Application of genomics, transcriptomics, and proteomics in probiotic research

Over the past few years, probiotics have been widely explored owing to their advantageous effects on human health and their benefits in the production of fermented products, especially probiotic beverages. Recent advancements in omics-based research and the availability of the whole genome sequences of several probiotic bacterial strains, particularly lactic acid bacteria and bifidobacteria, now provide useful resources to understand in-depth genetic physiology and metabolic functions of potential probiotic microbial sources. A combinatorial omics approach using genomics, transcriptomics, and proteomics is an effective strategy for gaining thorough insights into probiotic functions and modes of action from health and nutritional aspects. Specifically, comparative genomics among related bacterial strains can reveal the genetic basis of particular traits and also shed light on the evolution and underlying regulatory networks involved in probiotic-linked mechanisms. In this chapter, the recent application of omics-based approaches to understanding various beneficial probiotic functionalities and their mechanisms from a genetic perspective is discussed.