A previously unrecognized class of metal-dependent bile salt hydrolases (metalloBSHs) from the amidohydrolase superfamily catalyzes taurine-conjugated bile acid deconjugation in Desulfovibrionaceae bacteria through a metallocofactor-dependent mechanism distinct from canonical cysteine-dependent BSHs, with metalloBSH gene abundance correlating with altered bile acid metabolism across human gut microbiomes in multiple clinical cohorts.

Bile salt hydrolases (BSHs) are gut microbial enzymes that catalyze the deconjugation of glycine-or taurine-conjugated bile acids (BAs), a key step in shaping the BA pool in the human gastrointestinal tract and modulating host-gut microbiome interactions. All known BSHs are members of the N-terminal nucleophile (Ntn) hydrolase superfamily and share a conserved architecture and mechanism involving a nucleophilic active site cysteine. This knowledge has guided predictions and study of BSH activity in the gut microbiome as well as the development of BSH inhibitors. Here, we report the discovery and characterization of a previously unknown BSH from the human gut bacterium Bilophila wadsworthia that belongs to the metal-dependent amidohydrolase superfamily and exhibits robust and specific activity toward taurine-conjugated bile salts. We show this secreted enzyme, metalloBSH, utilizes a metallocofactor for BA deconjugation, a mechanism distinct from that of canonical Ntn-type BSHs. MetalloBSHs are conserved in B. wadsworthia and present in many other Desulfovibrionaceae found in vertebrate gut microbiomes. Analysis of multi-omic datasets indicates metalloBSHs are expressed in vivo and correlate with BA metabolism. Overall, our findings reshape our understanding of BSH activity in the gut microbiome and highlight the promise of activity guided discovery in revealing previously overlooked gut microbial enzymes.