fragments constituting each of these metagenomes were performed against genes conferring resistance to around 240 antibiotics. Potential antibiotic resistance genes conferring resistance against 53 different antibiotics were detected in the human gut microflora analysed in this study. In addition to several geography/country-specific patterns, four distinct clusters of gut microbiomes, referred to as ‘Resistotypes’, exhibiting similarities in their antibiotic resistance profiles, were identified. Groups of antibiotics having similarities in their resistance patterns within each of these clusters were also detected. Apart from this, mobile multi-drug resistance gene operons were detected in certain gut microbiomes. The study highlighted an alarmingly high abundance of antibiotic resistance genes in two infant gut microbiomes. The results obtained in the present study presents a holistic ‘big picture’ on the spectra of antibiotic resistance within our gut microbiota across different geographies. Such insights may help in implementation of new regulations and stringency on the existing ones. PMID:24391833

  15. An application of statistics to comparative metagenomics

    Directory of Open Access Journals (Sweden)

    Rohwer Forest

    2006-03-01

    Full Text Available Abstract Background Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments. Results Here we use a statistical method to compare curated subsystems, to predict the physiology, metabolism, and ecology from metagenomes. This approach can be used to identify those subsystems that are significantly different between metagenome sequences. Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenome when compared to non-redundant databases were identified. Conclusion The methodology described herein applies statistics to the comparisons of metabolic potential in metagenomes. This analysis reveals those subsystems that are more, or less, represented in the different environments that are compared. These differences in metabolic potential lead to several testable hypotheses about physiology and metabolism of microbes from these ecosystems.

  16. Effects of historic metal(loid) pollution on earthworm communities.

    Science.gov (United States)

    Lévêque, Thibaut; Capowiez, Yvan; Schreck, Eva; Mombo, Stéphane; Mazzia, Christophe; Foucault, Yann; Dumat, Camille

    2015-04-01

    The effects of metal(loid)s (Pb, Cd, Cu, Zn, As and Sb) from atmospheric fallout on earthworm communities were investigated in a fallow meadow located close to a 60-year-old lead recycling factory. We examined abundance and species diversity as well as the ratio of adult-to-juvenile earthworms, along five 140 m parallel transects. The influence of soil pollution on the earthworm community at the plot scale was put in context by measuring some physico-chemical soil characteristics (OM content, N content, pH), as well as total and bioavailable metal(loid) concentrations. Earthworms were absent in the highly polluted area (concentration from 30,000 to 5000 mg Pb·kg(-1) of dried soil), just near the factory (0-30 m area). A clear and almost linear relationship was observed between the proportion of juvenile versus mature earthworms and the pollution gradient, with a greater proportion of adults in the most polluted zones (only adult earthworms were observed from 30 to 50 m). Apporectodea longa was the main species present just near the smelter (80% of the earthworms were A. longa from 30 to 50 m). The earthworm density was found to increase progressively from five individuals·m(-2) at 30 m to 135 individuals·m(-2) at 140 m from the factory. On average, metal(loid) accumulation in earthworm tissues decreased linearly with distance from the factory. The concentration of exchangeable metal(loid)s in earthworm surface casts was higher than that of the overall soil. Finally, our field study clearly demonstrated that metal(loid) pollution has a direct impact on earthworm communities (abundance, diversity and proportion of juveniles) especially when Pb concentrations in soil were higher than 2050 mg·kg(-1). Copyright © 2014 Elsevier B.V. All rights reserved.

  17. [Meta-Mesh: metagenomic data analysis system].

    Science.gov (United States)

    Su, Xiaoquan; Song, Baoxing; Wang, Xuetao; Ma, Xinle; Xu, Jian; Ning, Kang

    2014-01-01

    With the current accumulation of metagenome data, it is possible to build an integrated platform for processing of rigorously selected metagenomic samples (also referred as "metagenomic communities" here) of interests. Any metagenomic samples could then be searched against this database to find the most similar sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories but not well annotated database, and only offer few functions for analysis. On the other hand, the few available methods to measure the similarity of metagenomic data could only compare a few pre-defined set of metagenome. It has long been intriguing scientists to effectively calculate similarities between microbial communities in a large repository, to examine how similar these samples are and to find the correlation of the meta-information of these samples. In this work we propose a novel system, Meta-Mesh, which includes a metagenomic database and its companion analysis platform that could systematically and efficiently analyze, compare and search similar metagenomic samples. In the database part, we have collected more than 7 000 high quality and well annotated metagenomic samples from the public domain and in-house facilities. The analysis platform supplies a list of online tools which could accept metagenomic samples, build taxonomical annotations, compare sample in multiple angle, and then search for similar samples against its database by a fast indexing strategy and scoring function. We also used case studies of "database search for identification" and "samples clustering based on similarity matrix" using human-associated habitat samples to demonstrate the performance of Meta-Mesh in metagenomic analysis. Therefore, Meta-Mesh would serve as a database and data analysis system to quickly parse and identify similar

  18. Metagenomic Detection Methods in Biopreparedness Outbreak Scenarios

    DEFF Research Database (Denmark)

    Karlsson, Oskar Erik; Hansen, Trine; Knutsson, Rickard

    2013-01-01

    of a clinical sample, creating a metagenome, in a single week of laboratory work. As new technologies emerge, their dissemination and capacity building must be facilitated, and criteria for use, as well as guidelines on how to report results, must be established. This article focuses on the use of metagenomics......, gaps in research, and future directions. Examples of metagenomic detection, as well as possible applications of the methods, are described in various biopreparedness outbreak scenarios....

  19. Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics?

    Directory of Open Access Journals (Sweden)

    Maryam Tidjani Alou

    2017-05-01

    Full Text Available Severe acute malnutrition is the world-leading cause of children under-five's death. Recent metagenomics studies have established a link between gut microbiota and severe acute malnutrition, describing an immaturity with a striking depletion in oxygen-sensitive prokaryotes. Amoxicillin and therapeutic diet cure most of the children with severe acute malnutrition but an irreversible disruption of the gut microbiota is suspected in the refractory and most severe cases. In these cases, therapeutic diet may be unable to reverse the microbiota alteration leading to persistent impaired development or death. In addition, as enteric sepsis is a major cause of death in this context, identification of missing gut microbes to be tested as probiotics (live bacteria that confer a benefit to the host to restore rapidly the healthy gut microbiota and prevent the gut pathogenic invasion is of foremost importance. In this study, stool samples of malnourished patients with kwashiorkor and healthy children were collected from Niger and Senegal and analyzed by culturomics and metagenomics. We found a globally decreased diversity, a decrease in the hitherto unknown diversity (new species isolation, a depletion in oxygen-sensitive prokaryotes including Methanobrevibacter smithii and an enrichment in potentially pathogenic Proteobacteria, Fusobacteria and Streptococcus gallolyticus. A complex of 12 species identified only in healthy children using culturomics and metagenomics were identified as probiotics candidates, providing a possible, defined, reproducible, safe, and convenient alternative to fecal transplantation to restore a healthy gut microbiota in malnourished children. Microbiotherapy based on selected strains has the potential to improve the current treatment of severe acute malnutrition and prevent relapse and death by reestablishing a healthy gut microbiota.

  20. Marine metagenomics as a source for bioprospecting

    KAUST Repository

    Kodzius, Rimantas

    2015-08-12

    This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals.

  1. Marine metagenomics as a source for bioprospecting.

    Science.gov (United States)

    Kodzius, Rimantas; Gojobori, Takashi

    2015-12-01

    This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals. Copyright © 2015. Published by Elsevier B.V.

  2. Metagenomics and the protein universe

    Science.gov (United States)

    Godzik, Adam

    2011-01-01

    Metagenomics sequencing projects have dramatically increased our knowledge of the protein universe and provided over one-half of currently known protein sequences; they have also introduced a much broader phylogenetic diversity into the protein databases. The full analysis of metagenomic datasets is only beginning, but it has already led to the discovery of thousands of new protein families, likely representing novel functions specific to given environments. At the same time, a deeper analysis of such novel families, including experimental structure determination of some representatives, suggests that most of them represent distant homologs of already characterized protein families, and thus most of the protein diversity present in the new environments are due to functional divergence of the known protein families rather than the emergence of new ones. PMID:21497084

  3. Functional metagenomics of extreme environments.

    Science.gov (United States)

    Mirete, Salvador; Morgante, Verónica; González-Pastor, José Eduardo

    2016-04-01

    The bioprospecting of enzymes that operate under extreme conditions is of particular interest for many biotechnological and industrial processes. Nevertheless, there is a considerable limitation to retrieve novel enzymes as only a small fraction of microorganisms derived from extreme environments can be cultured under standard laboratory conditions. Functional metagenomics has the advantage of not requiring the cultivation of microorganisms or previous sequence information to known genes, thus representing a valuable approach for mining enzymes with new features. In this review, we summarize studies showing how functional metagenomics was employed to retrieve genes encoding for proteins involved not only in molecular adaptation and resistance to extreme environmental conditions but also in other enzymatic activities of biotechnological interest. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Earthworm Effects without Earthworms: Inoculation of Raw Organic Matter with Worm-Worked Substrates Alters Microbial Community Functioning

    Science.gov (United States)

    Aira, Manuel; Domínguez, Jorge

    2011-01-01

    Background Earthworms are key organisms in organic matter decomposition because of the interactions they establish with soil microorganisms. They enhance decomposition rates through the joint action of direct effects (i.e. effects due to direct earthworm activity such as digestion, burrowing, etc) and indirect effects (i.e. effects derived from earthworm activities such as cast ageing). Here we test whether indirect earthworm effects affect microbial community functioning in the substrate, as when earthworms are present (i. e., direct effects). Methodology/Principal Findings To address these questions we inoculated fresh organic matter (pig manure) with worm-worked substrates (vermicompost) produced by three different earthworm species. Two doses of each vermicompost were used (2.5 and 10%). We hypothesized that the presence of worm-worked material in the fresh organic matter will result in an inoculum of different microorganisms and nutrients. This inoculum should interact with microbial communities in fresh organic matter, thus promoting modifications similar to those found when earthworms are present. Inoculation of worm-worked substrates provoked significant increases in microbial biomass and enzyme activities (β-glucosidase, cellulase, phosphatase and protease). These indirect effects were similar to, although lower than, those obtained in pig manure with earthworms (direct and indirect earthworm effects). In general, the effects were not dose-dependent, suggesting the existence of a threshold at which they were triggered. Conclusion/Significance Our data reveal that the relationships between earthworms and microorganisms are far from being understood, and suggest the existence of several positive feedbacks during earthworm activity as a result of the interactions between direct and indirect effects, since their combination produces stronger modifications to microbial biomass and enzyme activity. PMID:21298016

  5. Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria.

    Science.gov (United States)

    Wang, Weiwei; Jovel, Juan; Halloran, Brendan; Wine, Eytan; Patterson, Jordan; Ford, Glenn; OʼKeefe, Sandra; Meng, Bo; Song, Deyong; Zhang, Yong; Tian, Zhijian; Wasilenko, Shawn T; Rahbari, Mandana; Reza, Salman; Mitchell, Troy; Jordan, Tracy; Carpenter, Eric; Madsen, Karen; Fedorak, Richard; Dielemann, Levinus A; Ka-Shu Wong, Gane; Mason, Andrew L

    2015-06-01

    Inflammatory bowel diseases (IBD), Crohn's disease and ulcerative colitis, are poorly understood disorders affecting the intestinal tract. The current model for disease suggests that genetically susceptible patients develop intolerance to gut microflora, and chronic inflammation develops as a result of environmental insults. Although interest has mainly focused on studying genetic variants and gut bacterial flora, little is known about the potential of viral infection to contribute to disease. Accordingly, we conducted a metagenomic analysis to document the baseline virome in colonic biopsy samples from patients with IBD in order to assess the contribution of viral infection to IBD. Libraries were generated from colon RNA to create approximately 2 GB sequence data per library. Using a bioinformatic pipeline designed to detect viral sequences, more than 1000 viral reads were derived directly from tissue without any coculture or isolation procedure. Herein, we describe the complexity and abundance of viruses, bacteria/bacteriophage, and human endogenous retroviral sequences from 10 patients with IBD and 5 healthy subjects undergoing surveillance colonoscopy. Differences in gut microflora and the abundance of mammalian viruses and human endogenous retroviruses were readily detected in the metagenomic analyses. Specifically, patients with herpesviridae sequences in their colon demonstrated increased expression of human endogenous viral sequences and differences in the diversity of their microbiome. This study provides a promising metagenomic approach to describe the colonic microbiome that can be used to better understand virus-host and phage-bacteria interactions in IBD.

  6. Integrative workflows for metagenomic analysis.

    Science.gov (United States)

    Ladoukakis, Efthymios; Kolisis, Fragiskos N; Chatziioannou, Aristotelis A

    2014-01-01

    The rapid evolution of all sequencing technologies, described by the term Next Generation Sequencing (NGS), have revolutionized metagenomic analysis. They constitute a combination of high-throughput analytical protocols, coupled to delicate measuring techniques, in order to potentially discover, properly assemble and map allelic sequences to the correct genomes, achieving particularly high yields for only a fraction of the cost of traditional processes (i.e., Sanger). From a bioinformatic perspective, this boils down to many GB of data being generated from each single sequencing experiment, rendering the management or even the storage, critical bottlenecks with respect to the overall analytical endeavor. The enormous complexity is even more aggravated by the versatility of the processing steps available, represented by the numerous bioinformatic tools that are essential, for each analytical task, in order to fully unveil the genetic content of a metagenomic dataset. These disparate tasks range from simple, nonetheless non-trivial, quality control of raw data to exceptionally complex protein annotation procedures, requesting a high level of expertise for their proper application or the neat implementation of the whole workflow. Furthermore, a bioinformatic analysis of such scale, requires grand computational resources, imposing as the sole realistic solution, the utilization of cloud computing infrastructures. In this review article we discuss different, integrative, bioinformatic solutions available, which address the aforementioned issues, by performing a critical assessment of the available automated pipelines for data management, quality control, and annotation of metagenomic data, embracing various, major sequencing technologies and applications.

  7. Integrative Workflows for Metagenomic Analysis

    Directory of Open Access Journals (Sweden)

    Efthymios eLadoukakis

    2014-11-01

    Full Text Available The rapid evolution of all sequencing technologies, described by the term Next Generation Sequencing (NGS, have revolutionized metagenomic analysis. They constitute a combination of high-throughput analytical protocols, coupled to delicate measuring techniques, in order to potentially discover, properly assemble and map allelic sequences to the correct genomes, achieving particularly high yields for only a fraction of the cost of traditional processes (i.e. Sanger. From a bioinformatic perspective, this boils down to many gigabytes of data being generated from each single sequencing experiment, rendering the management or even the storage, critical bottlenecks with respect to the overall analytical endeavor. The enormous complexity is even more aggravated by the versatility of the processing steps available, represented by the numerous bioinformatic tools that are essential, for each analytical task, in order to fully unveil the genetic content of a metagenomic dataset. These disparate tasks range from simple, nonetheless non-trivial, quality control of raw data to exceptionally complex protein annotation procedures, requesting a high level of expertise for their proper application or the neat implementation of the whole workflow. Furthermore, a bioinformatic analysis of such scale, requires grand computational resources, imposing as the sole realistic solution, the utilization of cloud computing infrastructures. In this review article we discuss different, integrative, bioinformatic solutions available, which address the aforementioned issues, by performing a critical assessment of the available automated pipelines for data management, quality control and annotation of metagenomic data, embracing various, major sequencing technologies and applications.

  8. Uptake and elimination kinetics of heavy metals by earthworm ...

    African Journals Online (AJOL)

    Earthworm inoculation of petroleum hydrocarbon contaminated soil is thought to catalyze the bioremediation. Most bioremediation studies focus on the petroleum hydrocarbon content and not on the heavy metals. Here, the uptake kinetics of heavy metals by earthworm in used engine oil contaminated soil was investigated.

  9. Earthworms (Annelida: Oligochaeta) of the Columbia River basin assessment area.

    Science.gov (United States)

    Sam. James

    2000-01-01

    Earthworms are key components of many terrestrial ecosystems; however, little is known of their ecology, distribution, and taxonomy in the eastern interior Columbia River basin assessment area (hereafter referred to as the basin assessment area). This report summarizes the main issues about the ecology of earthworms and their impact on the physical and chemical status...

  10. Earthworms as colonizers of natural and cultivated soil environments

    NARCIS (Netherlands)

    Eijsackers, H.J.P.

    2011-01-01

    For cultivated soils, the important function of earthworms as ecosystem engineers and their major contribution to the composition and functioning of soil ecosystems with a varying species diversity has been extensively addressed. However, the role of earthworms as colonizers of virgin, uncultivated

  11. New earthworm (Clitellata: Lumbricidae records from Vitosha Mts. (Bulgaria

    Directory of Open Access Journals (Sweden)

    HRISTO VALCHOVSKI

    2016-10-01

    Full Text Available The paper deals with earthworm diversity from Vitosha Mountain (Bulgaria. During the investigation 10 earthworm species were collected altogether, belonging to 7 genera. Among them, two taxa are reported for the first time from the explored region. Aporrectodea caliginosa (Savigny, 1826 and Lumbricus terrestris Linnaeus, 1758 are proved to be new records from the territory of Vitosha Mountain.

  12. Earthworm (Clitellata: Lumbricidae records from the Rila Mountains (Bulgaria

    Directory of Open Access Journals (Sweden)

    HRISTO VALCHOVSKI

    2016-11-01

    Full Text Available The current study is a contribution to the knowledge of the earthworm diversity from the Rila Mountains (Bulgaria. During the investigation 13 earthworm species were collected altogether, belonging to eight genera. Among them Aporrectodea handlirschi (Rosa, 1897 and Aporrectodea caliginosa (Savigny, 1826 proved to be new records from the territory of the Rila Mountain.

  13. Responses of Earthworm to Aluminum Toxicity in Latosol

    Science.gov (United States)

    Jia-En Zhang; Jiayu Yu; Ying Ouyang; Huaqin. Xu

    2012-01-01

    Excess aluminum (Al) in soils due to acid rain leaching is toxic to water resources and harmful to soil organisms and plants. This study investigated adverse impacts of Al levels upon earthworms (Eisenia fetida) from the latosol (acidic red soil). Laboratory experiments were performed to examine the survival and avoidance of earthworms from high Al...

  14. Activity of earthworm in Latosol under simulated acid rain stress

    Science.gov (United States)

    Jia-En Zhang; Jiayu Yu; Ying Ouyang

    2015-01-01

    Acid rain is still an issue of environmental concerns. This study investigated the impacts of simulated acid rain (SAR) upon earthworm activity from the Latosol (acidic red soil). Laboratory experiment was performed by leaching the soil columns grown with earthworms (Eisenia fetida) at the SAR pH levels ranged from 2.0 to 6.5 over a 34-day period....

  15. Effects of metals on earthworm life cycles: a review.

    Science.gov (United States)

    Sivakumar, S

    2015-08-01

    Earthworms are abundant and ecologically very important organisms in the soil ecosystem. Impacts by pollutants on earthworm communities greatly influence the fertility of the terrestrial environment. In ecotoxicology, earthworms are good indicators of metal pollution. The observed median lethal concentrations (LC50) and the effective concentrations that cause 50% reduction of earthworm growth and reproduction (EC50) are referred to as toxicity concentrations or endpoints. In addition, the 'no observed effective concentration' (NOEC) is the estimation of the toxicity of metals on earthworms expressed as the highest concentration tested that does not show effects on growth and reproduction compared to controls. This article reviews the ecotoxicological parameters of LC50, EC50 and NOEC of a set of worms exposed to a number of metals in various tested media. In addition, this article reviews metal accumulation and the influences of soil characteristics on metal accumulation in earthworms. Morphological and behavioural responses are often used in earthworm toxicity studies. Therefore, earthworm responses due to metal toxicity are also discussed in this article.

  16. Antibiotic resistance potential of the healthy preterm infant gut microbiome

    Directory of Open Access Journals (Sweden)

    Graham Rose

    2017-01-01

    Full Text Available Background Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. Results Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. Conclusions We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.

  17. Using Short-Term Enrichments and Metagenomics to Obtain Genomes from uncultured Activated Sludge Microorganisms

    DEFF Research Database (Denmark)

    Karst, Søren Michael; Nielsen, Per Halkjær; Albertsen, Mads

    is that they depend on system-specific reference genomes in order to analyze the vast amounts of data (Albertsen et al., 2012). This limits the application of -omics to environments for which a comprehensive catalogue of reference genomes exists e.g. the human gut. Several strategies for obtaining microbial genomes...... exist today, but their ability to obtain complete genomes from complex microbial communities on a large scale is still inadequate (Lasken, 2012). In theory, conventional metagenomics should be able to recover genomes from complex communities, but in practice the approach is hampered by the presence...... of microdiversity. This leads to fragmented and chimeric de novo assemblies, which prevent the extraction of complete genomes. The new approach presented here involves reducing the impact of microdiversity and increasing genome extraction efficiency by what we term “metagenome triangulation”. The microdiversity...

  18. Effect of Soil Physical State on the Earthworms in Hungary

    Directory of Open Access Journals (Sweden)

    Marta Birkas

    2010-01-01

    Full Text Available Hungarian authors have long been discussing the role of earthworms in improving soil productivity. Earthworm counts in our higher quality soils are similar to those found in soils where more attention is paid to earthworm activity. Negative impacts that are independent of farming—such as sustained dry spells in the summer—also affect earthworm counts. Negative impacts that definitely depend on farming include land use causing soil moisture loss, deep stubble treatment leaving the soil without cover, and ploughing in the summer without subsequent pressing. The climate change is having both positive and negative impacts. Weather patterns are causing losses but adopting climate mitigating tillage are generating benefits. In the trials results so far show that tillage focusing on preserving soil moisture, structure, and organic materials, covering the surface in the critical months as well as adequate soil loosening are fundamental pre-requisites for making the soil a favourable habitat for earthworms.

  19. Exploring neighborhoods in the metagenome universe.

    Science.gov (United States)

    Aßhauer, Kathrin P; Klingenberg, Heiner; Lingner, Thomas; Meinicke, Peter

    2014-07-14

    The variety of metagenomes in current databases provides a rapidly growing source of information for comparative studies. However, the quantity and quality of supplementary metadata is still lagging behind. It is therefore important to be able to identify related metagenomes by means of the available sequence data alone. We have studied efficient sequence-based methods for large-scale identification of similar metagenomes within a database retrieval context. In a broad comparison of different profiling methods we found that vector-based distance measures are well-suitable for the detection of metagenomic neighbors. Our evaluation on more than 1700 publicly available metagenomes indicates that for a query metagenome from a particular habitat on average nine out of ten nearest neighbors represent the same habitat category independent of the utilized profiling method or distance measure. While for well-defined labels a neighborhood accuracy of 100% can be achieved, in general the neighbor detection is severely affected by a natural overlap of manually annotated categories. In addition, we present results of a novel visualization method that is able to reflect the similarity of metagenomes in a 2D scatter plot. The visualization method shows a similarly high accuracy in the reduced space as compared with the high-dimensional profile space. Our study suggests that for inspection of metagenome neighborhoods the profiling methods and distance measures can be chosen to provide a convenient interpretation of results in terms of the underlying features. Furthermore, supplementary metadata of metagenome samples in the future needs to comply with readily available ontologies for fine-grained and standardized annotation. To make profile-based k-nearest-neighbor search and the 2D-visualization of the metagenome universe available to the research community, we included the proposed methods in our CoMet-Universe server for comparative metagenome analysis.

  20. The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.

    Science.gov (United States)

    Milani, Christian; Duranti, Sabrina; Bottacini, Francesca; Casey, Eoghan; Turroni, Francesca; Mahony, Jennifer; Belzer, Clara; Delgado Palacio, Susana; Arboleya Montes, Silvia; Mancabelli, Leonardo; Lugli, Gabriele Andrea; Rodriguez, Juan Miguel; Bode, Lars; de Vos, Willem; Gueimonde, Miguel; Margolles, Abelardo; van Sinderen, Douwe; Ventura, Marco

    2017-12-01

    The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and

  1. EFFECT OF COMBINATIONS OF VERMICULITE AND EARTHWORM COMPOST IN THE DEVELOPMENT OF RANGPUR LIME ROOTSTOCK

    OpenAIRE

    Orioli, Fabrício Alberghini; Coopercitrus/Jales; Oliveira, Antônio Luís de; FAFRAM; Orioli Júnior, Valdeci; Unesp/Jaboticabal

    2008-01-01

    The present work was carried in protecting environment located in the Ranch Saint Luzia, situated in Monte Azul Paulista city. Rangpur lime rootstock was evaluated in different combinations of vermiculite and earthworm compost. The experiment was installed using a randomized block design, with five repetitions and seven treatments: 100% vermiculite; 100% earthworm compost; 50% vermiculite and 50% earthworm compost; 60% vermiculite and 40% earthworm compost; 70% vermiculite and 30% earthworm c...

  2. Statistical methods for detecting differentially abundant features in clinical metagenomic samples.

    Directory of Open Access Journals (Sweden)

    James Robert White

    2009-04-01

    Full Text Available Numerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more importantly, hope to reveal the secrets of the complex symbiotic relationship between us and our commensal bacterial microflora. An important prerequisite for such discoveries are computational tools that are able to rapidly and accurately compare large datasets generated from complex bacterial communities to identify features that distinguish them.We present a statistical method for comparing clinical metagenomic samples from two treatment populations on the basis of count data (e.g. as obtained through sequencing to detect differentially abundant features. Our method, Metastats, employs the false discovery rate to improve specificity in high-complexity environments, and separately handles sparsely-sampled features using Fisher's exact test. Under a variety of simulations, we show that Metastats performs well compared to previously used methods, and significantly outperforms other methods for features with sparse counts. We demonstrate the utility of our method on several datasets including a 16S rRNA survey of obese and lean human gut microbiomes, COG functional profiles of infant and mature gut microbiomes, and bacterial and viral metabolic subsystem data inferred from random sequencing of 85 metagenomes. The application of our method to the obesity dataset reveals differences between obese and lean subjects not reported in the original study. For the COG and subsystem datasets, we provide the first statistically rigorous assessment of the differences between these populations. The methods described in this paper are the first to address clinical metagenomic datasets comprising samples from multiple subjects. Our methods are robust across datasets of varied complexity and sampling level. While designed for metagenomic applications, our software

  3. Functional Metagenomics to Study Antibiotic Resistance.

    Science.gov (United States)

    Boolchandani, Manish; Patel, Sanket; Dantas, Gautam

    2017-01-01

    The construction and screening of metagenomic expression libraries has great potential to identify novel genes and their functions. Here, we describe metagenomic library preparation from fecal DNA, screening of libraries for antibiotic resistance genes (ARGs), massively parallel DNA sequencing of the enriched DNA fragments, and a computational pipeline for high-throughput assembly and annotation of functionally selected DNA.

  4. Metagenomic data analysis : computational methods and applications

    NARCIS (Netherlands)

    Gori, F.

