Determination of Microbial Diversity in Environmental Samples: Pitfalls of PCR-based rRNA Analysis

FEMS Microbiol Rev. 1997 Nov;21(3):213-29. doi: 10.1111/j.1574-6976.1997.tb00351.x.

Abstract

After nearly 10 years of PCR-based analysis of prokaryotic small-subunit ribosomal RNAs for ecological studies it seems necessary to summarize reported pitfalls of this approach which will most likely lead to an erroneous description on the microbial diversity of a given habitat. The following article will cover specific aspects of sample collection, cell lysis, nucleic acid extraction, PCR amplification, separation of amplified DNA, application of nucleic probes and data analysis.

Publication types

  • Comparative Study
  • Review

MeSH terms

  • Artifacts*
  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • DNA, Bacterial / analysis*
  • DNA, Bacterial / genetics
  • DNA, Bacterial / isolation & purification
  • DNA, Ribosomal / analysis*
  • DNA, Ribosomal / genetics
  • DNA, Ribosomal / isolation & purification
  • Environmental Microbiology*
  • Equipment Contamination
  • False Negative Reactions
  • False Positive Reactions
  • Mutagenesis
  • Polymerase Chain Reaction* / instrumentation
  • Polymerase Chain Reaction* / methods
  • RNA, Bacterial / genetics*
  • RNA, Bacterial / isolation & purification
  • RNA, Ribosomal / genetics*
  • RNA, Ribosomal / isolation & purification
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 16S / isolation & purification

Substances

  • DNA, Bacterial
  • DNA, Ribosomal
  • RNA, Bacterial
  • RNA, Ribosomal
  • RNA, Ribosomal, 16S