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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases</title><author><name sortKey="Brulc, Jennifer M" sort="Brulc, Jennifer M" uniqKey="Brulc J" first="Jennifer M." last="Brulc">Jennifer M. Brulc</name><affiliation><nlm:aff id="aff1">Department of Animal Sciences, University of Illinois, Urbana, IL 61801;</nlm:aff></affiliation></author><author><name sortKey="Antonopoulos, Dionysios A" sort="Antonopoulos, Dionysios A" uniqKey="Antonopoulos D" first="Dionysios A." last="Antonopoulos">Dionysios A. Antonopoulos</name><affiliation><nlm:aff id="aff2">Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439;</nlm:aff></affiliation></author><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><nlm:aff id="aff1">Department of Animal Sciences, University of Illinois, Urbana, IL 61801;</nlm:aff></affiliation><affiliation><nlm:aff id="aff10">The Institute for Genomic Biology, University of Illinois, Urbana, IL 61801</nlm:aff></affiliation></author><author><name sortKey="Wilson, Melissa K" sort="Wilson, Melissa K" uniqKey="Wilson M" first="Melissa K." last="Wilson">Melissa K. Wilson</name><affiliation><nlm:aff id="aff1">Department of Animal Sciences, University of Illinois, Urbana, IL 61801;</nlm:aff></affiliation></author><author><name sortKey="Yannarell, Anthony C" sort="Yannarell, Anthony C" uniqKey="Yannarell A" first="Anthony C." last="Yannarell">Anthony C. Yannarell</name><affiliation><nlm:aff id="aff1">Department of Animal Sciences, University of Illinois, Urbana, IL 61801;</nlm:aff></affiliation><affiliation><nlm:aff id="aff10">The Institute for Genomic Biology, University of Illinois, Urbana, IL 61801</nlm:aff></affiliation></author><author><name sortKey="Dinsdale, Elizabeth A" sort="Dinsdale, Elizabeth A" uniqKey="Dinsdale E" first="Elizabeth A." last="Dinsdale">Elizabeth A. Dinsdale</name><affiliation><nlm:aff id="aff3">Department of Biology, San Diego State University, San Diego, CA 92813;</nlm:aff></affiliation><affiliation><nlm:aff id="aff4">School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia;</nlm:aff></affiliation></author><author><name sortKey="Edwards, Robert E" sort="Edwards, Robert E" uniqKey="Edwards R" first="Robert E." last="Edwards">Robert E. Edwards</name><affiliation><nlm:aff id="aff3">Department of Biology, San Diego State University, San Diego, CA 92813;</nlm:aff></affiliation><affiliation><nlm:aff id="aff5">Center for Microbial Sciences, San Diego State University, San Diego, CA 92813;</nlm:aff></affiliation><affiliation><nlm:aff id="aff6">Department of Computer Sciences, San Diego State University, San Diego, CA 92813;</nlm:aff></affiliation><affiliation><nlm:aff id="aff7">Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439;</nlm:aff></affiliation></author><author><name sortKey="Frank, Edward D" sort="Frank, Edward D" uniqKey="Frank E" first="Edward D." last="Frank">Edward D. Frank</name><affiliation><nlm:aff id="aff7">Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439;</nlm:aff></affiliation></author><author><name sortKey="Emerson, Joanne B" sort="Emerson, Joanne B" uniqKey="Emerson J" first="Joanne B." last="Emerson">Joanne B. Emerson</name><affiliation><nlm:aff id="aff8">J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850;</nlm:aff></affiliation></author><author><name sortKey="Wacklin, Pirjo" sort="Wacklin, Pirjo" uniqKey="Wacklin P" first="Pirjo" last="Wacklin">Pirjo Wacklin</name><affiliation><nlm:aff id="aff8">J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850;</nlm:aff></affiliation></author><author><name sortKey="Coutinho, Pedro M" sort="Coutinho, Pedro M" uniqKey="Coutinho P" first="Pedro M." last="Coutinho">Pedro M. Coutinho</name><affiliation><nlm:aff wicri:cut="; and" id="aff9">Architecture et Fonction des Macromolecules Biologiques, Unité Mixte de Recherche 6098, Centre National de la Recherche Scientifique, Universites Aix-Marseille I and II, Case 932, 163 Avenue de Luminy, 13288 Marseille, France</nlm:aff></affiliation></author><author><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name><affiliation><nlm:aff wicri:cut="; and" id="aff9">Architecture et Fonction des Macromolecules