    2013-01-01

    Metagenomics is the study of the genomic content of microbial communities, acquired through DNA sequencing technology. The main advantage of metagenomics is that it can overcome the limitations of individual genome sequencing, that can work only on the few culturable microbes. Unfortunately, the

  5. Bacteroidales Secreted Antimicrobial Proteins Target Surface Molecules Necessary for Gut Colonization and Mediate Competition In Vivo.

    Science.gov (United States)

    Roelofs, Kevin G; Coyne, Michael J; Gentyala, Rahul R; Chatzidaki-Livanis, Maria; Comstock, Laurie E

    2016-08-23

    We recently showed that human gut Bacteroidales species secrete antimicrobial proteins (BSAPs), and we characterized in vitro the first such BSAP produced by Bacteroides fragilis In this study, we identified a second potent BSAP produced by the ubiquitous and abundant human gut species Bacteroides uniformis The two BSAPs contain a membrane attack complex/perforin (MACPF) domain but share very little sequence similarity. We identified the target molecules of BSAP-sensitive cells and showed that each BSAP targets a different class of surface molecule: BSAP-1 targets an outer membrane protein of sensitive B. fragilis strains, and BSAP-2 targets the O-antigen glycan of lipopolysaccharide (LPS) of sensitive B. uniformis strains. Species-wide genomic and phenotypic analyses of B. fragilis and B. uniformis showed that BSAP-producing strains circumvent killing by synthesizing an orthologous nontargeted surface molecule. The BSAP genes are adjacent to the gene(s) encoding their target replacements, suggesting coacquisition. Using a gnotobiotic mouse competitive-colonization model, we found that the BSAP surface targets are important for colonization of the mammalian gut, thereby explaining why they are maintained in sensitive strains and why they were replaced rather than deleted in BSAP-producing strains. Using isogenic BSAP-producing, -sensitive, and -resistant strains, we show that a BSAP-producing strain outcompetes a sensitive strain but not a resistant strain in the mammalian gut. Human gut metagenomic datasets reveal that BSAP-1-sensitive strains do not cooccur with BSAP-1-producing strains in human gut microbiotas, further supporting the idea that BSAPs are important competitive factors with relevance to the strain-level composition of the human gut microbiota. We know relatively little about the ecology of the human intestinal microbiota and the combination of factors that dictate which strains and species occupy an individual's gut microbial community

  6. The human gut resistome

    Science.gov (United States)

    van Schaik, Willem

    2015-01-01

    In recent decades, the emergence and spread of antibiotic resistance among bacterial pathogens has become a major threat to public health. Bacteria can acquire antibiotic resistance genes by the mobilization and transfer of resistance genes from a donor strain. The human gut contains a densely populated microbial ecosystem, termed the gut microbiota, which offers ample opportunities for the horizontal transfer of genetic material, including antibiotic resistance genes. Recent technological advances allow microbiota-wide studies into the diversity and dynamics of the antibiotic resistance genes that are harboured by the gut microbiota (‘the gut resistome’). Genes conferring resistance to antibiotics are ubiquitously present among the gut microbiota of humans and most resistance genes are harboured by strictly anaerobic gut commensals. The horizontal transfer of genetic material, including antibiotic resistance genes, through conjugation and transduction is a frequent event in the gut microbiota, but mostly involves non-pathogenic gut commensals as these dominate the microbiota of healthy individuals. Resistance gene transfer from commensals to gut-dwelling opportunistic pathogens appears to be a relatively rare event but may contribute to the emergence of multi-drug resistant strains, as is illustrated by the vancomycin resistance determinants that are shared by anaerobic gut commensals and the nosocomial pathogen Enterococcus faecium. PMID:25918444

  7. Metagenomics using next-generation sequencing.

    Science.gov (United States)

    Bragg, Lauren; Tyson, Gene W

    2014-01-01

    Traditionally, microbial genome sequencing has been restricted to the small number of species that can be grown in pure culture. The progressive development of culture-independent methods over the last 15 years now allows researchers to sequence microbial communities directly from environmental samples. This approach is commonly referred to as "metagenomics" or "community genomics". However, the term metagenomics is applied liberally in the literature to describe any culture-independent analysis of microbial communities. Here, we define metagenomics as shotgun ("random") sequencing of the genomic DNA of a sample taken directly from the environment. The metagenome can be thought of as a sampling of the collective genome of the microbial community. We outline the considerations and analyses that should be undertaken to ensure the success of a metagenomic sequencing project, including the choice of sequencing platform and methods for assembly, binning, annotation, and comparative analysis.

  8. Metagenomic applications in environmental monitoring and bioremediation.

    Science.gov (United States)

    Techtmann, Stephen M; Hazen, Terry C

    2016-10-01

    With the rapid advances in sequencing technology, the cost of sequencing has dramatically dropped and the scale of sequencing projects has increased accordingly. This has provided the opportunity for the routine use of sequencing techniques in the monitoring of environmental microbes. While metagenomic applications have been routinely applied to better understand the ecology and diversity of microbes, their use in environmental monitoring and bioremediation is increasingly common. In this review we seek to provide an overview of some of the metagenomic techniques used in environmental systems biology, addressing their application and limitation. We will also provide several recent examples of the application of metagenomics to bioremediation. We discuss examples where microbial communities have been used to predict the presence and extent of contamination, examples of how metagenomics can be used to characterize the process of natural attenuation by unculturable microbes, as well as examples detailing the use of metagenomics to understand the impact of biostimulation on microbial communities.

  9. The human gut chip "HuGChip", an explorative phylogenetic microarray for determining gut microbiome diversity at family level.

    Science.gov (United States)

    Tottey, William; Denonfoux, Jeremie; Jaziri, Faouzi; Parisot, Nicolas; Missaoui, Mohiedine; Hill, David; Borrel, Guillaume; Peyretaillade, Eric; Alric, Monique; Harris, Hugh M B; Jeffery, Ian B; Claesson, Marcus J; O'Toole, Paul W; Peyret, Pierre; Brugère, Jean-François

    2013-01-01

    Evaluating the composition of the human gut microbiota greatly facilitates studies on its role in human pathophysiology, and is heavily reliant on culture-independent molecular methods. A microarray designated the Human Gut Chip (HuGChip) was developed to analyze and compare human gut microbiota samples. The PhylArray software was used to design specific and sensitive probes. The DNA chip was composed of 4,441 probes (2,442 specific and 1,919 explorative probes) targeting 66 bacterial families. A mock community composed of 16S rRNA gene sequences from intestinal species was used to define the threshold criteria to be used to analyze complex samples. This was then experimentally verified with three human faecal samples and results were compared (i) with pyrosequencing of the V4 hypervariable region of the 16S rRNA gene, (ii) metagenomic data, and (iii) qPCR analysis of three phyla. When compared at both the phylum and the family level, high Pearson's correlation coefficients were obtained between data from all methods. The HuGChip development and validation showed that it is not only able to assess the known human gut microbiota but could also detect unknown species with the explorative probes to reveal the large number of bacterial sequences not yet described in the human gut microbiota, overcoming the main inconvenience encountered when developing microarrays.

  10. Dynamics and stabilization of the human gut microbiome during the first year of life

    DEFF Research Database (Denmark)

    Bäckhed, Gert Fredrik; Roswall, Josefine; Peng, Yangqing

    2015-01-01

    The gut microbiota is central to human health, but its establishment in early life has not been quantitatively and functionally examined. Applying metagenomic analysis on fecal samples from a large cohort of Swedish infants and their mothers, we characterized the gut microbiome during the first...... year of life and assessed the impact of mode of delivery and feeding on its establishment. In contrast to vaginally delivered infants, the gut microbiota of infants delivered by C-section showed significantly less resemblance to their mothers. Nutrition had a major impact on early microbiota...... of the microbiome. Our findings establish a framework for understanding the interplay between the gut microbiome and the human body in early life....

  11. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

    DEFF Research Database (Denmark)

    Forslund, Kristoffer; Hildebrand, Falk ; Nielsen, Trine N.

    2015-01-01

    for treatment yielded divergent conclusions regarding its associated gut microbial dysbiosis3,4. Here we show, using 784 available human gut metagenomes, how antidiabetic medication confounds these results, and analyse in detail the effects of the most widely used antidiabetic drug metformin. We provide support...... for microbial mediation of the therapeutic effects of metformin through short-chain fatty acid production, as well as for potential microbiota-mediated mechanisms behind known intestinal adverse effects in the form of a relative increase in abundance of Escherichia species. Controlling for metformin treatment......, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa3,4. These in turn cause functional microbiome shifts, in part alleviated by metformin-induced changes. Overall, the present study emphasizes the need to disentangle gut microbiota signatures...

  12. Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals.

    Directory of Open Access Journals (Sweden)

    Emma C L Finlayson-Trick

    Full Text Available Host diet influences the diversity and metabolic activities of the gut microbiome. Previous studies have shown that the gut microbiome provides a wide array of enzymes that enable processing of diverse dietary components. Because the primary diet of the porcupine, Erethizon dorsatum, is lignified plant material, we reasoned that the porcupine microbiome would be replete with enzymes required to degrade lignocellulose. Here, we report on the bacterial composition in the porcupine microbiome using 16S rRNA sequencing and bioinformatics analysis. We extended this analysis to the microbiomes of 20 additional mammals located in Shubenacadie Wildlife Park (Nova Scotia, Canada, enabling the comparison of bacterial diversity amongst three mammalian taxonomic orders (Rodentia, Carnivora, and Artiodactyla. 16S rRNA sequencing was validated using metagenomic shotgun sequencing on selected herbivores (porcupine, beaver and carnivores (coyote, Arctic wolf. In the microbiome, functionality is more conserved than bacterial composition, thus we mined microbiome data sets to identify conserved microbial functions across species in each order. We measured the relative gene abundances for cellobiose phosphorylase, endoglucanase, and beta-glucosidase to evaluate the cellulose-degrading potential of select mammals. The porcupine and beaver had higher proportions of genes encoding cellulose-degrading enzymes than the Artic wolf and coyote. These findings provide further evidence that gut microbiome diversity and metabolic capacity are influenced by host diet.

  13. The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp.

    OpenAIRE

    Vilanova, Cristina; Baixeras, Joaquín; Latorre, Amparo; Porcar, Manuel

    2016-01-01

    Some specialist insects feed on plants rich in secondary compounds, which pose a major selective pressure on both the phytophagous and the gut microbiota. However, microbial communities of toxic plant feeders are still poorly characterized. Here, we show the bacterial communities of the gut of two specialized Lepidoptera, Hyles euphorbiae and Brithys crini, which exclusively feed on latex-rich Euphorbia sp. and alkaloid-rich Pancratium maritimum, respectively. A metagenomic analysis based on ...

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

    OpenAIRE

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

    2016-01-01

    Diet and exercise underpin the risk of obesity-related metabolic disease. Diet alters the gut microbiota, which contributes to aspects of metabolic disease during obesity. Repeated exercise provides metabolic benefits during obesity. We assessed whether exercise could oppose changes in the taxonomic and predicted metagenomic characteristics of the gut microbiota during diet-induced obesity. We hypothesized that high-intensity interval training (HIIT) would counteract high-fat diet (HFD)-induc...

  15. Gut microbiota and obesity.

    Science.gov (United States)

    Gérard, Philippe

    2016-01-01

    The human intestine harbors a complex bacterial community called the gut microbiota. This microbiota is specific to each individual despite the existence of several bacterial species shared by the majority of adults. The influence of the gut microbiota in human health and disease has been revealed in the recent years. Particularly, the use of germ-free animals and microbiota transplant showed that the gut microbiota may play a causal role in the development of obesity and associated metabolic disorders, and lead to identification of several mechanisms. In humans, differences in microbiota composition, functional genes and metabolic activities are observed between obese and lean individuals suggesting a contribution of the gut microbiota to these phenotypes. Finally, the evidence linking gut bacteria to host metabolism could allow the development of new therapeutic strategies based on gut microbiota modulation to treat or prevent obesity.

  16. Pika population density is associated with composition and diversity of gut microbiota

    Directory of Open Access Journals (Sweden)

    Huan eLi

    2016-05-01

    Full Text Available Host population density is positively associated with the strength of social interactions or the frequency of physical contacts, and thus potentially influences microbial transmission among individuals. However, the relationship between host density and gut microbiota remains unknown. Here, we characterized the gut microbiota of plateau pikas (Ochotona curzoniae in wild experimental fields with different host population densities. The abundance of some gut microbes significantly correlated with host density, such as Ruminococcaceae, Lachnospiraceae and Staphylococcaceae. Intriguingly, host density was positively correlated with alpha diversity (Shannon diversity and observed species of gut microbial communities. The inter-individual gut microbiota within high-density groups were more similar to each other than those of low-density groups. Host density significantly explained the variations in the gut microbiota, even after controlling sex, weight, diet and geographical locations. Based on the PICRUSt metagenome prediction, positive correlations were observed between host density and the relative abundances of 12 gene functions involved in cellular processes, environmental information processing and metabolism. These results indicate the importance of host density as a factor in shaping gut microbial composition and diversity in plateau pikas, and may further help us understand the social transmission of gut microbiota.

  17. Pika Population Density Is Associated with the Composition and Diversity of Gut Microbiota.

    Science.gov (United States)

    Li, Huan; Qu, Jiapeng; Li, Tongtong; Li, Jiabao; Lin, Qiang; Li, Xiangzhen

    2016-01-01

    Host population density is positively associated with the strength of social interactions or the frequency of physical contacts, and thus potentially influences microbial transmission among individuals. However, the relationship between host density and gut microbiota remains unknown. Here, we characterized the gut microbiota of plateau pikas (Ochotona curzoniae) in wild experimental fields with different host population densities. The abundance of some gut microbes significantly correlated with host density, such as Ruminococcaceae, Lachnospiraceae, and Staphylococcaceae. Intriguingly, host density was positively correlated with alpha diversity (Shannon diversity and observed species) of gut microbial communities. The inter-individual gut microbiota within high-density groups were more similar to each other than those of low-density groups. Host density significantly explained the variations in the gut microbiota, even after controlling sex, weight, diet and geographical locations. Based on the PICRUSt metagenome prediction, positive correlations were observed between host density and the relative abundances of 12 gene functions involved in cellular processes, environmental information processing and metabolism. These results indicate the importance of host density as a factor in shaping gut microbial composition and diversity in plateau pikas, and may further help us understand the social transmission of gut microbiota.

  18. Invasive Asian Earthworms Negatively Impact Keystone Terrestrial Salamanders.

    Directory of Open Access Journals (Sweden)

    Julie L Ziemba

    Full Text Available Asian pheretimoid earthworms (e.g. Amynthas and Metaphire spp. are invading North American forests and consuming the vital detrital layer that forest floor biota [including the keystone species Plethodon cinereus (Eastern Red-backed Salamander], rely on for protection, food, and habitat. Plethodon cinereus population declines have been associated with leaf litter loss following the invasion of several exotic earthworm species, but there have been few studies on the specific interactions between pheretimoid earthworms and P. cinereus. Since some species of large and active pheretimoids spatially overlap with salamanders beneath natural cover objects and in detritus, they may distinctively compound the negative consequences of earthworm-mediated resource degradation by physically disturbing important salamander activities (foraging, mating, and egg brooding. We predicted that earthworms would exclude salamanders from high quality microhabitat, reduce foraging efficiency, and negatively affect salamander fitness. In laboratory trials, salamanders used lower quality microhabitat and consumed fewer flies in the presence of earthworms. In a natural field experiment, conducted on salamander populations from "non-invaded" and "pheretimoid invaded" sites in Ohio, salamanders and earthworms shared cover objects ~60% less than expected. Earthworm abundance was negatively associated with juvenile and male salamander abundance, but had no relationship with female salamander abundance. There was no effect of pheretimoid invasion on salamander body condition. Juvenile and non-resident male salamanders do not hold stable territories centered beneath cover objects such as rocks or logs, which results in reduced access to prey, greater risk of desiccation, and dispersal pressure. Habitat degradation and physical exclusion of salamanders from cover objects may hinder juvenile and male salamander performance, ultimately reducing recruitment and salamander abundance

  19. Invasive Asian Earthworms Negatively Impact Keystone Terrestrial Salamanders.

    Science.gov (United States)

    Ziemba, Julie L; Hickerson, Cari-Ann M; Anthony, Carl D

    2016-01-01

    Asian pheretimoid earthworms (e.g. Amynthas and Metaphire spp.) are invading North American forests and consuming the vital detrital layer that forest floor biota [including the keystone species Plethodon cinereus (Eastern Red-backed Salamander)], rely on for protection, food, and habitat. Plethodon cinereus population declines have been associated with leaf litter loss following the invasion of several exotic earthworm species, but there have been few studies on the specific interactions between pheretimoid earthworms and P. cinereus. Since some species of large and active pheretimoids spatially overlap with salamanders beneath natural cover objects and in detritus, they may distinctively compound the negative consequences of earthworm-mediated resource degradation by physically disturbing important salamander activities (foraging, mating, and egg brooding). We predicted that earthworms would exclude salamanders from high quality microhabitat, reduce foraging efficiency, and negatively affect salamander fitness. In laboratory trials, salamanders used lower quality microhabitat and consumed fewer flies in the presence of earthworms. In a natural field experiment, conducted on salamander populations from "non-invaded" and "pheretimoid invaded" sites in Ohio, salamanders and earthworms shared cover objects ~60% less than expected. Earthworm abundance was negatively associated with juvenile and male salamander abundance, but had no relationship with female salamander abundance. There was no effect of pheretimoid invasion on salamander body condition. Juvenile and non-resident male salamanders do not hold stable territories centered beneath cover objects such as rocks or logs, which results in reduced access to prey, greater risk of desiccation, and dispersal pressure. Habitat degradation and physical exclusion of salamanders from cover objects may hinder juvenile and male salamander performance, ultimately reducing recruitment and salamander abundance following Asian

  20. Transcriptional interactions suggest niche segregation among microorganisms in the human gut

    DEFF Research Database (Denmark)

    Plichta, Damian Rafal; Juncker, Agnieszka; dos Santos, Marcelo Bertalan Quintanilha

    2016-01-01

    The human gastrointestinal (GI) tract is the habitat for hundreds of microbial species, of which many cannot be cultivated readily, presumably because of the dependencies between species 1. Studies of microbial co-occurrence in the gut have indicated community substructures that may reflect...... functional and metabolic interactions between cohabiting species 2,3. To move beyond species co-occurrence networks, we systematically identified transcriptional interactions between pairs of coexisting gut microbes using metagenomics and microarray-based metatranscriptomics data from 233 stool samples from...

  1. The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity.

    Science.gov (United States)

    Tai, Ningwen; Wong, F Susan; Wen, Li

    2015-03-01

    Diabetes is a group of metabolic disorders characterized by persistent hyperglycemia and has become a major public health concern. Autoimmune type 1 diabetes (T1D) and insulin resistant type 2 diabetes (T2D) are the two main types. A combination of genetic and environmental factors contributes to the development of these diseases. Gut microbiota have emerged recently as an essential player in the development of T1D, T2D and obesity. Altered gut microbiota have been strongly linked to disease in both rodent models and humans. Both classic 16S rRNA sequencing and shot-gun metagenomic pyrosequencing analysis have been successfully applied to explore the gut microbiota composition and functionality. This review focuses on the association between gut microbiota and diabetes and discusses the potential mechanisms by which gut microbiota regulate disease development in T1D, T2D and obesity.

  2. Diversity of earthworms (Clitellata: Lumbricidae from Sredna Gora Mountain (Bulgaria

    Directory of Open Access Journals (Sweden)

    Valchovski, H.

    2016-07-01

    Full Text Available In the current study the diversity, zoogeographical position and distribution of earthworms from Sredna Gora Mountain (Bulgaria is presented. During the present investigation, altogether ten earthworm species belonging to seven genera were collected. Among them, seven taxa are reported for the first time from the Sredna Gora Mt.: Cernosvitovia rebeli, Dendrobaena alpina, Allolobophoridella eiseni, Dendrodrilus rubidus rubidus, Aporrectodea caliginosa, Aporrectodea rosea and Lumbricus terrestris. On the basis of the new and literature data here we provide the first list of lumbricid earthworms from Sredna Gora Mountain.

  3. Regulation of host metabolism and immunity by the gut microbiome

    DEFF Research Database (Denmark)

    Laursen, Janne Marie

    frequencies of butyrate-producing species associate with various lifestyle-associated disorders. In the present work, we used systems biology approaches to understand how bacterial components may associate with metabolic disease and mediate phenotypic shifts in pro-inflammatory immune cells. First, we...... 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...

  4. The severity of NAFLD is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota

    Science.gov (United States)

    Boursier, Jérôme; Mueller, Olaf; Barret, Matthieu; Machado, Mariana; Fizanne, Lionel; Araujo-Perez, Felix; Guy, Cynthia D.; Seed, Patrick C.; Rawls, John F.; David, Lawrence A.; Hunault, Gilles; Oberti, Frédéric; Calès, Paul; Diehl, Anna Mae

    2016-01-01

    Background & aims Several animal studies have emphasized the role of gut microbiota in non-alcoholic fatty liver disease (NAFLD). However, data about gut dysbiosis in human NAFLD remains scarce in the literature, especially studies including the whole spectrum of NAFLD lesions. We aimed to evaluate the association between gut dysbiosis and severe NAFLD lesions, i.e. non-alcoholic steatohepatitis (NASH) and fibrosis, in a well-characterized population of adult NAFLD. Methods 57 patients with biopsy-proven NAFLD were enrolled. The taxonomic composition of gut microbiota was determined using 16S ribosomal RNA gene sequencing of stool samples. Results 30 patients had F0/1 fibrosis stage at liver biopsy (10 with NASH), and 27 patients had significant F≥2 fibrosis (25 with NASH). Bacteroides abundance was significantly increased in NASH and F≥2 patients, whereas Prevotella abundance was decreased. Ruminococcus abundance was significantly higher in F≥2 patients. By multivariate analysis, Bacteroides abundance was independently associated with NASH and Ruminococcus with F≥2 fibrosis. Stratification according to the abundance of these 2 bacteria generated 3 patient subgroups with increasing severity of NAFLD lesions. Based on imputed metagenomic profiles, KEGG pathways significantly related to NASH and fibrosis F≥2 were mostly related to carbohydrate, lipid, and amino acid metabolism. Conclusion NAFLD severity associates with gut dysbiosis and a shift in metabolic function of the gut microbiota. We identified Bacteroides as independently associated with NASH and Ruminococcus with significant fibrosis. Thus, gut microbiota analysis adds information to classical predictors of NAFLD severity and suggests novel metabolic targets for pre/probiotics therapies. PMID:26600078

  5. Bioprospecting metagenomes: Glycosyl hydrolases for converting biomass

    Energy Technology Data Exchange (ETDEWEB)

    Li, L.; van der Lelie, D.; McCorkle, S. R.; Monchy, S.; Taghavi, S.

    2009-05-18

    Throughout immeasurable time, microorganisms evolved and accumulated remarkable physiological and functional heterogeneity, and now constitute the major reserve for genetic diversity on earth. Using metagenomics, namely genetic material recovered directly from environmental samples, this biogenetic diversification can be accessed without the need to cultivate cells. Accordingly, microbial communities and their metagenomes, isolated from biotopes with high turnover rates of recalcitrant biomass, such as lignocellulosic plant cell walls, have become a major resource for bioprospecting; furthermore, this material is a major asset in the search for new biocatalytics (enzymes) for various industrial processes, including the production of biofuels from plant feedstocks. However, despite the contributions from metagenomics technologies consequent upon the discovery of novel enzymes, this relatively new enterprise requires major improvements. In this review, we compare function-based metagenome screening and sequence-based metagenome data mining, discussing the advantages and limitations of both methods. We also describe the unusual enzymes discovered via metagenomics approaches, and discuss the future prospects for metagenome technologies.

  6. Bioprospecting metagenomes: glycosyl hydrolases for converting biomass

    Directory of Open Access Journals (Sweden)

    Monchy Sebastien

    2009-05-01

    Full Text Available Abstract Throughout immeasurable time, microorganisms evolved and accumulated remarkable physiological and functional heterogeneity, and now constitute the major reserve for genetic diversity on earth. Using metagenomics, namely genetic material recovered directly from environmental samples, this biogenetic diversification can be accessed without the need to cultivate cells. Accordingly, microbial communities and their metagenomes, isolated from biotopes with high turnover rates of recalcitrant biomass, such as lignocellulosic plant cell walls, have become a major resource for bioprospecting; furthermore, this material is a major asset in the search for new biocatalytics (enzymes for various industrial processes, including the production of biofuels from plant feedstocks. However, despite the contributions from metagenomics technologies consequent upon the discovery of novel enzymes, this relatively new enterprise requires major improvements. In this review, we compare function-based metagenome screening and sequence-based metagenome data mining, discussing the advantages and limitations of both methods. We also describe the unusual enzymes discovered via metagenomics approaches, and discuss the future prospects for metagenome technologies.

  7. Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, Alison L [ORNL; Cantarel, Brandi [University of Maryland School of Medicine, The, Baltimore, MD; Lamendella, Regina [Lawrence Berkeley National Laboratory (LBNL); Darzi, Youssef [Vrije Universiteit Brussel, Brussels, Belgium; Mongodin, Emmanuel [University of Maryland School of Medicine, The, Baltimore, MD; Pan, Chongle [ORNL; Shah, Manesh B [ORNL; Halfvarsson, J [Orebro University Hospital, Orebro, Sweden; Tysk, C [Orebro University Hospital, Orebro, Sweden; Henrissat, Bernard [Universite d' Aix-Marseille I & II; Raes, Jeroen [Vrije Universiteit Brussel, Brussels, Belgium; Verberkmoes, Nathan C [ORNL; Fraser-Liggett, C [University of Maryland; Hettich, Robert {Bob} L [ORNL; Jansson, Janet [Lawrence Berkeley National Laboratory (LBNL)

    2012-01-01

    Crohn's disease (CD) is an inflammatory bowel disease of complex etiology, although dysbiosis of the gut microbiota has been implicated in chronic immune-mediated inflammation associated with CD. Here we combined shotgun metagenomic and metaproteomic approaches to identify potential functional signatures of CD in stool samples from six twin pairs that were either healthy, or that had CD in the ileum (ICD) or colon (CCD). Integration of these omics approaches revealed several genes, proteins, and pathways that primarily differentiated ICD from healthy subjects, including depletion of many proteins in ICD. In addition, the ICD phenotype was associated with alterations in bacterial carbohydrate metabolism, bacterial-host interactions, as well as human host-secreted enzymes. This eco-systems biology approach underscores the link between the gut microbiota and functional alterations in the pathophysiology of Crohn's disease and aids in identification of novel diagnostic targets and disease specific biomarkers.

  8. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease.

