Culture-independent methods for identifying microbial communities in cheese

Food Microbiol. 2008 Oct;25(7):839-48. doi: 10.1016/ Epub 2008 Jun 10.


This review focuses on the culture-independent methods available for the description of both bacterial and fungal communities in cheese. Important steps of the culture-independent strategy, which relies on bulk DNA extraction from cheese and polymerase chain reaction (PCR) amplification of selected sequences, are discussed. We critically evaluate the identification techniques already used for monitoring microbial communities in cheese, including PCR-denaturing gradient gel electrophoresis (PCR-DGGE), PCR-temporal temperature gradient gel electrophoresis (PCR-TTGE) or single-strand conformation polymorphism-PCR (SSCP-PCR) as well as some other techniques that remain to be adapted to the study of cheese communities. Further, our analysis draws attention to the lack of data available on suitable DNA sequences for identifying fungal communities in cheese and proposes some potential DNA targets.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Bacteria / classification
  • Bacteria / isolation & purification*
  • Cheese / microbiology*
  • Chromatography, High Pressure Liquid
  • Colony Count, Microbial / methods
  • DNA, Bacterial / genetics
  • DNA, Bacterial / isolation & purification
  • DNA, Fungal / genetics
  • DNA, Fungal / isolation & purification
  • Electrophoresis, Agar Gel
  • Food Microbiology*
  • Oligonucleotide Array Sequence Analysis
  • Phylogeny
  • Polymerase Chain Reaction / methods
  • Polymorphism, Restriction Fragment Length
  • Polymorphism, Single-Stranded Conformational


  • DNA, Bacterial
  • DNA, Fungal