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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 research 2008 v.36 no.16 pp. 5180-5188
bacterial communities, biodiversity, clones, databases, feces, genomic libraries, humans, microorganisms, nucleotide sequences, ribosomal DNA, screening
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.