    Directory of Open Access Journals (Sweden)

    Alison R Erickson

    Full Text Available Crohn's disease (CD is an inflammatory bowel disease of complex etiology, although dysbiosis of the gut microbiota has been implicated in chronic immune-mediated inflammation associated with CD. Here we combined shotgun metagenomic and metaproteomic approaches to identify potential functional signatures of CD in stool samples from six twin pairs that were either healthy, or that had CD in the ileum (ICD or colon (CCD. Integration of these omics approaches revealed several genes, proteins, and pathways that primarily differentiated ICD from healthy subjects, including depletion of many proteins in ICD. In addition, the ICD phenotype was associated with alterations in bacterial carbohydrate metabolism, bacterial-host interactions, as well as human host-secreted enzymes. This eco-systems biology approach underscores the link between the gut microbiota and functional alterations in the pathophysiology of Crohn's disease and aids in identification of novel diagnostic targets and disease specific biomarkers.

  9. Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons.

    Science.gov (United States)

    Cao, Hong-Tai; Gibson, Travis E; Bashan, Amir; Liu, Yang-Yu

    2017-02-01

    The human gut microbiota is a very complex and dynamic ecosystem that plays a crucial role in health and well-being. Inferring microbial community structure and dynamics directly from time-resolved metagenomics data is key to understanding the community ecology and predicting its temporal behavior. Many methods have been proposed to perform the inference. Yet, as we point out in this review, there are several pitfalls along the way. Indeed, the uninformative temporal measurements and the compositional nature of the relative abundance data raise serious challenges in inference. Moreover, the inference results can be largely distorted when only focusing on highly abundant species by ignoring or grouping low-abundance species. Finally, the implicit assumptions in various regularization methods may not reflect reality. Those issues have to be seriously considered in ecological modeling of human gut microbiota. © 2016 WILEY Periodicals, Inc.

  10. Metagenomics and future perspectives in virus discovery.

    Science.gov (United States)

    Mokili, John L; Rohwer, Forest; Dutilh, Bas E

    2012-02-01

    Monitoring the emergence and re-emergence of viral diseases with the goal of containing the spread of viral agents requires both adequate preparedness and quick response. Identifying the causative agent of a new epidemic is one of the most important steps for effective response to disease outbreaks. Traditionally, virus discovery required propagation of the virus in cell culture, a proven technique responsible for the identification of the vast majority of viruses known to date. However, many viruses cannot be easily propagated in cell culture, thus limiting our knowledge of viruses. Viral metagenomic analyses of environmental samples suggest that the field of virology has explored less than 1% of the extant viral diversity. In the last decade, the culture-independent and sequence-independent metagenomic approach has permitted the discovery of many viruses in a wide range of samples. Phylogenetically, some of these viruses are distantly related to previously discovered viruses. In addition, 60-99% of the sequences generated in different viral metagenomic studies are not homologous to known viruses. In this review, we discuss the advances in the area of viral metagenomics during the last decade and their relevance to virus discovery, clinical microbiology and public health. We discuss the potential of metagenomics for characterization of the normal viral population in a healthy community and identification of viruses that could pose a threat to humans through zoonosis. In addition, we propose a new model of the Koch's postulates named the 'Metagenomic Koch's Postulates'. Unlike the original Koch's postulates and the Molecular Koch's postulates as formulated by Falkow, the metagenomic Koch's postulates focus on the identification of metagenomic traits in disease cases. The metagenomic traits that can be traced after healthy individuals have been exposed to the source of the suspected pathogen. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. Earthworms accumulate alanine in response to drought.

    Science.gov (United States)

    Holmstrup, Martin; Slotsbo, Stine; Henriksen, Per G; Bayley, Mark

    2016-09-01

    Earthworms have ecologically significant functions in tropical and temperate ecosystems and it is therefore important to understand how these animals survive during drought. In order to explore the physiological responses to dry conditions, we simulated a natural drought incident in a laboratory trial exposing worms in slowly drying soil for about one month, and then analyzed the whole-body contents of free amino acids (FAAs). We investigated three species forming estivation chambers when soils dry out (Aporrectodea tuberculata, Aporrectodea icterica and Aporrectodea longa) and one species that does not estivate during drought (Lumbricus rubellus). Worms subjected to drought conditions (Aporrectodea species and 300μmolg(-1) dry weight in L. rubellus. Proline was only weakly upregulated in some species as were a few other FAAs. Species forming estivation chambers (Aporrectodea spp.) did not show a better ability to conserve body water than the non-estivating species (L. rubellus) at the same drought level. These results suggest that the accumulation of alanine is an important adaptive trait in drought tolerance of earthworms in general. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Metals and terrestrial earthworms (Annelida: Oligochaeta)

    Science.gov (United States)

    Beyer, W.N.

    1981-01-01

    The toxicity of metals to earthworms and the residues of metals found in earthworms are reviewed. Meta 1 concentrations are rarely high enough to be toxic to worms, but copper may reduce populations in orchards heavily treated with fungicides and in soil contaminated with pig wastes. The metals in some industrial sewage sludges may interfere with using sludge in vermiculture. Storage ratios (the concentration of a metal in worms divided by the concentration in soil) tend to be highest in infertile soil and lowest in media rich in organic matter, such as sewage sludge. Cadmium, gold, and selenium are highly concentrated by worms. Lead concentrations in worms may be very high, but are generally lower than concentrations in soil. Body burdens of both copper and zinc seem to be regulated by worms. Because worms are part of the food webs of many wildlife species, and also because they are potentially valuable feed supplements for domestic animals, the possible toxic effects of cadmium and other metals should be studied. Worms can make metals more available to food webs and can redistribute them in soil.

  13. Glutathione S-transferases in earthworms (Lumbricidae).

    Science.gov (United States)

    Stenersen, J; Guthenberg, C; Mannervik, B

    1979-01-01

    Glutathione S-transferase activity (EC 2.5.1.18) was demonstrated in six species of earthworms of the family Lumbricidae: Eisenia foetida, Lumbricus terrestris, Lumbricus rebellus, Allolobophora longa, Allolobophora caliginosa and Allolobophora chlorotica. Considerable activity was obtained with 1-chlorl-2,4-dinitrobenzene and low activity with 3,4-dichloro-1-nitrobenzene, but no enzymic reaction was detectable with sulphobromophthalein 1,2-epoxy-3-(p-nitrophenoxy)propane of trans-4-phenylbut-3-en-2-one as substrates. Enzyme prepartations from L. rubellus and A. longa were the most active, whereas A. chlorotica gave the lowest activity. The ratio of the activities obtained with 1-chloro-2,4-dinitrobenzene and 3,4-cichloro-1-nitrobenzene was very different in the various species, but no phylogenetic pattern was evident. Isoelectric focusing gave rise to various activity peaks as measured with 1-chloro-2,4-dinitrobenzene as a substrate, and the activity profiles of the species examined appeared to follow a taxonomic pattern. The activity of Allolobophora had the highest peak in the alkaline region, whereas that of Lumbricus had the highest peak in the acid region. Eisenia showed a very complex activity profile, with the highest peak ne pH 7. As determined by an enzymic assay, all the species contained glutathione, on an average about 0.5 mumol/g wet wt. Conjugation with glutathione catalysed by glutathione S-transferases may consequently be an important detoxification mechanism in earthworms. PMID:486159

  14. Human gut microbiota: repertoire and variations.

    Science.gov (United States)

    Lagier, Jean-Christophe; Million, Matthieu; Hugon, Perrine; Armougom, Fabrice; Raoult, Didier

    2012-01-01

    The composition of human gut microbiota and their relationship with the host and, consequently, with human health and disease, presents several challenges to microbiologists. Originally dominated by culture-dependent methods for exploring this ecosystem, the advent of molecular tools has revolutionized our ability to investigate these relationships. However, many biases that have led to contradictory results have been identified. Microbial culturomics, a recent concept based on a use of several culture conditions with identification by MALDI-TOF followed by the genome sequencing of the new species cultured had allowed a complementarity with metagenomics. Culturomics allowed to isolate 31 new bacterial species, the largest human virus, the largest bacteria, and the largest Archaea from human. Moreover, some members of this ecosystem, such as Eukaryotes, giant viruses, Archaea, and Planctomycetes, have been neglected by the majority of studies. In addition, numerous factors, such as age, geographic provenance, dietary habits, antibiotics, or probiotics, can influence the composition of the microbiota. Finally, in addition to the countless biases associated with the study techniques, a considerable limitation to the interpretation of studies of human gut microbiota is associated with funding sources and transparency disclosures. In the future, studies independent of food industry funding and using complementary methods from a broad range of both culture-based and molecular tools will increase our knowledge of the repertoire of this complex ecosystem and host-microbiota mutualism.

  15. Gut microbiota, host gene expression, and aging.

    Science.gov (United States)

    Patrignani, Paola; Tacconelli, Stefania; Bruno, Annalisa

    2014-01-01

    Novel concepts of disease susceptibility and development suggest an important role of gastrointestinal microbiota and microbial pathogens. They can contribute to physiological systems and disease processes, even outside of the gastrointestinal tract. There is increasing evidence that genetics of the host influence and interact with gut microbiota. Moreover, aging-associated oxidative stress may cause morphologic alterations of bacterial cells, thus influencing the aggressive potential and virulence markers of an anaerobic bacterium and finally the type of interaction with the host. At the same time, microbiota may influence host gene expression and it is becoming apparent that it may occur through the regulation of microRNAs. They are short single-stranded noncoding RNAs that regulate posttranscriptional gene expression by affecting mRNA stability and/or translational repression of their target mRNAs. The introduction of -omics approaches (such as metagenomics, metaproteomics, and metatranscriptomics) in microbiota research will certainly advance our knowledge of this area. This will lead to greatly deepen our understanding of the molecular targets in the homeostatic interaction between the gut microbiota and the host and, thereby, promises to reveal new ways to treat diseases and maintain health.

  16. Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice

    Science.gov (United States)

    Li, Jun; Sung, Cecilia Ying Ju; Lee, Nikki; Ni, Yueqiong; Pihlajamäki, Jussi; Panagiotou, Gianni; El-Nezami, Hani

    2016-01-01

    The beneficial roles of probiotics in lowering the gastrointestinal inflammation and preventing colorectal cancer have been frequently demonstrated, but their immunomodulatory effects and mechanism in suppressing the growth of extraintestinal tumors remain unexplored. Here, we adopted a mouse model and metagenome sequencing to investigate the efficacy of probiotic feeding in controlling s.c. hepatocellular carcinoma (HCC) and the underlying mechanism suppressing the tumor progression. Our result demonstrated that Prohep, a novel probiotic mixture, slows down the tumor growth significantly and reduces the tumor size and weight by 40% compared with the control. From a mechanistic point of view the down-regulated IL-17 cytokine and its major producer Th17 cells, whose levels decreased drastically, played critical roles in tumor reduction upon probiotics feeding. Cell staining illustrated that the reduced Th17 cells in the tumor of the probiotic-treated group is mainly caused by the reduced frequency of migratory Th17 cells from the intestine and peripheral blood. In addition, shotgun-metagenome sequencing revealed the crosstalk between gut microbial metabolites and the HCC development. Probiotics shifted the gut microbial community toward certain beneficial bacteria, including Prevotella and Oscillibacter, that are known producers of antiinflammatory metabolites, which subsequently reduced the Th17 polarization and promoted the differentiation of antiinflammatory Treg/Tr1 cells in the gut. Overall, our study offers novel insights into the mechanism by which probiotic treatment modulates the microbiota and influences the regulation of the T-cell differentiation in the gut, which in turn alters the level of the proinflammatory cytokines in the extraintestinal tumor microenvironment. PMID:26884164

  17. EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.

    Science.gov (United States)

    Hunter, Sarah; Corbett, Matthew; Denise, Hubert; Fraser, Matthew; Gonzalez-Beltran, Alejandra; Hunter, Christopher; Jones, Philip; Leinonen, Rasko; McAnulla, Craig; Maguire, Eamonn; Maslen, John; Mitchell, Alex; Nuka, Gift; Oisel, Arnaud; Pesseat, Sebastien; Radhakrishnan, Rajesh; Rocca-Serra, Philippe; Scheremetjew, Maxim; Sterk, Peter; Vaughan, Daniel; Cochrane, Guy; Field, Dawn; Sansone, Susanna-Assunta

    2014-01-01

    Metagenomics is a relatively recently established but rapidly expanding field that uses high-throughput next-generation sequencing technologies to characterize the microbial communities inhabiting different ecosystems (including oceans, lakes, soil, tundra, plants and body sites). Metagenomics brings with it a number of challenges, including the management, analysis, storage and sharing of data. In response to these challenges, we have developed a new metagenomics resource (http://www.ebi.ac.uk/metagenomics/) that allows users to easily submit raw nucleotide reads for functional and taxonomic analysis by a state-of-the-art pipeline, and have them automatically stored (together with descriptive, standards-compliant metadata) in the European Nucleotide Archive.

  18. Gut-brain axis

    NARCIS (Netherlands)

    Romijn, Johannes A.; Corssmit, Eleonora P.; Havekes, Louis M.; Pijl, Hanno

    2008-01-01

    To summarize recent studies on the regulation and the functions of the gut-brain axis. Visual cues of food and food intake interact with the gut-brain axis at the level of the hypothalamus. However, the hypothalamic response to glucose intake is considerably altered in patients with type 2 diabetes

  19. Avoidance of Ag nanoparticles by earthworms, Eisenia fetida

    DEFF Research Database (Denmark)

    Mariyadas, Jennifer; Mónica, Amorim; Scott-Fordsmand, Janeck James

    2013-01-01

    Earthworms are key sentinel organisms playing an important role in improving the soil structure. Here we tested the avoidance behaviour of earthworms, Eisenia fetida to silver nanoparticles (Ag NPs). Silver nanoparticles are widely used in a range of consumer products mainly as antibacterial agents...... and thus causes potential risk to the environment once these particles are released into the environment [1]. In our tests, we were able to show that the earthworms avoided commercially fabricated silver nanoparticles in a dose and time dependent manner. The earthworms were exposed to 3 nanoparticles: NM......300K, Ag (PVP Coated), Ag (Non Coated) and a soluble salt AgNO3; the avoidance behaviour was noted for different time intervals. Immediate avoidance at 24 hours was observed for the highest concentrations for all the test substances. And, periodical avoidance was observed for other concentrations...

  20. Checklist of the earthworm fauna of Croatia (Oligochaeta: Lumbricidae).

    Science.gov (United States)

    Kutuzović, Davorka Hackenberger; Kutuzović, Branimir Hackenberger

    2013-01-01

    A checklist of the Croatian earthworm fauna (Oligochaeta: Lumbricidae) is presented, including published records and authors' personal data. This is the first checklist for Croatia only, with comprehensive information for each earthworm species regarding ecological category, habitat, distribution type and distribution in Croatia. The currently known earthworm fauna of Croatia comprises 68 species belonging to 17 genera, with Octodrilus being the species-richest genus (15 species). Chorologically these species can be allocated to 13 different types of distribution. Nineteen species are endemic of which 10 species are endemic to Croatia and 9 species are endemic to Croatia and neighbouring countries (Italy, Slovenia, Hungary, and Montenegro). The endemic earthworms are distributed in the areas of higher altitudes in the Continental and Alpine biogeographic region, mostly covered with forest or autochtonous vegetation.

  1. Descriptions of two new earthworm species, Iridodrilus abujaensis ...

    African Journals Online (AJOL)

    Two new eudriline earthworm species, Iridodrilus abujaensis and Iridodrilus furcothecata are described from collections made around the Federal Capital Territory and Wukari, Nigeria. They are distinguished by the forms of their external papillae, seminal vesicles, ovospermathecal systems and other characters.

  2. Human distal gut microbiome.

    Science.gov (United States)

    Marchesi, Julian R

    2011-12-01

    The distal gut and its associated microbiota is a new frontier in the quest to understand human biology and evolution. The renaissance in this field has been partly driven by advances in sequencing technology and also by the application of a variety of 'omic' technologies in a systems biology framework. In the initial stages of understanding what constitutes the gut, culture-independent methods, primarily inventories of 16S rRNA genes, have provided a clear view of the main taxonomic groups of Bacteria in the distal gut and we are now moving towards defining the functions that reside in the distal gut microbiome. This review will explore recent advances in the area of the distal gut and the use of a variety of omic approaches to determine what constitutes this fascinating collection of microbes. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  3. Earthworms lost from pesticides application in potato crops

    Science.gov (United States)

    Garcia-Santos, Glenda; Forrer, Karin; Binder, Claudia R.

    2010-05-01

    Bioturbation from earthworm's activity contributes to soil creep and soil carbon dynamics, and provide enough aeration conditions for agricultural practices all over the world. In developing countries where there is a long term misuse of pesticides for agricultural purposes, lost of these benefits from earthworms activity might already yielded negative effects in the current crop production. Little research has been performed on earthworms avoidance to pesticides in developing countries located in the tropics. Furthermore, the complete avoidance reaction (from attraction to 100% avoidance) from earthworms to most of the pesticides used in potato cultivation in developing countries like Colombia is incomplete as yet. Hence the aim of this study is to assess the lost of earthworm on the soils caused by different concentrations of pesticides and associated agricultural impacts caused by a lost in the soil bioturbation. As a first stage, we have studied earthworm's avoidance to pesticide concentration in a potato agricultural area located in Colombia. Local cultivated Eisenia fetida were exposed to four of the most frequent applied active ingredients in potato crops i.e. carbofuran, mancozeb, methamidophos and chlorpyriphos. Adult earthworm toxicity experiments were carried out in two soils, untreated grasslands under standard (ISO guidelines) and undisturbed conditions, and exposed to six different concentrations of the active ingredients. The results of the avoidance reaction on the standard soils were significant for carbofuran, mancoceb and chlorpyrifos. For each of the three active ingredients, we found i) overuse of pesticide, ii) applied dose of carbofuran, mancoceb and chlorpyrifos by the farmers potentially caused 20%, 11% and 9% of earthworms avoidance on the cultivated soils, respectively.

  4. Toward Accurate and Quantitative Comparative Metagenomics.

    Science.gov (United States)

    Nayfach, Stephen; Pollard, Katherine S

    2016-08-25

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. [Pathology and viral metagenomics, a recent history].

    Science.gov (United States)

    Bernardo, Pauline; Albina, Emmanuel; Eloit, Marc; Roumagnac, Philippe

    2013-05-01

    Human, animal and plant viral diseases have greatly benefited from recent metagenomics developments. Viral metagenomics is a culture-independent approach used to investigate the complete viral genetic populations of a sample. During the last decade, metagenomics concepts and techniques that were first used by ecologists progressively spread into the scientific field of viral pathology. The sample, which was first for ecologists a fraction of ecosystem, became for pathologists an organism that hosts millions of microbes and viruses. This new approach, providing without a priori high resolution qualitative and quantitative data on the viral diversity, is now revolutionizing the way pathologists decipher viral diseases. This review describes the very last improvements of the high throughput next generation sequencing methods and discusses the applications of viral metagenomics in viral pathology, including discovery of novel viruses, viral surveillance and diagnostic, large-scale molecular epidemiology, and viral evolution. © 2013 médecine/sciences – Inserm.

  6. Comparative metagenomics of the Red Sea

    KAUST Repository

    Mineta, Katsuhiko

    2016-01-26

    Metagenome produces a tremendous amount of data that comes from the organisms living in the environments. This big data enables us to examine not only microbial genes but also the community structure, interaction and adaptation mechanisms at the specific location and condition. The Red Sea has several unique characteristics such as high salinity, high temperature and low nutrition. These features must contribute to form the unique microbial community during the evolutionary process. Since 2014, we started monthly samplings of the metagenomes in the Red Sea under KAUST-CCF project. In collaboration with Kitasato University, we also collected the metagenome data from the ocean in Japan, which shows contrasting features to the Red Sea. Therefore, the comparative metagenomics of those data provides a comprehensive view of the Red Sea microbes, leading to identify key microbes, genes and networks related to those environmental differences.

  7. Tapping uncultured microorganisms through metagenomics for drug ...

    African Journals Online (AJOL)

    Tapping uncultured microorganisms through metagenomics for drug discovery. Abdelnasser Salah Shebl Ibrahim, Ali Abdullah Al-Salamah, Ashraf A Hatamleh, Mohammed S El-Shiekh, Shebl Salah S Ibrahim ...

  8. Effects of taurine on gut microbiota and metabolism in mice.

    Science.gov (United States)

    Yu, Haining; Guo, Zhengzhao; Shen, Shengrong; Shan, Weiguang

    2016-07-01

    As being a necessary amino acid, taurine plays an important role in the regulation of neuroendocrine functions and nutrition. In this study, effects of taurine on mice gut microbes and metabolism were investigated. BALB/C mice were randomly divided into three experimental groups: The first group was administered saline (CK), the second was administered 165 mg/kg natural taurine (NE) and the third one administered 165 mg/kg synthetic taurine (CS). Gut microbiota composition in mice feces was analyzed by metagenomics technology, and the content of short-chain fatty acids (SCFA) in mice feces was detected by gas chromatography (GC), while the concentrations of lipopolysaccharide (LPS) and superoxide dismutase (SOD) were detected by a LPS ELISA kit and a SOD assay kit, respectively. The results showed that the effect of taurine on gut microbiota could reduce the abundance of Proteobacteria, especially Helicobacter. Moreover, we found that the SCFA content was increased in feces of the NE group while LPS content was decreased in serum of the NE group; the SOD activity in serum and livers of the NE and CS groups were not changed significantly compare to that of the CK group. In conclusion, taurine could regulate the gut micro-ecology, which might be of benefit to health by inhibiting the growth of harmful bacteria, accelerating the production of SCFA and reducing LPS concentration.

  9. Gut Microbiota and Host Reaction in Liver Diseases

    Directory of Open Access Journals (Sweden)

    Hiroshi Fukui

    2015-10-01

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

  10. Earthworm dispersal assay for rapidly evaluating soil quality.

    Science.gov (United States)

    Kim, Shin Woong; Kim, Dokyung; Moon, Jongmin; Chae, Yooeun; Kwak, Jin Il; Park, Younsu; Jeong, Seung-Woo; An, Youn-Joo

    2017-10-01

    Earthworms enhance soil functioning and are therefore key species in the soil. Their presence is generally a positive sign for a terrestrial ecosystem, because these species serve as important biomarkers in soil quality evaluations. We describe a novel bioassay, the "dispersal assay," that is a simple and rapid technique for field-based soil quality evaluations. It is based on the premise that earthworms prefer optimal soils if given the choice. Thus, assay tubes containing a reference soil were inserted in target sites, and earthworms were placed into these tubes. According to their soil preference, the earthworms dispersed into the surrounding soil, remained in the initial soil within the tubes, avoided both by crawling up the tube, or died. Furthermore, sensitivity responses to metal concentrations, electrical conductivity, and soil pH were observed in field tests. Although the dispersal assay did not completely match traditional toxicity endpoints such as earthworm survival, we found that it can serve as an in situ screening test for assessing soil quality. Overall, our dispersal assay was relatively rapid (within 24 h), had low levels of variation, and showed high correlations between earthworm behavior and soil physicochemical properties. Environ Toxicol Chem 2017;36:2766-2772. © 2017 SETAC. © 2017 SETAC.

  11. Toxicity and bioaccumulation of ethofumesate enantiomers in earthworm Eisenia fetida.

    Science.gov (United States)

    Xu, Peng; Wang, Yinghuan; Zhang, Yanfeng; Li, Jianzhong; Wang, Huili

    2014-10-01

    Earthworms represent an important food source for many vertebrates and as a result, predators may encounter toxic effects via the food chain from consumption of contaminated worms. Therefore, including an assessment of xenobiotic to worms in risk assessment procedures is advisable. Here we studied the acute toxicity, bioaccumulation and elimination of ethofumesate enantiomers in earthworm, Eisenia fetida, in a soil. A slight difference in toxicity to earthworm between two enantiomers was found, and the calculated LC50 values for (+)-, rac- and (-)-ethofumesate were 4.51, 5.93 and 7.98 μg/cm(2), respectively, indicating that the acute toxicity of ethofumesate enantiomers was enantioselective. Earthworm can uptake ethofumesate but the bioaccumulation curve did not reach the steady state. In the elimination experiment, the concentrations of ethofumesate in earthworm declined following a first-order decay model with a short half life of 1.8d. The bioaccumulation and elimination of ethofumesate in earthworm were both nonenantioselective. In combination with other studies, a linear relationship between Log BSAFs and Log Kow was observed, and the Log BSAFs increased with increasing Log Kow. But the elimination rate did not show any correlation with the Kow value. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.

    Science.gov (United States)

    Lluch, Jérôme; Servant, Florence; Païssé, Sandrine; Valle, Carine; Valière, Sophie; Kuchly, Claire; Vilchez, Gaëlle; Donnadieu, Cécile; Courtney, Michael; Burcelin, Rémy; Amar, Jacques; Bouchez, Olivier; Lelouvier, Benjamin

    2015-01-01

    Substantial progress in high-throughput metagenomic sequencing methodologies has enabled the characterisation of bacteria from various origins (for example gut and skin). However, the recently-discovered bacterial microbiota present within animal internal tissues has remained unexplored due to technical difficulties associated with these challenging samples. We have optimized a specific 16S rDNA-targeted metagenomics sequencing (16S metabarcoding) pipeline based on the Illumina MiSeq technology for the analysis of bacterial DNA in human and animal tissues. This was successfully achieved in various mouse tissues despite the high abundance of eukaryotic DNA and PCR inhibitors in these samples. We extensively tested this pipeline on mock communities, negative controls, positive controls and tissues and demonstrated the presence of novel tissue specific bacterial DNA profiles in a variety of organs (including brain, muscle, adipose tissue, liver and heart). The high throughput and excellent reproducibility of the method ensured exhaustive and precise coverage of the 16S rDNA bacterial variants present in mouse tissues. This optimized 16S metagenomic sequencing pipeline will allow the scientific community to catalogue the bacterial DNA profiles of different tissues and will provide a database to analyse host/bacterial interactions in relation to homeostasis and disease.

  13. The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.

    Directory of Open Access Journals (Sweden)

    Jérôme Lluch

    Full Text Available Substantial progress in high-throughput metagenomic sequencing methodologies has enabled the characterisation of bacteria from various origins (for example gut and skin. However, the recently-discovered bacterial microbiota present within animal internal tissues has remained unexplored due to technical difficulties associated with these challenging samples.We have optimized a specific 16S rDNA-targeted metagenomics sequencing (16S metabarcoding pipeline based on the Illumina MiSeq technology for the analysis of bacterial DNA in human and animal tissues. This was successfully achieved in various mouse tissues despite the high abundance of eukaryotic DNA and PCR inhibitors in these samples. We extensively tested this pipeline on mock communities, negative controls, positive controls and tissues and demonstrated the presence of novel tissue specific bacterial DNA profiles in a variety of organs (including brain, muscle, adipose tissue, liver and heart.The high throughput and excellent reproducibility of the method ensured exhaustive and precise coverage of the 16S rDNA bacterial variants present in mouse tissues. This optimized 16S metagenomic sequencing pipeline will allow the scientific community to catalogue the bacterial DNA profiles of different tissues and will provide a database to analyse host/bacterial interactions in relation to homeostasis and disease.

  14. Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema.

