A metagenomic insight into our gut's microbiome
Identifieur interne : 002F02 ( Istex/Corpus ); précédent : 002F01; suivant : 002F03A metagenomic insight into our gut's microbiome
Auteurs : Patricia Lepage ; Marion C. Leclerc ; Marie Joossens ; Stanislas Mondot ; Hervé M. Blottière ; Jeroen Raes ; Dusko Ehrlich ; Joel DoréSource :
- Gut [ 0017-5749 ] ; 2013-01.
English descriptors
- KwdEn :
- Acad, Amino acids, Archaea, Bacteria, Bacterial chromosomes, Bacterial genes, Bacterial species, Bacteriophage, Basic science, Better understanding, Body regions, Bowel, Bowel disease, Bowel diseases, Carbohydrate metabolism, Clinical status, Clone, Cohort, Collective genomes, Colorectal cancer, Commensal, Commensal bacteria, Comprehensive data resource, Core microbiome, Digestive tract, Digestive tract disorders, Dysbiosis, Ecology, Ecosystem, Enterotypes, Environmental context, Epithelial, Escherichia coli, Faecal, Faecal microbiota, Fatty acids, Functional core, Functional genomics, Functional metagenomics, Gastrointestinal, Gastrointestinal tract, Gastrointestinal tract microbiota, Gene, Gene exchange, Genes encoding, Genome, Healthy individuals, Healthy people, High level, Human biology, Human body, Human cells, Human genome, Human health, Human intestine, Human microbiome, Human microbiomes, Human population, Immune system, Immunogenic properties, Intestinal, Intestinal microbiota, Irritable bowel syndrome, Mating preference, Metabolic network, Metabolism, Metabolomics, Metagenome, Metagenomic, Metagenomic analysis, Metagenomic clones, Metagenomic data, Metagenomic libraries, Metagenomic sequencing, Metagenomics, Metahit, Microbe, Microbial, Microbial communities, Microbial diversity, Microbial ecology, Microbial ecosystem, Microbial genes, Microbial pathways, Microbiol, Microbiome, Microbiome consortium, Microbiota, Microorganism, Mobile metagenome, Mucosal, Mucosal interfaces, Natl, Next generation sequencing, Obese individuals, Open reading frames, Pathway, Phage, Phage therapy, Phylogenetic, Proc, Proc natl acad, Quantitative metagenomics, Recent advances, Research group, Sequencing, Small subunit, Ulcerative colitis, Unaffected relatives, Vast majority.
- Teeft :
- Acad, Amino acids, Archaea, Bacteria, Bacterial chromosomes, Bacterial genes, Bacterial species, Bacteriophage, Basic science, Better understanding, Body regions, Bowel, Bowel disease, Bowel diseases, Carbohydrate metabolism, Clinical status, Clone, Cohort, Collective genomes, Colorectal cancer, Commensal, Commensal bacteria, Comprehensive data resource, Core microbiome, Digestive tract, Digestive tract disorders, Dysbiosis, Ecology, Ecosystem, Enterotypes, Environmental context, Epithelial, Escherichia coli, Faecal, Faecal microbiota, Fatty acids, Functional core, Functional genomics, Functional metagenomics, Gastrointestinal, Gastrointestinal tract, Gastrointestinal tract microbiota, Gene, Gene exchange, Genes encoding, Genome, Healthy individuals, Healthy people, High level, Human biology, Human body, Human cells, Human genome, Human health, Human intestine, Human microbiome, Human microbiomes, Human population, Immune system, Immunogenic properties, Intestinal, Intestinal microbiota, Irritable bowel syndrome, Mating preference, Metabolic network, Metabolism, Metabolomics, Metagenome, Metagenomic, Metagenomic analysis, Metagenomic clones, Metagenomic data, Metagenomic libraries, Metagenomic sequencing, Metagenomics, Metahit, Microbe, Microbial, Microbial communities, Microbial diversity, Microbial ecology, Microbial ecosystem, Microbial genes, Microbial pathways, Microbiol, Microbiome, Microbiome consortium, Microbiota, Microorganism, Mobile metagenome, Mucosal, Mucosal interfaces, Natl, Next generation sequencing, Obese individuals, Open reading frames, Pathway, Phage, Phage therapy, Phylogenetic, Proc, Proc natl acad, Quantitative metagenomics, Recent advances, Research group, Sequencing, Small subunit, Ulcerative colitis, Unaffected relatives, Vast majority.
