Phage–bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome
Identifieur interne : 000637 ( Istex/Curation ); précédent : 000636; suivant : 000638Phage–bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome
Auteurs : Margret E. Berg Miller [États-Unis] ; Carl J. Yeoman [États-Unis] ; Nicholas Chia [États-Unis] ; Susannah G. Tringe [États-Unis] ; Florent E. Angly [Australie] ; Robert A. Edwards [États-Unis] ; Harry J. Flint [Royaume-Uni] ; Raphael Lamed [Israël] ; Edward A. Bayer [Israël] ; Bryan A. White [États-Unis]Source :
- Environmental Microbiology [ 1462-2912 ] ; 2012-01.
Abstract
Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus‐enriched metagenomes (viromes) isolated from bovine rumen fluid and analysed the resulting data using comparative metagenomics. A high level of diversity was observed with up to 28 000 different viral genotypes obtained from each environment. The majority (∼78%) of sequences did not match any previously described virus. Prophages outnumbered lytic phages approximately 2:1 with the most abundant bacteriophage and prophage types being associated with members of the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling based on SEED subsystems revealed an enrichment of sequences with putative functional roles in DNA and protein metabolism, but a surprisingly low proportion of sequences assigned to carbohydrate and amino acid metabolism. We expanded our analysis to include previously described metagenomic data and 14 reference genomes. Clustered regularly interspaced short palindromic repeats (CRISPR) were detected in most of the microbial genomes, suggesting previous interactions between viral and microbial communities.
Url:
DOI: 10.1111/j.1462-2920.2011.02593.x
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000637
Links to Exploration step
ISTEX:08705BF8F57E6F36D4BE299E678D547AB1D3A814Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Phage–bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome</title>
<author><name sortKey="Berg Miller, Margret E" sort="Berg Miller, Margret E" uniqKey="Berg Miller M" first="Margret E." last="Berg Miller">Margret E. Berg Miller</name>
<affiliation wicri:level="1"><mods:affiliation>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Yeoman, Carl J" sort="Yeoman, Carl J" uniqKey="Yeoman C" first="Carl J." last="Yeoman">Carl J. Yeoman</name>
<affiliation wicri:level="1"><mods:affiliation>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Chia, Nicholas" sort="Chia, Nicholas" uniqKey="Chia N" first="Nicholas" last="Chia">Nicholas Chia</name>
<affiliation wicri:level="1"><mods:affiliation>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><mods:affiliation>Department of Physics, University of Illinois at Urbana‐Champaign, 1110 West Green St., Urbana, IL 61801, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Department of Physics, University of Illinois at Urbana‐Champaign, 1110 West Green St., Urbana, IL 61801</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Tringe, Susannah G" sort="Tringe, Susannah G" uniqKey="Tringe S" first="Susannah G." last="Tringe">Susannah G. Tringe</name>
<affiliation wicri:level="1"><mods:affiliation>DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Angly, Florent E" sort="Angly, Florent E" uniqKey="Angly F" first="Florent E." last="Angly">Florent E. Angly</name>
<affiliation wicri:level="1"><mods:affiliation>Australian Centre for Ecogenomics, University of Queensland, St. Lucia, Brisbane, Australia.</mods:affiliation>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Australian Centre for Ecogenomics, University of Queensland, St. Lucia, Brisbane</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Edwards, Robert A" sort="Edwards, Robert A" uniqKey="Edwards R" first="Robert A." last="Edwards">Robert A. Edwards</name>
<affiliation wicri:level="1"><mods:affiliation>Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Flint, Harry J" sort="Flint, Harry J" uniqKey="Flint H" first="Harry J." last="Flint">Harry J. Flint</name>
<affiliation wicri:level="1"><mods:affiliation>Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country>
<wicri:regionArea>Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lamed, Raphael" sort="Lamed, Raphael" uniqKey="Lamed R" first="Raphael" last="Lamed">Raphael Lamed</name>
<affiliation wicri:level="1"><mods:affiliation>Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel.</mods:affiliation>
<country xml:lang="fr">Israël</country>
<wicri:regionArea>Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Bayer, Edward A" sort="Bayer, Edward A" uniqKey="Bayer E" first="Edward A." last="Bayer">Edward A. Bayer</name>
<affiliation wicri:level="1"><mods:affiliation>Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel</mods:affiliation>
<country xml:lang="fr">Israël</country>
<wicri:regionArea>Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="White, Bryan A" sort="White, Bryan A" uniqKey="White B" first="Bryan A." last="White">Bryan A. White</name>
<affiliation wicri:level="1"><mods:affiliation>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801</wicri:regionArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">ISTEX</idno>
<idno type="RBID">ISTEX:08705BF8F57E6F36D4BE299E678D547AB1D3A814</idno>
<date when="2012" year="2012">2012</date>
<idno type="doi">10.1111/j.1462-2920.2011.02593.x</idno>
<idno type="url">https://api.istex.fr/document/08705BF8F57E6F36D4BE299E678D547AB1D3A814/fulltext/pdf</idno>
<idno type="wicri:Area/Istex/Corpus">000637</idno>
<idno type="wicri:Area/Istex/Curation">000637</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Phage–bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome</title>