    Directory of Open Access Journals (Sweden)

    Seungdae Oh

    Full Text Available Gut microbiota play an important role in human immunological processes, potentially affecting allergic diseases such as eczema. The diversity and structure of gut microbiota in infants with eczema have been previously documented. This study aims to evaluate by comparative metagenomics differences in genetic content in gut microbiota of infants with eczema and their matched controls. Stools were collected at the age of one month old from twelve infants from an at risk birth cohort in a case control manner. Clinical follow up for atopic outcomes were carried out at the age of 12 and 24 months. Microbial genomic DNA were extracted from stool samples and used for shotgun sequencing. Comparative metagenomic analysis showed that immune-regulatory TCAAGCTTGA motifs were significantly enriched in the six healthy controls (C communities compared to the six eczema subjects (E, with many encoded by Bifidobacterium (38% of the total motifs in the C communities. Draft genomes of five Bifidobacterium species populations (B. longum, B. bifidum, B. breve, B. dentium, and B. pseudocatenulatum were recovered from metagenomic datasets. The B. longum BFN-121-2 genome encoded more TCAAGCTTGA motifs (4.2 copies per one million genome sequence than other Bifidobacterium genomes. Additionally, the communities in the stool of controls (C were also significantly enriched in functions associated with tetrapyrrole biosynthesis compared to those of eczema (E. Our results show distinct immune-modulatory genomic properties of gut microbiota in infants associated with eczema and provide new insights into potential role of gut microbiota in affecting human immune homeostasis.

  15. Changes in the Functional Potential of the Gut Microbiome Following Probiotic Supplementation during Helicobacter Pylori Treatment.

    Science.gov (United States)

    Oh, Bumjo; Kim, Ji Won; Kim, Bong-Soo

    2016-12-01

    Probiotic supplementation is utilized to alleviate the side effects associated with antibiotic therapy for Helicobacter pylori infection. Several studies have described the effects of administration of probiotics on the gut microbiota during antibiotic therapy. However, most of these studies have focused on specific bacteria, thereby providing limited information on the functional roles of the altered microbiota. Therefore, we examined the impact of probiotic supplementation on the structure and functional dynamics of the gut microbiota during H. pylori eradication, using whole-metagenomic sequence analysis. Subjects were divided into two groups: the antibiotics group, which received only antibiotics, and the probiotics group, which received antibiotics with probiotic supplementation. The structural and functional profiles of gut microbiota was analyzed using metagenomic DNA extracted from the feces during treatment by Illumina MiSeq system. The overall alterations in microbiota, as revealed by whole metagenome sequencing, were similar with results from our previous 16S rRNA gene-based analysis. The proportional shift in functional gene families was greater in the antibiotics group than in the probiotics group. In particular, the proportion of genes related to selenocompound metabolism was reduced in the probiotics group, whereas genes associated with the metabolism of nucleotide sugars were increased. The functional alterations of gut microbiota may link to the reduction in intestinal irritation and maintenance of bacterial diversity observed following probiotic supplementation with antibiotic therapy. The potential beneficial roles of altered gut microbiota following probiotic supplementation are expected a reduction in side effects such as intestinal irritation and antibiotics resistance. © 2016 John Wiley & Sons Ltd.

  16. Individuality and temporal stability of the human gut microbiome

    Directory of Open Access Journals (Sweden)

    Shinichi Sunagawa

    2014-03-01

    Full Text Available Introduction: The breakthrough of next generation sequencing-technologies has enabled large-scale studies of natural microbial communities and the 16S rRNA genes have been widely used as a phylogenetic marker to study community structure. However, major limitations of this approach are that neither strain-level resolution nor genomic context of microorganisms can be provided. This information, however, is crucial to answer fundamental questions about the temporal stability and distinctiveness of natural microbial communities.Material and methods: We developed a methodological framework for metagenomic single nucleotide polymorphism (SNP variation analysis and applied it to publicly available data from 252 human fecal samples from 207 European and North American individuals. We further analyzed samples from 43 healthy subjects that were sampled at least twice over time intervals of up to one year and measured population similarities of dominant gut species.Results: We detected 10.3 million SNPs in 101 species, which nearly amounts to the number identified in more than 1,000 humans. Conclusion: The most striking result was that host-specific strains appear to be retained over long time periods. This indicates that individual-specific strains are not easily exchanged with the environment and furthermore, that an individuals appear to have a unique metagenomic genotype. This, in turn, is linked to implications for human gut physiology, such as the stability of antibiotic resistance potential.

  17. Metagenomics insights into food fermentations.

    Science.gov (United States)

    De Filippis, Francesca; Parente, Eugenio; Ercolini, Danilo

    2017-01-01

    This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High-throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

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

    Directory of Open Access Journals (Sweden)

    Xuemei Li

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

  19. Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut

    Science.gov (United States)

    Milani, Christian; Andrea Lugli, Gabriele; Duranti, Sabrina; Turroni, Francesca; Mancabelli, Leonardo; Ferrario, Chiara; Mangifesta, Marta; Hevia, Arancha; Viappiani, Alice; Scholz, Matthias; Arioli, Stefania; Sanchez, Borja; Lane, Jonathan; Ward, Doyle V.; Hickey, Rita; Mora, Diego; Segata, Nicola; Margolles, Abelardo; van Sinderen, Douwe; Ventura, Marco

    2015-01-01

    Bifidobacteria are common and frequently dominant members of the gut microbiota of many animals, including mammals and insects. Carbohydrates are considered key carbon sources for the gut microbiota, imposing strong selective pressure on the complex microbial consortium of the gut. Despite its importance, the genetic traits that facilitate carbohydrate utilization by gut microbiota members are still poorly characterized. Here, genome analyses of 47 representative Bifidobacterium (sub)species revealed the genes predicted to be required for the degradation and internalization of a wide range of carbohydrates, outnumbering those found in many other gut microbiota members. The glycan-degrading abilities of bifidobacteria are believed to reflect available carbon sources in the mammalian gut. Furthermore, transcriptome profiling of bifidobacterial genomes supported the involvement of various chromosomal loci in glycan metabolism. The widespread occurrence of bifidobacterial saccharolytic features is in line with metagenomic and metatranscriptomic datasets obtained from human adult/infant faecal samples, thereby supporting the notion that bifidobacteria expand the human glycobiome. This study also underscores the hypothesis of saccharidic resource sharing among bifidobacteria through species-specific metabolic specialization and cross feeding, thereby forging trophic relationships between members of the gut microbiota. PMID:26506949

  20. Gut Microbiota Contributes to the Growth of Fast-Growing Transgenic Common Carp (Cyprinus carpio L.)

    Science.gov (United States)

    Xie, Shouqi; Hu, Wei; Yu, Yuhe; Hu, Zihua

    2013-01-01

    Gut microbiota has shown tight and coordinated connection with various functions of its host such as metabolism, immunity, energy utilization, and health maintenance. To gain insight into whether gut microbes affect the metabolism of fish, we employed fast-growing transgenic common carp (Cyprinus carpio L.) to study the connections between its large body feature and gut microbes. Metagenome-based fingerprinting and high-throughput sequencing on bacterial 16S rRNA genes indicated that fish gut was dominated by Proteobacteria, Fusobacteria, Bacteroidetes and Firmicutes, which displayed significant differences between transgenic fish and wild-type controls. Analyses to study the association of gut microbes with the fish metabolism discovered three major phyla having significant relationships with the host metabolic factors. Biochemical and histological analyses indicated transgenic fish had increased carbohydrate but decreased lipid metabolisms. Additionally, transgenic fish has a significantly lower Bacteroidetes:Firmicutes ratio than that of wild-type controls, which is similar to mammals between obese and lean individuals. These findings suggest that gut microbiotas are associated with the growth of fast growing transgenic fish, and the relative abundance of Firmicutes over Bacteroidetes could be one of the factors contributing to its fast growth. Since the large body size of transgenic fish displays a proportional body growth, which is unlike obesity in human, the results together with the findings from others also suggest that the link between obesity and gut microbiota is likely more complex than a simple Bacteroidetes:Firmicutes ratio change. PMID:23741344

  1. MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota.

    Science.gov (United States)

    Zhang, Xu; Ning, Zhibin; Mayne, Janice; Moore, Jasmine I; Li, Jennifer; Butcher, James; Deeke, Shelley Ann; Chen, Rui; Chiang, Cheng-Kang; Wen, Ming; Mack, David; Stintzi, Alain; Figeys, Daniel

    2016-06-24

    The gut microbiota has been shown to be closely associated with human health and disease. While next-generation sequencing can be readily used to profile the microbiota taxonomy and metabolic potential, metaproteomics is better suited for deciphering microbial biological activities. However, the application of gut metaproteomics has largely been limited due to the low efficiency of protein identification. Thus, a high-performance and easy-to-implement gut metaproteomic approach is required. In this study, we developed a high-performance and universal workflow for gut metaproteome identification and quantification (named MetaPro-IQ) by using the close-to-complete human or mouse gut microbial gene catalog as database and an iterative database search strategy. An average of 38 and 33 % of the acquired tandem mass spectrometry (MS) spectra was confidently identified for the studied mouse stool and human mucosal-luminal interface samples, respectively. In total, we accurately quantified 30,749 protein groups for the mouse metaproteome and 19,011 protein groups for the human metaproteome. Moreover, the MetaPro-IQ approach enabled comparable identifications with the matched metagenome database search strategy that is widely used but needs prior metagenomic sequencing. The response of gut microbiota to high-fat diet in mice was then assessed, which showed distinct metaproteome patterns for high-fat-fed mice and identified 849 proteins as significant responders to high-fat feeding in comparison to low-fat feeding. We present MetaPro-IQ, a metaproteomic approach for highly efficient intestinal microbial protein identification and quantification, which functions as a universal workflow for metaproteomic studies, and will thus facilitate the application of metaproteomics for better understanding the functions of gut microbiota in health and disease.

  2. Challenges and Opportunities of Airborne Metagenomics

    KAUST Repository

    Behzad, H.

    2015-05-06

    Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles.

  3. The Amordad database engine for metagenomics.

    Science.gov (United States)

    Behnam, Ehsan; Smith, Andrew D

    2014-10-15

    Several technical challenges in metagenomic data analysis, including assembling metagenomic sequence data or identifying operational taxonomic units, are both significant and well known. These forms of analysis are increasingly cited as conceptually flawed, given the extreme variation within traditionally defined species and rampant horizontal gene transfer. Furthermore, computational requirements of such analysis have hindered content-based organization of metagenomic data at large scale. In this article, we introduce the Amordad database engine for alignment-free, content-based indexing of metagenomic datasets. Amordad places the metagenome comparison problem in a geometric context, and uses an indexing strategy that combines random hashing with a regular nearest neighbor graph. This framework allows refinement of the database over time by continual application of random hash functions, with the effect of each hash function encoded in the nearest neighbor graph. This eliminates the need to explicitly maintain the hash functions in order for query efficiency to benefit from the accumulated randomness. Results on real and simulated data show that Amordad can support logarithmic query time for identifying similar metagenomes even as the database size reaches into the millions. Source code, licensed under the GNU general public license (version 3) is freely available for download from http://smithlabresearch.org/amordad andrewds@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Off to the (Earthworm) Races: A Quick and Flexible Lab Experiment for Introductory Zoology Courses.

    Science.gov (United States)

    Switzer, Paul V.; Fritz, Ann H.

    2001-01-01

    Presents a hands-on, investigative lab activity for use in an introductory zoology course. Tests the behavioral hypothesis that substrate texture affects earthworm locomotor ability. Provides background information on earthworm locomotion followed by details of the lab exercise. (NB)

  5. Warming shifts ‘worming’: effects of experimental warming on invasive earthworms in northern North America

    OpenAIRE

    Nico Eisenhauer; Artur Stefanski; Fisichelli, Nicholas A.; Karen Rice; Roy Rich; Reich, Peter B.

    2014-01-01

    Climate change causes species range shifts and potentially alters biological invasions. The invasion of European earthworm species across northern North America has severe impacts on native ecosystems. Given the long and cold winters in that region that to date supposedly have slowed earthworm invasion, future warming is hypothesized to accelerate earthworm invasions into yet non-invaded regions. Alternatively, warming-induced reductions in soil water content (SWC) can also decrease earthworm...

  6. The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders

    OpenAIRE

    Liu, Ya-Jun; Zaprasis, Adrienne; Liu, Shuang-Jiang; Drake, Harold L; Horn, Marcus A

    2010-01-01

    2-Methyl-4-chlorophenoxyacetic acid (MCPA) is a widely used phenoxyalkanoic acid (PAA) herbicide. Earthworms represent the dominant macrofauna and enhance microbial activities in many soils. Thus, the effect of the model earthworm Aporrectodea caliginosa (Oligochaeta, Lumbricidae) on microbial MCPA degradation was assessed in soil columns with agricultural soil. MCPA degradation was quicker in soil with earthworms than without earthworms. Quantitative PCR was inhibition-corrected per nucleic ...

  7. Correlation between earthworms and plant litter decomposition in a tropical wet forest of Puerto Rico.

    Science.gov (United States)

    Jennifer Dechainea; Honghua Ruanb; Yaniria Sanchez-de Leon; Xiaoming Zou

    2005-01-01

    Earthworms are recognized to play an important role in the decomposition of organic materials. To test the use of earthworms as an indicator of plant litter decomposition, we examined the abundance and biomass of earthworms in relation to plant litter decomposition in a tropical wet forest of Puerto Rico. We collected earthworms at 0–0.1m and 0.1–0.25m soil depths from...

  8. Mole: an open near real-time database-centric Earthworm subsystem

    OpenAIRE

    Quintiliani, Matteo; Pintore, Stefano

    2012-01-01

    Mole is an open-source and cross-platform Earthworm subsystem made up of a MySQL database schema, an Earthworm module, and a web interface. Although it sprang from INGV requirements, Mole is as general-purpose as possible in order to provide a high-level communication layer to Earthworm. In this sense, Mole intends to be a starting point for the Earthworm community to fire up a development effort for a new “Open Interactive Earthworm”.

  9. Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota.

    Science.gov (United States)

    Bolaños, Luis M; Rosenblueth, Mónica; Castillo-Ramírez, Santiago; Figuier-Huttin, Gilles; Martínez-Romero, Esperanza

    2016-05-01

    Scorpions are considered 'living fossils' that have conserved ancestral anatomical features and have adapted to numerous habitats. However, their gut microbiota diversity has not been studied. Here, we characterized the gut microbiota of two scorpion species, Vaejovis smithi and Centruroides limpidus. Our results indicate that scorpion gut microbiota is species-specific and that food deprivation reduces bacterial diversity. 16S rRNA gene phylogenetic analysis revealed novel bacterial lineages showing a low level of sequence identity to any known bacteria. Furthermore, these novel bacterial lineages were each restricted to a different scorpion species. Additionally, our results of the predicted metagenomic profiles revealed a core set of pathways that were highly abundant in both species, and mostly related to amino acid, carbohydrate, vitamin and cofactor metabolism. Notably, the food-deprived V. smithi shotgun metagenome matched almost completely the metabolic features of the prediction. Finally, comparisons among predicted metagenomic profiles showed that toxic compound degradation pathways were more abundant in recently captured C. limpidus scorpions. This study gives a first insight into the scorpion gut microbiota and provides a reference for future studies on the gut microbiota from other arachnid species. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  10. A geographically-diverse collection of 418 human gut microbiome pathway genome databases

    KAUST Repository

    Hahn, Aria S.

    2017-04-11

    Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the Pathway Tools software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GutCyc provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn’s disease, and type 2 diabetes. GutCyc data products are searchable online, or may be downloaded and explored locally using MetaPathways and Pathway Tools.

  11. Trophic dynamics in a simple experimental ecosystem: Interactions among centipedes, Collembola and introduced earthworms

    Science.gov (United States)

    Meixiang Gao; Melanie K. Taylor; Mac A. Callaham

    2017-01-01

    Invasive earthworms in North America are known to have dramatic influences on soil ecosystems, including negative effects on other soil fauna. In general, studies examining this phenomenon have focused on invasive earthworm impacts on organisms at the same or lower trophic level as the earthworms themselves (i.e., detritivores and decomposers). In contrast, there have...

  12. Darwin, Earthworms & Circadian Rhythms: A Fertile Field for Science Fair Experiments

    Science.gov (United States)

    Burns, John T.; Scurti, Paul J.; Furda, Amy M.

    2009-01-01

    This article discusses why the study of earthworms has fascinated many scientists, and why earthworms make ideal experimental animals for students to test in the laboratory. Although earthworms may appear to be primitive, they are governed by both circadian and seasonal rhythms, just as more advanced organisms are. They possess an intelligence…

  13. A Fluorescent Marking and Re-count Technique Using the Invasive Earthworm, Pontoscolex corethrurus (Annelida: Oligochaeta)

    Science.gov (United States)

    Grizelle Gonzalez; Elianid Espinoza; Zhigang Liu; Xiaoming. Zou

    2006-01-01

    We used a fluorescence technique to mark and re-count the invasive earthworm, Pontoscolex corethrurus from PVC tubes established in a forest and a recently abandoned pasture in Puerto Rico to test the effects of the labeling treatment on earthworm population survival over time. A fluorescent marker was injected into the earthworms in the middle third section of the...

  14. Earthworm assemblages as affected by field margin strips and tillage intensity: An on-farm approach

    NARCIS (Netherlands)

    Crittenden, S.; Huerta, E.; Goede, de R.G.M.; Pulleman, M.M.

    2015-01-01

    Earthworm species contribute to soil ecosystem functions in varying ways. Important soil functions like structural maintenance and nutrient cycling are affected by earthworms, thus it is essential to understand how arable farm management influences earthworm species. One aim of arable field margin

  15. Species-specific earthworm population responses in relation to flooding dynamics in a Dutch floodplain soil

    NARCIS (Netherlands)

    Zorn, M.I.; Gestel, van C.A.M.; Eijsackers, H.J.P.

    2005-01-01

    Earthworms dominate the animal biomass in moist floodplain soils. They are known to survive long periods in aerated water, but little is known about earthworm population dynamics in floodplain systems with changing inundation frequencies. This study determined earthworm population dynamics in a

  16. Species-specific earthworm population responses in relation to flooding dynamics in a Dutch floodplain soil.

    NARCIS (Netherlands)

    Zorn, M.I.; van Gestel, C.A.M.; Eijsackers, H.J.P.

    2005-01-01

    Earthworms dominate the animal biomass in moist floodplain soils. They are known to survive long periods in aerated water, but little is known about earthworm population dynamics in floodplain systems with changing inundation frequencies. This study determined earthworm population dynamics in a

  17. Earthworm (Eisenia andrei Avoidance of Soils Treated with Cypermethrin

    Directory of Open Access Journals (Sweden)

    Mara M. de Andréa

    2011-11-01

    Full Text Available The pyrethroid insecticide cypermethrin is used for agricultural and public health campaigns. Its residues may contaminate soils and the beneficial soil organisms, like the earthworms, that may ingest the contaminated soil particles. Due to its ecological relevance, earthworms Eisenia andrei/fetida have been used in different ecotoxicological tests. The avoidance of soils treated with cypermethrin by compost worms Eisenia andrei was studied here as a bioindicator of the influence of treatment dosage and the pesticide formulation in three different agricultural soils indicated by the Brazilian environmental authorities for ecotoxicological tests. This earthworms’ behavior was studied here as a first attempt to propose the test for regulation purposes. The two-compartment test systems, where the earthworms were placed for a two-day exposure period, contained samples of untreated soil alone or together with soil treated with technical grade or wettable powder formulation of cypermethrin. After 48 h, there was no mortality, but the avoidance was clear because all earthworms were found in the untreated section of each type of soil (p < 0.05. No differences were found by the Fisher’s exact test (p ≤ 1.000 for each soil and treatment, demonstrating that the different soil characteristics, the cypermethrin concentrations and formulation, as well as the smaller amounts of soil and earthworms did not influence the avoidance behavior of the earthworms to cypermethrin. The number and range of treatments used in this study do not allow a detailed recommendation of the conditions applied here, but to the best of our knowledge, this is the first reported attempt to identify the avoidance of pesticide treated tropical soils by earthworms.

  18. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

    Directory of Open Access Journals (Sweden)

    Stevens R

    2008-09-01

    Full Text Available Abstract Background Random community genomes (metagenomes are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers. Results A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats. Conclusion The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis – the availability of high-performance computing for annotating the data. http://metagenomics.nmpdr.org

  19. The metagenomic data life-cycle: standards and best practices

    Energy Technology Data Exchange (ETDEWEB)

    ten Hoopen, Petra; Finn, Robert D.; Bongo, Lars Ailo; Corre, Erwan; Fosso, Bruno; Meyer, Folker; Mitchell, Alex; Pelletier, Eric; Pesole, Graziano; Santamaria, Monica; Willassen, Nils Peder; Cochrane, Guy

    2017-06-16

    Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing. Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community but greater awareness and adoption is still needed. We emphasise the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.

  20. Metagenome Analysis: a Powerful Tool for Enzyme Bioprospecting.

    Science.gov (United States)

    Madhavan, Aravind; Sindhu, Raveendran; Parameswaran, Binod; Sukumaran, Rajeev K; Pandey, Ashok

    2017-10-01

    Microorganisms are found throughout every corner of nature, and vast number of microorganisms is difficult to cultivate by classical microbiological techniques. The advent of metagenomics has revolutionized the field of microbial biotechnology. Metagenomics allow the recovery of genetic material directly from environmental niches without any cultivation techniques. Currently, metagenomic tools are widely employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the uncultivable component of microbial communities. The employment of next-generation sequencing techniques for metagenomics resulted in the generation of large sequence data sets derived from various environments, such as soil, the human body and ocean water. This review article describes the state-of-the-art techniques and tools in metagenomics and discusses the potential of metagenomic approaches for the bioprospecting of industrial enzymes from various environmental samples. We also describe the unusual novel enzymes discovered via metagenomic approaches and discuss the future prospects for metagenome technologies.

  1. Metagenomics of Glassy-Winged Sharpshooter, Homalodisca vitripennis (Hemiptera: Cicadellidae)

    Science.gov (United States)

    A Metagenomics approach was used to identify unknown organisms which live in association with the glassy-winged sharpshooter, Homalodisca vitripennis (Hemiptera: Cicadellidae). Metagenomics combines molecular biology and genetics to identify, and characterize genetic material from unique biological ...

  2. Interactive metagenomic visualization in a Web browser.

    Science.gov (United States)

    Ondov, Brian D; Bergman, Nicholas H; Phillippy, Adam M

    2011-09-30

    A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.

  3. Metagenomic Guilt by Association: An Operonic Perspective

    Science.gov (United States)

    Vey, Gregory

    2013-01-01

    Next-generation sequencing projects continue to drive a vast accumulation of metagenomic sequence data. Given the growth rate of this data, automated approaches to functional annotation are indispensable and a cornerstone heuristic of many computational protocols is the concept of guilt by association. The guilt by association paradigm has been heavily exploited by genomic context methods that offer functional predictions that are complementary to homology-based annotations, thereby offering a means to extend functional annotation. In particular, operon methods that exploit co-directional intergenic distances can provide homology-free functional annotation through the transfer of functions among co-operonic genes, under the assumption that guilt by association is indeed applicable. Although guilt by association is a well-accepted annotative device, its applicability to metagenomic functional annotation has not been definitively demonstrated. Here a large-scale assessment of metagenomic guilt by association is undertaken where functional associations are predicted on the basis of co-directional intergenic distances. Specifically, functional annotations are compared within pairs of adjacent co-directional genes, as well as operons of various lengths (i.e. number of member genes), in order to reveal new information about annotative cohesion versus operon length. The results suggests that co-directional gene pairs offer reduced confidence for metagenomic guilt by association due to difficulty in resolving the existence of functional associations when intergenic distance is the sole predictor of pairwise gene interactions. However, metagenomic operons, particularly those with substantial lengths, appear to be capable of providing a superior basis for metagenomic guilt by association due to increased annotative stability. The need for improved recognition of metagenomic operons is discussed, as well as the limitations of the present work. PMID:23940763

  4. Interactive metagenomic visualization in a Web browser

    Directory of Open Access Journals (Sweden)

    Phillippy Adam M

    2011-09-01

    Full Text Available Abstract Background A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables. Results Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools. Conclusions Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.

  5. High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea faeces.

    Directory of Open Access Journals (Sweden)

    Trish J Lavery

    Full Text Available Metagenomic analysis was used to examine the taxonomic diversity and metabolic potential of an Australian sea lion (Neophoca cinerea gut microbiome. Bacteria comprised 98% of classifiable sequences and of these matches to Firmicutes (80% were dominant, with Proteobacteria and Actinobacteria representing 8% and 2% of matches respectively. The relative proportion of Firmicutes (80% to Bacteriodetes (2% is similar to that in previous studies of obese humans and obese mice, suggesting the gut microbiome may confer a predisposition towards the excess body fat that is needed for thermoregulation within the cold oceanic habitats foraged by Australian sea lions. Core metabolic functions, including carbohydrate utilisation (14%, protein metabolism (9% and DNA metabolism (7% dominated the metagenome, but in comparison to human and fish gut microbiomes there was a significantly higher proportion of genes involved in phosphorus metabolism (2.4% and iron scavenging mechanisms (1%. When sea lions defecate at sea, the relatively high nutrient metabolism potential of bacteria in their faeces may accelerate the dissolution of nutrients from faecal particles, enhancing their persistence in the euphotic zone where they are available to stimulate marine production.

  6. Earthworm species influence on carbon-mineral association in a sugar maple forest in northern Minnesota

    Science.gov (United States)

    Lyttle, A.; Yoo, K.; Aufdenkampe, A. K.; Hale, C. M.; Sebestyen, S. D.

    2011-12-01

    Non-native European earthworms are invading previously earthworm-free hardwood forests in the northern Great Lakes Region. Whereas earthworms' impacts on soil morphology and geochemical properties have been well documented in agricultural settings, the role of earthworms in biogeochemical cycles of undisturbed forests remains poorly understood. The forest soils that were recently invaded by exotic earthworms, therefore, provide a unique opportunity to understand how and how much earthworms contribute to biogeochemistry of non-agricultural environments. Increased degree and extent of soil mixing is one of the better known consequences of the earthworm invasion. Our hypothesis is that invasive earthworms positively affect carbon (C) stabilization by enhancing contacts between organic matter and minerals. We are studying C-mineral complexation along a well-established earthworm chronosequence in a sugar maple forest in northern Minnesota. We have observed changes in total earthworm biomass, A horizon C storage, and total specific surface area (SSA) of minerals as the invasion progresses. Because each earthworm species has different feeding and dwelling habits, biogeochemical imprints of the invasion reflect not only earthworms' biomass but also their species composition. All earthworm species show an increase in their biomass with greater time length since the invasion, though epigeic earthworms tend to be the pioneer species. As the total earthworm biomass increases, we find greater incorporation of organic C into the A horizon; the O horizon thickness decreases from 8 to 0 cm as the A horizon thickens from ~5 cm to ~12 cm. While leaf litter biomass is negatively correlated with total earthworm biomass, dramatic decreases in litter biomass are coupled with considerable increases in the biomass of epi-endogeic species. Despite the general decrease in C storage in the A horizon with greater degree of invasion, the storages fluctuate along the transect because

  7. The Re-colonization Ability of a Native Earthworm, Estherella spp., in Forests and Pastures in Puerto Rico

    Science.gov (United States)

    Ching-Yu Huang; Grizelle Gonzalez; Paul F. Hendrix

    2006-01-01

    Populations of some native earthworm species are decreasing or disappearing due to human activities like habitat disturbance and introduction of exotic earthworms. Habitat disturbance can cause changes in soil physical structure and nutrient cycling, which may reduce native earthworm populations prior to the invasion of exotic earthworms. Our purpose was 1) to...