Abstract
Advances in sequencing technology and the development of metagenomic and bioinformatics methods have opened up new ways to investigate the 1014 microorganisms inhabiting the human gut. The gene composition of human gut microbiome in a large and deeply sequenced cohort highlighted an overall non-redundant genome size 150 times larger than the human genome. The in silico predictions based on metagenomic sequencing are now actively followed, compared and challenged using additional ‘omics’ technologies. Interactions between the microbiota and its host are of key interest in several pathologies and applying meta-omics to describe the human gut microbiome will give a better understanding of this crucial crosstalk at mucosal interfaces. Adding to the growing appreciation of the importance of the microbiome is the discovery that numerous phages, that is, viruses of prokaryotes infecting bacteria (bacteriophages) or archaea with a high host specificity, inhabit the human gut and impact microbial activity. In addition, gene exchanges within the gut microbiota have proved to be more frequent than anticipated. Taken together, these innovative exploratory technologies are expected to unravel new information networks critical for gut homeostasis and human health. Among the challenges faced, the in vivo validation of these networks, together with their integration into the prediction and prognosis of disease, may require further working hypothesis and collaborative efforts.
Url:
DOI: 10.1136/gutjnl-2011-301805
Links to Exploration step
ISTEX:F995F34D52E9F6B4B8175B38F2C40C300F004FBDLe document en format XML
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France</mods:affiliation></affiliation><affiliation><mods:affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</mods:affiliation></affiliation></author><author><name sortKey="Dore, Joel" sort="Dore, Joel" uniqKey="Dore J" first="Joel" last="Doré">Joel Doré</name><affiliation><mods:affiliation>INRA, MICALIS UMR1319, Jouy-en-Josas, France</mods:affiliation></affiliation><affiliation><mods:affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Gut</title><title level="j" type="abbrev">Gut</title><idno type="ISSN">0017-5749</idno><idno type="eISSN">1468-3288</idno><imprint><publisher>BMJ Publishing Group Ltd and British Society of Gastroenterology</publisher><date type="published" when="2013-01">2013-01</date><biblScope unit="volume">62</biblScope><biblScope unit="issue">1</biblScope><biblScope unit="page" from="146">146</biblScope></imprint><idno type="ISSN">0017-5749</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0017-5749</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Acad</term><term>Amino acids</term><term>Archaea</term><term>Bacteria</term><term>Bacterial chromosomes</term><term>Bacterial genes</term><term>Bacterial species</term><term>Bacteriophage</term><term>Basic science</term><term>Better understanding</term><term>Body regions</term><term>Bowel</term><term>Bowel disease</term><term>Bowel diseases</term><term>Carbohydrate metabolism</term><term>Clinical status</term><term>Clone</term><term>Cohort</term><term>Collective genomes</term><term>Colorectal cancer</term><term>Commensal</term><term>Commensal bacteria</term><term>Comprehensive data resource</term><term>Core microbiome</term><term>Digestive tract</term><term>Digestive tract disorders</term><term>Dysbiosis</term><term>Ecology</term><term>Ecosystem</term><term>Enterotypes</term><term>Environmental context</term><term>Epithelial</term><term>Escherichia coli</term><term>Faecal</term><term>Faecal microbiota</term><term>Fatty acids</term><term>Functional core</term><term>Functional genomics</term><term>Functional metagenomics</term><term>Gastrointestinal</term><term>Gastrointestinal tract</term><term>Gastrointestinal tract microbiota</term><term>Gene</term><term>Gene exchange</term><term>Genes encoding</term><term>Genome</term><term>Healthy individuals</term><term>Healthy people</term><term>High level</term><term>Human biology</term><term>Human body</term><term>Human cells</term><term>Human genome</term><term>Human health</term><term>Human intestine</term><term>Human microbiome</term><term>Human microbiomes</term><term>Human population</term><term>Immune system</term><term>Immunogenic properties</term><term>Intestinal</term><term>Intestinal microbiota</term><term>Irritable bowel syndrome</term><term>Mating preference</term><term>Metabolic network</term><term>Metabolism</term><term>Metabolomics</term><term>Metagenome</term><term>Metagenomic</term><term>Metagenomic analysis</term><term>Metagenomic clones</term><term>Metagenomic data</term><term>Metagenomic libraries</term><term>Metagenomic sequencing</term><term>Metagenomics</term><term>Metahit</term><term>Microbe</term><term>Microbial</term><term>Microbial communities</term><term>Microbial diversity</term><term>Microbial ecology</term><term>Microbial ecosystem</term><term>Microbial genes</term><term>Microbial pathways</term><term>Microbiol</term><term>Microbiome</term><term>Microbiome consortium</term><term>Microbiota</term><term>Microorganism</term><term>Mobile metagenome</term><term>Mucosal</term><term>Mucosal interfaces</term><term>Natl</term><term>Next generation sequencing</term><term>Obese individuals</term><term>Open reading 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bacteria</term><term>Comprehensive data resource</term><term>Core microbiome</term><term>Digestive tract</term><term>Digestive tract disorders</term><term>Dysbiosis</term><term>Ecology</term><term>Ecosystem</term><term>Enterotypes</term><term>Environmental context</term><term>Epithelial</term><term>Escherichia