Methods for the study of microbial communities in fermented foods

The importance of ecological concepts to understand the presence and growth of microorganisms in foods is presently recognized. The production of fermented foods under controlled conditions and its safety assurance depend on the knowledge and control of their microbiota. Traditional fermented foods are obtained by natural fermentations (in which no inoculum is added) and contain complex microbiotas, which are difficult to describe through the use of traditional microbiological methods. The microbial structure of these foods can be studied with different approaches. One of them consists on the typification of isolated microorganisms with methods based on DNA as RFLP, ribotyping, AFLP, ARDRA and RAPD. In order to detect non-culturable or not yet cultured microorganisms, nucleic acids are directly extracted from foods and the microbial diversity is determined from them. Examples of these techniques are the construction of 16S rDNA clone libraries and fingerprinting techniques, such as DGGE and TGGE. Recent advances on the application of these techniques on the study of fermented foods are presented.