Abstract: The application of culture-independent methods in food industry is still in the preliminary stage. In this paper, the application of the most common culture-independent approaches for describing both bacterial and fungal communities in cheese and for monitoring microbial community in cheese manufacturing and ripening process has been reviewed. The most commonly used DNA fingerprinting techniques for investigating microbial communities in cheese are introduced, which include PCR-DGGE, PCR-TTGE, SSCP-PCR, DHPLC and other techniques. Furthermore, the benefits, pitfalls and perspectives of culture-independent methods in cheese are discussed. Based on the discussion, a polyphasic approach with the combination of culture-dependent and culture-independent methods may be the best strategy to achieve more accurate structures of microbial communities.

Key words: culture-independent methods, cheese, DNA fingerprinting techniques, microbial communities