  8. 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

  9. Alzheimer's disease and gut microbiota.

    Science.gov (United States)

    Hu, Xu; Wang, Tao; Jin, Feng

    2016-10-01

    Alzheimer's disease (AD) is a most common neurodegenerative disorder, which associates with impaired cognition. Gut microbiota can modulate host brain function and behavior via microbiota-gut-brain axis, including cognitive behavior. Germ-free animals, antibiotics, probiotics intervention and diet can induce alterations of gut microbiota and gut physiology and also host cognitive behavior, increasing or decreasing risks of AD. The increased permeability of intestine and blood-brain barrier induced by gut microbiota disturbance will increase the incidence of neurodegeneration disorders. Gut microbial metabolites and their effects on host neurochemical changes may increase or decrease the risk of AD. Pathogenic microbes infection will also increase the risk of AD, and meanwhile, the onset of AD support the "hygiene hypothesis". All the results suggest that AD may begin in the gut, and is closely related to the imbalance of gut microbiota. Modulation of gut microbiota through personalized diet or beneficial microbiota intervention will probably become a new treatment for AD.

  10. The systemic imprint of growth and its uses in ecological (meta)genomics.

    Science.gov (United States)

    Vieira-Silva, Sara; Rocha, Eduardo P C

    2010-01-15

    Microbial minimal generation times range from a few minutes to several weeks. They are evolutionarily determined by variables such as environment stability, nutrient availability, and community diversity. Selection for fast growth adaptively imprints genomes, resulting in gene amplification, adapted chromosomal organization, and biased codon usage. We found that these growth-related traits in 214 species of bacteria and archaea are highly correlated, suggesting they all result from growth optimization. While modeling their association with maximal growth rates in view of synthetic biology applications, we observed that codon usage biases are better correlates of growth rates than any other trait, including rRNA copy number. Systematic deviations to our model reveal two distinct evolutionary processes. First, genome organization shows more evolutionary inertia than growth rates. This results in over-representation of growth-related traits in fast degrading genomes. Second, selection for these traits depends on optimal growth temperature: for similar generation times purifying selection is stronger in psychrophiles, intermediate in mesophiles, and lower in thermophiles. Using this information, we created a predictor of maximal growth rate adapted to small genome fragments. We applied it to three metagenomic environmental samples to show that a transiently rich environment, as the human gut, selects for fast-growers, that a toxic environment, as the acid mine biofilm, selects for low growth rates, whereas a diverse environment, like the soil, shows all ranges of growth rates. We also demonstrate that microbial colonizers of babies gut grow faster than stabilized human adults gut communities. In conclusion, we show that one can predict maximal growth rates from sequence data alone, and we propose that such information can be used to facilitate the manipulation of generation times. Our predictor allows inferring growth rates in the vast majority of uncultivable

  11. The systemic imprint of growth and its uses in ecological (metagenomics.

    Directory of Open Access Journals (Sweden)

    Sara Vieira-Silva

    2010-01-01

    Full Text Available Microbial minimal generation times range from a few minutes to several weeks. They are evolutionarily determined by variables such as environment stability, nutrient availability, and community diversity. Selection for fast growth adaptively imprints genomes, resulting in gene amplification, adapted chromosomal organization, and biased codon usage. We found that these growth-related traits in 214 species of bacteria and archaea are highly correlated, suggesting they all result from growth optimization. While modeling their association with maximal growth rates in view of synthetic biology applications, we observed that codon usage biases are better correlates of growth rates than any other trait, including rRNA copy number. Systematic deviations to our model reveal two distinct evolutionary processes. First, genome organization shows more evolutionary inertia than growth rates. This results in over-representation of growth-related traits in fast degrading genomes. Second, selection for these traits depends on optimal growth temperature: for similar generation times purifying selection is stronger in psychrophiles, intermediate in mesophiles, and lower in thermophiles. Using this information, we created a predictor of maximal growth rate adapted to small genome fragments. We applied it to three metagenomic environmental samples to show that a transiently rich environment, as the human gut, selects for fast-growers, that a toxic environment, as the acid mine biofilm, selects for low growth rates, whereas a diverse environment, like the soil, shows all ranges of growth rates. We also demonstrate that microbial colonizers of babies gut grow faster than stabilized human adults gut communities. In conclusion, we show that one can predict maximal growth rates from sequence data alone, and we propose that such information can be used to facilitate the manipulation of generation times. Our predictor allows inferring growth rates in the vast majority of

  12. Proximal Soil Sensing - A Contribution for Species Habitat Distribution Modelling of Earthworms in Agricultural Soils?

    Science.gov (United States)

    Schirrmann, Michael; Joschko, Monika; Gebbers, Robin; Kramer, Eckart; Zörner, Mirjam; Barkusky, Dietmar; Timmer, Jens

    2016-01-01

    Earthworms are important for maintaining soil ecosystem functioning and serve as indicators of soil fertility. However, detection of earthworms is time-consuming, which hinders the assessment of earthworm abundances with high sampling density over entire fields. Recent developments of mobile terrestrial sensor platforms for proximal soil sensing (PSS) provided new tools for collecting dense spatial information of soils using various sensing principles. Yet, the potential of PSS for assessing earthworm habitats is largely unexplored. This study investigates whether PSS data contribute to the spatial prediction of earthworm abundances in species distribution models of agricultural soils. Proximal soil sensing data, e.g., soil electrical conductivity (EC), pH, and near infrared absorbance (NIR), were collected in real-time in a field with two management strategies (reduced tillage / conventional tillage) and sandy to loam soils. PSS was related to observations from a long-term (11 years) earthworm observation study conducted at 42 plots. Earthworms were sampled from 0.5 x 0.5 x 0.2 m³ soil blocks and identified to species level. Sensor data were highly correlated with earthworm abundances observed in reduced tillage but less correlated with earthworm abundances observed in conventional tillage. This may indicate that management influences the sensor-earthworm relationship. Generalized additive models and state-space models showed that modelling based on data fusion from EC, pH, and NIR sensors produced better results than modelling without sensor data or data from just a single sensor. Regarding the individual earthworm species, particular sensor combinations were more appropriate than others due to the different habitat requirements of the earthworms. Earthworm species with soil-specific habitat preferences were spatially predicted with higher accuracy by PSS than more ubiquitous species. Our findings suggest that PSS contributes to the spatial modelling of

  13. An earthworm-like robot using origami-ball structures

    Science.gov (United States)

    Fang, Hongbin; Zhang, Yetong; Wang, K. W.

    2017-04-01

    Earthworms possess extraordinary on-ground and underground mobility, which inspired researchers to mimic their morphology characteristics and locomotion mechanisms to develop crawling robots. One of the bottlenecks that constrain the development and wide-spread application of earthworm-like robots is the process of design, fabrication and assembly of the robot frameworks. Here we present a new earthworm-like robot design and prototype by exploring and utilizing origami ball structures. The origami ball is able to antagonistically output both axial and radial deformations, similar as an earthworm's body segment. The origami folding techniques also introduce many advantages to the robot development, including precise and low cost fabrication and high customizability. Starting from a flat polymer film, we adopt laser machining technique to engrave the crease pattern and manually fold the patterned flat film into an origami ball. Coupling the ball with a servomotor-driven linkage yields a robot segment. Connecting six segments in series, we obtain an earthworm-like origami robot prototype. The prototype is tested in a tube to evaluate its locomotion performance. It shows that the robot could crawl effectively in the tube, manifesting the feasibility of the origami-based design. In addition, test results indicate that the robot's locomotion could be tailored by employing different peristalsis-wave based gaits. The robot design and prototype reported in this paper could foster a new breed of crawling robots with simply design, fabrication, and assemble processes, and improved locomotion performance.

  14. Viral Metagenomics: MetaView Software

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, C; Smith, J

    2007-10-22

    The purpose of this report is to design and develop a tool for analysis of raw sequence read data from viral metagenomics experiments. The tool should compare read sequences of known viral nucleic acid sequence data and enable a user to attempt to determine, with some degree of confidence, what virus groups may be present in the sample. This project was conducted in two phases. In phase 1 we surveyed the literature and examined existing metagenomics tools to educate ourselves and to more precisely define the problem of analyzing raw read data from viral metagenomic experiments. In phase 2 we devised an approach and built a prototype code and database. This code takes viral metagenomic read data in fasta format as input and accesses all complete viral genomes from Kpath for sequence comparison. The system executes at the UNIX command line, producing output that is stored in an Oracle relational database. We provide here a description of the approach we came up with for handling un-assembled, short read data sets from viral metagenomics experiments. We include a discussion of the current MetaView code capabilities and additional functionality that we believe should be added, should additional funding be acquired to continue the work.

  15. Metagenomics for pathogen detection in public health

    Science.gov (United States)

    2013-01-01

    Traditional pathogen detection methods in public health infectious disease surveillance rely upon the identification of agents that are already known to be associated with a particular clinical syndrome. The emerging field of metagenomics has the potential to revolutionize pathogen detection in public health laboratories by allowing the simultaneous detection of all microorganisms in a clinical sample, without a priori knowledge of their identities, through the use of next-generation DNA sequencing. A single metagenomics analysis has the potential to detect rare and novel pathogens, and to uncover the role of dysbiotic microbiomes in infectious and chronic human disease. Making use of advances in sequencing platforms and bioinformatics tools, recent studies have shown that metagenomics can even determine the whole-genome sequences of pathogens, allowing inferences about antibiotic resistance, virulence, evolution and transmission to be made. We are entering an era in which more novel infectious diseases will be identified through metagenomics-based methods than through traditional laboratory methods. The impetus is now on public health laboratories to integrate metagenomics techniques into their diagnostic arsenals. PMID:24050114

  16. Preliminary High-Throughput Metagenome Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Dusheyko, Serge; Furman, Craig; Pangilinan, Jasmyn; Shapiro, Harris; Tu, Hank

    2007-03-26

    Metagenome data sets present a qualitatively different assembly problem than traditional single-organism whole-genome shotgun (WGS) assembly. The unique aspects of such projects include the presence of a potentially large number of distinct organisms and their representation in the data set at widely different fractions. In addition, multiple closely related strains could be present, which would be difficult to assemble separately. Failure to take these issues into account can result in poor assemblies that either jumble together different strains or which fail to yield useful results. The DOE Joint Genome Institute has sequenced a number of metagenomic projects and plans to considerably increase this number in the coming year. As a result, the JGI has a need for high-throughput tools and techniques for handling metagenome projects. We present the techniques developed to handle metagenome assemblies in a high-throughput environment. This includes a streamlined assembly wrapper, based on the JGI?s in-house WGS assembler, Jazz. It also includes the selection of sensible defaults targeted for metagenome data sets, as well as quality control automation for cleaning up the raw results. While analysis is ongoing, we will discuss preliminary assessments of the quality of the assembly results (http://fames.jgi-psf.org).

  17. Shotgun metagenomic data streams: surfing without fear

    Energy Technology Data Exchange (ETDEWEB)

    Berendzen, Joel R [Los Alamos National Laboratory

    2010-12-06

    Timely information about bio-threat prevalence, consequence, propagation, attribution, and mitigation is needed to support decision-making, both routinely and in a crisis. One DNA sequencer can stream 25 Gbp of information per day, but sampling strategies and analysis techniques are needed to turn raw sequencing power into actionable knowledge. Shotgun metagenomics can enable biosurveillance at the level of a single city, hospital, or airplane. Metagenomics characterizes viruses and bacteria from complex environments such as soil, air filters, or sewage. Unlike targeted-primer-based sequencing, shotgun methods are not blind to sequences that are truly novel, and they can measure absolute prevalence. Shotgun metagenomic sampling can be non-invasive, efficient, and inexpensive while being informative. We have developed analysis techniques for shotgun metagenomic sequencing that rely upon phylogenetic signature patterns. They work by indexing local sequence patterns in a manner similar to web search engines. Our methods are laptop-fast and favorable scaling properties ensure they will be sustainable as sequencing methods grow. We show examples of application to soil metagenomic samples.

  18. Metazen – metadata capture for metagenomes

    Science.gov (United States)

    2014-01-01

    Background As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution. Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. Unfortunately, these tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools. Results Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata. Conclusions Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility. PMID:25780508

  19. Application of earthworm humus and Bradyrhizobium japonicum in Glycine max (L.) Merrill

    OpenAIRE

    Ricardo Gómez Machado; Marta Travieso Torres; Luis Antonio Tamayo López; Yoannia Gretel Pupo Blanco

    2017-01-01

    The experiment was developed in the Granma University's productive area, with the objective of evaluating the alone and combined earthworm humus application effect with Bradyrhizobium japonicum on G7R-315 variety soybean cultivation. Six treatments were evaluated: T1 Control, T2 B. japonicum, T3 earthworm humus (6 t ha-1), T4 B. japonicum + earthworm humus (6 t ha-1), T5 earthworm humus (8 t ha-1), T6 B. japonicum + earthworm humus (8 t ha-1) on a brown soil. A randomized block design was use...

  20. Gut Microbiota-brain Axis

    OpenAIRE

    Wang, Hong-Xing; Wang, Yu-Ping

    2016-01-01

    Objective: To systematically review the updated information about the gut microbiota-brain axis. Data Sources: All articles about gut microbiota-brain axis published up to July 18, 2016, were identified through a literature search on PubMed, ScienceDirect, and Web of Science, with the keywords of “gut microbiota”, “gut-brain axis”, and “neuroscience”. Study Selection: All relevant articles on gut microbiota and gut-brain axis were included and carefully reviewed, with no limitation of s...

  1. Mnemiopsis leidyi Gut Harbors Seasonally Variant and Commensal Microbial Assemblages

    Science.gov (United States)

    Mariita, R. M.; Hossain, M. J.; Liles, M. R.; Moss, A.

    2016-02-01

    Studies have shown that with widespread use of antibiotics in human and domestic animal populations, antibiotic resistance becomes increasingly common in the environment. Estuaries provide ideal conditions for acquisition and dissemination of drug resistance genes because they serve as sinks for pollution. This study aimed to identify M. leidyi microbial diversity and richness and their potential to act as vectors for antibiotic resistance determinants (ARDs). M. leidyi, although native to study area are highly invasive. Metagenomic analyses indicate that there are temporal variations of bacterioplankton assemblages in M. leidyi gut. Overall, Proteobacteria and Actinobacteria are the most abundant phyla. Despite the temporal dynamics in the microbial assemblages in M. leidyi gut, they seem to retain Propionibacterium acnes (gut microbiota in some insects) and select proteobacteria across all seasons. The results contradict previous studies that suggest that M. leidyi does not have constant a microbiota, but only seasonally variant microbial assemblages. Here we reveal the presence of M. leidyi gut ARDs in winter and summer, probably because of the ctenophores' positive geotaxis during rough surface conditions. Genes responsible for resistance to fluoroquinolones, multidrug resistance efflux pumps, mercuric reductase, copper homeostasis and blaR1 genes were observed. This is the first study to demonstrate that M. leidyi harbors constant microbiota and provides a baseline for understanding M. leidyi gut microbial and ARDs ecology. It also suggests that M. leidyi bacterial taxonomic and functional dynamics is influenced by season. Funding: Alabama EPSCoR GRSP fellowship, AU-CMB fellowship, NSF EPS-1158862, USDA-Hatch 370225-310100 (AGM, ML).

  2. Structure and function of the healthy pre-adolescent pediatric gut microbiome.

    Science.gov (United States)

    Hollister, Emily B; Riehle, Kevin; Luna, Ruth Ann; Weidler, Erica M; Rubio-Gonzales, Michelle; Mistretta, Toni-Ann; Raza, Sabeen; Doddapaneni, Harsha V; Metcalf, Ginger A; Muzny, Donna M; Gibbs, Richard A; Petrosino, Joseph F; Shulman, Robert J; Versalovic, James

    2015-08-26

    The gut microbiome influences myriad host functions, including nutrient acquisition, immune modulation, brain development, and behavior. Although human gut microbiota are recognized to change as we age, information regarding the structure and function of the gut microbiome during childhood is limited. Using 16S rRNA gene and shotgun metagenomic sequencing, we characterized the structure, function, and variation of the healthy pediatric gut microbiome in a cohort of school-aged, pre-adolescent children (ages 7-12 years). We compared the healthy pediatric gut microbiome with that of healthy adults previously recruited from the same region (Houston, TX, USA). Although healthy children and adults harbored similar numbers of taxa and functional genes, their composition and functional potential differed significantly. Children were enriched in Bifidobacterium spp., Faecalibacterium spp., and members of the Lachnospiraceae, while adults harbored greater abundances of Bacteroides spp. From a functional perspective, significant differences were detected with respect to the relative abundances of genes involved in vitamin synthesis, amino acid degradation, oxidative phosphorylation, and triggering mucosal inflammation. Children's gut communities were enriched in functions which may support ongoing development, while adult communities were enriched in functions associated with inflammation, obesity, and increased risk of adiposity. Previous studies suggest that the human gut microbiome is relatively stable and adult-like after the first 1 to 3 years of life. Our results suggest that the healthy pediatric gut microbiome harbors compositional and functional qualities that differ from those of healthy adults and that the gut microbiome may undergo a more prolonged development than previously suspected.

  3. Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies.

    Science.gov (United States)

    Santiago-Rodriguez, Tasha M; Fornaciari, Gino; Luciani, Stefania; Toranzos, Gary A; Marota, Isolina; Giuffra, Valentina; Cano, Raul J

    2017-11-07

    Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. The Italian nobility mummies exhibited a higher bacterial diversity as compared to the Inca mummies when using 16S ribosomal (rRNA) gene amplicon sequencing, but both groups showed bacterial and fungal taxa when using shotgun metagenomic sequencing that may resemble both the thanatomicrobiome and extant human gut microbiomes. Identification of sequences associated with plants, animals, and carbohydrate-active enzymes (CAZymes) may provide further insights into the dietary habits of Inca and Italian nobility mummies. Putative antibiotic-resistance genes in the Inca and Italian nobility mummies support a human gut resistome prior to the antibiotic therapy era. The higher proportion of putative antibiotic-resistance genes in the Inca compared to Italian nobility mummies may support the hypotheses that a greater exposure to the environment may result in a greater acquisition of antibiotic-resistance genes. The present study adds knowledge of the microbiome resulting from the process of mummification of the human gut, insights of ancient dietary habits, and the preserved putative human gut resistome prior the antibiotic therapy era.

  4. Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies

    Directory of Open Access Journals (Sweden)

    Tasha M. Santiago-Rodriguez

    2017-11-01

    Full Text Available Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. The Italian nobility mummies exhibited a higher bacterial diversity as compared to the Inca mummies when using 16S ribosomal (rRNA gene amplicon sequencing, but both groups showed bacterial and fungal taxa when using shotgun metagenomic sequencing that may resemble both the thanatomicrobiome and extant human gut microbiomes. Identification of sequences associated with plants, animals, and carbohydrate-active enzymes (CAZymes may provide further insights into the dietary habits of Inca and Italian nobility mummies. Putative antibiotic-resistance genes in the Inca and Italian nobility mummies support a human gut resistome prior to the antibiotic therapy era. The higher proportion of putative antibiotic-resistance genes in the Inca compared to Italian nobility mummies may support the hypotheses that a greater exposure to the environment may result in a greater acquisition of antibiotic-resistance genes. The present study adds knowledge of the microbiome resulting from the process of mummification of the human gut, insights of ancient dietary habits, and the preserved putative human gut resistome prior the antibiotic therapy era.

  5. The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study.

    Science.gov (United States)

    Rothenberg, Sarah E; Keiser, Sharon; Ajami, Nadim J; Wong, Matthew C; Gesell, Jonathan; Petrosino, Joseph F; Johs, Alexander

    2016-02-03

    The mechanisms by which gut microbiota contribute to methylmercury metabolism remain unclear. Among a cohort of pregnant mothers, the objectives of our pilot study were to determine (1) associations between gut microbiota and mercury concentrations in biomarkers (stool, hair and cord blood) and (2) the contributions of gut microbial mercury methylation/demethylation to stool methylmercury. Pregnant women (36-39 weeks gestation, n=17) donated hair and stool specimens, and cord blood was collected for a subset (n=7). The diversity of gut microbiota was determined using 16S rRNA gene profiling (n=17). For 6 stool samples with highest/lowest methylmercury concentrations, metagenomic whole genome shotgun sequencing was employed to search for the mercury methylation gene (hgcA), and two mer operon genes involved in methylmercury detoxification (merA and merB). Seventeen bacterial genera were significantly correlated (increasing or decreasing) with stool methylmercury, stool inorganic mercury, or hair total mercury; however, aside from one genus, there was no overlap between biomarkers. There were no definitive matches for hgcA or merB, while merA was detected at low concentrations in all six samples. Proportional differences in stool methylmercury were not likely attributed to gut microbiota through methylation/demethylation. Gut microbiota potentially altered methylmercury metabolism using indirect pathways. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  6. Gut microbiome populations are associated with structure-specific changes in white matter architecture.

    Science.gov (United States)

    Ong, Irene M; Gonzalez, Jose G; McIlwain, Sean J; Sawin, Emily A; Schoen, Andrew J; Adluru, Nagesh; Alexander, Andrew L; Yu, John-Paul J

    2018-01-10

    Altered gut microbiome populations are associated with a broad range of neurodevelopmental disorders including autism spectrum disorder and mood disorders. In animal models, modulation of gut microbiome populations via dietary manipulation influences brain function and behavior and has been shown to ameliorate behavioral symptoms. With striking differences in microbiome-driven behavior, we explored whether these behavioral changes are also accompanied by corresponding changes in neural tissue microstructure. Utilizing diffusion tensor imaging, we identified global changes in white matter structural integrity occurring in a diet-dependent manner. Analysis of 16S ribosomal RNA sequencing of gut bacteria also showed changes in bacterial populations as a function of diet. Changes in brain structure were found to be associated with diet-dependent changes in gut microbiome populations using a machine learning classifier for quantitative assessment of the strength of microbiome-brain region associations. These associations allow us to further test our understanding of the gut-brain-microbiota axis by revealing possible links between altered and dysbiotic gut microbiome populations and changes in brain structure, highlighting the potential impact of diet and metagenomic effects in neuroimaging.

  7. Viral metagenomics: are we missing the giants?

    Science.gov (United States)

    Halary, S; Temmam, S; Raoult, D; Desnues, C

    2016-06-01

    Amoeba-infecting giant viruses are recently discovered viruses that have been isolated from diverse environments all around the world. In parallel to isolation efforts, metagenomics confirmed their worldwide distribution from a broad range of environmental and host-associated samples, including humans, depicting them as a major component of eukaryotic viruses in nature and a possible resident of the human/animal virome whose role is still unclear. Nevertheless, metagenomics data about amoeba-infecting giant viruses still remain scarce, mainly because of methodological limitations. Efforts should be pursued both at the metagenomic sample preparation level and on in silico analyses to better understand their roles in the environment and in human/animal health and disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Interactions between the nematode parasite of pigs, Ascaris suum, and the earthworm Aporrectodea longa.

    Science.gov (United States)

    Kraglund, H O; Grønvold, J; Roepstorff, A; Rawat, H

    1998-01-01

    Pig faeces in which Ascaris suum eggs had been embryonating for 57 days were placed in buckets of soil containing either 30 or no earth-worms (Aporrectodea longa). When present, earthworms consumed the faeces and transported the eggs down into the soil, without inflicting any visible damage on the eggs. In later experiments 10 earthworms from the above experiment were fed to each of ten pigs, and another 40 earthworms were dissected. None of the 10 pigs became infected with A. suum through consumption of earthworms, and none of the dissected earthworms were found to contain A. suum larvae. This experiment indicates that A. longa did not act as a paratenic host for A. suum but shows that earthworms are very efficient in transporting A. suum eggs from faeces deposited on the soil surface into the soil.

  9. Earthworm bioturbation influences the phytoavailability of metals released by particles in cultivated soils.

    Science.gov (United States)

    Leveque, Thibaut; Capowiez, Yvan; Schreck, Eva; Xiong, Tiantian; Foucault, Yann; Dumat, Camille

    2014-08-01

    The influence of earthworm activity on soil-to-plant metal transfer was studied by carrying out six weeks mesocosms experiments with or without lettuce and/or earthworms in soil with a gradient of metal concentrations due to particles fallouts. Soil characteristics, metal concentrations in lettuce and earthworms were measured and soil porosity in the mesocosms was determined. Earthworms increased the soil pH, macroporosity and soil organic matter content due to the burying of wheat straw provided as food. Earthworm activities increased the metals concentrations in lettuce leaves. Pb and Cd concentrations in lettuce leaves can increase up to 46% with earthworm activities … These results and the low correlation between estimated by CaCl2 and EDTA and measured pollutant phytoavailability suggest that earthworm bioturbation was the main cause of the increase. Bioturbation could affect the proximity of pollutants to the roots and soil organic matter. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Second contribution to the knowledge of earthworms (Lumbricidae in Montenegro

    Directory of Open Access Journals (Sweden)

    Stojanović Mirjana M.

    2003-01-01

    Full Text Available This paper contains the results of qualitative analysis of Lumbricidae (Oligochaeta in Montenegro, during the period 1997-2003. The research has included natural and cultivated biotopes. The presence of 15 species was established and the habitats, localities and their zoogeographical position are given. In Montenegro we found four species for the first time Dendrobaena jastrebensis, D. vejdovskyi, Octodrilus bretcheri and Lumbricus terrestris. The complete list of earthworm species in Montenegro includes 45 taxa. With respects to the zoogeographic situation of the earthworms in Montenegro, the largest number belongs to endemic (10 and European (10 species. But 8 taxa are south-European, 9 Holarctic, 7 cosmopolitan, and 1 Palearctic. The degree of endemism of the earthworm fauna of Montenegro is quite high, exceeding 22.2%.

  11. Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study.

