Completion of the gut microbial epi-bile acid pathway

Bile acids are detergent molecules that solubilize dietary lipids and lipid-soluble vitamins. Humans synthesize bile acids with alpha-orientation hydroxyl groups which can be biotransformed by gut microbiota to toxic, hydrophobic bile acids, such as deoxycholic acid (DCA). Gut microbiota can also convert hydroxyl groups from the alpha-orientation through an oxo-intermediate to the beta-orientation, resulting in more hydrophilic, less toxic bile acids. This interconversion is catalyzed by regio- (C-3 vs. C-7) and stereospecific (alpha vs. beta) hydroxysteroid dehydrogenases (HSDHs). So far, genes encoding the urso- (7 alpha-HSDH & 7 beta-HSDH) and iso- (3 alpha-HSDH & 3 beta-HSDH) bile acid pathways have been described. Recently, multiple human gut clostridia were reported to encode 12 alpha-HSDH, which interconverts DCA and 12-oxolithocholic acid (12-oxoLCA). 12 beta-HSDH completes the epi-bile acid pathway by converting 12-oxoLCA to the 12 beta-bile acid denoted epiDCA; however, a gene(s) encoding this enzyme has yet to be identified. We confirmed 12 beta-HSDH activity in cultures of Clostridium paraputrificum ATCC 25780. From six candidate C. paraputrificum ATCC 25780 oxidoreductase genes, we discovered the first gene (DR024_RS09610) encoding bile acid 12 beta-HSDH. Phylogenetic analysis revealed unforeseen diversity for 12 beta-HSDH, leading to validation of two additional bile acid 12 beta-HSDHs through a synthetic biology approach. By comparison to a previous phylogenetic analysis of 12 alpha-HSDH, we identified the first potential C-12 epimerizing strains: Collinsella tanakaei YIT 12063 and Collinsella stercoris DSM 13279. A Hidden Markov Model search against human gut metagenomes located putative 12 beta-HSDH genes in about 30% of subjects within the cohorts analyzed, indicating this gene is relevant in the human gut microbiome.

Automated summary

Intestinal microbiota can convert the orientation of bile acids, altering their water solubility and toxicity, while relevant genes have been identified and shown potential importance.