Specificity and sensitivity of eubacterial primers utilized for molecular profiling of bacteria within complex microbial ecosystems

S. A. Huws, J. E. Edwards, E. J. Kim, N. D. Scollan

Research output: Contribution to journalArticlepeer-review

116 Scopus citations

Abstract

Efficient profiling of eubacterial diversity within complex communities requires that primers are specific for eubacterial 16S rRNA. Specificity of published primers against eubacterial and archaeal 16S rRNA as well as protozoal and fungal 18S rRNA was assessed in silico. The specificity and sensitivity of the V3 and V6-V8 (F968gc and R1401) Denaturing Gradient Gel Electrophoresis (DGGE) primers was subsequently verified using rumen-derived samples. An assessment of the effects of employing touchdown PCR cycling conditions was also made. For DGGE profiling of eubacteria within rumen samples, primers F968gc and R1401 proved the most specific and sensitive providing that touchdown PCR is not used.

Original languageEnglish
Pages (from-to)565-569
Number of pages5
JournalJournal of Microbiological Methods
Volume70
Issue number3
DOIs
StatePublished - Sep 2007

Keywords

  • ARISA
  • Community
  • Cytophage-Flexibacter-Bacteroides
  • DGGE
  • Diversity
  • Profiling
  • Ruminant
  • T-RFLP

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