coli</term><term>Faecal</term><term>Faecal microbiota</term><term>Fatty acids</term><term>Functional core</term><term>Functional genomics</term><term>Functional metagenomics</term><term>Gastrointestinal</term><term>Gastrointestinal tract</term><term>Gastrointestinal tract microbiota</term><term>Gene</term><term>Gene exchange</term><term>Genes encoding</term><term>Genome</term><term>Healthy individuals</term><term>Healthy people</term><term>High level</term><term>Human biology</term><term>Human body</term><term>Human cells</term><term>Human genome</term><term>Human health</term><term>Human intestine</term><term>Human microbiome</term><term>Human microbiomes</term><term>Human population</term><term>Immune system</term><term>Immunogenic properties</term><term>Intestinal</term><term>Intestinal microbiota</term><term>Irritable bowel syndrome</term><term>Mating preference</term><term>Metabolic network</term><term>Metabolism</term><term>Metabolomics</term><term>Metagenome</term><term>Metagenomic</term><term>Metagenomic analysis</term><term>Metagenomic clones</term><term>Metagenomic data</term><term>Metagenomic libraries</term><term>Metagenomic sequencing</term><term>Metagenomics</term><term>Metahit</term><term>Microbe</term><term>Microbial</term><term>Microbial communities</term><term>Microbial diversity</term><term>Microbial ecology</term><term>Microbial ecosystem</term><term>Microbial genes</term><term>Microbial pathways</term><term>Microbiol</term><term>Microbiome</term><term>Microbiome consortium</term><term>Microbiota</term><term>Microorganism</term><term>Mobile metagenome</term><term>Mucosal</term><term>Mucosal interfaces</term><term>Natl</term><term>Next generation sequencing</term><term>Obese individuals</term><term>Open reading frames</term><term>Pathway</term><term>Phage</term><term>Phage therapy</term><term>Phylogenetic</term><term>Proc</term><term>Proc natl acad</term><term>Quantitative metagenomics</term><term>Recent advances</term><term>Research group</term><term>Sequencing</term><term>Small subunit</term><term>Ulcerative colitis</term><term>Unaffected relatives</term><term>Vast majority</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract">Advances in sequencing technology and the development of metagenomic and bioinformatics methods have opened up new ways to investigate the 1014 microorganisms inhabiting the human gut. The gene composition of human gut microbiome in a large and deeply sequenced cohort highlighted an overall non-redundant genome size 150 times larger than the human genome. The in silico predictions based on metagenomic sequencing are now actively followed, compared and challenged using additional ‘omics’ technologies. Interactions between the microbiota and its host are of key interest in several pathologies and applying meta-omics to describe the human gut microbiome will give a better understanding of this crucial crosstalk at mucosal interfaces. Adding to the growing appreciation of the importance of the microbiome is the discovery that numerous phages, that is, viruses of prokaryotes infecting bacteria (bacteriophages) or archaea with a high host specificity, inhabit the human gut and impact microbial activity. In addition, gene exchanges within the gut microbiota have proved to be more frequent than anticipated. Taken together, these innovative exploratory technologies are expected to unravel new information networks critical for gut homeostasis and human health. Among the challenges faced, the in vivo validation of these networks, together with their integration into the prediction and prognosis of disease, may require further working hypothesis and collaborative efforts.</div></front></TEI><istex><corpusName>bmj</corpusName><keywords><teeft><json:string>microbiota</json:string><json:string>microbiome</json:string><json:string>metagenomic</json:string><json:string>metagenomics</json:string><json:string>genome</json:string><json:string>phage</json:string><json:string>intestinal</json:string><json:string>microbial</json:string><json:string>microbe</json:string><json:string>enterotypes</json:string><json:string>sequencing</json:string><json:string>ecosystem</json:string><json:string>dysbiosis</json:string><json:string>metagenome</json:string><json:string>bowel</json:string><json:string>faecal</json:string><json:string>acad</json:string><json:string>recent 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exchange</json:string><json:string>bacteria</json:string></teeft></keywords><author><json:item><name>Patricia Lepage</name><affiliations><json:string>INRA, MICALIS UMR1319, Jouy-en-Josas, France</json:string><json:string>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</json:string><json:string>E-mail: patricia.lepage@jouy.inra.fr</json:string></affiliations></json:item><json:item><name>Marion C Leclerc</name><affiliations><json:string>INRA, MICALIS UMR1319, Jouy-en-Josas, France</json:string><json:string>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</json:string></affiliations></json:item><json:item><name>Marie Joossens</name><affiliations><json:string>Research Group of Bioinformatics and (Eco-)systems Biology, Department of Structural Biology, VIB, Brussels, Belgium</json:string><json:string>Microbiology Unit, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, Belgium</json:string><json:string>IBD Research Group, TARGID, Department of Gastroenterology, KU Leuven, Leuven, Belgium</json:string></affiliations></json:item><json:item><name>Stanislas Mondot</name><affiliations><json:string>CSIRO, Division of Livestock Industries, Queensland Biosciences Precinct, St