<author><name sortKey="Berg Miller, Margret E" sort="Berg Miller, Margret E" uniqKey="Berg Miller M" first="Margret E." last="Berg Miller">Margret E. Berg Miller</name>
<affiliation wicri:level="1"><mods:affiliation>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Yeoman, Carl J" sort="Yeoman, Carl J" uniqKey="Yeoman C" first="Carl J." last="Yeoman">Carl J. Yeoman</name>
<affiliation wicri:level="1"><mods:affiliation>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Chia, Nicholas" sort="Chia, Nicholas" uniqKey="Chia N" first="Nicholas" last="Chia">Nicholas Chia</name>
<affiliation wicri:level="1"><mods:affiliation>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><mods:affiliation>Department of Physics, University of Illinois at Urbana‐Champaign, 1110 West Green St., Urbana, IL 61801, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Department of Physics, University of Illinois at Urbana‐Champaign, 1110 West Green St., Urbana, IL 61801</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Tringe, Susannah G" sort="Tringe, Susannah G" uniqKey="Tringe S" first="Susannah G." last="Tringe">Susannah G. Tringe</name>
<affiliation wicri:level="1"><mods:affiliation>DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Angly, Florent E" sort="Angly, Florent E" uniqKey="Angly F" first="Florent E." last="Angly">Florent E. Angly</name>
<affiliation wicri:level="1"><mods:affiliation>Australian Centre for Ecogenomics, University of Queensland, St. Lucia, Brisbane, Australia.</mods:affiliation>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Australian Centre for Ecogenomics, University of Queensland, St. Lucia, Brisbane</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Edwards, Robert A" sort="Edwards, Robert A" uniqKey="Edwards R" first="Robert A." last="Edwards">Robert A. Edwards</name>
<affiliation wicri:level="1"><mods:affiliation>Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Flint, Harry J" sort="Flint, Harry J" uniqKey="Flint H" first="Harry J." last="Flint">Harry J. Flint</name>
<affiliation wicri:level="1"><mods:affiliation>Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">Royaume-Uni</country>
<wicri:regionArea>Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lamed, Raphael" sort="Lamed, Raphael" uniqKey="Lamed R" first="Raphael" last="Lamed">Raphael Lamed</name>
<affiliation wicri:level="1"><mods:affiliation>Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel.</mods:affiliation>
<country xml:lang="fr">Israël</country>
<wicri:regionArea>Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Bayer, Edward A" sort="Bayer, Edward A" uniqKey="Bayer E" first="Edward A." last="Bayer">Edward A. Bayer</name>
<affiliation wicri:level="1"><mods:affiliation>Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel</mods:affiliation>
<country xml:lang="fr">Israël</country>
<wicri:regionArea>Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="White, Bryan A" sort="White, Bryan A" uniqKey="White B" first="Bryan A." last="White">Bryan A. White</name>
<affiliation wicri:level="1"><mods:affiliation>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801, USA.</mods:affiliation>
<country xml:lang="fr" wicri:curation="lc">États-Unis</country>
<wicri:regionArea>Institute for Genomic Biology, University of Illinois at Urbana‐Champaign, 1206 W. Gregory Dr, Urbana, IL 61801</wicri:regionArea>
</affiliation>
</author>
</analytic>
<monogr></monogr>
<series><title level="j">Environmental Microbiology</title>
<idno type="ISSN">1462-2912</idno>
<idno type="eISSN">1462-2920</idno>
<imprint><publisher>Blackwell Publishing Ltd</publisher>
<pubPlace>Oxford, UK</pubPlace>
<date type="published" when="2012-01">2012-01</date>
<biblScope unit="volume">14</biblScope>
<biblScope unit="issue">1</biblScope>
<biblScope unit="page" from="207">207</biblScope>
<biblScope unit="page" to="227">227</biblScope>
</imprint>
<idno type="ISSN">1462-2912</idno>
</series>
<idno type="istex">08705BF8F57E6F36D4BE299E678D547AB1D3A814</idno>
<idno type="DOI">10.1111/j.1462-2920.2011.02593.x</idno>
<idno type="ArticleID">EMI2593</idno>
</biblStruct>
</sourceDesc>
<seriesStmt><idno type="ISSN">1462-2912</idno>
</seriesStmt>
</fileDesc>
<profileDesc><textClass></textClass>
<langUsage><language ident="en">en</language>
</langUsage>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus‐enriched metagenomes (viromes) isolated from bovine rumen fluid and analysed the resulting data using comparative metagenomics. A high level of diversity was observed with up to 28 000 different viral genotypes obtained from each environment. The majority (∼78%) of sequences did not match any previously described virus. Prophages outnumbered lytic phages approximately 2:1 with the most abundant bacteriophage and prophage types being associated with members of the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling based on SEED subsystems revealed an enrichment of sequences with putative functional roles in DNA and protein metabolism, but a surprisingly low proportion of sequences assigned to carbohydrate and amino acid metabolism. We expanded our analysis to include previously described metagenomic data and 14 reference genomes. Clustered regularly interspaced short palindromic repeats (CRISPR) were detected in most of the microbial genomes, suggesting previous interactions between viral and microbial communities.</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Istex/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000637 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Istex/Curation/biblio.hfd -nk 000637 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Istex |étape= Curation |type= RBID |clé= ISTEX:08705BF8F57E6F36D4BE299E678D547AB1D3A814 |texte= Phage–bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome }}
This area was generated with Dilib version V0.6.25. |