The metabolic pathways encoded by the human gut microbiome constantly interact with host gene products through numerous bioactive molecules. Primary bile acids (BAs) are synthesized within hepatocytes and released into the duodenum to facilitate absorption of lipids or fat-soluble vitamins. Some BAs (approximately 5%) escape into the colon, where gut commensal bacteria convert them into various intestinal BAs that are important hormones that regulate host cholesterol metabolism and energy balance via several nuclear receptors and/or G-protein-coupled receptors^,. These receptors have pivotal roles in shaping host innate immune responses^,. However, the effect of this host–microorganism biliary network on the adaptive immune system remains poorly characterized. Here we report that both dietary and microbial factors influence the composition of the gut BA pool and modulate an important population of colonic FOXP3⁺ regulatory T (T_reg) cells expressing the transcription factor RORγ. Genetic abolition of BA metabolic pathways in individual gut symbionts significantly decreases this T_reg cell population. Restoration of the intestinal BA pool increases colonic RORγ⁺ T_reg cell counts and ameliorates host susceptibility to inflammatory colitis via BA nuclear receptors. Thus, a pan-genomic biliary network interaction between hosts and their bacterial symbionts can control host immunological homeostasis via the resulting metabolites.