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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Classification and quantification of bacteriophage taxa in human gut metagenomes</title><author><name sortKey="Waller, Alison S" sort="Waller, Alison S" uniqKey="Waller A" first="Alison S" last="Waller">Alison S. Waller</name><affiliation><nlm:aff id="aff1"><institution>Structural and Computational Biology Unit, European Molecular Biology Laboratory</institution>, Heidelberg,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Yamada, Takuji" sort="Yamada, Takuji" uniqKey="Yamada T" first="Takuji" last="Yamada">Takuji Yamada</name><affiliation><nlm:aff id="aff2"><institution>Department of Biological Information, Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology</institution>, Yokohama,<country>Japan</country></nlm:aff></affiliation></author><author><name sortKey="Kristensen, David M" sort="Kristensen, David M" uniqKey="Kristensen D" first="David M" last="Kristensen">David M. Kristensen</name><affiliation><nlm:aff id="aff3"><institution>National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH)</institution>, Bethesda, MD,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Kultima, Jens Roat" sort="Kultima, Jens Roat" uniqKey="Kultima J" first="Jens Roat" last="Kultima">Jens Roat Kultima</name><affiliation><nlm:aff id="aff1"><institution>Structural and Computational Biology Unit, European Molecular Biology Laboratory</institution>, Heidelberg,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Sunagawa, Shinichi" sort="Sunagawa, Shinichi" uniqKey="Sunagawa S" first="Shinichi" last="Sunagawa">Shinichi Sunagawa</name><affiliation><nlm:aff id="aff1"><institution>Structural and Computational Biology Unit, European Molecular Biology Laboratory</institution>, Heidelberg,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Koonin, Eugene V" sort="Koonin, Eugene V" uniqKey="Koonin E" first="Eugene V" last="Koonin">Eugene V. Koonin</name><affiliation><nlm:aff id="aff3"><institution>National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH)</institution>, Bethesda, MD,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Bork, Peer" sort="Bork, Peer" uniqKey="Bork P" first="Peer" last="Bork">Peer Bork</name><affiliation><nlm:aff id="aff1"><institution>Structural and Computational Biology Unit, European Molecular Biology Laboratory</institution>, Heidelberg,<country>Germany</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24621522</idno><idno type="pmc">4069399</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4069399</idno><idno type="RBID">PMC:4069399</idno><idno type="doi">10.1038/ismej.2014.30</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000017</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Classification and quantification of bacteriophage taxa in human gut metagenomes</title><author><name sortKey="Waller, Alison S" sort="Waller, Alison S" uniqKey="Waller A" first="Alison S" last="Waller">Alison S. Waller</name><affiliation><nlm:aff id="aff1"><institution>Structural and Computational Biology Unit, European Molecular Biology Laboratory</institution>, Heidelberg,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Yamada, Takuji" sort="Yamada, Takuji" uniqKey="Yamada T" first="Takuji" last="Yamada">Takuji Yamada</name><affiliation><nlm:aff id="aff2"><institution>Department of Biological Information, Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology</institution>, Yokohama,<country>Japan</country></nlm:aff></affiliation></author><author><name sortKey="Kristensen, David M" sort="Kristensen, David M" uniqKey="Kristensen D" first="David M" last="Kristensen">David M. Kristensen</name><affiliation><nlm:aff id="aff3"><institution>National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH)</institution>, Bethesda, MD,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Kultima, Jens Roat" sort="Kultima, Jens Roat" uniqKey="Kultima J" first="Jens Roat" last="Kultima">Jens Roat Kultima</name><affiliation><nlm:aff id="aff1"><institution>Structural and Computational Biology Unit, European Molecular Biology Laboratory</institution>, Heidelberg,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Sunagawa, Shinichi" sort="Sunagawa, Shinichi" uniqKey="Sunagawa S" first="Shinichi" last="Sunagawa">Shinichi Sunagawa</name><affiliation><nlm:aff id="aff1"><institution>Structural and Computational Biology Unit, European Molecular Biology Laboratory</institution>, Heidelberg,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Koonin, Eugene V" sort="Koonin, Eugene V" uniqKey="Koonin E" first="Eugene V" last="Koonin">Eugene V. Koonin</name><affiliation><nlm:aff id="aff3"><institution>National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH)</institution>, Bethesda, MD,<country>USA</country></nlm:aff></affiliation></author><author><name sortKey="Bork, Peer" sort="Bork, Peer" uniqKey="Bork P" first="Peer" last="Bork">Peer Bork</name><affiliation><nlm:aff id="aff1"><institution>Structural and Computational Biology Unit, European Molecular Biology Laboratory</institution>, Heidelberg,<country>Germany</country></nlm:aff></affiliation></author></analytic><series><title level="j">The ISME Journal</title><idno type="ISSN">1751-7362</idno><idno type="eISSN">1751-7370</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Bacteriophages have key roles in microbial communities, to a large extent shaping the taxonomic and functional composition of the microbiome, but data on the connections between phage diversity and the composition of communities are scarce. Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. On average, five phage taxa were identified in each sample, with up to three of these being highly abundant. The abundances of most phage taxa vary by up to four orders of magnitude between the samples, and several taxa that are highly abundant in some samples are absent in others. Significant correlations exist between the abundances of some phage taxa and human host metadata: for example, ‘<italic>Group 936 lactococcal phages'</italic> are more prevalent and abundant in Danish samples than in samples from Spain or the United States of America. Quantification of phages that exist as integrated prophages revealed that the abundance profiles of prophages are highly individual-specific and remain unique to an individual over a 1-year time period, and prediction of prophage lysis across the samples identified hundreds of prophages that are apparently active in the gut and vary across the samples, in terms of presence and lytic state. Finally, a prophage–host network of the human gut was established and includes numerous novel host–phage associations.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">ISME J</journal-id><journal-id journal-id-type="iso-abbrev">ISME J</journal-id><journal-title-group><journal-title>The ISME Journal</journal-title></journal-title-group><issn pub-type="ppub">1751-7362</issn><issn pub-type="epub">1751-7370</issn><publisher><publisher-name>Nature Publishing Group</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24621522</article-id><article-id pub-id-type="pmc">4069399</article-id><article-id pub-id-type="pii">ismej201430</article-id><article-id pub-id-type="doi">10.1038/ismej.2014.30</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Article</subject></subj-group></article-categories><title-group><article-title>Classification and quantification of bacteriophage taxa in human gut metagenomes</article-title><alt-title alt-title-type="running">Bacteriophage taxa in human gut metagenomes</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Waller</surname><given-names>Alison S</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Yamada</surname><given-names>Takuji</given-names></name><xref ref-type="aff" rid="aff2">2</xref></contrib><contrib contrib-type="author"><name><surname>Kristensen</surname><given-names>David M</given-names></name><xref ref-type="aff" rid="aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Kultima</surname><given-names>Jens Roat</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Sunagawa</surname><given-names>Shinichi</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Koonin</surname><given-names>Eugene V</given-names></name><xref ref-type="aff" rid="aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Bork</surname><given-names>Peer</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="corresp" rid="caf1">*</xref></contrib><aff id="aff1"><label>1</label><institution>Structural and Computational Biology Unit, European Molecular Biology Laboratory</institution>, Heidelberg,<country>Germany</country></aff><aff id="aff2"><label>2</label><institution>Department of Biological Information, Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology</institution>, Yokohama,<country>Japan</country></aff><aff id="aff3"><label>3</label><institution>National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH)</institution>, Bethesda, MD,<country>USA</country></aff></contrib-group><author-notes><corresp id="caf1"><label>*</label><institution>Structural and Computational Biology Unit, European Molecular Biology Laboratory</institution>, Meyerhofstrasse 1, Heidelberg 69117, <country>Germany</country>. E-mail: <email>bork@embl.de</email></corresp></author-notes><pub-date pub-type="ppub"><month>07</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>13</day><month>03</month><year>2014</year></pub-date><volume>8</volume><issue>7</issue><fpage>1391</fpage><lpage>1402</lpage><history><date date-type="received"><day>14</day><month>08</month><year>2013</year></date><date date-type="rev-recd"><day>17</day><month>01</month><year>2014</year></date><date date-type="accepted"><day>24</day><month>01</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014 International Society for Microbial Ecology</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>International Society for Microbial Ecology</copyright-holder></permissions><abstract><p>Bacteriophages have key roles in microbial communities, to a large extent shaping the taxonomic and functional composition of the microbiome, but data on the connections between phage diversity and the composition of communities are scarce. Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. On average, five phage taxa were identified in each sample, with up to three of these being highly abundant. The abundances of most phage taxa vary by up to four orders of magnitude between the samples, and several taxa that are highly abundant in some samples are absent in others. Significant correlations exist between the abundances of some phage taxa and human host metadata: for example, ‘<italic>Group 936 lactococcal phages'</italic> are more prevalent and abundant in Danish samples than in samples from Spain or the United States of America. Quantification of phages that exist as integrated prophages revealed that the abundance profiles of prophages are highly individual-specific and remain unique to an individual over a 1-year time period, and prediction of prophage lysis across the samples identified hundreds of prophages that are apparently active in the gut and vary across the samples, in terms of presence and lytic state. Finally, a prophage–host network of the human gut was established and includes numerous novel host–phage associations.</p></abstract><kwd-group><kwd>human gut</kwd><kwd>metagenomics</kwd><kwd>phage</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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