Food as Medicine: Enhancing Crop Breeding and Food Processing to Shift the Gut Microbiome for Prevention and Treatment of Chronic Diseases

Prebiotics are useful tools for shifting the gut microbiome and metabolome to confer immune, metabolic, and preventive benefits for human disease. However, there are emerging concerns about methods for discovering optimal candidate compounds and their sustainable production for long-term success in targeting mechanisms of disease. In this perspective, we review the current state of prebiotics moving from nutrition to function in health, highlighting the opportunities for using food as medicine in treating a model disease, inflammatory bowel disease, discussing the ways crop breeding can be used to identify and improve the functional (beyond nutritional) value of a prebiotic and the critical role that food processing plays in sustaining the integrity and scalability of the prebiotic compound while influencing consumer adoption of these agents. This information supports a trajectory for the future of food as medicine to be moving from population-scale dietary guidelines to personalized or precision nutrition guidelines, from "eat more fiber" to "eat this specific type of fiber that has been enhanced in and processed from this specific genotype of food crop". This could include developing designer fibers by crop breeding to develop panels of genotypes with different fiber structures that deliver reliable shifts in the microbiome and metabolome for most patients with the targeted disease. Finally, there needs to be a commitment to sustainability of the plant-derived product so that future generations will have access to the same benefits of the food as medicine initially developed for disease prevention and treatment.