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Bile acids (BAs) comprise a diverse group of cholesterol metabolites with multiple modes of action. Much of the role of BAs and their receptors in energy homeostasis has been discerned from studies on genetic and/or pharmacologic manipulations. Additionally, changes in BA metabolism and transport have been reported in settings of insulin resistance, obesity, and liver dysfunction. Thus, BA-based interventions have been proposed for treatment of metabolic diseases. However, the heterogeneity of endogenous BAs lends to different affinities for and potencies in activating the various BA receptors, and the effects of altering BA composition per se are incompletely understood. In this dissertation, we aimed to characterize the effects of altering BA composition by stimulating intestinal organoids with distinct BA pools modeled after those in humans and mice. Unexpectedly, we found that BA composition regulated expression of the manganese transporter encoded by Slc30a10 and manganese efflux from cells, suggesting a role for BAs in metal homeostasis. We also identified genes that were similarly and differentially regulated by the distinct mouse and human BA pools. Overall, our studies reveal a pathway by which BAs could modulate micronutrient metabolism, which might also mediate known effects of BAs on macronutrient metabolism.