Xanthogranulomatous cholecystitis (XGC) is characterized histologically by the accumulation of numerous foamy macrophages in the gallbladder, resulting in thickening of the gallbladder wall. Moreover, XGC is frequently diagnosed as gallbladder carcinoma. Escherichia coli antigens have been detected immunohistologically in XGC lesions, and E. coli was reported to be involved in the pathogenesis of XGC, with scavenger receptor class A and CXCL16-CXCR interactions. These resulted suggested that E. coli infections of the gallbladder play an important role in the onset and/or early stages of XGC. However, it is unclear whether other pathogens are associated with the cause and progression of XGC. In this study, we analyzed the microbiota in bile samples from XGC patients to reveal the cause and progression of XGC.