Lucia, Queensland, Australia</json:string></affiliations></json:item><json:item><name>Hervé M Blottière</name><affiliations><json:string>INRA, MICALIS UMR1319, Jouy-en-Josas, France</json:string><json:string>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</json:string></affiliations></json:item><json:item><name>Jeroen Raes</name><affiliations><json:string>Research Group of Bioinformatics and (Eco-)systems Biology, Department of Structural Biology, VIB, Brussels, Belgium</json:string><json:string>Microbiology Unit, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, Belgium</json:string></affiliations></json:item><json:item><name>Dusko Ehrlich</name><affiliations><json:string>INRA, MICALIS UMR1319, Jouy-en-Josas, France</json:string><json:string>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</json:string></affiliations></json:item><json:item><name>Joel Doré</name><affiliations><json:string>INRA, MICALIS UMR1319, Jouy-en-Josas, France</json:string><json:string>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Bacterial interactions</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>genetics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>IBD</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>mucus</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>intestinal microbiology</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>metagenomics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>carbohydrates</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>anaerobic bacterial fermentation</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>molecular biology</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>mucins</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>inflammatory diseases</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>bacterial adherence</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>short chain fatty acids</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>IBD basic research</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>intestinal microbiota</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Crohn's disease</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>stool markers</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>inflammatory bowel disease</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>intestinal bacteria</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>ribosomal RNA</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>colonic microflora</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>enteric bacterial microflora</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>RNA expression</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>gut inflammation</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>intestinal bacteria</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>immune response</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>mucosal immunology</value></json:item></subject><articleId><json:string>gutjnl-2011-301805</json:string></articleId><arkIstex>ark:/67375/NVC-21HVKLZV-P</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>review-article</json:string></originalGenre><abstract>Advances in sequencing technology and the development of metagenomic and bioinformatics methods have opened up new ways to investigate the 1014 microorganisms inhabiting the human gut. The gene composition of human gut microbiome in a large and deeply sequenced cohort highlighted an overall non-redundant genome size 150 times larger than the human genome. The in silico predictions based on metagenomic sequencing are now actively followed, compared and challenged using additional ‘omics’ technologies. Interactions between the microbiota and its host are of key interest in several pathologies and applying meta-omics to describe the human gut microbiome will give a better understanding of this crucial crosstalk at mucosal interfaces. Adding to the growing appreciation of the importance of the microbiome is the discovery that numerous phages, that is, viruses of prokaryotes infecting bacteria (bacteriophages) or archaea with a high host specificity, inhabit the human gut and impact microbial activity. In addition, gene exchanges within the gut microbiota have proved to be more frequent than anticipated. Taken together, these innovative exploratory technologies are expected to unravel new information networks critical for gut homeostasis and human health. Among the challenges faced, the in vivo validation of these networks, together with their integration into the prediction and prognosis of disease, may require further working hypothesis and collaborative efforts.</abstract><qualityIndicators><score>9.556</score><pdfWordCount>8076</pdfWordCount><pdfCharCount>57154</pdfCharCount><pdfVersion>1.4</pdfVersion><pdfPageCount>13</pdfPageCount><pdfPageSize>595.163 x 793.587 pts</pdfPageSize><refBibsNative>true</refBibsNative><abstractWordCount>213</abstractWordCount><abstractCharCount>1484</abstractCharCount><keywordCount>27</keywordCount></qualityIndicators><title>A metagenomic insight into our gut's 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Dore</json:string></persName><placeName><json:string>Germany</json:string><json:string>Korea</json:string><json:string>St Lucia</json:string><json:string>UK</json:string><json:string>Canada</json:string><json:string>American</json:string><json:string>Europe</json:string><json:string>Denmark</json:string><json:string>France</json:string><json:string>Republic of