A metabolic pathway for bile acid dehydroxylation by the gut microbiome

Abstract

The gut microbiota synthesize hundreds of molecules, many of which are known to impact host physiology. Among the most abundant metabolites are the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA), which accumulate at ~500 µM and are known to block C. difficile growth 1 , promote hepatocellular carcinoma 2 , and modulate host metabolism via the GPCR TGR5 3 . More broadly, DCA, LCA and their derivatives are a major component of the recirculating bile acid pool 4 ; the size and composition of this pool are a target of therapies for primary biliary cholangitis and nonalcoholic steatohepatitis. Despite the clear impact of DCA and LCA on host physiology, incomplete knowledge of their biosynthetic genes and a lack of genetic tools in their native producer limit our ability to modulate secondary bile acid levels in the host. Here, we complete the pathway to DCA/LCA by assigning and characterizing enzymes for each of the steps in its reductive arm, revealing a strategy in which the A-B rings of the steroid core are transiently converted into an electron acceptor for two reductive steps carried out by Fe-S flavoenzymes. Using anaerobic in vitro reconstitution, we establish that a set of six enzymes is necessary and sufficient for the 8-step conversion of cholic acid to DCA. We then engineer the pathway into Clostridium sporogenes, conferring production of DCA and LCA on a non-producing commensal and demonstrating that a microbiome-derived pathway can be expressed and controlled heterologously. These data establish a complete pathway to two central components of the bile acid pool, and provide a road map for deorphaning and engineering pathways from the microbiome as a critical step toward controlling the metabolic output of the gut microbiota.

Protein Phosphatase 1 Regulatory Subunit 3B Genotype at rs4240624 Has a Major Effect on Gallbladder Bile Composition

“…Lower bile acid concentration probably influences the composition of the microbiota and hence may increase bile acid dehydroxylation. (40) Variants of PPP1R3B have not been associated with gallstones. (41) Intriguingly, our preliminary data with limited number of subjects with gallstone disease data available showed that 2 out of 25 (8%) subjects with genotype AA had gallstones compared to 5 out of 15 (33%) with genotype AG (P = 0.021).…”

Identification of unique bile acid-metabolizing bacteria from the microbiome of centenarians

“…a-diversities were calculated using Shannon index and b-diversity was calculated using Bray-Curtis dissimilarity based on relative abundances at species levels (Vegan package in R). The non-redundant gene catalogue was queried using USEARCH ublast 53 with proteins in the bai operon of C. scindens 26 or proteins in the bacterial isolates reported here as 5AR, 5BR, 3bHSDH I, or 3bHSDH II to identify and annotate homologous proteins with at least 40% identity and 80% coverage to the query sequence. An identical processing pipeline has been applied to the dataset describing the gut microbiome in Sardinian centenarians 8 .…”

Alleviation of Cholesterol Gallstones by Lactobacillus Targeting the Gut Microbiota Depends on Global Farnesoid X Receptor-Mediated Bile Acid Metabolism

“…Serum bile acids (BAs), as important signaling molecules, participate in the regulation of BA metabolism and the activation of several kinds of bile acid receptors [25]. Most BAs come from reabsorption in the intestinal epithelium after being processed by gut microbes and then entering the enterohepatic circulation [26,27]. Therefore, we measured total bile acid (TBA) and the composition of BAs in serum to examine differences induced by LR and LP treatment.…”