Gastrointestinal diseases, both infectious and cancerous, account for over 1 billion human illnesses each year. Rice bran is a globally-available and affordable food source accessible to populations on all continents. Rice bran alone is a rich source of fats, proteins, vitamins and minerals. However, when health-promoting probiotics ferment rice bran, we observe elevations in many of its health promoting compounds and pathogen-fighting effects. This mouse model study revealed that fermented rice bran health changes occur in-part due to changes in the gut microbiome and compounds that these microbes produce, and it gives us a framework for more critically-evaluating these compounds and their roles in health and disease prevention. Probiotic-fermented rice bran could be applied as an adjunctive or alternative treatment when managing infectious or neoplastic gastrointestinal diseases.