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Nucleic Acids Research Advance Access published online on August 5, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn496
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© 2008 The Author(s)
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.

Genomics

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

Chaysavanh Manichanh1,2,*, Charles E. Chapple3, Lionel Frangeul4, Karine Gloux5, Roderic Guigo2,3 and Joel Dore5

1Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, 2Bioinformatics and Genomics Program, Center for Genomic Regulation, Barcelona, 3Genome Bioinformatics Laboratory, GRIB—IMIM/UPF, E-08003 Barcelona, Spain, 4Genopole, Institut Pasteur, Paris and 5INRA, UR910, F-78352 Jouy-en-Josas, France

*To whom correspondence should be addressed. Tel: +34 933 160 167; Fax: +34 933 160 019; Email: chaysavanh.manichanh{at}jouy.inra.fr

Received December 14, 2007. Revised July 11, 2008. Accepted July 17, 2008.

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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