A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

The construction of metagenomic libraries has permitted the study of microorganisms resistant to isolation and the analysis of 16S rDNA sequences has been used for over two decades to examine bacterial biodiversity. Here, we show that the analysis of random sequence reads (RSRs) instead of 16S is a...

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Autores: Guigó Serra, Roderic, Manichanh, Chaysavanh, Chapple, Charles E., Frangeul, Lionel, Gloux, Karine, Dore, Joel
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2008
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/6242
Acceso en línea:http://hdl.handle.net/10230/6242
http://dx.doi.org/10.1093/nar/gkn496
Access Level:acceso abierto
Palabra clave:ADN
Interaccions ADN -- Proteïnes
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spelling A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic libraryGuigó Serra, RodericManichanh, ChaysavanhChapple, Charles E.Frangeul, LionelGloux, KarineDore, JoelADNInteraccions ADN -- ProteïnesThe construction of metagenomic libraries has permitted the study of microorganisms resistant to isolation and the analysis of 16S rDNA sequences has been used for over two decades to examine bacterial biodiversity. Here, we show that the analysis of random sequence reads (RSRs) instead of 16S is a suitable shortcut to estimate the biodiversity of a bacterial community from metagenomic libraries. We generated 10,010 RSRs from a metagenomic library of microorganisms found in human faecal samples. Then searched them using the program BLASTN against a prokaryotic sequence database to assign a taxon to each RSR. The results were compared with those obtained by screening and analysing the clones containing 16S rDNA sequences in the whole library. We found that the biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA. We also show that RSRs are suitable to compare the biodiversity between different metagenomic libraries. RSRs can thus provide a good estimate of the biodiversity of a metagenomic library and, as an alternative to 16S, this approach is both faster and cheaper.Oxford University Press201020102008info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/6242http://dx.doi.org/10.1093/nar/gkn496reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésNucleic Acids Research 2008;36(16):e5180© 2008 Roderic Guigó et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by-nc/2.0/uk/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/62422026-05-29T05:05:01Z
dc.title.none.fl_str_mv A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
title A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
spellingShingle A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
Guigó Serra, Roderic
ADN
Interaccions ADN -- Proteïnes
title_short A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
title_full A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
title_fullStr A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
title_full_unstemmed A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
title_sort A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
dc.creator.none.fl_str_mv Guigó Serra, Roderic
Manichanh, Chaysavanh
Chapple, Charles E.
Frangeul, Lionel
Gloux, Karine
Dore, Joel
author Guigó Serra, Roderic
author_facet Guigó Serra, Roderic
Manichanh, Chaysavanh
Chapple, Charles E.
Frangeul, Lionel
Gloux, Karine
Dore, Joel
author_role author
author2 Manichanh, Chaysavanh
Chapple, Charles E.
Frangeul, Lionel
Gloux, Karine
Dore, Joel
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv ADN
Interaccions ADN -- Proteïnes
topic ADN
Interaccions ADN -- Proteïnes
description The construction of metagenomic libraries has permitted the study of microorganisms resistant to isolation and the analysis of 16S rDNA sequences has been used for over two decades to examine bacterial biodiversity. Here, we show that the analysis of random sequence reads (RSRs) instead of 16S is a suitable shortcut to estimate the biodiversity of a bacterial community from metagenomic libraries. We generated 10,010 RSRs from a metagenomic library of microorganisms found in human faecal samples. Then searched them using the program BLASTN against a prokaryotic sequence database to assign a taxon to each RSR. The results were compared with those obtained by screening and analysing the clones containing 16S rDNA sequences in the whole library. We found that the biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA. We also show that RSRs are suitable to compare the biodiversity between different metagenomic libraries. RSRs can thus provide a good estimate of the biodiversity of a metagenomic library and, as an alternative to 16S, this approach is both faster and cheaper.
publishDate 2008
dc.date.none.fl_str_mv 2008
2010
2010
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/6242
http://dx.doi.org/10.1093/nar/gkn496
url http://hdl.handle.net/10230/6242
http://dx.doi.org/10.1093/nar/gkn496
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Nucleic Acids Research 2008;36(16):e5180
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by-nc/2.0/uk/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc/2.0/uk/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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