A review of the molecular approaches to investigate the diversity and activity of cheese microbiota

The cheese microbiota is characterized by the presence of a large variety of bacteria, yeasts, and molds, and many factors influence their growth and survival. The microbial community in cheese at various stages of ripening has been extensively studied by microbiological techniques based on the cultivation of the microorganisms on media and phenotypic or genotypic characterization of a fraction of the community (culture-dependent methods). Culture-independent methods based on DNA or RNA extraction offer the possibility of profiling uncultivable members of the microbial community as well as distinguishing those that are metabolically active. In this review, the status of research on available molecular tools used to characterize the microbiota in the cheese matrix are described and discussed in order to assess the metabolic functionality of the microbial community, its diversity, as well as the identification of species and their comparative quantification. Combining culture-dependent and culture-independent approaches can contribute to improving the strain selection process by understanding the basis of technological performance. Defined starter and adjunct cultures will improve and standardize cheese quality and safety. Future perspectives include the application of methods such as high-throughput quantitative reverse transcription PCR and pyrosequencing to quantify the contribution of the microbial community to cheese ripening.