China</json:string><json:string>Italy</json:string><json:string>Spain</json:string><json:string>Netherlands</json:string></placeName><ref_url><json:string>http://www.human-microbiome.org/</json:string><json:string>http://commonfund.nih.gov/hmp/overview.aspx</json:string><json:string>http://ms.lbl.gov/</json:string><json:string>http://www.genomesonline.org/cgi-bin/index.cgi</json:string><json:string>http://www.metahit.eu/</json:string><json:string>http://www.microbiome-standards.org/</json:string></ref_url><ref_bibl><json:string>Qin et al</json:string><json:string>Lakhdari et al</json:string><json:string>Paterson et al</json:string><json:string>Wang et al</json:string><json:string>Tasse et al</json:string><json:string>Turnbaugh et al</json:string><json:string>Frias-Lopez et al</json:string><json:string>October 2005</json:string><json:string>Minot et al</json:string><json:string>Breitbart et al</json:string><json:string>Reyes et al</json:string></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/NVC-21HVKLZV-P</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - gastroenterology & hepatology</json:string></wos><scienceMetrix><json:string>1 - health sciences</json:string><json:string>2 - clinical medicine</json:string><json:string>3 - gastroenterology & hepatology</json:string></scienceMetrix><scopus><json:string>1 - Health Sciences</json:string><json:string>2 - Medicine</json:string><json:string>3 - Gastroenterology</json:string></scopus><inist><json:string>1 - sciences appliquees, technologies et medecines</json:string><json:string>2 - sciences biologiques et medicales</json:string><json:string>3 - sciences biologiques fondamentales et appliquees. psychologie</json:string></inist></categories><publicationDate>2013</publicationDate><copyrightDate>2013</copyrightDate><doi><json:string>10.1136/gutjnl-2011-301805</json:string></doi><id>F995F34D52E9F6B4B8175B38F2C40C300F004FBD</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/document/F995F34D52E9F6B4B8175B38F2C40C300F004FBD/fulltext/pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/document/F995F34D52E9F6B4B8175B38F2C40C300F004FBD/fulltext/zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/document/F995F34D52E9F6B4B8175B38F2C40C300F004FBD/fulltext/tei"><teiHeader><fileDesc><titleStmt><title level="a">A metagenomic insight into our gut's 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For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions</p></licence><p scheme="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-7M42M2QJ-2">bmj</p></availability><date>2012-04-23</date></publicationStmt><notesStmt><note type="review-article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-L5L7X3NF-P">review-article</note><note type="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a">A metagenomic insight into our gut's microbiome</title><author xml:id="author-0000" corresp="yes"><persName><forename type="first">Patricia</forename><surname>Lepage</surname></persName><email>patricia.lepage@jouy.inra.fr</email><affiliation>INRA, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</affiliation></author><author xml:id="author-0001"><persName><forename type="first">Marion C</forename><surname>Leclerc</surname></persName><affiliation>INRA, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</affiliation></author><author xml:id="author-0002"><persName><forename type="first">Marie</forename><surname>Joossens</surname></persName><affiliation>Research Group of Bioinformatics and (Eco-)systems Biology, Department of Structural Biology, VIB, Brussels, Belgium</affiliation><affiliation>Microbiology Unit, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, Belgium</affiliation><affiliation>IBD Research Group, TARGID, Department of Gastroenterology, KU Leuven, Leuven, Belgium</affiliation></author><author xml:id="author-0003"><persName><forename type="first">Stanislas</forename><surname>Mondot</surname></persName><affiliation>CSIRO, Division of Livestock Industries, Queensland Biosciences Precinct, St Lucia, Queensland, Australia</affiliation></author><author xml:id="author-0004"><persName><forename type="first">Hervé M</forename><surname>Blottière</surname></persName><affiliation>INRA, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</affiliation></author><author xml:id="author-0005"><persName><forename type="first">Jeroen</forename><surname>Raes</surname></persName><affiliation>Research Group of Bioinformatics and (Eco-)systems Biology, Department of Structural Biology, VIB, Brussels, Belgium</affiliation><affiliation>Microbiology Unit, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, Belgium</affiliation></author><author xml:id="author-0006"><persName><forename type="first">Dusko</forename><surname>Ehrlich</surname></persName><affiliation>INRA, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</affiliation></author><author xml:id="author-0007"><persName><forename type="first">Joel</forename><surname>Doré</surname></persName><affiliation>INRA, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</affiliation></author><idno type="istex">F995F34D52E9F6B4B8175B38F2C40C300F004FBD</idno><idno type="ark">ark:/67375/NVC-21HVKLZV-P</idno><idno type="DOI">10.1136/gutjnl-2011-301805</idno><idno type="href">gutjnl-62-146.pdf</idno><idno type="article-id">gutjnl-2011-301805</idno><idno type="PMID">22525886</idno><idno type="local">gutjnl;62/1/146</idno></analytic><monogr><title level="j">Gut</title><title level="j" type="abbrev">Gut</title><idno type="pISSN">0017-5749</idno><idno type="eISSN">1468-3288</idno><idno type="publisher-id">gut</idno><idno type="PublisherID-hwp">gutjnl</idno><idno type="PublisherID-nlm-ta">Gut</idno><imprint><publisher>BMJ Publishing Group Ltd and British Society of