    Science.gov (United States)

    Abayasekara, Lalanika M; Perera, Jennifer; Chandrasekharan, Vishvanath; Gnanam, Vaz S; Udunuwara, Nisala A; Liyanage, Dileepa S; Bulathsinhala, Nuwani E; Adikary, Subhashanie; Aluthmuhandiram, Janith V S; Thanaseelan, Chrishanthi S; Tharmakulasingam, D Portia; Karunakaran, Tharaga; Ilango, Janahan

    2017-09-19

    Infectious disease is the leading cause of death worldwide, and diagnosis of polymicrobial and fungal infections is increasingly challenging in the clinical setting. Conventionally, molecular detection is still the best method of species identification in clinical samples. However, the limitations of Sanger sequencing make diagnosis of polymicrobial infections one of the biggest hurdles in treatment. The development of massively parallel sequencing or next generation sequencing (NGS) has revolutionized the field of metagenomics, with wide application of the technology in identification of microbial communities in environmental sources, human gut and others. However, to date there has been no commercial application of this technology in infectious disease diagnostic settings. Credence Genomics Rapid Infection Detection™ test, is a molecular based diagnostic test that uses next generation sequencing of bacterial 16S rRNA gene and fungal ITS1 gene region to provide accurate identification of species within a clinical sample. Here we present a study comparing 16S and ITS1 metagenomic identification against conventional culture for clinical samples. Using culture results as gold standard, a comparison was conducted using patient specimens from a clinical microbiology lab. Metagenomics based results show a 91.8% concordance rate for culture positive specimens and 52.8% concordance rate with culture negative samples. 10.3% of specimens were also positive for fungal species which was not investigated by culture. Specificity and sensitivity for metagenomics analysis is 91.8 and 52.7% respectively. 16S based metagenomic identification of bacterial species within a clinical specimen is on par with conventional culture based techniques and when coupled with clinical information can lead to an accurate diagnostic tool for infectious disease diagnosis.

  12. 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

  13. A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda

    Science.gov (United States)

    Blomström, Anne-Lie; Lalander, Cecilia; Komakech, Allan John; Vinnerås, Björn; Boqvist, Sofia

    2016-01-01

    Background Vermicomposting is a mesophilic process using earthworms to efficiently and at low cost process large volumes of organic waste. It has been suggested to not only increase soil fertility but also increase biomass of beneficial bacteria while reducing harmful bacteria. The aim of this study was to set up a strategy to investigate and characterise the viral as well as the bacterial composition of a vermicomposting system. Material and methods The vermicomposting unit used in this study was placed at the Makerere University Agricultural Research Institute Kabanyolo on the outskirts of Kampala, Uganda, and was fed with 80% cattle manure and 20% food waste. On Day 172, the compost was terminated and compost samples were collected from three layers of the unit: the top, the middle and the bottom layer. A metagenomic approach was then applied to characterise the viral and bacterial composition of the vermicomposting system. Results and discussion A high abundance and diversity of bacteria were identified. Proteobacteria was the largest phyla in the compost (mainly Alpha-, Gamma- and Betaproteobacteria), constituting almost 65% of the bacterial reads in the data sets. DNA samples from several possible pathogenic bacteria, such as Salmonella spp., Escherichia coli, Enterobacter spp., Enterococcus spp. and Clostridium spp, were detected in the vermicompost, suggesting that there might still be harmful bacteria in the vermicast. Phages constituted the main viral group; apart from phages, mainly insect viruses were identified. The only animal or human virus identified was kobuvirus. In summary, metagenomic analysis was shown to be an efficient technology to characterise the microbial composition of vermicast. The data from this study contribute to a better understanding of the microbes present in this kind of composting system and can help determine measures necessary for safe manure handling. PMID:27834174

  14. A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda

    Directory of Open Access Journals (Sweden)

    Anne-Lie Blomström

    2016-11-01

    Full Text Available Background: Vermicomposting is a mesophilic process using earthworms to efficiently and at low cost process large volumes of organic waste. It has been suggested to not only increase soil fertility but also increase biomass of beneficial bacteria while reducing harmful bacteria. The aim of this study was to set up a strategy to investigate and characterise the viral as well as the bacterial composition of a vermicomposting system. Material and methods: The vermicomposting unit used in this study was placed at the Makerere University Agricultural Research Institute Kabanyolo on the outskirts of Kampala, Uganda, and was fed with 80% cattle manure and 20% food waste. On Day 172, the compost was terminated and compost samples were collected from three layers of the unit: the top, the middle and the bottom layer. A metagenomic approach was then applied to characterise the viral and bacterial composition of the vermicomposting system. Results and discussion: A high abundance and diversity of bacteria were identified. Proteobacteria was the largest phyla in the compost (mainly Alpha-, Gamma- and Betaproteobacteria, constituting almost 65% of the bacterial reads in the data sets. DNA samples from several possible pathogenic bacteria, such as Salmonella spp., Escherichia coli, Enterobacter spp., Enterococcus spp. and Clostridium spp, were detected in the vermicompost, suggesting that there might still be harmful bacteria in the vermicast. Phages constituted the main viral group; apart from phages, mainly insect viruses were identified. The only animal or human virus identified was kobuvirus. In summary, metagenomic analysis was shown to be an efficient technology to characterise the microbial composition of vermicast. The data from this study contribute to a better understanding of the microbes present in this kind of composting system and can help determine measures necessary for safe manure handling.

  15. Challenges and opportunities of airborne metagenomics.

    Science.gov (United States)

    Behzad, Hayedeh; Gojobori, Takashi; Mineta, Katsuhiko

    2015-05-06

    Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. Gene Prediction in Metagenomic Fragments with Deep Learning

    Directory of Open Access Journals (Sweden)

    Shao-Wu Zhang

    2017-01-01

    Full Text Available Next generation sequencing technologies used in metagenomics yield numerous sequencing fragments which come from thousands of different species. Accurately identifying genes from metagenomics fragments is one of the most fundamental issues in metagenomics. In this article, by fusing multifeatures (i.e., monocodon usage, monoamino acid usage, ORF length coverage, and Z-curve features and using deep stacking networks learning model, we present a novel method (called Meta-MFDL to predict the metagenomic genes. The results with 10 CV and independent tests show that Meta-MFDL is a powerful tool for identifying genes from metagenomic fragments.

  17. Gene Prediction in Metagenomic Fragments with Deep Learning.

    Science.gov (United States)

    Zhang, Shao-Wu; Jin, Xiang-Yang; Zhang, Teng

    2017-01-01

    Next generation sequencing technologies used in metagenomics yield numerous sequencing fragments which come from thousands of different species. Accurately identifying genes from metagenomics fragments is one of the most fundamental issues in metagenomics. In this article, by fusing multifeatures (i.e., monocodon usage, monoamino acid usage, ORF length coverage, and Z-curve features) and using deep stacking networks learning model, we present a novel method (called Meta-MFDL) to predict the metagenomic genes. The results with 10 CV and independent tests show that Meta-MFDL is a powerful tool for identifying genes from metagenomic fragments.

  18. Origami-based earthworm-like locomotion robots.

    Science.gov (United States)

    Fang, Hongbin; Zhang, Yetong; Wang, K W

    2017-10-16

    Inspired by the morphology characteristics of the earthworms and the excellent deformability of origami structures, this research creates a novel earthworm-like locomotion robot through exploiting the origami techniques. In this innovation, appropriate actuation mechanisms are incorporated with origami ball structures into the earthworm-like robot 'body', and the earthworm's locomotion mechanism is mimicked to develop a gait generator as the robot 'centralized controller'. The origami ball, which is a periodic repetition of waterbomb units, could output significant bidirectional (axial and radial) deformations in an antagonistic way similar to the earthworm's body segment. Such bidirectional deformability can be strategically programmed by designing the number of constituent units. Experiments also indicate that the origami ball possesses two outstanding mechanical properties that are beneficial to robot development: one is the structural multistability in the axil direction that could contribute to the robot control implementation; and the other is the structural compliance in the radial direction that would increase the robot robustness and applicability. To validate the origami-based innovation, this research designs and constructs three robot segments based on different axial actuators: DC-motor, shape-memory-alloy springs, and pneumatic balloon. Performance evaluations reveal their merits and limitations, and to prove the concept, the DC-motor actuation is selected for building a six-segment robot prototype. Learning from earthworms' fundamental locomotion mechanism-retrograde peristalsis wave, seven gaits are automatically generated; controlled by which, the robot could achieve effective locomotion with qualitatively different modes and a wide range of average speeds. The outcomes of this research could lead to the development of origami locomotion robots with low fabrication costs, high customizability, light weight, good scalability, and excellent re-configurability.

  19. Bioavailability of nonextractable (bound) pesticide residues to earthworms.

    Science.gov (United States)

    Gevao, B; Mordaunt, C; Semple, K T; Piearce, T G; Jones, K C

    2001-02-01

    There is an ongoing debate regarding whether nonextractable (bound) pesticide residues in soils are occluded or may remain bioavailable in the long term in the environment. This study investigated the release of 14C-labeled residues, which were previously nonextractable after exhaustive extraction with organic solvents in soils, and their uptake by earthworms (Aporrectodea longa). After a 100-day incubation of soils treated with 14C-labeled atrazine, isoproturon, and dicamba and exhaustive Soxhlet extractions with methanol and dichloromethane, nonextracted 14C-labeled residues remaining in the soils were 18, 70, and 67%, respectively. Adding clean soil in the ratio of 7:1 increased the volumes of these extracted soils. After earthworms had lived in these previously extracted soils for 28 days, 0.02-0.2% of previously bound 14C activity was absorbed into the earthworm tissue. Uptake by earthworms was found to be 2-10 times higher in soils containing freshly introduced 14C-labeled pesticides as compared to soils containing nonextractable 14C-labeled residues. The differential bioavailability observed between freshly introduced 14C-labeled pesticides and those previously nonextractable may be related to the ease of transfer of the 14C activity into the solution phase. By the end of the 28-day incubation period, 3, 23, and 24% of previously nonextractable 14C-labeled isoproturon, dicamba, and atrazine residues, respectively, were extracted by solvents or mineralized to 14CO2. The amounts of 14C activity released were not significantly different in the presence or in the absence of earthworms in soils containing previously nonextractable residues. However, the formation of bound residues was 2, 2, and 4 times lower for freshly introduced 14C-labeled isoproturon, dicamba, and atrazine, respectively, suggesting that the presence of earthworms retarded bound residue formation.

  20. Enantioseletive bioaccumulation of tebuconazole in earthworm Eisenia fetida.

    Science.gov (United States)

    Yu, Dingyi; Li, Jianzhong; Zhang, Yanfeng; Wang, Huili; Guo, Baoyuan; Zheng, Lin

    2012-01-01

    Methods of extraction and determination of tebuconazole enantiomers in earthworm (Eisenia fetida) were developed by capillary electrophoresis (CE) and high performance liquid chromatography (HPLC). Both CE and HPLC have excellent resolution and recovery. The linearity ranges were 2.9-102.4 mg/kg and 3.0-99.6 mg/kg for (+)-R-tebuconazole and (-)-S-tebuconazole respectively in CE, and from 0.56 to 1000 mg/kg for both enantiomers in HPLC. Enantioselective bioaccumulation in earthworms from soil was investigated under laboratory condition at concentrations of 10 and 50 mg/kg dw in soil. The uptake kinetics of (+)-R-tebuconazole fitted the first-order kinetics well with r2 0.97 and 0.94 under 10 and 50 mg/kg dw exposure condition, respectively, while (-)-S-tebuconazole with r2 0.75 and 0.22 did not show the same. Bioaccumulation of tebuconazole in earthworm tissues was enantioselective with a preferential accumulation of (+)-R-tebuconazole. The (+)-R-tebuconazole might also have biomagnifying effect potential in earthworm food chain with biota-sediment accumulation factor (BSAF) of 1.64 kg OC/kg lip in 10 mg/kg dw exposure group and 2.61 kg OC/kg lip in 50 mg/kg dw exposure group from soil to earthworm after 36 days. Although (-)-S-tebuconazole shares the same physicochemical properties with (+)-R-tebuconazole, it did not biomagnify. BSAFs of (-)-S-tebuconazole were 0.50 kg OC/kg lip (10 mg/kg dw tebuconazole exposure) and 0.28 kg OC/kg lip (50 mg/kg dw tebuconazole exposure) after 36 days, which was possibly owing to biotransformation or metabolism in earthworm tissues.

  1. Comparative toxicity of chemicals to earthworms

    Energy Technology Data Exchange (ETDEWEB)

    Callahan, C.A.; Shirazi, M.A. (Environmental Protection Agency, Corvallis, OR (United States)); Neuhauser, E.F. (Niagara Mohawk Power Corp., Syracuse, NY (United States))

    1994-02-01

    The concentration-response (mortality) relationships of four species of earthworms, Eisenia fetida (Savigny), Allolobophora tuberculata (Eisen), Eudrilus eugeniae (Kinberg), and Perionyx excavatus (Perrier) are summarized for 62 chemicals and two test protocols. A Weibull function is used to summarize these data for each chemical in terms of sensitivity and toxicity, in addition to the LC50. The estimation of the Weibull parameters a and k summarize the entire concentration-response relationship. This technique should be applicable to a variety of testing protocols with different species whenever the goal is summarizing the shape of the concentration-response curves to fully evaluate chemical impact on organisms. In some cases for these data four orders of magnitude separate LC50s of the soil test and the contact test for the same chemical and species. All four species appear to be similar in range of toxicity and tolerance to these chemicals, suggesting that Eisenia fetida and may be representative of these four species and these chemicals.

  2. Soil type influence on Ag Nanoparticles by earthworms, Eisenia fetida

    DEFF Research Database (Denmark)

    Mariyadas, Jennifer; Mónica, Amorim; Scott-Fordsmand, Janeck James

    2014-01-01

    Earthworms are key sentinel organisms playing an important role in improving the soil structure. Here we tested the importance of soil type on the toxicity to silver nanoparticles (Ag NPs) to earthworms, Eisenia fetida. Silver nanoparticles are widely used in a range of consumer products mainly...... matter content, clay and cation exchange capacity along with the metal solution activity will provide insight into the bioavailability of metals in different soils, hence For each of the soil type the fate of the AgNPs was also measured....

  3. New data to the earthworm fauna of Israel (Oligochaeta, Lumbricidae

    Directory of Open Access Journals (Sweden)

    Szederjesi, T.

    2013-11-01

    Full Text Available Elaborating several smaller earthworm samples collected in different parts of Israel resulted in recording 20 earthworm species including Bimastos parvus (Eisen, 1874 a North American peregrine which represents new record for the country. Three other species; Dendrobaena nevoi Csuzdi & Pavlíček, 1999, Healyella jordanis (Csuzdi & Pavlíček, 1999and Perelia shamsi Csuzdi & Pavlíček, 2005 were first recorded after their original descriptions. The present list of lumbricidearthworms recorded for Israel is raised to 28.

  4. Metagenomics as a Tool for Enzyme Discovery: Hydrolytic Enzymes from Marine-Related Metagenomes.

    Science.gov (United States)

    Popovic, Ana; Tchigvintsev, Anatoly; Tran, Hai; Chernikova, Tatyana N; Golyshina, Olga V; Yakimov, Michail M; Golyshin, Peter N; Yakunin, Alexander F

    2015-01-01

    This chapter discusses metagenomics and its application for enzyme discovery, with a focus on hydrolytic enzymes from marine metagenomic libraries. With less than one percent of culturable microorganisms in the environment, metagenomics, or the collective study of community genetics, has opened up a rich pool of uncharacterized metabolic pathways, enzymes, and adaptations. This great untapped pool of genes provides the particularly exciting potential to mine for new biochemical activities or novel enzymes with activities tailored to peculiar sets of environmental conditions. Metagenomes also represent a huge reservoir of novel enzymes for applications in biocatalysis, biofuels, and bioremediation. Here we present the results of enzyme discovery for four enzyme activities, of particular industrial or environmental interest, including esterase/lipase, glycosyl hydrolase, protease and dehalogenase.

  5. Gut Microbiome and Antibiotics.

    Science.gov (United States)

    Iizumi, Tadasu; Battaglia, Thomas; Ruiz, Victoria; Perez Perez, Guillermo I

    2017-12-05

    Despite that the human gastrointestinal tract is the most populated ecological niche by bacteria in the human body, much is still unknown about its characteristics. This site is highly susceptible to the effects of many external factors that may affect in the quality and the quantity of the microbiome. Specific factors such as diet, personal hygiene, pharmacological drugs and the use of antibiotics can produce a significant impact on the gut microbiota. The effect of these factors is more relevant early in life, when the gut microbiota has not yet fully established. In this review, we discussed the effect of type and doses of the antibiotics on the gut microbiota and what the major consequences in the use and abuse of these antimicrobial agents. Copyright © 2017 IMSS. Published by Elsevier Inc. All rights reserved.

  6. Villification of the gut

    Science.gov (United States)

    Tallinen, Tuomas; Shyer, Amy E.; Tabin, Clifford J.; Mahadevan, L.

    2014-03-01

    The villi of the human and chick gut are formed in similar stepwise progressions, wherein the mesenchyme and attached epithelium first fold into longitudinal ridges, then a zigzag pattern, and lastly individual villi. We combine biological manipulations and quantitative modeling to show that these steps of villification depend on the sequential differentiation of the distinct smooth muscle layers of the gut, which restrict the expansion of the growing endoderm and mesenchyme, generating compressive stresses that lead to their buckling and folding. Our computational model incorporates measured elastic properties and growth rates in the developing gut, recapitulating the morphological patterns seen during villification in a variety of species. Our study provides a mechanical basis for the genesis of these epithelial protrusions that are essential for providing sufficient surface area for nutrient absorption.

  7. Hot topics in gut microbiota

    OpenAIRE

    Doré, Joël; Simrén, Magnus; Buttle, Lisa; Guarner, Francisco

    2013-01-01

    The study of gut microbiota is a rapidly moving field of research, and the impact of gut microbial communities on human health is widely perceived as one of the most exciting advancements in biomedicine in recent years. The gut microbiota plays a key role in digestion, metabolism and immune function, and has widespread impact beyond the gastrointestinal tract. Changes in the biodiversity of the gut microbiota are associated with far reaching consequences on host health and development. Furthe...

  8. Application of metagenomics in poultry research

    Science.gov (United States)

    The complicated microbiota in the gut of agriculturally important animals has a direct impact on animal health, fitness, and performance. The advent of high-throughput nucleic acid sequencing has allowed our laboratory to assemble a more complete—albeit more complicated—picture of the gut microbiota...

  9. Diet, gut microbiota and cognition.

    Science.gov (United States)

    Proctor, Cicely; Thiennimitr, Parameth; Chattipakorn, Nipon; Chattipakorn, Siriporn C

    2017-02-01

    The consumption of a diet high in fat and sugar can lead to the development of obesity, type 2 diabetes mellitus (T2DM), cardiovascular disease and cognitive decline. In the human gut, the trillions of harmless microorganisms harboured in the host's gastrointestinal tract are called the 'gut microbiota'. Consumption of a diet high in fat and sugar changes the healthy microbiota composition which leads to an imbalanced microbial population in the gut, a phenomenon known as "gut dysbiosis". It has been shown that certain types of gut microbiota are linked to the pathogenesis of obesity. In addition, long-term consumption of a high fat diet is associated with cognitive decline. It has recently been proposed that the gut microbiota is part of a mechanistic link between the consumption of a high fat diet and the impaired cognition of an individual, termed "microbiota-gut-brain axis". In this complex relationship between the gut, the brain and the gut microbiota, there are several types of gut microbiota and host mechanisms involved. Most of these mechanisms are still poorly understood. Therefore, this review comprehensively summarizes the current evidence from mainly in vivo (rodent and human) studies of the relationship between diet, gut microbiota and cognition. The possible mechanisms that the diet and the gut microbiota have on cognition are also presented and discussed.

  10. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

    Science.gov (United States)

    Olson, Nathan D; Treangen, Todd J; Hill, Christopher M; Cepeda-Espinoza, Victoria; Ghurye, Jay; Koren, Sergey; Pop, Mihai

    2017-08-07

    Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation. © The Author 2017. Published by Oxford University Press.

  11. Assembly of viral genomes from metagenomes

    Directory of Open Access Journals (Sweden)

    Saskia L Smits

    2014-12-01

    Full Text Available Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.

  12. The metagenomic approach and causality in virology

    Directory of Open Access Journals (Sweden)

    Silvana Beres Castrignano

    2015-01-01

    Full Text Available Nowadays, the metagenomic approach has been a very important tool in the discovery of new viruses in environmental and biological samples. Here we discuss how these discoveries may help to elucidate the etiology of diseases and the criteria necessary to establish a causal association between a virus and a disease.

  13. Towards a more complete metagenomics toolkit

    Science.gov (United States)

    The emerging scientific discipline of metagenomics has not only created a myriad of opportunities for biologists to reveal new insights into the microbial underpinnings of our environment, but has also presented a number of interesting challenges for bioinformatics algorithms and software developers...

  14. Applications of metagenomics for industrial bioproducts

    Science.gov (United States)

    Recent progress in mining the rich genetic resource of non-culturable microbes has led to the discovery of new genes, enzymes, and natural products. The impact of metagenomics is witnessed in the development of commodity and fine chemicals, agrochemicals and pharmaceuticals where the benefit of enz...

  15. Bracken: estimating species abundance in metagenomics data

    Directory of Open Access Journals (Sweden)

    Jennifer Lu

    2017-01-01

    Full Text Available Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.

  16. Clustering metagenomic sequences with interpolated Markov models

    Science.gov (United States)

    2010-01-01

    Background Sequencing of environmental DNA (often called metagenomics) has shown tremendous potential to uncover the vast number of unknown microbes that cannot be cultured and sequenced by traditional methods. Because the output from metagenomic sequencing is a large set of reads of unknown origin, clustering reads together that were sequenced from the same species is a crucial analysis step. Many effective approaches to this task rely on sequenced genomes in public databases, but these genomes are a highly biased sample that is not necessarily representative of environments interesting to many metagenomics projects. Results We present SCIMM (Sequence Clustering with Interpolated Markov Models), an unsupervised sequence clustering method. SCIMM achieves greater clustering accuracy than previous unsupervised approaches. We examine the limitations of unsupervised learning on complex datasets, and suggest a hybrid of SCIMM and supervised learning method Phymm called PHYSCIMM that performs better when evolutionarily close training genomes are available. Conclusions SCIMM and PHYSCIMM are highly accurate methods to cluster metagenomic sequences. SCIMM operates entirely unsupervised, making it ideal for environments containing mostly novel microbes. PHYSCIMM uses supervised learning to improve clustering in environments containing microbial strains from well-characterized genera. SCIMM and PHYSCIMM are available open source from http://www.cbcb.umd.edu/software/scimm. PMID:21044341

  17. Clustering metagenomic sequences with interpolated Markov models.

    Science.gov (United States)

    Kelley, David R; Salzberg, Steven L

    2010-11-02

    Sequencing of environmental DNA (often called metagenomics) has shown tremendous potential to uncover the vast number of unknown microbes that cannot be cultured and sequenced by traditional methods. Because the output from metagenomic sequencing is a large set of reads of unknown origin, clustering reads together that were sequenced from the same species is a crucial analysis step. Many effective approaches to this task rely on sequenced genomes in public databases, but these genomes are a highly biased sample that is not necessarily representative of environments interesting to many metagenomics projects. We present SCIMM (Sequence Clustering with Interpolated Markov Models), an unsupervised sequence clustering method. SCIMM achieves greater clustering accuracy than previous unsupervised approaches. We examine the limitations of unsupervised learning on complex datasets, and suggest a hybrid of SCIMM and supervised learning method Phymm called PHYSCIMM that performs better when evolutionarily close training genomes are available. SCIMM and PHYSCIMM are highly accurate methods to cluster metagenomic sequences. SCIMM operates entirely unsupervised, making it ideal for environments containing mostly novel microbes. PHYSCIMM uses supervised learning to improve clustering in environments containing microbial strains from well-characterized genera. SCIMM and PHYSCIMM are available open source from http://www.cbcb.umd.edu/software/scimm.

  18. Clustering metagenomic sequences with interpolated Markov models

    Directory of Open Access Journals (Sweden)

    Kelley David R

    2010-11-01

    Full Text Available Abstract Background Sequencing of environmental DNA (often called metagenomics has shown tremendous potential to uncover the vast number of unknown microbes that cannot be cultured and sequenced by traditional methods. Because the output from metagenomic sequencing is a large set of reads of unknown origin, clustering reads together that were sequenced from the same species is a crucial analysis step. Many effective approaches to this task rely on sequenced genomes in public databases, but these genomes are a highly biased sample that is not necessarily representative of environments interesting to many metagenomics projects. Results We present SCIMM (Sequence Clustering with Interpolated Markov Models, an unsupervised sequence clustering method. SCIMM achieves greater clustering accuracy than previous unsupervised approaches. We examine the limitations of unsupervised learning on complex datasets, and suggest a hybrid of SCIMM and supervised learning method Phymm called PHYSCIMM that performs better when evolutionarily close training genomes are available. Conclusions SCIMM and PHYSCIMM are highly accurate methods to cluster metagenomic sequences. SCIMM operates entirely unsupervised, making it ideal for environments containing mostly novel microbes. PHYSCIMM uses supervised learning to improve clustering in environments containing microbial strains from well-characterized genera. SCIMM and PHYSCIMM are available open source from http://www.cbcb.umd.edu/software/scimm.

  19. Soil Penetration by Earthworms and Plant Roots—Mechanical Energetics of Bioturbation of Compacted Soils

    Science.gov (United States)

    2015-01-01

    We quantify mechanical processes common to soil penetration by earthworms and growing plant roots, including the energetic requirements for soil plastic displacement. The basic mechanical model considers cavity expansion into a plastic wet soil involving wedging by root tips or earthworms via cone-like penetration followed by cavity expansion due to pressurized earthworm hydroskeleton or root radial growth. The mechanical stresses and resulting soil strains determine the mechanical energy required for bioturbation under different soil hydro-mechanical conditions for a realistic range of root/earthworm geometries. Modeling results suggest that higher soil water content and reduced clay content reduce the strain energy required for soil penetration. The critical earthworm or root pressure increases with increased diameter of root or earthworm, however, results are insensitive to the cone apex (shape of the tip). The invested mechanical energy per unit length increase with increasing earthworm and plant root diameters, whereas mechanical energy per unit of displaced soil volume decreases with larger diameters. The study provides a quantitative framework for estimating energy requirements for soil penetration work done by earthworms and plant roots, and delineates intrinsic and external mechanical limits for bioturbation processes. Estimated energy requirements for earthworm biopore networks are linked to consumption of soil organic matter and suggest that earthworm populations are likely to consume a significant fraction of ecosystem net primary production to sustain their subterranean activities. PMID:26087130

  20. The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome

    Science.gov (United States)

    Wang, Hang; Sangwan, Naseer; Li, Hong-Yi; Su, Jian-Qiang; Oyang, Wei-Yin; Zhang, Zhi-Jian; Gilbert, Jack A; Zhu, Yong-Guan; Ping, Fan; Zhang, Han-Luo

    2017-01-01

    The overuse of antibiotics as veterinary feed additives is potentially contributing to a significant reservoir of antibiotic resistance in agricultural farmlands via the application of antibiotic-contaminated manure. Vermicomposting of swine manure using housefly larvae is a promising biotechnology for waste reduction and control of antibiotic pollution. To determine how vermicomposting influences antibiotic resistance traits in swine manure, we explored the resistome and associated bacterial community dynamics during larvae gut transit over 6 days of treatment. In total, 94 out of 158 antibiotic resistance genes (ARGs) were significantly attenuated (by 85%), while 23 were significantly enriched (3.9-fold) following vermicomposting. The manure-borne bacterial community showed a decrease in the relative abundance of Bacteroidetes, and an increase in Proteobacteria, specifically Ignatzschineria, following gut transit. ARG attenuation was significantly correlated with changes in microbial community succession, especially reduction in Clostridiales and Bacteroidales. Six genomes were assembled from the manure, vermicompost (final product) and gut samples, including Pseudomonas, Providencia, Enterococcus, Bacteroides and Alcanivorax. Transposon-linked ARGs were more abundant in gut-associated bacteria compared with those from manure and vermicompost. Further, ARG-transposon gene cassettes had a high degree of synteny between metagenomic assemblies from gut and vermicompost samples, highlighting the significant contribution of gut microbiota through horizontal gene transfer to the resistome of vermicompost. In conclusion, the larvae gut microbiome significantly influences manure-borne community succession and the antibiotic resistome during animal manure processing. PMID:27458785

  1. 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

  2. Aggregate formation and soil carbon sequestration by earthworms at the ORNL FACE experiment

    Science.gov (United States)

    Sanchez-de Leon, Y.; Gonzalez-Meler, M. A.; Lugo-Perez, J.; Wise, D. H.; Jastrow, J. D.

