Community dynamics of complex starter cultures for Gouda-type cheeses and its functional consequences

Lactic acid bacteria (LAB) are used as starter and adjunct cultures for the production of artisanal and industrial fermented milk products such as yoghurt and cheese.  Artisanal fermentations is propagated with the transfer of an inoculum from old batch of fermented food to the new batch (back-slopping) to initiate the fermentation with the activity of the indigenous microbiota present in the inoculum. In industrial production, these inocula with indigenous microbiota are replaced with the starter cultures that contain lower numbers of LAB species for better controlled fermentation process and consistent final product quality. Cheese manufacturing is still performed in both artisanal ways and with the use of starter cultures. Gouda cheese starter cultures constitute several strains from the subspecies of Lactococcus lactisand Leuconostocs mesenteroidesin different combinations. The mixed and undefined type of starter culture may harbour variable number of strains that contribute unique functionalities to the cheese manufacturing process. Therefore, understanding, controlling and predicting the cheese manufacturing processes require the determination of strain level diversity in the starter culture, their collective and specific metabolic complement, and their activity throughout the cheese manufacturing process, including the interactions between the strains. The first two studies that are covered in this thesis describes the development of a high resolution AFLP fingerprinting tool allowing the discrimination of closely related strains in the starter culture and the subsequent analysis of the microbial community of  Gouda cheese starter with this implemented technique and with metagenomics. Furthermore, the thesis includes the development of another tool to selectively amplify DNA only from live fraction of the microbial community in cheese using propidium monoazide (PMA), which is required to study community dynamics with culture independent approaches. The last study in the thesis describes the effects of the variation in propagation regime on the community composition of a mixed starter culture and connects the composition change to the functionalities that impact on flavour development during cheese manufacturing. Overall, the approaches presented in this thesis are intended to eventually enable accurate prediction and control of the cheese manufacturing process using (un)defined starter cultures, but may also allow rational design and development of new starter cultures.