Background: The metabolic benefits induced by gastric bypass - currently the most effective treatment for morbid obesity - are associated with BA delivery to the distal intestine. However, mechanistic insights into BA signaling in the mediation of metabolic benefits remain an area of focus. Methods: The BD mouse model, in which the gallbladder is anastomosed to the distal jejunum, was utilized to test BA specific role in the regulation of glucose and lipid homeostasis. Metabolic phenotype, including body weight and composition, glucose tolerance, energy expenditure, thermogenesis genes, total BA and BA composition in the circulation and portal vein, and gut microbiota were examined. Results: BD improves metabolic phenotype in line with increased circulating primary BAs and regulation of enterohormones. BD-induced hypertrophy of the proximal intestine in the absence of BAs was reversed by BA oral gavage, but without influencing BD metabolic benefits. BD enhanced energy expenditure was associated with elevated TGR5, D2 and thermogenic genes, including UCP1, PRDM16, PGC1α/β and PDGFRα, in epididymal white adipose tissue (eWAT) and inguinal WAT (iWAT), but not in brown adipose tissue (BAT). BD altered the gut microbiota profile, i.e. decreasing Firmicutes and increasing Bacteriodetes and Akkermansia being positively correlated with increased circulating primary BAs. Conclusions: Our study demonstrates that enhancement of BA signaling regulates glucose and lipid homeostasis, promotes thermogenesis, and modulates the gut microbiota, which collectively resulted in an improved metabolic phenotype.