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Applied and Environmental Microbiology, August 2007, p. 5261-5267, Vol. 73, No. 16
0099-2240/07/$08.00+0     doi:10.1128/AEM.00062-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy{triangledown} ,{dagger}

Qiong Wang,1 George M. Garrity,1,2 James M. Tiedje,1,2 and James R. Cole1*

Center for Microbial Ecology,1 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 488242

Received 10 January 2007/ Accepted 18 June 2007

The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (≥95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.

* Corresponding author. Mailing address: Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824. Phone: (517) 432-4998. Fax: (517) 353-8957. E-mail: colej{at}msu.edu

{triangledown} Published ahead of print on 22 June 2007.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, August 2007, p. 5261-5267, Vol. 73, No. 16
0099-2240/07/$08.00+0     doi:10.1128/AEM.00062-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



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