Omics for the study of probiotic microorganisms

Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. They are mainly, although not exclusively, bacteria from the genera Lactobacillus and Bifidobacterium. Traditionally, these bacteria have been used by the food industry taking into account their technological behavior, without paying much attention to their biological effects. However, current omics technologies provide a range of high-throughput methods which are extremely useful for unraveling the beneficial effects of probiotics, allowing a rational selection of strains, with specific health-promoting activities, to be included in functional foods. The genome sequence of several Lactobacillus and Bifidobacterium strains is now available, and provides the basis for the implementation of omics technologies (mainly transcriptomics, proteomics, and metagenomics) in the emerging field of probiotics. They have been used with the aim of understanding the biological processes behind the potential beneficial effects attributed to these bacteria, such as their immunomodulatory activity, the capacity to compete with enteropathogens, the intestinal colonization processes, and the crosstalk mechanisms with the host. Furthermore, they are useful to determine markers of robustness, which can help to predict their performance under the technological processes in food manufacturing and during the passage through the gastrointestinal tract, including resistance to different stress factors. This review summarizes how omics are contributing to understanding the functions of probiotics and their mechanisms of action.