The probiotics sector is constantly expanding, with new products being introduced all the time. This has prompted scientists to conduct research in the hopes of discovering probiotic strains that show solid proof of improved health and disease outcomes. These opportunistic objectives have yet to be reached, as indicated by the fact that there are currently no approved health claims attributed to probiotic supplements. This is most likely due to individual variability in commensal bacteria as well as fundamental differences across probiotic strains. The use of new omics technologies will improve our understanding of the intricate host-bacteria interactions, but research techniques must be well-planned in order to produce useful data that can be interpreted biologically. There has been a surge in interest in the use of probiotic supplements as mediators in health and disease in recent years. This appeal is primarily motivated by mounting evidence of the involvement of the microbiota with disease pathophysiological processes in the human body.