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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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Detalles Bibliográficos
Autores principales: Manichanh, Chaysavanh, Chapple, Charles E., Frangeul, Lionel, Gloux, Karine, Guigo, Roderic, Dore, Joel
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2532719/
https://www.ncbi.nlm.nih.gov/pubmed/18682527
http://dx.doi.org/10.1093/nar/gkn496
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author Manichanh, Chaysavanh
Chapple, Charles E.
Frangeul, Lionel
Gloux, Karine
Guigo, Roderic
Dore, Joel
author_facet Manichanh, Chaysavanh
Chapple, Charles E.
Frangeul, Lionel
Gloux, Karine
Guigo, Roderic
Dore, Joel
author_sort Manichanh, Chaysavanh
collection PubMed
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.
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spelling pubmed-25327192008-09-16 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library Manichanh, Chaysavanh Chapple, Charles E. Frangeul, Lionel Gloux, Karine Guigo, Roderic Dore, Joel Nucleic Acids Res Genomics 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. Oxford University Press 2008-09 2008-08-05 /pmc/articles/PMC2532719/ /pubmed/18682527 http://dx.doi.org/10.1093/nar/gkn496 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genomics
Manichanh, Chaysavanh
Chapple, Charles E.
Frangeul, Lionel
Gloux, Karine
Guigo, Roderic
Dore, Joel
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
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_short A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
title_sort comparison of random sequence reads versus 16s rdna sequences for estimating the biodiversity of a metagenomic library
topic Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2532719/
https://www.ncbi.nlm.nih.gov/pubmed/18682527
http://dx.doi.org/10.1093/nar/gkn496
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