Gastroenterology</publisher><date type="published" when="2013-01"></date><biblScope unit="volume">62</biblScope><biblScope unit="issue">1</biblScope><biblScope unit="page" from="146">146</biblScope></imprint></monogr></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2012-04-23</date></creation><langUsage><language ident="en">en</language></langUsage><abstract><p>Advances in sequencing technology and the development of metagenomic and bioinformatics methods have opened up new ways to investigate the 1014 microorganisms inhabiting the human gut. The gene composition of human gut microbiome in a large and deeply sequenced cohort highlighted an overall non-redundant genome size 150 times larger than the human genome. The in silico predictions based on metagenomic sequencing are now actively followed, compared and challenged using additional ‘omics’ technologies. Interactions between the microbiota and its host are of key interest in several pathologies and applying meta-omics to describe the human gut microbiome will give a better understanding of this crucial crosstalk at mucosal interfaces. Adding to the growing appreciation of the importance of the microbiome is the discovery that numerous phages, that is, viruses of prokaryotes infecting bacteria (bacteriophages) or archaea with a high host specificity, inhabit the human gut and impact microbial activity. In addition, gene exchanges within the gut microbiota have proved to be more frequent than anticipated. Taken together, these innovative exploratory technologies are expected to unravel new information networks critical for gut homeostasis and human health. Among the challenges faced, the in vivo validation of these networks, together with their integration into the prediction and prognosis of disease, may require further working hypothesis and collaborative efforts.</p></abstract><textClass><keywords scheme="keyword"><list><head>keywords</head><item><term>Bacterial interactions</term></item><item><term>genetics</term></item><item><term>IBD</term></item><item><term>mucus</term></item><item><term>intestinal microbiology</term></item><item><term>metagenomics</term></item><item><term>carbohydrates</term></item><item><term>anaerobic bacterial fermentation</term></item><item><term>molecular biology</term></item><item><term>mucins</term></item><item><term>inflammatory diseases</term></item><item><term>bacterial adherence</term></item><item><term>short chain fatty acids</term></item><item><term>IBD basic research</term></item><item><term>intestinal microbiota</term></item><item><term>Crohn's disease</term></item><item><term>stool markers</term></item><item><term>inflammatory bowel disease</term></item><item><term>intestinal bacteria</term></item><item><term>ribosomal RNA</term></item><item><term>colonic microflora</term></item><item><term>enteric bacterial microflora</term></item><item><term>RNA expression</term></item><item><term>gut inflammation</term></item><item><term>intestinal bacteria</term></item><item><term>immune response</term></item><item><term>mucosal immunology</term></item></list></keywords></textClass><textClass><keywords scheme="Journal Subject"><list><head>hwp-journal-coll</head><item><term>GUT Recent advances in basic science</term></item></list></keywords></textClass><textClass><keywords scheme="Journal Subject"><list><head>hwp-journal-coll</head><item><term>Gut Education</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2012-04-23">Created</change><change when="2013-01">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/document/F995F34D52E9F6B4B8175B38F2C40C300F004FBD/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="corpus bmj" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="no"</istex:xmlDeclaration><istex:docType PUBLIC="-//NLM//DTD Journal Archiving and Interchange DTD v2.3 20070202//EN" URI="archivearticle.dtd" name="istex:docType"></istex:docType><istex:document><article article-type="review-article"><front><journal-meta><journal-id journal-id-type="hwp">gutjnl</journal-id><journal-id journal-id-type="nlm-ta">Gut</journal-id><journal-id journal-id-type="publisher-id">gut</journal-id><journal-title>Gut</journal-title><abbrev-journal-title abbrev-type="publisher">Gut</abbrev-journal-title><abbrev-journal-title>Gut</abbrev-journal-title><issn pub-type="ppub">0017-5749</issn><issn pub-type="epub">1468-3288</issn><publisher><publisher-name>BMJ Publishing Group Ltd and British Society of Gastroenterology</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">gutjnl-2011-301805</article-id><article-id pub-id-type="doi">10.1136/gutjnl-2011-301805</article-id><article-id pub-id-type="other">gutjnl;62/1/146</article-id><article-id pub-id-type="other">gutjnl;gutjnl-2011-301805</article-id><article-id pub-id-type="pmid">22525886</article-id><article-id pub-id-type="other">146</article-id><article-id pub-id-type="other">gutjnl-2011-301805</article-id><article-categories><subj-group subj-group-type="heading"><subject>Recent advances in basic science</subject></subj-group><subj-group subj-group-type="hwp-journal-coll"><subject>GUT Recent advances in basic science</subject></subj-group><subj-group subj-group-type="hwp-journal-coll"><subject>Gut Education</subject></subj-group></article-categories><title-group><article-title>A metagenomic insight into our gut's microbiome</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Lepage</surname><given-names>Patricia</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Leclerc</surname><given-names>Marion C</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Joossens</surname><given-names>Marie</given-names></name><xref