Biologiques, Unité Mixte de Recherche 6098, Centre National de la Recherche Scientifique, Universites Aix-Marseille I and II, Case 932, 163 Avenue de Luminy, 13288 Marseille, France</nlm:aff></affiliation></author><author><name sortKey="Nelson, Karen E" sort="Nelson, Karen E" uniqKey="Nelson K" first="Karen E." last="Nelson">Karen E. Nelson</name><affiliation><nlm:aff id="aff8">J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850;</nlm:aff></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><nlm:aff id="aff1">Department of Animal Sciences, University of Illinois, Urbana, IL 61801;</nlm:aff></affiliation><affiliation><nlm:aff id="aff10">The Institute for Genomic Biology, University of Illinois, Urbana, IL 61801</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19181843</idno><idno type="pmc">2633212</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633212</idno><idno type="RBID">PMC:2633212</idno><idno type="doi">10.1073/pnas.0806191105</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">001B22</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001B22</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases</title><author><name sortKey="Brulc, Jennifer M" sort="Brulc, Jennifer M" uniqKey="Brulc J" first="Jennifer M." last="Brulc">Jennifer M. Brulc</name><affiliation><nlm:aff id="aff1">Department of Animal Sciences, University of Illinois, Urbana, IL 61801;</nlm:aff></affiliation></author><author><name sortKey="Antonopoulos, Dionysios A" sort="Antonopoulos, Dionysios A" uniqKey="Antonopoulos D" first="Dionysios A." last="Antonopoulos">Dionysios A. Antonopoulos</name><affiliation><nlm:aff id="aff2">Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439;</nlm:aff></affiliation></author><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><nlm:aff id="aff1">Department of Animal Sciences, University of Illinois, Urbana, IL 61801;</nlm:aff></affiliation><affiliation><nlm:aff id="aff10">The Institute for Genomic Biology, University of Illinois, Urbana, IL 61801</nlm:aff></affiliation></author><author><name sortKey="Wilson, Melissa K" sort="Wilson, Melissa K" uniqKey="Wilson M" first="Melissa K." last="Wilson">Melissa K. Wilson</name><affiliation><nlm:aff id="aff1">Department of Animal Sciences, University of Illinois, Urbana, IL 61801;</nlm:aff></affiliation></author><author><name sortKey="Yannarell, Anthony C" sort="Yannarell, Anthony C" uniqKey="Yannarell A" first="Anthony C." last="Yannarell">Anthony C. Yannarell</name><affiliation><nlm:aff id="aff1">Department of Animal Sciences, University of Illinois, Urbana, IL 61801;</nlm:aff></affiliation><affiliation><nlm:aff id="aff10">The Institute for Genomic Biology, University of Illinois, Urbana, IL 61801</nlm:aff></affiliation></author><author><name sortKey="Dinsdale, Elizabeth A" sort="Dinsdale, Elizabeth A" uniqKey="Dinsdale E" first="Elizabeth A." last="Dinsdale">Elizabeth A. Dinsdale</name><affiliation><nlm:aff id="aff3">Department of Biology, San Diego State University, San Diego, CA 92813;</nlm:aff></affiliation><affiliation><nlm:aff id="aff4">School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia;</nlm:aff></affiliation></author><author><name sortKey="Edwards, Robert E" sort="Edwards, Robert E" uniqKey="Edwards R" first="Robert E." last="Edwards">Robert E. Edwards</name><affiliation><nlm:aff id="aff3">Department of Biology, San Diego State University, San Diego, CA 92813;</nlm:aff></affiliation><affiliation><nlm:aff id="aff5">Center for Microbial Sciences, San Diego State University, San Diego, CA 92813;</nlm:aff></affiliation><affiliation><nlm:aff id="aff6">Department of Computer Sciences, San Diego State University, San Diego, CA 92813;</nlm:aff></affiliation><affiliation><nlm:aff id="aff7">Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439;</nlm:aff></affiliation></author><author><name sortKey="Frank, Edward D" sort="Frank, Edward D" uniqKey="Frank E" first="Edward D." last="Frank">Edward D. Frank</name><affiliation><nlm:aff id="aff7">Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439;</nlm:aff></affiliation></author><author><name sortKey="Emerson, Joanne B" sort="Emerson, Joanne B" uniqKey="Emerson J" first="Joanne