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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics</title><author><name sortKey="Weber, Marc" sort="Weber, Marc" uniqKey="Weber M" first="Marc" last="Weber">Marc Weber</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Teeling, Hanno" sort="Teeling, Hanno" uniqKey="Teeling H" first="Hanno" last="Teeling">Hanno Teeling</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Huang, Sixing" sort="Huang, Sixing" uniqKey="Huang S" first="Sixing" last="Huang">Sixing Huang</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Waldmann, Jost" sort="Waldmann, Jost" uniqKey="Waldmann J" first="Jost" last="Waldmann">Jost Waldmann</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><institution>Institute of Marine Biotechnology e.V</institution>., Greifswald,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Kassabgy, Mariette" sort="Kassabgy, Mariette" uniqKey="Kassabgy M" first="Mariette" last="Kassabgy">Mariette Kassabgy</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Fuchs, Bernhard M" sort="Fuchs, Bernhard M" uniqKey="Fuchs B" first="Bernhard M" last="Fuchs">Bernhard M. Fuchs</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Klindworth, Anna" sort="Klindworth, Anna" uniqKey="Klindworth A" first="Anna" last="Klindworth">Anna Klindworth</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Klockow, Christine" sort="Klockow, Christine" uniqKey="Klockow C" first="Christine" last="Klockow">Christine Klockow</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff3"><institution>Jacobs University Bremen gGmbH</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Wichels, Antje" sort="Wichels, Antje" uniqKey="Wichels A" first="Antje" last="Wichels">Antje Wichels</name><affiliation><nlm:aff id="aff4"><institution>Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland</institution>, Helgoland,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Gerdts, Gunnar" sort="Gerdts, Gunnar" uniqKey="Gerdts G" first="Gunnar" last="Gerdts">Gunnar Gerdts</name><affiliation><nlm:aff id="aff4"><institution>Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland</institution>, Helgoland,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Amann, Rudolf" sort="Amann, Rudolf" uniqKey="Amann R" first="Rudolf" last="Amann">Rudolf Amann</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Glockner, Frank Oliver" sort="Glockner, Frank Oliver" uniqKey="Glockner F" first="Frank Oliver" last="Glöckner">Frank Oliver Glöckner</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff3"><institution>Jacobs University Bremen gGmbH</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21160538</idno><idno type="pmc">3105762</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105762</idno><idno type="RBID">PMC:3105762</idno><idno type="doi">10.1038/ismej.2010.180</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000022</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics</title><author><name sortKey="Weber, Marc" sort="Weber, Marc" uniqKey="Weber M" first="Marc" last="Weber">Marc Weber</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Teeling, Hanno" sort="Teeling, Hanno" uniqKey="Teeling H" first="Hanno" last="Teeling">Hanno Teeling</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Huang, Sixing" sort="Huang, Sixing" uniqKey="Huang S" first="Sixing" last="Huang">Sixing Huang</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Waldmann, Jost" sort="Waldmann, Jost" uniqKey="Waldmann J" first="Jost" last="Waldmann">Jost Waldmann</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff2"><institution>Institute of Marine Biotechnology e.V</institution>., Greifswald,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Kassabgy, Mariette" sort="Kassabgy, Mariette" uniqKey="Kassabgy M" first="Mariette" last="Kassabgy">Mariette Kassabgy</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Fuchs, Bernhard M" sort="Fuchs, Bernhard M" uniqKey="Fuchs B" first="Bernhard M" last="Fuchs">Bernhard M. Fuchs</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Klindworth, Anna" sort="Klindworth, Anna" uniqKey="Klindworth A" first="Anna" last="Klindworth">Anna Klindworth</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Klockow, Christine" sort="Klockow, Christine" uniqKey="Klockow C" first="Christine" last="Klockow">Christine Klockow</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff3"><institution>Jacobs University Bremen gGmbH</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Wichels, Antje" sort="Wichels, Antje" uniqKey="Wichels A" first="Antje" last="Wichels">Antje Wichels</name><affiliation><nlm:aff id="aff4"><institution>Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland</institution>, Helgoland,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Gerdts, Gunnar" sort="Gerdts, Gunnar" uniqKey="Gerdts G" first="Gunnar" last="Gerdts">Gunnar Gerdts</name><affiliation><nlm:aff id="aff4"><institution>Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland</institution>, Helgoland,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Amann, Rudolf" sort="Amann, Rudolf" uniqKey="Amann R" first="Rudolf" last="Amann">Rudolf Amann</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation></author><author><name sortKey="Glockner, Frank Oliver" sort="Glockner, Frank Oliver" uniqKey="Glockner F" first="Frank Oliver" last="Glöckner">Frank Oliver Glöckner</name><affiliation><nlm:aff id="aff1"><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></nlm:aff></affiliation><affiliation><nlm:aff id="aff3"><institution>Jacobs University Bremen gGmbH</institution>, Bremen,<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="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence <italic>in situ</italic> hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at <ext-link ext-link-type="uri" xlink:href="http://www.megx.net/toolbox/taxsom">http://www.megx.net/toolbox/taxsom</ext-link>. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion.</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-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">21160538</article-id><article-id pub-id-type="pmc">3105762</article-id><article-id pub-id-type="pii">ismej2010180</article-id><article-id pub-id-type="doi">10.1038/ismej.2010.180</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Article</subject></subj-group></article-categories><title-group><article-title>Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics</article-title><alt-title alt-title-type="running">SOMs for linking biodiversity and functions in metagenomics</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Weber</surname><given-names>Marc</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Teeling</surname><given-names>Hanno</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="corresp" rid="caf1">*</xref></contrib><contrib contrib-type="author"><name><surname>Huang</surname><given-names>Sixing</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Waldmann</surname><given-names>Jost</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>Kassabgy</surname><given-names>Mariette</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Fuchs</surname><given-names>Bernhard M</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Klindworth</surname><given-names>Anna</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Klockow</surname><given-names>Christine</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Wichels</surname><given-names>Antje</given-names></name><xref ref-type="aff" rid="aff4">4</xref></contrib><contrib contrib-type="author"><name><surname>Gerdts</surname><given-names>Gunnar</given-names></name><xref ref-type="aff" rid="aff4">4</xref></contrib><contrib contrib-type="author"><name><surname>Amann</surname><given-names>Rudolf</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Glöckner</surname><given-names>Frank Oliver</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff3">3</xref></contrib><aff id="aff1"><label>1</label><institution>Max Planck Institute for Marine Microbiology</institution>, Bremen,<country>Germany</country></aff><aff id="aff2"><label>2</label><institution>Institute of Marine Biotechnology e.V</institution>., Greifswald,<country>Germany</country></aff><aff id="aff3"><label>3</label><institution>Jacobs University Bremen gGmbH</institution>, Bremen,<country>Germany</country></aff><aff id="aff4"><label>4</label><institution>Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland</institution>, Helgoland,<country>Germany</country></aff></contrib-group><author-notes><corresp id="caf1"><label>*</label><institution>Department of Molecular Ecology/Microbial Genomics Group, Max Planck Institute for Marine Microbiology</institution>, Celsiusstrasse 1, Bremen 28359, <country>Germany</country>. E-mail: <email>hteeling@mpi-bremen.de</email></corresp></author-notes><pub-date pub-type="ppub"><month>05</month><year>2011</year></pub-date><pub-date pub-type="epub"><day>16</day><month>12</month><year>2010</year></pub-date><volume>5</volume><issue>5</issue><fpage>918</fpage><lpage>928</lpage><history><date date-type="received"><day>21</day><month>06</month><year>2010</year></date><date date-type="rev-recd"><day>27</day><month>10</month><year>2010</year></date><date date-type="accepted"><day>27</day><month>10</month><year>2010</year></date></history><permissions><copyright-statement>Copyright © 2011 International Society for Microbial Ecology</copyright-statement><copyright-year>2011</copyright-year><copyright-holder>International Society for Microbial Ecology</copyright-holder></permissions><abstract><p>Next-generation sequencing (NGS) technologies have enabled the application of broad-scale sequencing in microbial biodiversity and metagenome studies. Biodiversity is usually targeted by classifying 16S ribosomal RNA genes, while metagenomic approaches target metabolic genes. However, both approaches remain isolated, as long as the taxonomic and functional information cannot be interrelated. Techniques like self-organizing maps (SOMs) have been applied to cluster metagenomes into taxon-specific bins in order to link biodiversity with functions, but have not been applied to broad-scale NGS-based metagenomics yet. Here, we provide a novel implementation, demonstrate its potential and practicability, and provide a web-based service for public usage. Evaluation with published data sets mimicking varyingly complex habitats resulted into classification specificities and sensitivities of close to 100% to above 90% from phylum to genus level for assemblies exceeding 8 kb for low and medium complexity data. When applied to five real-world metagenomes of medium complexity from direct pyrosequencing of marine subsurface waters, classifications of assemblies above 2.5 kb were in good agreement with fluorescence <italic>in situ</italic> hybridizations, indicating that biodiversity was mostly retained within the metagenomes, and confirming high classification specificities. This was validated by two protein-based classifications (PBCs) methods. SOMs were able to retrieve the relevant taxa down to the genus level, while surpassing PBCs in resolution. In order to make the approach accessible to a broad audience, we implemented a feature-rich web-based SOM application named TaxSOM, which is freely available at <ext-link ext-link-type="uri" xlink:href="http://www.megx.net/toolbox/taxsom">http://www.megx.net/toolbox/taxsom</ext-link>. TaxSOM can classify reads or assemblies exceeding 2.5 kb with high accuracy and thus assists in linking biodiversity and functions in metagenome studies, which is a precondition to study microbial ecology in a holistic fashion.</p></abstract><kwd-group><kwd>binning</kwd><kwd>metagenomics</kwd><kwd>molecular ecology</kwd><kwd>self-organizing map (SOM)</kwd><kwd>taxonomic classification</kwd><kwd>TaxSOM</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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