ref-type="aff" rid="aff3">3</xref><xref ref-type="aff" rid="aff4">4</xref><xref ref-type="aff" rid="aff5">5</xref></contrib><contrib contrib-type="author"><name><surname>Mondot</surname><given-names>Stanislas</given-names></name><xref ref-type="aff" rid="aff6">6</xref></contrib><contrib contrib-type="author"><name><surname>Blottière</surname><given-names>Hervé M</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Raes</surname><given-names>Jeroen</given-names></name><xref ref-type="aff" rid="aff3">3</xref><xref ref-type="aff" rid="aff4">4</xref></contrib><contrib contrib-type="author"><name><surname>Ehrlich</surname><given-names>Dusko</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Doré</surname><given-names>Joel</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff2">2</xref></contrib></contrib-group><aff id="aff1"><label>1</label>INRA, MICALIS UMR1319, Jouy-en-Josas, France</aff><aff id="aff2"><label>2</label>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</aff><aff id="aff3"><label>3</label>Research Group of Bioinformatics and (Eco-)systems Biology, Department of Structural Biology, VIB, Brussels, Belgium</aff><aff id="aff4"><label>4</label>Microbiology Unit, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, Belgium</aff><aff id="aff5"><label>5</label>IBD Research Group, TARGID, Department of Gastroenterology, KU Leuven, Leuven, Belgium</aff><aff id="aff6"><label>6</label>CSIRO, Division of Livestock Industries, Queensland Biosciences Precinct, St Lucia, Queensland, Australia</aff><author-notes><corresp><label>Correspondence to</label> Dr Patricia Lepage, MICALIS, Building 405, Domaine de Vilvert, INRA, 78350 Jouy-en-Josas, France; <email>patricia.lepage@jouy.inra.fr</email></corresp></author-notes><pub-date pub-type="ppub"><month>1</month><year>2013</year></pub-date><pub-date pub-type="epub"><day>23</day><month>4</month><year>2012</year></pub-date><volume>62</volume><volume-id pub-id-type="other">62</volume-id><volume-id pub-id-type="other">62</volume-id><issue>1</issue><issue-id pub-id-type="other">gutjnl;62/1</issue-id><issue-id pub-id-type="other">1</issue-id><issue-id pub-id-type="other">62/1</issue-id><fpage>146</fpage><permissions><copyright-statement>Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions</copyright-statement><copyright-year>2012</copyright-year></permissions><self-uri content-type="pdf" xlink:role="full-text" xlink:href="gutjnl-62-146.pdf"></self-uri><abstract><p>Advances in sequencing technology and the development of metagenomic and bioinformatics methods have opened up new ways to investigate the 10<sup>14</sup> microorganisms inhabiting the human gut. The gene composition of human gut microbiome in a large and deeply sequenced cohort highlighted an overall non-redundant genome size 150 times larger than the human genome. The <italic>in silico</italic> predictions based on metagenomic sequencing are now actively followed, compared and challenged using additional ‘omics’ technologies. Interactions between the microbiota and its host are of key interest in several pathologies and applying meta-omics to describe the human gut microbiome will give a better understanding of this crucial crosstalk at mucosal interfaces. Adding to the growing appreciation of the importance of the microbiome is the discovery that numerous phages, that is, viruses of prokaryotes infecting bacteria (bacteriophages) or archaea with a high host specificity, inhabit the human gut and impact microbial activity. In addition, gene exchanges within the gut microbiota have proved to be more frequent than anticipated. Taken together, these innovative exploratory technologies are expected to unravel new information networks critical for gut homeostasis and human health. Among the challenges faced, the <italic>in vivo</italic> validation of these networks, together with their integration into the prediction and prognosis of disease, may require further working hypothesis and collaborative efforts.</p></abstract><kwd-group><kwd>Bacterial interactions</kwd><kwd>genetics</kwd><kwd>IBD</kwd><kwd>mucus</kwd><kwd>intestinal microbiology</kwd><kwd>metagenomics</kwd><kwd>carbohydrates</kwd><kwd>anaerobic bacterial fermentation</kwd><kwd>molecular biology</kwd><kwd>mucins</kwd><kwd>inflammatory diseases</kwd><kwd>bacterial adherence</kwd><kwd>short chain fatty acids</kwd><kwd>IBD basic research</kwd><kwd>intestinal microbiota</kwd><kwd>Crohn's disease</kwd><kwd>stool markers</kwd><kwd>inflammatory bowel disease</kwd><kwd>intestinal bacteria</kwd><kwd>ribosomal RNA</kwd><kwd>colonic microflora</kwd><kwd>enteric bacterial microflora</kwd><kwd>RNA expression</kwd><kwd>gut inflammation</kwd><kwd>intestinal bacteria</kwd><kwd>immune response</kwd><kwd>mucosal immunology</kwd></kwd-group></article-meta></front></article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo><title>A metagenomic insight into our gut's microbiome</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>A metagenomic insight into our gut's microbiome</title></titleInfo><name type="personal" displayLabel="corresp"><namePart type="given">Patricia</namePart><namePart type="family">Lepage</namePart><affiliation>INRA, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><affiliation>E-mail: patricia.lepage@jouy.inra.fr</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Marion C</namePart><namePart type="family">Leclerc</namePart><affiliation>INRA, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Marie</namePart><namePart type="family">Joossens</namePart><affiliation>Research Group of Bioinformatics and (Eco-)systems Biology, Department of Structural