AEM Accepts, published online ahead of print on 22 June 2007
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Appl. Environ. Microbiol. doi:10.1128/AEM.00062-07
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

A Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

Qiong Wang, George M. Garrity, James M. Tiedje, and James R. Cole*

Center for Microbial Ecology, and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824

* To whom correspondence should be addressed. Email: colej{at}msu.edu.


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Abstract

The 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 Prokaryotes. 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 the corpus of 5014 type strain sequences from Bergey's Outline, the RDP Classifier was also tested with a corpus of 23095 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 accuracy 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 variable regions V2 and V4 giving the lowest error rates. The RDP Classifier is suitable both for analysis of single rRNA sequences and for 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 Library Compare are available online at http://rdp.cme.msu.edu/.




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