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

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<h2>A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library</h2>
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<p><strong>Chaysavanh Manichanh1,2,*, Charles E. Chapple3, Lionel Frangeul4, Karine Gloux5, Roderic Guigo2,3 and Joel Dore5 </strong></p>
<p><sup>1</sup>Digestive System Research Unit, University Hospital Vall d'Hebron, Ciberehd, <sup>2</sup>Bioinformatics and Genomics Program, Center for Genomic Regulation, Barcelona, <sup>3</sup>Genome Bioinformatics Laboratory, GRIB&mdash;IMIM/UPF, E-08003 Barcelona, Spain, <sup>4</sup>Genopole, Institut Pasteur, Paris and <sup>5</sup>INRA, UR910, F-78352 Jouy-en-Josas, France</p>
<p><font size="-1">*To whom correspondence should be addressed. Tel: +34 933 160 167; Fax: +34 933 160 019; Email: <span id="em0"><a href="mailto:chaysavanh.manichanh@jouy.inra.fr">chaysavanh.manichanh@jouy.inra.fr</a></span> <script type="text/javascript"><!--
var u = "chaysavanh.manichanh", d = "jouy.inra.fr"; document.getElementById("em0").innerHTML = '<a href="mailto:' + u + '@' + d + '">' + u + '@' + d + '<\/a>'//--></script></font></p>
<p><font size="-1">Received December 14, 2007.</font> <font size="-1">Revised July 11, 2008.</font> <font size="-1">Accepted July 17, 2008.</font></p>
<p><!-- ABS -->The construction of metagenomic libraries has permitted the<sup> </sup>study of microorganisms resistant to isolation and the analysis<sup> </sup>of 16S rDNA sequences has been used for over two decades to<sup> </sup>examine bacterial biodiversity. Here, we show that the analysis<sup> </sup>of random sequence reads (RSRs) instead of 16S is a suitable<sup> </sup>shortcut to estimate the biodiversity of a bacterial community<sup> </sup>from metagenomic libraries. We generated 10 010 RSRs from a<sup> </sup>metagenomic library of microorganisms found in human faecal<sup> </sup>samples. Then searched them using the program BLASTN against<sup> </sup>a prokaryotic sequence database to assign a taxon to each RSR.<sup> </sup>The results were compared with those obtained by screening and<sup> </sup>analysing the clones containing 16S rDNA sequences in the whole<sup> </sup>library. We found that the biodiversity observed by RSR analysis<sup> </sup>is consistent with that obtained by 16S rDNA. We also show that<sup> </sup>RSRs are suitable to compare the biodiversity between different<sup> </sup>metagenomic libraries. RSRs can thus provide a good estimate<sup> </sup>of the biodiversity of a metagenomic library and, as an alternative<sup> </sup>to 16S, this approach is both faster and cheaper.<sup> </sup></p>

Revision as of 01:52, 3 May 2010

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