Reconstruction of Ribosomal RNA Genes from Metagenomic Data
Identifieur interne : 000472 ( Main/Exploration ); précédent : 000471; suivant : 000473Reconstruction of Ribosomal RNA Genes from Metagenomic Data
Auteurs : Lu Fan ; Kerensa Mcelroy ; Torsten ThomasSource :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
Direct sequencing of environmental DNA (metagenomics) has a great potential for describing the 16S rRNA gene diversity of microbial communities. However current approaches using this 16S rRNA gene information to describe community diversity suffer from low taxonomic resolution or chimera problems. Here we describe a new strategy that involves stringent assembly and data filtering to reconstruct full-length 16S rRNA genes from metagenomicpyrosequencing data. Simulations showed that reconstructed 16S rRNA genes provided a true picture of the community diversity, had minimal rates of chimera formation and gave taxonomic resolution down to genus level. The strategy was furthermore compared to PCR-based methods to determine the microbial diversity in two marine sponges. This showed that about 30% of the abundant phylotypes reconstructed from metagenomic data failed to be amplified by PCR. Our approach is readily applicable to existing metagenomic datasets and is expected to lead to the discovery of new microbial phylotypes.
Url:
DOI: 10.1371/journal.pone.0039948
PubMed: 22761935
PubMed Central: 3384625
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Reconstruction of Ribosomal RNA Genes from Metagenomic Data</title><author><name sortKey="Fan, Lu" sort="Fan, Lu" uniqKey="Fan L" first="Lu" last="Fan">Lu Fan</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Mcelroy, Kerensa" sort="Mcelroy, Kerensa" uniqKey="Mcelroy K" first="Kerensa" last="Mcelroy">Kerensa Mcelroy</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Thomas, Torsten" sort="Thomas, Torsten" uniqKey="Thomas T" first="Torsten" last="Thomas">Torsten Thomas</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22761935</idno><idno type="pmc">3384625</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384625</idno><idno type="RBID">PMC:3384625</idno><idno type="doi">10.1371/journal.pone.0039948</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000606</idno><idno type="wicri:Area/Pmc/Curation">000606</idno><idno type="wicri:Area/Pmc/Checkpoint">000383</idno><idno type="wicri:Area/Ncbi/Merge">000331</idno><idno type="wicri:Area/Ncbi/Curation">000331</idno><idno type="wicri:Area/Ncbi/Checkpoint">000331</idno><idno type="wicri:Area/Main/Merge">000473</idno><idno type="wicri:Area/Main/Curation">000472</idno><idno type="wicri:Area/Main/Exploration">000472</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Reconstruction of Ribosomal RNA Genes from Metagenomic Data</title><author><name sortKey="Fan, Lu" sort="Fan, Lu" uniqKey="Fan L" first="Lu" last="Fan">Lu Fan</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Mcelroy, Kerensa" sort="Mcelroy, Kerensa" uniqKey="Mcelroy K" first="Kerensa" last="Mcelroy">Kerensa Mcelroy</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Thomas, Torsten" sort="Thomas, Torsten" uniqKey="Thomas T" first="Torsten" last="Thomas">Torsten Thomas</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Direct sequencing of environmental DNA (metagenomics) has a great potential for describing the 16S rRNA gene diversity of microbial communities. However current approaches using this 16S rRNA gene information to describe community diversity suffer from low taxonomic resolution or chimera problems. Here we describe a new strategy that involves stringent assembly and data filtering to reconstruct full-length 16S rRNA genes from metagenomicpyrosequencing data. Simulations showed that reconstructed 16S rRNA genes provided a true picture of the community diversity, had minimal rates of chimera formation and gave taxonomic resolution down to genus level. The strategy was furthermore compared to PCR-based methods to determine the microbial diversity in two marine sponges. This showed that about 30% of the abundant phylotypes reconstructed from metagenomic data failed to be amplified by PCR. Our approach is readily applicable to existing metagenomic datasets and is expected to lead to the discovery of new microbial phylotypes.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Pace, Nr" uniqKey="Pace N">NR Pace</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tringe, Sg" uniqKey="Tringe S">SG Tringe</name></author><author><name sortKey="Hugenholtz, P" uniqKey="Hugenholtz P">P Hugenholtz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hong, S" uniqKey="Hong S">S Hong</name></author><author><name sortKey="Bunge, J" uniqKey="Bunge J">J Bunge</name></author><author><name sortKey="Leslin, C" uniqKey="Leslin C">C Leslin</name></author><author><name sortKey="Jeon, S" uniqKey="Jeon S">S Jeon</name></author><author><name sortKey="Epstein, Ss" uniqKey="Epstein S">SS Epstein</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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Meyer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peterson, J" uniqKey="Peterson J">J Peterson</name></author><author><name sortKey="Garges, S" uniqKey="Garges S">S Garges</name></author><author><name sortKey="Giovanni, M" uniqKey="Giovanni M">M Giovanni</name></author><author><name sortKey="Mcinnes, P" uniqKey="Mcinnes P">P McInnes</name></author><author><name sortKey="Wang, L" uniqKey="Wang L">L Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Siqueira, Jf" uniqKey="Siqueira J">JF Siqueira</name></author><author><name sortKey="Fouad, Af" uniqKey="Fouad A">AF Fouad</name></author><author><name sortKey="Rocas, In" uniqKey="Rocas I">IN Rôças</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Fan, Lu" sort="Fan, Lu" uniqKey="Fan L" first="Lu" last="Fan">Lu Fan</name><name sortKey="Mcelroy, Kerensa" sort="Mcelroy, Kerensa" uniqKey="Mcelroy K" first="Kerensa" last="Mcelroy">Kerensa Mcelroy</name><name sortKey="Thomas, Torsten" sort="Thomas, Torsten" uniqKey="Thomas T" first="Torsten" last="Thomas">Torsten Thomas</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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