    2012-12-01

    Earthworms have an important role in soil carbon sequestration, but their contribution to carbon sequestration in soils exposed to elevated atmospheric CO2 concentrations has been largely overlooked. Previous studies at the Oak Ridge National Laboratory Free Air CO2 Experiment (ORNL FACE) site showed that the formation of soil aggregates is a key mechanism for soil carbon sequestration. We did a microcosm experiment to quantify earthworm-mediated aggregate formation and compare between two earthworm species with different feeding habits (endogeic vs. epi-edogeic). In addition, we wanted to identify the carbon source (soil, leaf litter or root litter) within aggregates formed by earthworms. We used 13C-depleted soil and 15N-enriched sweetgum (Liquidambar styraciflua) leaf and root litter collected from the ORNL FACE site to assess soil aggregate formation of the native, endogeic earthworm Diplocardia sp. and European, epi-endogeic earthworm Lumbricus rubellus. Both earthworm species are present at the ORNL FACE site. We crushed, sieved ( 250 μm) were higher in treatments with earthworms (III and IV) than in treatments without earthworms (I and II) (p = 0.02). Within macroaggregates, most of the carbon was soil-derived. Leaf and root-derived carbon was found in treatment IV only. Our results suggest that earthworms at the ORNL FACE site directly contribute to the formation of soil aggregates, thus contributing to soil carbon sequestration. Carbon source within macroaggregates correspond with earthworm feeding habits, with endogeic earthworms (Diplocardia sp.) feeding mostly on mineral soil and epi-endogeic earthworm (L. rubellus) feeding on both plant residues and soil organic matter.

  3. Invasion by Exotic Earthworms Alters Biodiversity and Communities of Litter- and Soil-dwelling Oribatid Mites

    Directory of Open Access Journals (Sweden)

    John C. Maerz

    2011-03-01

    Full Text Available Exotic earthworms are drivers of biotic communities in invaded North American forest stands. Here we used ecologically important oribatid mite (Arachnida: Acari communities, as model organisms to study the responses of litter- and soil-dwelling microarthropod communities to exotic earthworm invasion in a northern temperate forest. Litter- and soil-dwelling mites were sampled in 2008–2009 from forest areas: (1 with no earthworms; (2 those with epigeic and endogeic species, including Lumbricus rubellus Hoffmeister; and (3 those with epigeic, endogeic, and anecic earthworms including L. terrestris L. Species richness and diversity of litter- and soil-dwelling (0–2 cm soil depth oribatid mites was 1–2 times higher in sites without earthworms than in sites with worms. Similarly, litter-dwelling oribatid mites were between 72 and 1,210 times more abundant in earthworm-free sites than in sites with worms. Among earthworm invaded sites, abundance of litter-dwelling oribatid mites in sites without the anecic L. terrestris was twice as high in May and 28 times higher in October, compared to sites with L. terrestris. Species richness, diversity, and abundance of oribatid mites were greater in litter-layers than in the soil-layers that showed a varied response to earthworm invasion. Species compositions of both litter- and soil-dwelling oribatid mite communities of forests with no earthworms were markedly different from those with earthworms. We conclude that exotic earthworm invasions are associated with significant declines of species diversity, numbers, and compositional shifts in litter- and soil-inhabiting communities. These faunal shifts may contribute to earthworm effects on soil processes and food web dynamics in historically earthworm-free, northern temperate forests.

  4. The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders.

    Science.gov (United States)

    Liu, Ya-Jun; Zaprasis, Adrienne; Liu, Shuang-Jiang; Drake, Harold L; Horn, Marcus A

    2011-03-01

    2-Methyl-4-chlorophenoxyacetic acid (MCPA) is a widely used phenoxyalkanoic acid (PAA) herbicide. Earthworms represent the dominant macrofauna and enhance microbial activities in many soils. Thus, the effect of the model earthworm Aporrectodea caliginosa (Oligochaeta, Lumbricidae) on microbial MCPA degradation was assessed in soil columns with agricultural soil. MCPA degradation was quicker in soil with earthworms than without earthworms. Quantitative PCR was inhibition-corrected per nucleic acid extract and indicated that copy numbers of tfdA-like and cadA genes (both encoding oxygenases initiating aerobic PAA degradation) in soil with earthworms were up to three and four times higher than without earthworms, respectively. tfdA-like and 16S rRNA gene transcript copy numbers in soil with earthworms were two and six times higher than without earthworms, respectively. Most probable numbers (MPNs) of MCPA degraders approximated 4 × 10(5) g(dw)(-1) in soil before incubation and in soil treated without earthworms, whereas MPNs of earthworm-treated soils were approximately 150 × higher. The aerobic capacity of soil to degrade MCPA was higher in earthworm-treated soils than in earthworm-untreated soils. Burrow walls and 0-5 cm depth bulk soil displayed higher capacities to degrade MCPA than did soil from 5-10 cm depth bulk soil, expression of tfdA-like genes in burrow walls was five times higher than in bulk soil and MCPA degraders were abundant in burrow walls (MPNs of 5 × 10(7) g(dw)(-1)). The collective data indicate that earthworms stimulate abundance and activity of MCPA degraders endogenous to soil by their burrowing activities and might thus be advantageous for enhancing PAA degradation in soil.

  5. The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders

    Science.gov (United States)

    Liu, Ya-Jun; Zaprasis, Adrienne; Liu, Shuang-Jiang; Drake, Harold L; Horn, Marcus A

    2011-01-01

    2-Methyl-4-chlorophenoxyacetic acid (MCPA) is a widely used phenoxyalkanoic acid (PAA) herbicide. Earthworms represent the dominant macrofauna and enhance microbial activities in many soils. Thus, the effect of the model earthworm Aporrectodea caliginosa (Oligochaeta, Lumbricidae) on microbial MCPA degradation was assessed in soil columns with agricultural soil. MCPA degradation was quicker in soil with earthworms than without earthworms. Quantitative PCR was inhibition-corrected per nucleic acid extract and indicated that copy numbers of tfdA-like and cadA genes (both encoding oxygenases initiating aerobic PAA degradation) in soil with earthworms were up to three and four times higher than without earthworms, respectively. tfdA-like and 16S rRNA gene transcript copy numbers in soil with earthworms were two and six times higher than without earthworms, respectively. Most probable numbers (MPNs) of MCPA degraders approximated 4 × 105 gdw−1 in soil before incubation and in soil treated without earthworms, whereas MPNs of earthworm-treated soils were approximately 150 × higher. The aerobic capacity of soil to degrade MCPA was higher in earthworm-treated soils than in earthworm-untreated soils. Burrow walls and 0–5 cm depth bulk soil displayed higher capacities to degrade MCPA than did soil from 5–10 cm depth bulk soil, expression of tfdA-like genes in burrow walls was five times higher than in bulk soil and MCPA degraders were abundant in burrow walls (MPNs of 5 × 107 gdw−1). The collective data indicate that earthworms stimulate abundance and activity of MCPA degraders endogenous to soil by their burrowing activities and might thus be advantageous for enhancing PAA degradation in soil. PMID:20740027

  6. Extracellular vesicles derived from gut microbiota, especially Akkermansia muciniphila, protect the progression of dextran sulfate sodium-induced colitis.

    Directory of Open Access Journals (Sweden)

    Chil-Sung Kang

    Full Text Available Gut microbiota play an important part in the pathogenesis of mucosal inflammation, such as inflammatory bowel disease (IBD. However, owing to the complexity of the gut microbiota, our understanding of the roles of commensal and pathogenic bacteria in the maintenance of immune homeostasis in the gut is evolving only slowly. Here, we evaluated the role of gut microbiota and their secreting extracellular vesicles (EV in the development of mucosal inflammation in the gut. Experimental IBD model was established by oral application of dextran sulfate sodium (DSS to C57BL/6 mice. The composition of gut microbiota and bacteria-derived EV in stools was evaluated by metagenome sequencing using bacterial common primer of 16S rDNA. Metagenomics in the IBD mouse model showed that the change in stool EV composition was more drastic, compared to the change of bacterial composition. Oral DSS application decreased the composition of EV from Akkermansia muciniphila and Bacteroides acidifaciens in stools, whereas increased EV from TM7 phylum, especially from species DQ777900_s and AJ400239_s. In vitro pretreatment of A. muciniphila-derived EV ameliorated the production of a pro-inflammatory cytokine IL-6 from colon epithelial cells induced by Escherichia coli EV. Additionally, oral application of A. muciniphila EV also protected DSS-induced IBD phenotypes, such as body weight loss, colon length, and inflammatory cell infiltration of colon wall. Our data provides insight into the role of gut microbiota-derived EV in regulation of intestinal immunity and homeostasis, and A. muciniphila-derived EV have protective effects in the development of DSS-induced colitis.

  7. The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota.

    Science.gov (United States)

    Boursier, Jérôme; Mueller, Olaf; Barret, Matthieu; Machado, Mariana; Fizanne, Lionel; Araujo-Perez, Felix; Guy, Cynthia D; Seed, Patrick C; Rawls, John F; David, Lawrence A; Hunault, Gilles; Oberti, Frédéric; Calès, Paul; Diehl, Anna Mae

    2016-03-01

    Several animal studies have emphasized the role of gut microbiota in nonalcoholic fatty liver disease (NAFLD). However, data about gut dysbiosis in human NAFLD remain scarce in the literature, especially studies including the whole spectrum of NAFLD lesions. We aimed to evaluate the association between gut dysbiosis and severe NAFLD lesions, that is, nonalcoholic steatohepatitis (NASH) and fibrosis, in a well-characterized population of adult NAFLD. Fifty-seven patients with biopsy-proven NAFLD were enrolled. Taxonomic composition of gut microbiota was determined using 16S ribosomal RNA gene sequencing of stool samples. Thirty patients had F0/F1 fibrosis stage at liver biopsy (10 with NASH), and 27 patients had significant F≥2 fibrosis (25 with NASH). Bacteroides abundance was significantly increased in NASH and F≥2 patients, whereas Prevotella abundance was decreased. Ruminococcus abundance was significantly higher in F≥2 patients. By multivariate analysis, Bacteroides abundance was independently associated with NASH and Ruminococcus with F≥2 fibrosis. Stratification according to the abundance of these two bacteria generated three patient subgroups with increasing severity of NAFLD lesions. Based on imputed metagenomic profiles, Kyoto Encyclopedia of Genes and Genomes pathways significantly related to NASH and fibrosis F≥2 were mostly related to carbohydrate, lipid, and amino acid metabolism. NAFLD severity associates with gut dysbiosis and a shift in metabolic function of the gut microbiota. We identified Bacteroides as independently associated with NASH and Ruminococcus with significant fibrosis. Thus, gut microbiota analysis adds information to classical predictors of NAFLD severity and suggests novel metabolic targets for pre-/probiotics therapies. © 2015 by the American Association for the Study of Liver Diseases.

  8. The Human Gut Microbiota

    NARCIS (Netherlands)

    Harmsen, Hermie J. M.; de Goffau, Marcus. C.; Schwiertz, A

    2016-01-01

    The microbiota in our gut performs many different essential functions that help us to stay healthy. These functions include vitamin production, regulation of lipid metabolism and short chain fatty acid production as fuel for epithelial cells and regulation of gene expression. There is a very

  9. Philosophy with Guts

    Science.gov (United States)

    Sherman, Robert R.

    2014-01-01

    Western philosophy, from Plato on, has had the tendency to separate feeling and thought, affect and cognition. This article argues that a strong philosophy (metaphorically, with "guts") utilizes both in its work. In fact, a "complete act of thought" also will include action. Feeling motivates thought, which formulates ideas,…

  10. Food and the gut

    African Journals Online (AJOL)

    1994-11-09

    Nov 9, 1994 ... More women enter medicine: young doctors' family origin and career choice. Medical ... A. R. P. Walker pioneered the research into the association between food, gut function and disease patterns in ... unusual dietary and social changes is great, but there is a threshold level below which the adaptation ...

  11. Genomics: A gut prediction

    NARCIS (Netherlands)

    Vos, de W.M.; Nieuwdorp, M.

    2013-01-01

    Microbial cells make up the majority of cells in the human body, and most of these reside in the intestinal tract. Researchers have long recognized that some intestinal microorganisms are associated with health, but the beneficial impact of most of the gut's microbes on human metabolism has been

  12. Food and the gut

    African Journals Online (AJOL)

    1994-11-09

    Nov 9, 1994 ... saturated fat and cholesteroL' The obesity commonly seen in black women is not associated with ..... of lactose in a milk diet given over a 24-hour period.40 This brings into question the clinical relevance of adult ..... Circulating antibodies to cow's milk proteins in ulcerative colitis. Gut 1972; 13: 796-801. 45.

  13. Gut microbiota and malnutrition.

    Science.gov (United States)

    Million, Matthieu; Diallo, Aldiouma; Raoult, Didier

    2017-05-01

    Malnutrition is the leading cause of death worldwide in children under the age of five, and is the focus of the first World Health Organization (WHO) Millennium Development Goal. Breastfeeding, food and water security are major protective factors against malnutrition and critical factors in the maturation of healthy gut microbiota, characterized by a transient bifidobacterial bloom before a global rise in anaerobes. Early depletion in gut Bifidobacterium longum, a typical maternal probiotic, known to inhibit pathogens, represents the first step in gut microbiota alteration associated with severe acute malnutrition (SAM). Later, the absence of the Healthy Mature Anaerobic Gut Microbiota (HMAGM) leads to deficient energy harvest, vitamin biosynthesis and immune protection, and is associated with diarrhea, malabsorption and systemic invasion by microbial pathogens. A therapeutic diet and infection treatment may be unable to restore bifidobacteria and HMAGM. Besides refeeding and antibiotics, future trials including non-toxic missing microbes and nutrients necessary to restore bifidobacteria and HMAGM, including prebiotics and antioxidants, are warranted in children with severe or refractory disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. GUT FERMENTATION SYNDROME

    African Journals Online (AJOL)

    boaz

    individuals who became intoxicated after consuming carbohydrates, which became fermented in the gastrointestinal tract. These claims of intoxication without drinking alcohol, and the findings on endogenous alcohol fermentation are now called Gut. Fermentation Syndrome. This review will concentrate on understanding ...

  15. Marked variation between winter and spring gut microbiota in free-ranging Tibetan Macaques (Macaca thibetana)

    Science.gov (United States)

    Sun, Binghua; Wang, Xi; Bernstein, Sofi; Huffman, Michael A.; Xia, Dong-Po; Gu, Zhiyuan; Chen, Rui; Sheeran, Lori K.; Wagner, R. S; Li, Jinhua

    2016-01-01

    Variation in the availability and distribution of food resources is a strong selective pressure on wild primates. We explored variation in Tibetan macaque gut microbiota composition during winter and spring seasons. Our results showed that gut microbial composition and diversity varied by season. In winter, the genus Succinivibrio, which promotes the digestion of cellulose and hemicellulose, was significantly increased. In spring, the abundance of the genus Prevotella, which is associated with digestion of carbohydrates and simple sugars, was significantly increased. PICRUSt analysis revealed that the predicted metagenomes related to the glycan biosynthesis and metabolic pathway was significantly increased in winter samples, which would aid in the digestion of glycan extracted from cellulose and hemicellulose. The predicted metagenomes related to carbohydrate and energy metabolic pathways were significantly increased in spring samples, which could facilitate a monkey’s recovery from acute energy loss experienced during winter. We propose that shifts in the composition and function of the gut microbiota provide a buffer against seasonal fluctuations in energy and nutrient intake, thus enabling these primates to adapt to variations in food supply and quality. PMID:27180722

  16. Altered metabolism of gut microbiota contributes to chronic immune activation in HIV-infected individuals.

    Science.gov (United States)

    Vázquez-Castellanos, J F; Serrano-Villar, S; Latorre, A; Artacho, A; Ferrús, M L; Madrid, N; Vallejo, A; Sainz, T; Martínez-Botas, J; Ferrando-Martínez, S; Vera, M; Dronda, F; Leal, M; Del Romero, J; Moreno, S; Estrada, V; Gosalbes, M J; Moya, A

    2015-07-01

    Altered interplay between gut mucosa and microbiota during treated HIV infection may possibly contribute to increased bacterial translocation and chronic immune activation, both of which are predictors of morbidity and mortality. Although a dysbiotic gut microbiota has recently been reported in HIV+ individuals, the metagenome gene pool associated with HIV infection remains unknown. The aim of this study is to characterize the functional gene content of gut microbiota in HIV+ patients and to define the metabolic pathways of this bacterial community, which is potentially associated with immune dysfunction. We determined systemic markers of innate and adaptive immunity in a cohort of HIV-infected individuals on successful antiretroviral therapy without comorbidities and in healthy non-HIV-infected subjects. Metagenome sequencing revealed an altered functional profile, with enrichment of the genes involved in various pathogenic processes, lipopolysaccharide biosynthesis, bacterial translocation, and other inflammatory pathways. In contrast, we observed depletion of genes involved in amino acid metabolism and energy processes. Bayesian networks showed significant interactions between the bacterial community, their altered metabolic pathways, and systemic markers of immune dysfunction. This study reveals altered metabolic activity of microbiota and provides novel insight into the potential host-microbiota interactions driving the sustained inflammatory state in successfully treated HIV-infected patients.

  17. Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease

    Science.gov (United States)

    Petriz, Bernardo A.; Franco, Octávio L.

    2017-01-01

    Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota such as the human gut. The advances in molecular separation methods coupled with mass spectrometry (e.g. LC-MS/MS) and proteome bioinformatics have been fundamental in these novel large-scale metaproteomic studies, which have further been performed in a wide range of samples including soil, plant and human environments. Metaproteomic studies will make major progress if a comprehensive database covering the genes and expresses proteins from all gut microbial species is developed. To this end, we here present some of the main limitations of metaproteomic studies in complex microbiota environments such as the gut, also addressing the up-to-date pipelines in sample preparation prior to fractionation/separation and mass spectrometry analysis. In addition, a novel approach to the limitations of metagenomic databases is also discussed. Finally, prospects are addressed regarding the application of metaproteomic analysis using a unified host-microbiome gene database and other meta-OMICs platforms.

  18. Greenhouse-gas emissions from soils increased by earthworms

    NARCIS (Netherlands)

    Lubbers, I.M.; Groenigen, van K.J.; Fonte, S.J.; Six, J.; Brussaard, L.; Groenigen, van J.W.

    2013-01-01

    Earthworms play an essential part in determining the greenhouse-gas balance of soils worldwide, and their influence is expected to grow over the next decades. They are thought to stimulate carbon sequestration in soil aggregates, but also to increase emissions of the main greenhouse gases carbon

  19. Methodological Considerations in the Study of Earthworms in Forest Ecosystems

    Science.gov (United States)

    Dylan Rhea-Fournier; Grizelle Gonzalez

    2017-01-01

    Decades of studies have shown that soil macrofauna, especially earthworms, play dominant engineering roles in soils, affecting physical, chemical, and biological components of ecosystems. Quantifying these effects would allow crucial improvement in biogeochemical budgets and modeling, predicting response of land use and disturbance, and could be applied to...

  20. Feeding activity of the earthworm Eisenia andrei in artificial soil.

    NARCIS (Netherlands)

    Jager, D.T.; Fleuren, R.H.L.J.; Roelofs, W.; de Groot, A.C.

    2003-01-01

    Quantitative information on the feeding activity of earthworms is scarce but this information is valuable in many eco(toxico)logical studies. In this study, the feeding activity of the compost worm Eisenia andrei is examined in artificial soil (OECD medium), with and without a high-quality food

  1. Drivers of earthworm incidence and abundance across European forests

    DEFF Research Database (Denmark)

    Wandeler, Hans De; Sousa-Silva, Rita; Ampoorter, Evy

    2016-01-01

    Earthworms have a significant influence on the structure, composition and functioning of forest ecosystems, but in spite of their role as ecosystem engineers, little is known on the factors controlling their distribution across European forests. Optimised sampling techniques, as well as more adva...

  2. Impact of Biochar on Earthworm Populations: A Review

    Directory of Open Access Journals (Sweden)

    Sharon L. Weyers

    2011-01-01

    Full Text Available Despite the overwhelming importance of earthworm activity in the soil system, there are a limited number of studies that have examined the impact resulting from biochar addition to soil. Biochar is part of the black carbon continuum of chemo-thermal converted biomass. This review summarizes existing data pertaining to earthworms where biochar and other black carbon substances, including slash-and-burn charcoals and wood ash, have been applied. After analyzing existing studies on black carbon, we identified that these additions have a range from short-term negative impacts to long-term null effects on earthworm population density and total biomass. Documented cases of mortality were found with certain biochar-soil combinations; the cause is not fully understood, but hypothesized to be related to pH, whether the black carbon is premoistened, affects feeding behaviors, or other unknown factors. With wood ashes, negative impacts were overcome with addition of other carbon substrates. Given that field data is limited, soils amended with biochar did not appear to cause significant long-term impacts. However, this may indicate that the magnitude of short-term negative impacts on earthworm populations can be reduced with time.

  3. Exploring the pathways of earthworm-induced phosphorus availability

    NARCIS (Netherlands)

    Ros, Mart B.H.; Hiemstra, Tjisse; Groenigen, van Jan Willem; Chareesri, Anupol; Koopmans, Gerwin F.

    2017-01-01

    As many soils are unable to supply sufficient amounts of phosphorus (P) to plants, P availability is often a growth-limiting factor. Literature shows that levels of readily available P can be considerably higher in earthworm casts than in the surrounding bulk soil, possibly resulting in increased

  4. Diversity and host specificity of the Verminephrobacter–earthworm symbiosis

    DEFF Research Database (Denmark)

    Lund, Marie Braad; Davidson, Seana; Holmstrup, Martin

    2010-01-01

    Symbiotic bacteria of the genus Verminephrobacter (Betaproteobacteria) were detected in the nephridia of 19 out of 23 investigated earthworm species (Oligochaeta: Lumbricidae) by 16S rRNA gene sequence analysis and fluorescence in situ hybridization (FISH). While all four Lumbricus species and th...

  5. Phenotypic and functional characterization of earthworm coelomocyte subsets

    DEFF Research Database (Denmark)

    Engelmann, Péter; Hayashi, Yuya; Bodo, Kornélia

    2016-01-01

    Flow cytometry is a common approach to study invertebrate immune cells including earthworm coelomocytes. However, the link between light-scatter- and microscopy-based phenotyping remains obscured. Here we show, by means of light scatter-based cell sorting, both subpopulations (amoebocytes and ele...

  6. Do earthworms increase N2O emissions in ploughed grassland?

    NARCIS (Netherlands)

    Bertora, C.; Vliet, van P.C.J.; Hummelink, E.W.J.; Groenigen, van J.W.

    2007-01-01

    Earthworm activity has been reported to lead to increased production of the greenhouse gas nitrous oxide (N2O). This is due to emissions from worms themselves, their casts and drilosphere, as well as to general changes in soil structure. However, it remains to be determined how important this effect

  7. Earthworm communities along an elevation gradient in Northeastern Puerto Rico.

    Science.gov (United States)

    Grizelle Gonzalez; Emerita Garcia; Veronica Cruz; Sonia Borges; Marcela Zalamea; Maria M. Rivera

    2007-01-01

    In this study, we describe earthworm communities along an elevation gradient of eight forest types in Northeastern Puerto Rico, and determine whether their abundance, biomass and/or diversity is related to climatic, soil physical/chemical and/or biotic characteristics. We found that the density, biomass, and diversity of worms varied significantly among forest types....

  8. Policy and management responses to earthworm invasions in North America

    Science.gov (United States)

    Mac A. Callaham; Grizelle Gonzalez; Cynthia M Hale; Liam Henegham; Sharon L. Lachnicht; Xiaoming Zou

    2006-01-01

    The introduction, establishment and spread of non-native earthworm species in North America have been ongoing for centuries. These introductions have occurred across the continent and in some ecosystems have resulted in considerable modifications to ecosystem processes and functions associated with above- and belowground foodwebs. However, many areas of North America...

  9. Earthworm survival in used engine oil contaminated soil spiked with ...

    African Journals Online (AJOL)

    The ability of L. terrestris to survive in bioremediated used engine oil contaminated soil was evaluated and it was observed that100% of earthworms survived in both motorcycle and truck engine used engine oil contaminated soil for concentration as high as 150 g used engine oil/kg soil for a period of 30 days. The highest ...

  10. Comparative Microbial Analysis of Earthworm Casts Collected From ...

    African Journals Online (AJOL)

    A comparative assessment of the physicochemical parameters and microbial profile of three types of earthworm casts (Pellet, Mass and Turret) were determined. The total viable count (TVC), coliform counts, yeast and mould counts were determined using standard procedures. The pH ranged from 7.8 for Mass cast to 8.6 for ...

  11. Impact of biochar on earthworm populations: A review

    Science.gov (United States)

    Despite the overwhelming importance of earthworm activity in the soil system, there are a limited number of studies that have examined the impact resulting from biochar addition to soil. Biochar is part of the black carbon continuum of chemo-thermal converted biomass. This review summarizes existing...

  12. Bioaccumulation of heavy metals in earthworms collected from ...

    African Journals Online (AJOL)

    Activities in abattoirs and direct release of its waste into the environment are on the increase due to high protein demand in the country; and there is a need for proper assessment of abattoir soil for pollution. This study evaluated bioaccumulations of heavy metals in indigenous earthworm from abattoir soils as a measure of ...

  13. Earthworm Biomass Measurement: A Science Activity for Middle School.

    Science.gov (United States)

    Haskett, Jonathan; Levine, Elissa; Carey, Pauline B.; Niepold III, Frank

    2000-01-01

    Describes an activity on biomass measurement which, in this case, is the weight of a group of living things in a given area. The earthworm activity gives students a greater understanding of ecology, practical math applications, and the scientific method. (ASK)

  14. The Earthworms (Oligochaeta: Lumbricidae)of Wyoming, USA, Revisited.

    Science.gov (United States)

    This survey of the earthworms from 22 of the 23 counties of Wyoming recorded 13 species of terrestrial Oligochaeta, all members of the family Lumbricidae. One of these species, Aporrectodea limicola, is reported for the first time from the state. Current nomenclature is applied to historical records...

