3. New tools for the microbial ecology of fermented foods

3.1 From cultural and phenotypic approaches to molecular approaches and high-throughput sequencing technologies

The study of the diversity of microbial ecosystems has long relied on the Pasteurian approach based on the isolation, culture on synthetic media and identification of micro-organisms. This was an essential first approach to understanding the microorganisms in an ecosystem. Long and tedious, however, it underestimates the true diversity of cheese microbial communities, as it is impossible to detect non-cultivable micro-organisms or cells in a dormant state.

Advances in molecular biology, combined with the development of protocols enabling DNA to be extracted directly from cheese, have made it possible to introduce culture-independent approaches that...