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

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Manichanh C, Chapple CE, Frangeul L, Gloux K, Guigo R, Dore J. A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res. 2008; 36(16): 5180-5188. DOI: 10.1093/nar/gkn496
http://hdl.handle.net/10230/6242
To cite or link this document: http://hdl.handle.net/10230/6242
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Manichanh, Chaysavanh
dc.contributor.author Chapple, Charles E.
dc.contributor.author Frangeul, Lionel
dc.contributor.author Gloux, Karine
dc.contributor.author Dore, Joel
dc.date.accessioned 2010-06-10T14:41:23Z
dc.date.available 2010-06-10T14:41:23Z
dc.date.issued 2008
dc.identifier.citation Manichanh C, Chapple CE, Frangeul L, Gloux K, Guigo R, Dore J. A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res. 2008; 36(16): 5180-5188. DOI: 10.1093/nar/gkn496
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10230/6242
dc.description.abstract 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.
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Nucleic Acids Research 2008; 36(16): 5180-5188
dc.rights © 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.
dc.rights.uri http://creativecommons.org/licenses/by-nc/2.0/uk/
dc.subject.other ADN
dc.subject.other Interaccions ADN -- Proteïnes
dc.title A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/nar/gkn496
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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