An introduction to the analysis of shotgun metagenomic data
Identifieur interne : 000542 ( Ncbi/Merge ); précédent : 000541; suivant : 000543An introduction to the analysis of shotgun metagenomic data
Auteurs : Thomas J. SharptonSource :
- Frontiers in Plant Science [ 1664-462X ] ; 2014.
Abstract
Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms and clarified the relationship between host-associated microbial communities and host phenotype. Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function. But, the analysis of metagenomic sequences is complicated due to the complex structure of the data. Fortunately, new tools and data resources have been developed to circumvent these complexities and allow researchers to determine which microbes are present in the community and what they might be doing. This review describes the analytical strategies and specific tools that can be applied to metagenomic data and the considerations and caveats associated with their use. Specifically, it documents how metagenomes can be analyzed to quantify community structure and diversity, assemble novel genomes, identify new taxa and genes, and determine which metabolic pathways are encoded in the community. It also discusses several methods that can be used compare metagenomes to identify taxa and functions that differentiate communities.
Url:
DOI: 10.3389/fpls.2014.00209
PubMed: 24982662
PubMed Central: 4059276
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">An introduction to the analysis of shotgun metagenomic data</title><author><name sortKey="Sharpton, Thomas J" sort="Sharpton, Thomas J" uniqKey="Sharpton T" first="Thomas J." last="Sharpton">Thomas J. Sharpton</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24982662</idno><idno type="pmc">4059276</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059276</idno><idno type="RBID">PMC:4059276</idno><idno type="doi">10.3389/fpls.2014.00209</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000699</idno><idno type="wicri:Area/Pmc/Curation">000699</idno><idno type="wicri:Area/Pmc/Checkpoint">000240</idno><idno type="wicri:Area/Ncbi/Merge">000542</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">An introduction to the analysis of shotgun metagenomic data</title><author><name sortKey="Sharpton, Thomas J" sort="Sharpton, Thomas J" uniqKey="Sharpton T" first="Thomas J." last="Sharpton">Thomas J. Sharpton</name></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</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>Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms and clarified the relationship between host-associated microbial communities and host phenotype. Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function. But, the analysis of metagenomic sequences is complicated due to the complex structure of the data. Fortunately, new tools and data resources have been developed to circumvent these complexities and allow researchers to determine which microbes are present in the community and what they might be doing. This review describes the analytical strategies and specific tools that can be applied to metagenomic data and the considerations and caveats associated with their use. Specifically, it documents how metagenomes can be analyzed to quantify community structure and diversity, assemble novel genomes, identify new taxa and genes, and determine which metabolic pathways are encoded in the community. It also discusses several methods that can be used compare metagenomes to identify taxa and functions that differentiate communities.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Abubucker, S" uniqKey="Abubucker S">S. Abubucker</name></author><author><name sortKey="Segata, N" uniqKey="Segata N">N. Segata</name></author><author><name sortKey="Goll, J" uniqKey="Goll J">J. Goll</name></author><author><name sortKey="Schubert, A M" uniqKey="Schubert A">A. M. Schubert</name></author><author><name sortKey="Izard, J" uniqKey="Izard J">J. 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Borodovsky</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="review-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Plant Sci</journal-id><journal-id journal-id-type="iso-abbrev">Front Plant Sci</journal-id><journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id><journal-title-group><journal-title>Frontiers in Plant Science</journal-title></journal-title-group><issn pub-type="epub">1664-462X</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24982662</article-id><article-id pub-id-type="pmc">4059276</article-id><article-id pub-id-type="doi">10.3389/fpls.2014.00209</article-id><article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject><subj-group><subject>Review Article</subject></subj-group></subj-group></article-categories><title-group><article-title>An introduction to the analysis of shotgun metagenomic data</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Sharpton</surname><given-names>Thomas J.</given-names></name><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/136632"></uri></contrib></contrib-group><aff><institution>Department of Microbiology and Department of Statistics, Oregon State University</institution><country>Corvallis, OR, USA</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: <italic>Ann E. Stapleton, University of North Carolina at Wilmington, USA</italic></p></fn><fn fn-type="edited-by"><p>Reviewed by: <italic>Asa Ben-Hur, Colorado State University, USA; Jeffrey Blanchard, University of Massachusetts at Amherst, USA</italic></p></fn><corresp id="fn001">*Correspondence: <italic>Thomas J. Sharpton, Department of Microbiology and Department of Statistics, Oregon State University, 220 Nash Hall, Corvallis, OR 97331, USA e-mail: <email xlink:type="simple">thomas.sharpton@oregonstate.edu</email></italic></corresp><fn fn-type="other" id="fn002"><p>This article was submitted to Plant Genetics and Genomics, a section of the journal Frontiers in Plant Science.</p></fn></author-notes><pub-date pub-type="epreprint"><day>20</day><month>3</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>16</day><month>6</month><year>2014</year></pub-date><pub-date pub-type="collection"><year>2014</year></pub-date><volume>5</volume><elocation-id>209</elocation-id><history><date date-type="received"><day>14</day><month>2</month><year>2014</year></date><date date-type="accepted"><day>29</day><month>4</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014 Sharpton.</copyright-statement><copyright-year>2014</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p> This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><p>Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms and clarified the relationship between host-associated microbial communities and host phenotype. Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function. But, the analysis of metagenomic sequences is complicated due to the complex structure of the data. Fortunately, new tools and data resources have been developed to circumvent these complexities and allow researchers to determine which microbes are present in the community and what they might be doing. This review describes the analytical strategies and specific tools that can be applied to metagenomic data and the considerations and caveats associated with their use. Specifically, it documents how metagenomes can be analyzed to quantify community structure and diversity, assemble novel genomes, identify new taxa and genes, and determine which metabolic pathways are encoded in the community. It also discusses several methods that can be used compare metagenomes to identify taxa and functions that differentiate communities.</p></abstract><kwd-group><kwd>metagenome</kwd><kwd>bioinformatics</kwd><kwd>microbiota</kwd><kwd>microbiome</kwd><kwd>microbial diversity</kwd><kwd>host–microbe interactions</kwd><kwd>review</kwd></kwd-group><counts><fig-count count="3"></fig-count><table-count count="1"></table-count><equation-count count="0"></equation-count><ref-count count="147"></ref-count><page-count count="14"></page-count><word-count count="0"></word-count></counts></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Sharpton, Thomas J" sort="Sharpton, Thomas J" uniqKey="Sharpton T" first="Thomas J." last="Sharpton">Thomas J. Sharpton</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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