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Appl. Environ. Microbiol. doi:10.1128/AEM.02272-07
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Critical Evaluation of Two Commonly-Used Primers for Amplification of Bacterial 16S rRNA Genes

Department of Microbiology, Host-Microbe Systems Theme, Institute for Genomic Biology, National Center for Supercomputing Applications, and College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, and Carle Foundation Hospital, Urbana, IL 61801

^* To whom correspondence should be addressed. Email: gary{at}life.uiuc.edu.

	Abstract

Ribosomal RNA-based studies, which have become the most common method for assessing microbial communities, rely upon faithful amplification of the corresponding genes from the original DNA sample. We report here an analysis and reevaluation of commonly-used primers for amplifying the DNA between positions 27 and 1492 of bacterial 16S rRNA genes (numbered by the Escherichia coli rRNA). We propose a formulation for a forward primer (27f) that includes three sequences not usually present. We compare our proposed formulation to two common alternatives using linear amplification — providing an assessment that is independent of a reverse primer — and in combination with the 1492 reverse primer (1492r) under the polymerase chain reaction (PCR) conditions appropriate for making community rDNA clone libraries. In analyses of DNA from human vaginal samples, our formulation was better at maintaining the original rRNA gene ratio of Lactobacillus spp. to Gardnerella spp., particularly under more stringent amplification conditions. Because our 27f formulation remains relatively simple, having seven distinct primer sequences, there is minimal loss of overall amplification efficiency and specificity.