B." last="Emerson">Joanne B. Emerson</name><affiliation><nlm:aff id="aff8">J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850;</nlm:aff></affiliation></author><author><name sortKey="Wacklin, Pirjo" sort="Wacklin, Pirjo" uniqKey="Wacklin P" first="Pirjo" last="Wacklin">Pirjo Wacklin</name><affiliation><nlm:aff id="aff8">J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850;</nlm:aff></affiliation></author><author><name sortKey="Coutinho, Pedro M" sort="Coutinho, Pedro M" uniqKey="Coutinho P" first="Pedro M." last="Coutinho">Pedro M. Coutinho</name><affiliation><nlm:aff wicri:cut="; and" id="aff9">Architecture et Fonction des Macromolecules Biologiques, Unité Mixte de Recherche 6098, Centre National de la Recherche Scientifique, Universites Aix-Marseille I and II, Case 932, 163 Avenue de Luminy, 13288 Marseille, France</nlm:aff></affiliation></author><author><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name><affiliation><nlm:aff wicri:cut="; and" id="aff9">Architecture et Fonction des Macromolecules Biologiques, Unité Mixte de Recherche 6098, Centre National de la Recherche Scientifique, Universites Aix-Marseille I and II, Case 932, 163 Avenue de Luminy, 13288 Marseille, France</nlm:aff></affiliation></author><author><name sortKey="Nelson, Karen E" sort="Nelson, Karen E" uniqKey="Nelson K" first="Karen E." last="Nelson">Karen E. Nelson</name><affiliation><nlm:aff id="aff8">J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850;</nlm:aff></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><nlm:aff id="aff1">Department of Animal Sciences, University of Illinois, Urbana, IL 61801;</nlm:aff></affiliation><affiliation><nlm:aff id="aff10">The Institute for Genomic Biology, University of Illinois, Urbana, IL 61801</nlm:aff></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><idno type="eISSN">1091-6490</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly sampled pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid sample (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood).</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">Proc Natl Acad Sci U S A</journal-id><journal-id journal-id-type="hwp">pnas</journal-id><journal-id journal-id-type="pmc">pnas</journal-id><journal-id journal-id-type="publisher-id">PNAS</journal-id><journal-title-group><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title></journal-title-group><issn pub-type="ppub">0027-8424</issn><issn pub-type="epub">1091-6490</issn><publisher><publisher-name>National Academy of Sciences</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19181843</article-id><article-id pub-id-type="pmc">2633212</article-id><article-id pub-id-type="publisher-id">4473</article-id><article-id pub-id-type="doi">10.1073/pnas.0806191105</article-id><article-categories><subj-group subj-group-type="heading"><subject>Biological Sciences</subject><subj-group><subject>Microbiology</subject></subj-group></subj-group></article-categories><title-group><article-title>Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Brulc</surname><given-names>Jennifer M.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Antonopoulos</surname><given-names>Dionysios A.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Berg Miller</surname><given-names>Margret E.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff10"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wilson</surname><given-names>Melissa K.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yannarell</surname><given-names>Anthony C.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff10"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Dinsdale</surname><given-names>Elizabeth A.</given-names></name><xref ref-type="aff" rid="aff3"><sup>d</sup></xref><xref ref-type="aff" rid="aff4"><sup>e</sup></xref></contrib><contrib contrib-type="author"><name><surname>Edwards</surname><given-names>Robert E.</given-names></name><xref ref-type="aff" rid="aff3"><sup>d</sup></xref><xref ref-type="aff" rid="aff5"><sup>f</sup></xref><xref ref-type="aff" rid="aff6"><sup>g</sup></xref><xref ref-type="aff" rid="aff7"><sup>h</sup></xref></contrib><contrib contrib-type="author"><name><surname>Frank</surname><given-names>Edward D.