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Nucleic Acids Research Advance Access originally published online on August 22, 2008
Nucleic Acids Research 2008 36(18):e120; doi:10.1093/nar/gkn491
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Nucleic Acids Research, 2008, Vol. 36, No. 18 e120
© 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.

Methods Online

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

Zongzhi Liu1, Todd Z. DeSantis2, Gary L. Andersen2 and Rob Knight1,*

1Department of Chemistry and Biochemistry, UCB 215, University of Colorado at Boulder, Boulder, CO 80309-0215 and 2Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720, USA

*To whom correspondence should be addressed. Tel: +1 303 492 1984; Fax: +1 303 492 7744; Email: rob.knight{at}colorado.edu

Received June 16, 2008. Revised July 15, 2008. Accepted July 16, 2008.

The recent introduction of massively parallel pyrosequencers allows rapid, inexpensive analysis of microbial community composition using 16S ribosomal RNA (rRNA) sequences. However, a major challenge is to design a workflow so that taxonomic information can be accurately and rapidly assigned to each read, so that the composition of each community can be linked back to likely ecological roles played by members of each species, genus, family or phylum. Here, we use three large 16S rRNA datasets to test whether taxonomic information based on the full-length sequences can be recaptured by short reads that simulate the pyrosequencer outputs. We find that different taxonomic assignment methods vary radically in their ability to recapture the taxonomic information in full-length 16S rRNA sequences: most methods are sensitive to the region of the 16S rRNA gene that is targeted for sequencing, but many combinations of methods and rRNA regions produce consistent and accurate results. To process large datasets of partial 16S rRNA sequences obtained from surveys of various microbial communities, including those from human body habitats, we recommend the use of Greengenes or RDP classifier with fragments of at least 250 bases, starting from one of the primers R357, R534, R798, F343 or F517.


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