Probiotics and prebiotics have gotten a lot of interest in the scientific, clinical, and public realms in recent years. This aids in the understanding of how these organisms work in the gut, both in vivo and in situ. Data from these types of techniques is currently being used to improve our understanding of how these bacteria interact with gut epithelial cells. This type of genome functional study will considerably expand our understanding of how probiotic bacteria work mechanistically. This will result in a more scientific approach to strain selection for probiotic applications, as well as a stronger scientific justification for adopting specific strains for specific probiotic functions. While the discovery-based genomics paradigm in probiotic LAB has revealed important parts of probiotic processes, it has also exposed the complexity of interactions with the resident microbiota and mucosal immune system. However, this problem has brought with it a fantastic opportunity.