Strategies for Studying the Microbiome of Fermented Foods

The advent of next-generation sequencing (NGS) technologies represented a watershed moment in microbiological research, opening up the possibility to study sub-dominant groups, late-growing species, and previously uncultivable microorganisms within the fermentation process. The first NGS platform developed was the Roche 454. Since then, DNA sequencing has undergone gradual evolution, leading to its categorization based on read size. This classification includes short-read or ‘second-generation’ platforms such Ion Torrent, Illumina, and SOLID sequencers, as well as long-read or ‘third-generation’ platforms exemplified by Pacific Biosciences and Oxford Nanopore. To date, targeted rDNA gene sequencing and metagenomics have been the main strategies for understanding both the taxonomic composition and the different types of interactions, for example, mutualism, commensalism, parasitism, competition, and amensalism that occur in the microbiome of fermented foods. In addition, NGS has also been applied in industry as a quality control tool to identify both pathogenic and spoilage microorganisms and their possible routes of contamination, which include surfaces, human contact, and the environment itself. Finally, NGS has also been used to identify microbial strains that can improve the organoleptic properties and shelf life of the final product. This chapter aims to characterize the strategies for studying microbiome by NGS and to demonstrate how this technology has increased our understanding of fermented foods.