The process of food fermentation has improved the safety qualities of raw materials and produced novel foods with improved organoleptic properties. The scientific community has taken notice of the empirical finding that certain items might have a health benefit. To determine which of these compounds might be effective against particular diseases, several researches have been carried out in both animal and human hosts. Despite the growing body of research, regulatory agencies have only approved a relatively small number of items as functional meals. This problem may be greatly exacerbated by inconsistent data and a lack of thorough preclinical characterization of functional products. The improved accessibility of omics platforms and bioinformatics methods for thorough data analysis nowadays can help with the systematic investigation of microbe-microbe, microbe-matrix, and microbe-host interactions and offer insightful information about maximizing their positive impacts. Food science still has difficulties integrating these platforms, but with concerted efforts and cross-disciplinary cooperation, a new age in the discipline might be on the horizon.