Compared to drugs food is characterized by a large spectrum of chemicals inducing a broad spectrum of cellular responses of low signal intensity. Because of this complexity, advances in nutritional science have long been lagging behind compared to pharmacology. The advent of functional genomics and its application to nutritional science has changed this situation and nutritionists now obtain an unprecedented amount of molecular and mechanistic information from human studies. This paper presents and selectively illustrates the concepts of nutrigenomics, nutrigenetics, nutriepigenetics, and nutritional systems biology. The potential application of nutrigenomics to the field of fermented food is finally discussed. Highlights ► The science of nutrigenomics is reshaping food and nutrition research. ► Personalized nutrition is a phenotypic science that integrates genetic and epigenetic factors. ► Omics technologies promote the translational of food science into nutritional knowledge. ► Bacterial genomics link food fermentation to gut metabolism and health in humans.