Classification and quantification of bacteriophage taxa in human gut metagenomes
Identifieur interne : 000017 ( Pmc/Corpus ); précédent : 000016; suivant : 000018Classification and quantification of bacteriophage taxa in human gut metagenomes
Auteurs : Alison S. Waller ; Takuji Yamada ; David M. Kristensen ; Jens Roat Kultima ; Shinichi Sunagawa ; Eugene V. Koonin ; Peer BorkSource :
- The ISME Journal [ 1751-7362 ] ; 2014.
Abstract
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, ‘
Url:
DOI: 10.1038/ismej.2014.30
PubMed: 24621522
PubMed Central: 4069399
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PMC:4069399Le document en format XML
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<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>
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<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>
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<issn pub-type="ppub">1751-7362</issn>
<issn pub-type="epub">1751-7370</issn>
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<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>
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<contrib contrib-type="author"><name><surname>Yamada</surname>
<given-names>Takuji</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
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<contrib contrib-type="author"><name><surname>Kristensen</surname>
<given-names>David M</given-names>
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<contrib contrib-type="author"><name><surname>Kultima</surname>
<given-names>Jens Roat</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
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<contrib contrib-type="author"><name><surname>Sunagawa</surname>
<given-names>Shinichi</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
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<contrib contrib-type="author"><name><surname>Koonin</surname>
<given-names>Eugene V</given-names>
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<xref ref-type="aff" rid="aff3">3</xref>
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<contrib contrib-type="author"><name><surname>Bork</surname>
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<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="corresp" rid="caf1">*</xref>
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<aff id="aff1"><label>1</label>
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<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>
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, Bethesda, MD,<country>USA</country>
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<author-notes><corresp id="caf1"><label>*</label>
<institution>Structural and Computational Biology Unit, European Molecular Biology Laboratory</institution>
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. 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>
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</front>
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