</given-names></name><xref ref-type="aff" rid="aff7"><sup>h</sup></xref></contrib><contrib contrib-type="author"><name><surname>Emerson</surname><given-names>Joanne B.</given-names></name><xref ref-type="aff" rid="aff8"><sup>i</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wacklin</surname><given-names>Pirjo</given-names></name><xref ref-type="aff" rid="aff8"><sup>i</sup></xref></contrib><contrib contrib-type="author"><name><surname>Coutinho</surname><given-names>Pedro M.</given-names></name><xref ref-type="aff" rid="aff9"><sup>j</sup></xref></contrib><contrib contrib-type="author"><name><surname>Henrissat</surname><given-names>Bernard</given-names></name><xref ref-type="aff" rid="aff9"><sup>j</sup></xref></contrib><contrib contrib-type="author"><name><surname>Nelson</surname><given-names>Karen E.</given-names></name><xref ref-type="aff" rid="aff8"><sup>i</sup></xref></contrib><contrib contrib-type="author"><name><surname>White</surname><given-names>Bryan A.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff10"><sup>c</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><aff id="aff1"><sup>a</sup>Department of Animal Sciences, University of Illinois, Urbana, IL 61801;</aff><aff id="aff2"><sup>b</sup>Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL 60439;</aff><aff id="aff3"><sup>d</sup>Department of Biology, San Diego State University, San Diego, CA 92813;</aff><aff id="aff4"><sup>e</sup>School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia;</aff><aff id="aff5"><sup>f</sup>Center for Microbial Sciences, San Diego State University, San Diego, CA 92813;</aff><aff id="aff6"><sup>g</sup>Department of Computer Sciences, San Diego State University, San Diego, CA 92813;</aff><aff id="aff7"><sup>h</sup>Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439;</aff><aff id="aff8"><sup>i</sup>J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850;</aff><aff id="aff9"><sup>j</sup>Architecture et Fonction des Macromolecules Biologiques, Unité Mixte de Recherche 6098, Centre National de la Recherche Scientifique, Universites Aix-Marseille I and II, Case 932, 163 Avenue de Luminy, 13288 Marseille, France; and</aff><aff id="aff10"><sup>c</sup>The Institute for Genomic Biology, University of Illinois, Urbana, IL 61801</aff></contrib-group><author-notes><corresp id="cor1"><sup>1</sup>To whom correspondence should be addressed. E-mail: <email>bwhite44@illinois.edu</email></corresp><fn fn-type="com"><p>Communicated by Jillian F. Banfield, University of California, Berkeley, CA, June 27, 2008</p></fn><fn fn-type="con"><p>Author contributions: B.A.W. designed research; J.M.B., M.E.B.M., M.K.W., J.B.E., P.W., P.M.C., and B.H. performed research; J.M.B., D.A.A., A.C.Y., E.A.D., R.E.E., E.D.F., J.B.E., P.W., P.M.C., B.H., K.E.N., and B.A.W. analyzed data; and J.M.B., D.A.A., A.C.Y., E.A.D., R.E.E., E.D.F., B.H., K.E.N., and B.A.W. wrote the paper.</p></fn></author-notes><pub-date pub-type="ppub"><day>10</day><month>2</month><year>2009</year></pub-date><pub-date pub-type="epub"><day>30</day><month>1</month><year>2009</year></pub-date><pub-date pub-type="pmc-release"><day>30</day><month>1</month><year>2009</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
epub date downloaded from Highwire. </pmc-comment>
<volume>106</volume><issue>6</issue><fpage>1948</fpage><lpage>1953</lpage><history><date date-type="received"><day>10</day><month>9</month><year>2007</year></date></history><permissions><copyright-statement>© 2009 by The National Academy of Sciences of the USA</copyright-statement><license license-type="open-access"><license-p>Freely available online through the PNAS open access option.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="zpq00609001948.pdf"></self-uri><abstract><p>The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly sampled pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid sample (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood).</p></abstract><kwd-group><kwd>CAZymes</kwd><kwd>cellulases</kwd><kwd>plant cell wall</kwd><kwd>pyrosequencing</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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