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

S A Huws, Joan Elizabeth Edwards, Eun J Kim, N D Scollan

Research output: Contribution to journalArticle

77 Citations (Scopus)

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)565-9
Number of pages5
JournalJournal of Microbiological Methods
Volume70
Issue number3
DOIs
Publication statusPublished - Sep 2007

Keywords

  • Animals
  • Bacteria
  • Base Sequence
  • DNA Primers
  • DNA, Ribosomal
  • Electrophoresis, Polyacrylamide Gel
  • Fungi
  • Polymerase Chain Reaction
  • Polymorphism, Restriction Fragment Length
  • RNA, Ribosomal, 16S
  • Ruminants
  • Sensitivity and Specificity
  • Journal Article
  • Research Support, Non-U.S. Gov't

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