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Improvement of phylum- and class-specific primers for real-time PCR of bacterial taxa

Lookup NU author(s): Tristano Bacchetti De Gregoris, Dr Nicholas Aldred, Professor Tony Clare, Professor Grant Burgess


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Mapping the distribution of phylogenetically distinct bacteria in natural environments is of primary importance to an understanding of ecological dynamics. Here we present a quantitative PCR (qPCR) assay for the analysis of higher taxa composition in natural communities that advances previously available methods by allowing quantification of several taxa during the same qPCR run. Existing primers targeting the 16S rRNA gene specific for Firmicutes, Actinobacteria, Bacteroidetes and for the α and γ subdivisions of the Proteobacteria were improved by largely increasing the coverage of the taxon they target without diminishing their specificity. The qPCR assay was validated in vitro testing artificial mixtures of 16S rRNA sequences and used to characterise the composition of natural communities developing in young marine biofilms. The possible contribution of the proposed technique in revealing ecological dynamics affecting higher bacterial taxa is discussed.

Publication metadata

Author(s): Bacchetti De Gregoris T, Aldred N, Clare AS, Burgess JG

Publication type: Article

Publication status: Published

Journal: Journal of Microbiological Methods

Year: 2011

Volume: 86

Issue: 3

Pages: 351-356

Print publication date: 17/06/2011

ISSN (print): 0167-7012

ISSN (electronic): 1872-8359

Publisher: Elsevier BV


DOI: 10.1016/j.mimet.2011.06.010


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Funder referenceFunder name
N00014-08-1-1240US Office of Naval Research
NER/S/A/2005/13338ANatural Environment Research Council, England, UK