A diagram illustrating the major findings of the present study. Briefly, 1) PBDEs decreased bacterial diversity, but increased the taxa A. muciniphila and Allobaculum spp., 2) PBDEs increased unconjugated BAs in the serum, liver, SIC, and LIC of CV mice, 3) the lack of gut microbiome led to a shift in BA composition toward an increase in T-α/βMCA in GF mice, and 4) PBDEs down-regulated host enzymes and transporters involved in BA metabolism in a gut microbiota-dependent manner.