Improvement of phylum- and class-specific primers for real-time PCR of bacterial taxa (2011)

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

    Abstract: 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.

      • Date: 17-06-2011
      • Journal: Journal of Microbiological Methods
      • Volume: 86
      • Issue: 3
      • Pages: 351-356
      • Publisher: Elsevier BV
      • Publication type: Article
      • Bibliographic status: Published

      Dr Nicholas Aldred
      Research Associate

      Professor Grant Burgess
      Professor of Marine Biotechnology

      Professor Tony Clare
      Professor of Marine Science and Coordinator of marineNewcastle