Study of the dynamics of microbial communities in fermented foods and selection and use of functional cultures

Fermentation is a widespread technological process in culinary traditions all over the world, not only because assures the preservation and the safety of products but also because provides foods with excellent sensory and organoleptic characteristics. Moreover, the growing interest in functional foods has led to involve fermented foods as excellent food matrices by which to design functional products. Today is known that fermented foods are characterized by complex microbial communities that play needful and specific role of pro-technological interest improving the food safety, the shelf-life and the sensory profile of the end product. Moreover, in the last decades the demand by consumers for foods able to improve the human health is growing. In that context, fermented foods containing probiotic microorganisms cover a large slice in the sector of functional foods. This research thesis was finalized on the study of microbial ecosystems of fermented foods and the selection of functional strains and their potential use to design safer and healthier products. The goals were pursued through the study of microbial ecosystem of fermented foods and the monitoring of starter and pathogenic bacteria by next generation sequencing (NGS) techniques and dependent-culture methods, and the isolation and characterization of starter and probiotic cultures and their application in food matrices. In this research project the use of both NGS techniques and culture-dependent methods to investigate the microbial diversity of fermented foods provided a complete overview of microbial populations that occur in fermented foods. Culture-independent methods, as NGS techniques, are able to describe the bacterial ecosystem at species level, which are hard to highlight using culture-based methods. Nevertheless, isolation and characterization are still needed to date because represent the unique way to select strains to use as starter, protective, functional and probiotic cultures in fermented foods. On this purpose, one of the goals of the research is focused on the screening of LAB strains and their selection for abilities of pro-technological, protective and probiotic interest for the industry of fermented foods.