Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes

Jeremy A. Frank, Claudia I. Reich, Shobha Sharma, Jon S. Weisbaum, Brenda A. Wilson, Gary J. Olsen

Research output: Contribution to journalArticle

Abstract

rRNA-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 according to 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 by using linear amplification - providing an assessment that is independent of a reverse primer - and in combination with the 1492 reverse primer (1492r) under the PCR conditions appropriate for making community rRNA gene clone libraries. For 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 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.

Original languageEnglish (US)
Pages (from-to)2461-2470
Number of pages10
JournalApplied and environmental microbiology
Volume74
Issue number8
DOIs
StatePublished - Apr 1 2008

Fingerprint

rRNA Genes
amplification
ribosomal RNA
gene
Gardnerella
DNA
DNA Primers
genes
Gene Amplification
Lactobacillus
Gene Library
Clone Cells
Escherichia coli
DNA primers
microbial community
clone
Polymerase Chain Reaction
microbial communities
polymerase chain reaction
evaluation

ASJC Scopus subject areas

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology

Cite this

Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. / Frank, Jeremy A.; Reich, Claudia I.; Sharma, Shobha; Weisbaum, Jon S.; Wilson, Brenda A.; Olsen, Gary J.

In: Applied and environmental microbiology, Vol. 74, No. 8, 01.04.2008, p. 2461-2470.

Research output: Contribution to journalArticle

Frank, Jeremy A. ; Reich, Claudia I. ; Sharma, Shobha ; Weisbaum, Jon S. ; Wilson, Brenda A. ; Olsen, Gary J. / Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. In: Applied and environmental microbiology. 2008 ; Vol. 74, No. 8. pp. 2461-2470.
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