Biology, VIB, Brussels, Belgium</affiliation><affiliation>Microbiology Unit, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, Belgium</affiliation><affiliation>IBD Research Group, TARGID, Department of Gastroenterology, KU Leuven, Leuven, Belgium</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Stanislas</namePart><namePart type="family">Mondot</namePart><affiliation>CSIRO, Division of Livestock Industries, Queensland Biosciences Precinct, St Lucia, Queensland, Australia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Hervé M</namePart><namePart type="family">Blottière</namePart><affiliation>INRA, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jeroen</namePart><namePart type="family">Raes</namePart><affiliation>Research Group of Bioinformatics and (Eco-)systems Biology, Department of Structural Biology, VIB, Brussels, Belgium</affiliation><affiliation>Microbiology Unit, Department of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, Belgium</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Dusko</namePart><namePart type="family">Ehrlich</namePart><affiliation>INRA, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Joel</namePart><namePart type="family">Doré</namePart><affiliation>INRA, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><affiliation>AgroParisTech, MICALIS UMR1319, Jouy-en-Josas, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="review-article" displayLabel="review-article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-L5L7X3NF-P">review-article</genre><originInfo><publisher>BMJ Publishing Group Ltd and British Society of Gastroenterology</publisher><dateIssued encoding="w3cdtf">2013-01</dateIssued><dateCreated encoding="w3cdtf">2012-04-23</dateCreated><copyrightDate encoding="w3cdtf">2013</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><abstract>Advances in sequencing technology and the development of metagenomic and bioinformatics methods have opened up new ways to investigate the 1014 microorganisms inhabiting the human gut. The gene composition of human gut microbiome in a large and deeply sequenced cohort highlighted an overall non-redundant genome size 150 times larger than the human genome. The in silico predictions based on metagenomic sequencing are now actively followed, compared and challenged using additional ‘omics’ technologies. Interactions between the microbiota and its host are of key interest in several pathologies and applying meta-omics to describe the human gut microbiome will give a better understanding of this crucial crosstalk at mucosal interfaces. Adding to the growing appreciation of the importance of the microbiome is the discovery that numerous phages, that is, viruses of prokaryotes infecting bacteria (bacteriophages) or archaea with a high host specificity, inhabit the human gut and impact microbial activity. In addition, gene exchanges within the gut microbiota have proved to be more frequent than anticipated. Taken together, these innovative exploratory technologies are expected to unravel new information networks critical for gut homeostasis and human health. Among the challenges faced, the in vivo validation of these networks, together with their integration into the prediction and prognosis of disease, may require further working hypothesis and collaborative efforts.</abstract><subject><genre>keywords</genre><topic>Bacterial interactions</topic><topic>genetics</topic><topic>IBD</topic><topic>mucus</topic><topic>intestinal microbiology</topic><topic>metagenomics</topic><topic>carbohydrates</topic><topic>anaerobic bacterial fermentation</topic><topic>molecular biology</topic><topic>mucins</topic><topic>inflammatory diseases</topic><topic>bacterial adherence</topic><topic>short chain fatty acids</topic><topic>IBD basic research</topic><topic>intestinal microbiota</topic><topic>Crohn's disease</topic><topic>stool markers</topic><topic>inflammatory bowel disease</topic><topic>intestinal bacteria</topic><topic>ribosomal RNA</topic><topic>colonic microflora</topic><topic>enteric bacterial microflora</topic><topic>RNA expression</topic><topic>gut inflammation</topic><topic>intestinal bacteria</topic><topic>immune response</topic><topic>mucosal immunology</topic></subject><relatedItem type="host"><titleInfo><title>Gut</title></titleInfo><titleInfo type="abbreviated"><title>Gut</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><subject><genre>hwp-journal-coll</genre><topic>GUT Recent advances in basic science</topic></subject><subject><genre>hwp-journal-coll</genre><topic>Gut Education</topic></subject><identifier type="ISSN">0017-5749</identifier><identifier type="eISSN">1468-3288</identifier><identifier type="PublisherID">gut</identifier><identifier type="PublisherID-hwp">gutjnl</identifier><identifier type="PublisherID-nlm-ta">Gut</identifier><part><date>2013</date><detail type="volume"><caption>vol.</caption><number>62</number></detail><detail type="issue"><caption>no.</caption><number>1</number></detail><extent unit="pages"><start>146</start></extent></part></relatedItem><identifier type="istex">F995F34D52E9F6B4B8175B38F2C40C300F004FBD</identifier><identifier type="ark">ark:/67375/NVC-21HVKLZV-P</identifier><identifier type="DOI">10.1136/gutjnl-2011-301805</identifier><identifier type="href">gutjnl-62-146.pdf</identifier><identifier type="ArticleID">gutjnl-2011-301805</identifier><identifier type="PMID">22525886</identifier><identifier type="local">gutjnl;62/1/146</identifier><accessCondition type="use and reproduction" contentType="copyright">Published by the BMJ Publishing Group Limited. 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