ABSTRACT
New knowledge on novel informatic techniques such as metagenomics, scalable computing platforms, and annotated reference databases of microbial genomes has greatly accelerated the profitable use of food microbial genetic resources. The enormous diversity of microbiota facilitates cohabitation and leads to a variety of relationships in food through symbiotic, pathogenic, antagonistic, and competitive associations. This chapter summarizes recent food microbiome studies exploiting the links between food and its associated microbial cluster through conventional and high-throughput sequencing techniques. Special emphasis is placed on the workhorses of traditional fermented foods (microbes such as bacteria and yeast) that stabilize the lipids, sugar, and proteins that are fragile in milk, meat, and fruits. Unraveling the molecular interactions in the food-microbe matrix will be the key challenge in the future industrial adaption of foodborne microbes. Though this omics science is potentially exciting, linking the food microbiome and human gut functions will ensure the safety, authenticity, and traceability of food commodities.
