Metagenomics for the identification and characterization of microorganisms in fermented foods

Food fermentation is an ancient food processing operation that has survived the test of time and still remains an important aspect of food processing. The quantity and quality of the ecosystem in fermented foods vary based on the substrate and fermenting conditions such as temperature, pH, and duration. To ensure improved fermented food products with optimum quality, knowledge of the participating microorganisms is critical. It is important to identify the fermenting microorganisms and understand their activities, physiology, and interactions with each other and with the environment. Once these are known, the fermentation process can be optimized and standardized to derive products with improved safety and quality as well as scaled up for industrial applications. In this regard, metagenomics stands out as an analytical technique for the identification and characterization of microbial communities because it permits high-resolution analysis of genetic materials acquired directly from environmental samples in their natural ecology, without the need for pure isolates. This is in contrast to conventional methods of microbial characterization that provides limited insights into the microbial diversity, hence leaving food processing experts with little or no evidence to associate biochemical changes and adequately describe food transformation patterns and products following fermentation, which limit scientific and technological developments in this area. This chapter therefore presents a critical appraisal of the applications of metagenomic techniques for the identification and characterization of microbial communities in fermented food products. Indeed, metagenomics has the potential to considerably expand the understanding and applications of fermented food microbiomes by providing comprehensive insights into the microbial diversity, composition, and their functional ecology.