  15. Growth response of Amaranthus caudatus to earthworm casts and ...

    African Journals Online (AJOL)

    The effect of earth worm cast on the physiomorphological differences of Amaranthus caudatus was studied in the green house of the Department of Agronomy, University of Ibadan for seven weeks in 1998. Earthworm casts were collected from soils cultivated with maize, cassava and oil palm fields and secondary forest.

  16. Enteric pathogen modification by anaecic earthworm, Lampito Mauritii

    African Journals Online (AJOL)

    The biosolids from municipal wastewater treatment plant contains several enteric microbial pathogens, predominantly Salmonella and Escherichia species in the range of 15-18 x 104 CFU/g and 11-12 x 104 CFU/g respectively. The present study investigates the influence of earthworm, Lampito mauritii on enteric pathogen ...

  17. Fractures and the gut microbiome.

    Science.gov (United States)

    McGinty, Tara; Mallon, Paddy W G

    2018-01-01

    The role of the gut microbiome in the pathogenesis of several inflammatory, non-AIDS comorbidities, such as cardiovascular disease, cognitive impairment and liver disease has become a focus of recent research. Low bone mineral density (BMD) and increased fracture incidence in people living with HIV (PLWH) is also widely reported, however, the relationship between alterations in the gut microbiome and bone disease in PLWH has not been previously reviewed. Murine models that manipulate the gut microbiome, either through breeding of 'germ-free' mice or antibiotic-depleted gut microbiome, show differences in bone mineral density and bone mass in those with altered gut microbiome. This effect is reported to be driven via changes in the gut-immune-skeletal axis, with changes favouring bone resorption. Several inflammatory conditions wherever bone loss is a prominent feature, such as rheumatoid arthritis and inflammatory bowel disease, have also reported alterations in the gut microbiome, which are associated with bone loss, again through changes in the gut-immune-skeletal axis. The interplay between the gut microbiome and the immune-skeletal axis in HIV represents a complex relationship. Alterations in the gut microbiome, which induce an activated immune phenotype and inflammatory milieu are associated with non-AIDS comorbidities in PLWH and bone loss in several other conditions characterized by chronic immune activation and inflammation. It is, therefore, likely that there are comparable effects between altered gut microbiome and bone loss in HIV, however, further research is required to better define this relationship in populations of PLWH.

  18. Accumulation of heavy metals in the earthworm Eisenia foetida

    Energy Technology Data Exchange (ETDEWEB)

    Hartenstein, R. (State Univ. of New York, Syracuse); Neuhauser, E.F.; Collier, J.

    1980-01-01

    Conversion of waste-activated sludge into egesta by the earthworm Eisenia foetida resulted in neither an increase nor decrease of 0.1 N HCl-extractable cadmium, copper, nickel, lead, or zinc. The addition of 2500 ppM copper as copper sulfate to activated sludge caused 100% mortality whthin 1 week, though feeding upon nonamended activated sludges with up to 1500 ppM copper over several months was innocuous. Amendment of sludge with 10, 50, and 100 ppM Cd as CdSO/sub 4/ resulted in 3.90-, 2.04-, and 1.44-fold concentrations in the earthworm over the quantities present in the sludge, with a range of 118 to 170 ppM being found on exposure to the highest level for periods of 1 to 5 weeks at 25/sup 0/C. In field trials with nonamended sludge, however, containing 12 to 27 ppM Cd, biweekly sampling for 28 weeks revealed accumulations in E. foetida ranging from 8 to 46 ppM; control earthworms not exposed to culture media with easily measurable Cd levels contained 0.3 to 2 ppM Cd. Upwards to about 50 ppM Ni, 325 ppM Pb, and 250 ppM Zn accumulated from sludges amended with ionic soluble forms of these metals. In the field, where these metals ranged from 2 to 46, 1 to 53, and 68 to 210 ppM, respectively, an upper concentration of about 50 ppM Ni, 55 ppM Pb, and 250 ppM Zn were found in the earthworm. Distinctions were made between accumulable and concentratable and a discussion is provided to show that each of the most problematic heavy metals, Cd, Zn, Ni, Pb, and Cu, may accumulate or concentrate in the earthworm.

  19. Avoidance, biomass and survival response of soil dwelling (endogeic) earthworms to OECD artificial soil: potential implications for earthworm ecotoxicology.

    Science.gov (United States)

    Brami, C; Glover, A R; Butt, K R; Lowe, C N

    2017-05-01

    Soil dwelling earthworms are now adopted more widely in ecotoxicology, so it is vital to establish if standardised test parameters remain applicable. The main aim of this study was to determine the influence of OECD artificial soil on selected soil-dwelling, endogeic earthworm species. In an initial experiment, biomass change in mature Allolobophora chlorotica was recorded in Standard OECD Artificial Soil (AS) and also in Kettering Loam (KL). In a second experiment, avoidance behaviour was recorded in a linear gradient with varying proportions of AS and KL (100% AS, 75% AS + 25% KL, 50% KS + 50% KL, 25% AS + 75% KL, 100% KL) with either A. chlorotica or Octolasion cyaneum. Results showed a significant decrease in A. chlorotica biomass in AS relative to KL, and in the linear gradient, both earthworm species preferentially occupied sections containing higher proportions of KL over AS. Soil texture and specifically % composition and particle size of sand are proposed as key factors that influenced observed results. This research suggests that more suitable substrates are required for ecotoxicology tests with soil dwelling earthworms.

  20. Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment.

    Directory of Open Access Journals (Sweden)

    Jessica L Danzeisen

    Full Text Available With increasing pressures to reduce or eliminate the use of antimicrobials for growth promotion purposes in production animals, there is a growing need to better understand the effects elicited by these agents in order to identify alternative approaches that might be used to maintain animal health. Antibiotic usage at subtherapeutic levels is postulated to confer a number of modulations in the microbes within the gut that ultimately result in growth promotion and reduced occurrence of disease. This study examined the effects of the coccidiostat monensin and the growth promoters virginiamycin and tylosin on the broiler chicken cecal microbiome and metagenome. Using a longitudinal design, cecal contents of commercial chickens were extracted and examined using 16S rRNA and total DNA shotgun metagenomic pyrosequencing. A number of genus-level enrichments and depletions were observed in response to monensin alone, or monensin in combination with virginiamycin or tylosin. Of note, monensin effects included depletions of Roseburia, Lactobacillus and Enterococcus, and enrichments in Coprococcus and Anaerofilum. The most notable effect observed in the monensin/virginiamycin and monensin/tylosin treatments, but not in the monensin-alone treatments, was enrichments in Escherichia coli. Analysis of the metagenomic dataset identified enrichments in transport system genes, type I fimbrial genes, and type IV conjugative secretion system genes. No significant differences were observed with regard to antimicrobial resistance gene counts. Overall, this study provides a more comprehensive glimpse of the chicken cecum microbial community, the modulations of this community in response to growth promoters, and targets for future efforts to mimic these effects using alternative approaches.

  1. Genometa--a fast and accurate classifier for short metagenomic shotgun reads.

    Directory of Open Access Journals (Sweden)

    Colin F Davenport

    Full Text Available Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer.The Genometa program, a step by step tutorial and Java source code are freely available from http://genomics1.mh-hannover.de/genometa/ and on http://code.google.com/p/genometa/. This program has been tested on Ubuntu Linux and Windows XP/7.

  2. Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment.

    Science.gov (United States)

    Danzeisen, Jessica L; Kim, Hyeun Bum; Isaacson, Richard E; Tu, Zheng Jin; Johnson, Timothy J

    2011-01-01

    With increasing pressures to reduce or eliminate the use of antimicrobials for growth promotion purposes in production animals, there is a growing need to better understand the effects elicited by these agents in order to identify alternative approaches that might be used to maintain animal health. Antibiotic usage at subtherapeutic levels is postulated to confer a number of modulations in the microbes within the gut that ultimately result in growth promotion and reduced occurrence of disease. This study examined the effects of the coccidiostat monensin and the growth promoters virginiamycin and tylosin on the broiler chicken cecal microbiome and metagenome. Using a longitudinal design, cecal contents of commercial chickens were extracted and examined using 16S rRNA and total DNA shotgun metagenomic pyrosequencing. A number of genus-level enrichments and depletions were observed in response to monensin alone, or monensin in combination with virginiamycin or tylosin. Of note, monensin effects included depletions of Roseburia, Lactobacillus and Enterococcus, and enrichments in Coprococcus and Anaerofilum. The most notable effect observed in the monensin/virginiamycin and monensin/tylosin treatments, but not in the monensin-alone treatments, was enrichments in Escherichia coli. Analysis of the metagenomic dataset identified enrichments in transport system genes, type I fimbrial genes, and type IV conjugative secretion system genes. No significant differences were observed with regard to antimicrobial resistance gene counts. Overall, this study provides a more comprehensive glimpse of the chicken cecum microbial community, the modulations of this community in response to growth promoters, and targets for future efforts to mimic these effects using alternative approaches.

  3. Genometa--a fast and accurate classifier for short metagenomic shotgun reads.

    Science.gov (United States)

    Davenport, Colin F; Neugebauer, Jens; Beckmann, Nils; Friedrich, Benedikt; Kameri, Burim; Kokott, Svea; Paetow, Malte; Siekmann, Björn; Wieding-Drewes, Matthias; Wienhöfer, Markus; Wolf, Stefan; Tümmler, Burkhard; Ahlers, Volker; Sprengel, Frauke

    2012-01-01

    Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species) and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer. The Genometa program, a step by step tutorial and Java source code are freely available from http://genomics1.mh-hannover.de/genometa/ and on http://code.google.com/p/genometa/. This program has been tested on Ubuntu Linux and Windows XP/7.

  4. Role of Gut Microbiota in the Aetiology of Obesity: Proposed Mechanisms and Review of the Literature

    Science.gov (United States)

    Gerasimidis, Konstantinos; Edwards, Christine Ann; Shaikh, M. Guftar

    2016-01-01

    The aetiology of obesity has been attributed to several factors (environmental, dietary, lifestyle, host, and genetic factors); however none of these fully explain the increase in the prevalence of obesity worldwide. Gut microbiota located at the interface of host and environment in the gut are a new area of research being explored to explain the excess accumulation of energy in obese individuals and may be a potential target for therapeutic manipulation to reduce host energy storage. Several mechanisms have been suggested to explain the role of gut microbiota in the aetiology of obesity such as short chain fatty acid production, stimulation of hormones, chronic low-grade inflammation, lipoprotein and bile acid metabolism, and increased endocannabinoid receptor system tone. However, evidence from animal and human studies clearly indicates controversies in determining the cause or effect relationship between the gut microbiota and obesity. Metagenomics based studies indicate that functionality rather than the composition of gut microbiota may be important. Further mechanistic studies controlling for environmental and epigenetic factors are therefore required to help unravel obesity pathogenesis. PMID:27703805

  5. Role of Gut Microbiota in the Aetiology of Obesity: Proposed Mechanisms and Review of the Literature

    Directory of Open Access Journals (Sweden)

    Muhammad Jaffar Khan

    2016-01-01

    Full Text Available The aetiology of obesity has been attributed to several factors (environmental, dietary, lifestyle, host, and genetic factors; however none of these fully explain the increase in the prevalence of obesity worldwide. Gut microbiota located at the interface of host and environment in the gut are a new area of research being explored to explain the excess accumulation of energy in obese individuals and may be a potential target for therapeutic manipulation to reduce host energy storage. Several mechanisms have been suggested to explain the role of gut microbiota in the aetiology of obesity such as short chain fatty acid production, stimulation of hormones, chronic low-grade inflammation, lipoprotein and bile acid metabolism, and increased endocannabinoid receptor system tone. However, evidence from animal and human studies clearly indicates controversies in determining the cause or effect relationship between the gut microbiota and obesity. Metagenomics based studies indicate that functionality rather than the composition of gut microbiota may be important. Further mechanistic studies controlling for environmental and epigenetic factors are therefore required to help unravel obesity pathogenesis.

  6. Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice.

    Science.gov (United States)

    Kim, Min-Soo; Bae, Jin-Woo

    2016-05-01

    Gut microbial biogeography is a key feature of host-microbe relationships. In gut viral ecology, biogeography and responses to dietary intervention remain poorly understood. Here, we conducted a metagenomic study to determine the composition of the mucosal and luminal viromes of the gut and to evaluate the impact of a Western diet on gut viral ecology. We found that mucosal and luminal viral assemblages comprised predominantly temperate phages. The mucosal virome significantly differed from the luminal virome in low-fat diet-fed lean mice, where spatial variation correlated with bacterial microbiota from the mucosa and lumen. The mucosal and luminal viromes of high-fat, high-sucrose 'Western' diet-fed obese mice were significantly enriched with temperate phages of the Caudovirales order. Interestingly, this community alteration occurred to a greater extent in the mucosa than lumen, leading to loss of spatial differences; however, these changes recovered after switching to a low-fat diet. Temperate phages enriched in the Western diet-induced obese mice were associated with the Bacilli, Negativicutes and Bacteroidia classes and temperate phages from the Bacteroidia class particularly encoded stress and niche-specific functions advantageous to bacterial host adaptation. This study illustrates a biogeographic view of the gut virome and phage-bacterial host connections under the diet-induced microbial dysbiosis. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin.

    Science.gov (United States)

    Rampelli, Simone; Turroni, Silvia; Schnorr, Stephanie L; Soverini, Matteo; Quercia, Sara; Barone, Monica; Castagnetti, Andrea; Biagi, Elena; Gallinella, Giorgio; Brigidi, Patrizia; Candela, Marco

    2017-11-01

    It is a matter of fact that the human gut microbiome also includes a non-bacterial fraction represented by eukaryotic cells and viruses. To further explore the gut microbiome variation in human populations, here we characterized the human DNA viral community from publicly available gut metagenome data sets from human populations with different geographical origin and lifestyle. In particular, such data sets encompass microbiome information from two western urban societies (USA and Italy), as well as two traditional hunter-gatherer communities (the Hadza from Tanzania and Matses from Peru) and one pre-agricultural tribe (Tunapuco from Peru). Our results allowed for the first taxonomic reconstruction of the complex viral metacommunities within the human gut. The core virome structure included herpesviruses, papillomaviruses, polyomaviruses, adenoviruses and anelloviruses. Using Random Forests and a co-occurrence analysis approach, we identified the viruses that distinguished populations according to their geographical origin and/or lifestyle. This paves the way for new research aimed at investigating the biological role of the gut virome in human physiology, and the importance of our viral counterpart in the microbiome-host co-evolutionary process. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  8. Role of Gut Microbiota in the Aetiology of Obesity: Proposed Mechanisms and Review of the Literature.

    Science.gov (United States)

    Khan, Muhammad Jaffar; Gerasimidis, Konstantinos; Edwards, Christine Ann; Shaikh, M Guftar

    2016-01-01

    The aetiology of obesity has been attributed to several factors (environmental, dietary, lifestyle, host, and genetic factors); however none of these fully explain the increase in the prevalence of obesity worldwide. Gut microbiota located at the interface of host and environment in the gut are a new area of research being explored to explain the excess accumulation of energy in obese individuals and may be a potential target for therapeutic manipulation to reduce host energy storage. Several mechanisms have been suggested to explain the role of gut microbiota in the aetiology of obesity such as short chain fatty acid production, stimulation of hormones, chronic low-grade inflammation, lipoprotein and bile acid metabolism, and increased endocannabinoid receptor system tone. However, evidence from animal and human studies clearly indicates controversies in determining the cause or effect relationship between the gut microbiota and obesity. Metagenomics based studies indicate that functionality rather than the composition of gut microbiota may be important. Further mechanistic studies controlling for environmental and epigenetic factors are therefore required to help unravel obesity pathogenesis.

  9. "Omic" investigations of protozoa and worms for a deeper understanding of the human gut "parasitome".

    Science.gov (United States)

    Marzano, Valeria; Mancinelli, Livia; Bracaglia, Giorgia; Del Chierico, Federica; Vernocchi, Pamela; Di Girolamo, Francesco; Garrone, Stefano; Tchidjou Kuekou, Hyppolite; D'Argenio, Patrizia; Dallapiccola, Bruno; Urbani, Andrea; Putignani, Lorenza

    2017-11-01

    The human gut has been continuously exposed to a broad spectrum of intestinal organisms, including viruses, bacteria, fungi, and parasites (protozoa and worms), over millions of years of coevolution, and plays a central role in human health. The modern lifestyles of Western countries, such as the adoption of highly hygienic habits, the extensive use of antimicrobial drugs, and increasing globalisation, have dramatically altered the composition of the gut milieu, especially in terms of its eukaryotic "citizens." In the past few decades, numerous studies have highlighted the composition and role of human intestinal bacteria in physiological and pathological conditions, while few investigations exist on gut parasites and particularly on their coexistence and interaction with the intestinal microbiota. Studies of the gut "parasitome" through "omic" technologies, such as (meta)genomics, transcriptomics, proteomics, and metabolomics, are herein reviewed to better understand their role in the relationships between intestinal parasites, host, and resident prokaryotes, whether pathogens or commensals. Systems biology-based profiles of the gut "parasitome" under physiological and severe disease conditions can indeed contribute to the control of infectious diseases and offer a new perspective of omics-assisted tropical medicine.

  10. Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods.

    Science.gov (United States)

    Huang, Andrew D; Luo, Chengwei; Pena-Gonzalez, Angela; Weigand, Michael R; Tarr, Cheryl L; Konstantinidis, Konstantinos T

    2017-02-01

    Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based culture-independent approaches, such as shotgun metagenomics, could sidestep these limitations and potentially reveal a pathogen-specific signature on the microbiome that would have implications not only for diagnostics but also for better understanding disease progression and pathogen ecology. However, metagenomics have not yet been validated for foodborne pathogen detection. Toward closing these gaps, we applied shotgun metagenomics to stool samples collected from two geographically isolated (Alabama and Colorado) foodborne outbreaks, where the etiologic agents were identified by culture-dependent methods as distinct strains of Salmonella enterica subsp. enterica serovar Heidelberg. Metagenomic investigations were consistent with the culture-based findings and revealed, in addition, the in situ abundance and level of intrapopulation diversity of the pathogen, the possibility of coinfections with Staphylococcus aureus, overgrowth of commensal Escherichia coli, and significant shifts in the gut microbiome during infection relative to reference healthy samples. Additionally, we designed our bioinformatics pipeline to deal with several challenges associated with the analysis of clinical samples, such as the high frequency of coeluting human DNA sequences and assessment of the virulence potential of pathogens. Comparisons of these results to those of other studies revealed that in several, but not all, cases of diarrheal outbreaks, the disease and healthy states of the gut microbial community might be distinguishable, opening new possibilities for diagnostics. Diagnostic testing for enteric pathogens has relied for decades on culture-based techniques, but a total of 38.4 million cases of foodborne illness

  11. Heavy Metals Bioaccumulation by Iranian and Australian Earthworms (Eisenia fetida in the Sewage Sludge Vermicomposting

    Directory of Open Access Journals (Sweden)

    MR Shahmansouri, H Pourmoghadas, AR Parvaresh, H Alidadi

    2005-01-01

    Full Text Available Vermicomposting of organic waste has an important part to play in an integrated waste management strategy. In this study, the possibility of heavy metals accumulation with two groups of Iranian and Australian earthworms in sewage sludge vermicompost was investigated. Eisenia fetida was the species of earthworms used in the vermicomposting process. The bioaccumulation of Cr, Cd, Pb, Cu, and Zn as heavy metals by Iranian and Australian earthworms was studied. The results indicated that heavy metals concentration decreased with increasing vermicomposting time. Comparison of the two groups of earthworms showed that the Iranian earthworms consumed higher quantities of micronutrients such as Cu and Zn comparing with the Australian earthworms, while the bioaccumulation of non-essential elements such as Cr, Cd, and Pb by the Australian group was higher. The significant decrease in heavy metal concentrations in the final vermicompost indicated the capability of both Iranian and Australian E.fetida species in accumulating heavy metals in their body tissues.

  12. Application of earthworm humus and Bradyrhizobium japonicum in Glycine max (L. Merrill

    Directory of Open Access Journals (Sweden)

    Ricardo Gómez Machado

    2017-10-01

    Full Text Available The experiment was developed in the Granma University's productive area, with the objective of evaluating the alone and combined earthworm humus application effect with Bradyrhizobium japonicum on G7R-315 variety soybean cultivation. Six treatments were evaluated: T1 Control, T2 B. japonicum, T3 earthworm humus (6 t ha-1, T4 B. japonicum + earthworm humus (6 t ha-1, T5 earthworm humus (8 t ha-1, T6 B. japonicum + earthworm humus (8 t ha-1 on a brown soil. A randomized block design was used with three replicas. The evaluated variables were: number per plant leguminous; weigh from 100 seeds and agricultural yield. The data obtained were processed by double classification variance analysis, applied a Turkey's multivariate statistical analysis. It was found that treatments that included the earthworm humus, the evaluated variables shown superior significantly results and it differed of the control treatment and to the aloneB. japonicum application.

  13. Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites.

    Science.gov (United States)

    Rossmassler, Karen; Dietrich, Carsten; Thompson, Claire; Mikaelyan, Aram; Nonoh, James O; Scheffrahn, Rudolf H; Sillam-Dussès, David; Brune, Andreas

    2015-11-26

    Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Here, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential between the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among wood- and litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. Community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. The high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.

  14. Metagenomic studies of the Red Sea.

    Science.gov (United States)

    Behzad, Hayedeh; Ibarra, Martin Augusto; Mineta, Katsuhiko; Gojobori, Takashi

    2016-02-01

    Metagenomics has significantly advanced the field of marine microbial ecology, revealing the vast diversity of previously unknown microbial life forms in different marine niches. The tremendous amount of data generated has enabled identification of a large number of microbial genes (metagenomes), their community interactions, adaptation mechanisms, and their potential applications in pharmaceutical and biotechnology-based industries. Comparative metagenomics reveals that microbial diversity is a function of the local environment, meaning that unique or unusual environments typically harbor novel microbial species with unique genes and metabolic pathways. The Red Sea has an abundance of unique characteristics; however, its microbiota is one of the least studied among marine environments. The Red Sea harbors approximately 25 hot anoxic brine pools, plus a vibrant coral reef ecosystem. Physiochemical studies describe the Red Sea as an oligotrophic environment that contains one of the warmest and saltiest waters in the world with year-round high UV radiations. These characteristics are believed to have shaped the evolution of microbial communities in the Red Sea. Over-representation of genes involved in DNA repair, high-intensity light responses, and osmoregulation were found in the Red Sea metagenomic databases suggesting acquisition of specific environmental adaptation by the Red Sea microbiota. The Red Sea brine pools harbor a diverse range of halophilic and thermophilic bacterial and archaeal communities, which are potential sources of enzymes for pharmaceutical and biotechnology-based application. Understanding the mechanisms of these adaptations and their function within the larger ecosystem could also prove useful in light of predicted global warming scenarios where global ocean temperatures are expected to rise by 1-3°C in the next few decades. In this review, we provide an overview of the published metagenomic studies that were conducted in the Red Sea, and

  15. Biotic interaction between earthworms and pesticide degrading bacteria - Impact on the detoxification service of soil

    OpenAIRE

    Monard, Cécile; Vandenkoornhuyse, Philippe; Martin-Laurent, Fabrice; Binet, Françoise

    2010-01-01

    Earthworms are efficient soil engineers that change the physical and chemical properties of soil and act in turn on soil microbial communities. Earthworm bioturbation will thus impact microbial processes in soil and also the generated ecosystemic services such as detoxification function. By using RNA based Stable Isotope Probing we demonstrated that the bacterial communities responsive to 13 C enrichments in earthworm casts were different from those in bulk soil resulting in different degrada...

  16. Earthworms, soil-aggregates and organic matter decomposition in agro-ecosystems in the Netherlands

    OpenAIRE

    Marinissen, J.C.

    1995-01-01

    The relationships between earthworm populations, soil aggregate stability and soil organic matter dynamics were studied at an experimental farm in The Netherlands.

    Arable land in general is not favourable for earthworm growth. In the Lovinkhoeve fields under conventional management earthworm populations were brought to the verge of extinction in a few years. Main causes are soil fumigation against nematodes and unfavourable food conditions. Organic matter inputs and N-content...

  17. Ecological properties of earthworm burrows in an organically managed grass-clover system

    OpenAIRE

    Krogh, Paul Henning; Lamandé, Mathieu; Eriksen, Jørgen; Holmstrup, Martin

    2001-01-01

    Earthworms have long been recognized for their soil engineering capacities. Since the creation of the ecosystem service concept the utilitarian perception of nature has gained a lot of attention and funding for research. Hence, we selected earthworms and their burrowing activities to enable an assessment of their influence on water movement and nutrient release. The study went on in autumn where earthworm population densities and their burrowing activities were quantified in plots of third ye...

  18. Accumulation of methylmercury in the earthworm, Eisenia foetida, and its effect on regeneration

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, W.N.; Cromartie, E.; Moment, G.B.

    1985-08-01

    Earthworms provide an appropriate model for evaluating the environmental hazards of metals in soil, and they are also excellent organisms for studying the process of regeneration. Two studies have found that concentrations of mercury in earthworms were higher than those in the soil where they lived. This study investigates the accumulation of methylmercury in the earthworm, Eisenia foetida (Savigny), and its effect on regeneration after excision of the caudal end.

  19. New earthworm records from Turkey, with description of three new species (Oligochaeta: Lumbricidae).

    Science.gov (United States)

    Szederjesi, Tímea; Pavlíček, Tomás; Coşkun, Yüksel; Csuzdi, Csaba

    2014-02-13

    Identifying the earthworm material recently collected in different parts of Turkey (Marmara Region, Upper Mesopotamia, Hatay Province and East Anatolia) resulted in records of 29 earthworm species including three lumbricids new to science: Dendrobaena cevdeti, D. szalokii and Eisenia patriciae spp. nov. In addition, Dendrobaena cognettii is reported for the first time from the country. With this contribution, the number of earthworm species and subspecies registered in Turkey is raised to 80.

  20. Earthworm (Pheretima aspergillum) extract stimulates osteoblast activity and inhibits osteoclast differentiation

    OpenAIRE

    Fu, Yuan-Tsung; Chen, Kuo-Yu; Chen, Yueh-Sheng; Yao, Chun-Hsu

    2014-01-01

    Background The potential benefits of earthworm (Pheretima aspergillum) for healing have received considerable attention recently. Osteoblast and osteoclast activities are very important in bone remodeling, which is crucial to repair bone injuries. This study investigated the effects of earthworm extract on bone cell activities. Methods Osteoblast-like MG-63 cells and RAW 264.7 macrophage cells were used for identifying the cellular effects of different concentrations of earthworm extract on o...