Another renaissance for bile acid gastrointestinal microbiology

Abstract

The field of bile acid microbiology in the gastrointestinal tract is going through a current rebirth after a peak of activity in the late 1970s and early 1980s. This renewed activity is a result of many factors, including the discovery near the turn of the century that bile acids are potent signalling molecules and technological advances in next-generation sequencing, computation, culturomics, gnotobiology, and metabolomics. We describe the current state of the field with particular emphasis on questions that have remained unanswered for many decades in both bile acid synthesis by the host and metabolism by the gut microbiota. Current knowledge of established enzymatic pathways, including bile salt hydrolase, hydroxysteroid dehydrogenases involved in the oxidation and epimerization of bile acid hydroxy groups, the Hylemon-Bjӧrkhem pathway of bile acid C7-dehydroxylation, and the formation of secondary allo-bile acids, is described. We cover aspects of bile acid conjugation and esterification as well as evidence for bile acid C3-dehydroxylation and C12-dehydroxylation that are less well understood but potentially critical for our understanding of bile acid metabolism in the human gut. The physiological consequences of bile acid metabolism for human health, important caveats and cautionary notes on experimental design and interpretation of data reflecting bile acid metabolism are also explored.

Fig. 1|. Bile acid structure and function.

a, Generic form of a bile acid with functional groups (R) defined for select bile acids listed in the corresponding insert table. b, Structural comparisons of 5β-bile acids (R₅ = 5β-H), whose A/B rings are cis. and 5α-bile acids (R₅ = 5α-H), in which A/B rings are trans. c, Bile acids have a ‘Janus-like’ quality in that their faces have distinct properties that lend to detergent function, 1°, primary; 2°, secondary; NA. not applicable.

Fig. 2|. The enterohepatlc circulation or bile acids.

Primary bile acids (yellow) are synthesized de novo in hepatocytes from cholesterol and secreted into bile through transport protein BSEP. During a meal, the gallbladder contracts, releasing bile into the duodenum, where mixed micelles composed of phosphdipods. fatty acids, cholesterol and lipid-soluble vitamins form and are surrounded by amphipathic conjugated bile acids. When conjugated bile acids reach the terminal ileum, they are transposed into enterocytes by the illeal sodium-bile acid cotransporter (JBAT), bound to FABP6 and transported into portal circulation via OSTα and OSTβ expressed basolaterally on enterocytes. As part of the negative feedback function of bile acid synthesis, intracellular bile acids activate the nuclear farnesoild X receptor (FXR) in enterocytes, resulting in upregulation in the synthesis and secretion of the protein FGF15/19 into the portal circulation. FGF15/19 binds to fibroblast growth factor receptor FGFR4/β-Klortho receptor-dependent manner resulting in inhibition of CYP7AL the rate-limiting enzyme in bile acid biosynthesis in the liver. Bile acids returning to the liver are transported by NTCP. Activation of FXR in hepatocytes represses CYP7A1 expression dependent on small heterodimer partner (SHP) and liver-related homologue 1(LRHI). This process allows bile acid levels to remain in steady state. TCRS activation in intestinal stem cells promotes regeneration of enterocytes. Roughly 5% of bile acids (400–800 mg per day) escape fieal transport and enter the large Intestine, which is the major route by which cholesterol is removed from the body. In the large intestine, bile acid structure and function are diversified by the gut microbiota. Part of this diversification is increasing the hydrophobicity of bile acids in the large intestine, allowing passive absorption into colonocytes and entry into the portal circulation, where secondary bile acids (mainly decoycholic acid (DCA)) accumulate to roughly one-quarter of the bile acid pool in healthy humans.

Fig. 3|. Targeting microbiota-bile acid interactions as potential therapeutic approaches for gastrointestinal and metabolic diseases.

a, Studies have demonstrated the potential utility of selecting for bacterial strain-dependent bacteriophages to remove microbial strains that have a causal rolle in diseases such as inflammatory bowel disease. b, Synthetic biology offers the potential to rationally design commensal or probiotic bacteria to modulate bile acid metabolism in vivo. c, The development of specific inhibitors against the microblome is expected to provide therapeutic potential. The development of bile salt hydrolase (BSH) enayme inhibitors has allowed interrogation of the effects of altering bile acid metabolism^,,; other studies indicate that inhibitors against bar enzymes might also be therapeutically Important. d, Chemoproteomic profiling using click chemistry bile acid probes allows the discovery of novel bacterial enzymes involved in bile acid metabolism. After the bile acid probe covalently bonds to a bile acid binding enzyme (BAZyme), proteomic mass spectrometry allows the identification of gene sequence candidates. e, Cheminformatics couples metabolomics with computation to obtain metabolite networks in which some nodes represent novel metabolites that repeal previously unknown bacterial metabolism. BAZyme, bile acid enzyme.

Fig. 4|. Bile acid biotransformations in the human large intestine.

Conjugated primary bile acids (taurocholic acid (TCA), glycocholic acid (GCA), taurochenodeoxycholic acid (TCDCA), glycochenodeoxycholic acid (GCDCA)) enter the large intestineand are deconjugated by the enzyme bile salt hydrolase (BSID by diverse gut bacterial taxa (Table 1). BSH is also reported to reconjugate free bile acids with a wide range of amino acids (AAs) yielding microbially conjugated bile acids (MCBAs). The primary bile acids cholic acid (CA) and chenodeoxycholic acid i.CDCA) can be oxidized to 7-oxoCA and 7-oxoCDCA, respectively, by the enzyme 7α hydroxysteroid dehydrogenase(ursA) (Table 1) and epimerized to ursochollc acid (UCA) and ursodeoxycholic acid (UDCA), respectively, by the enzyme 7β-hydroxysteroid dehydrogenase(ursB). CA and CDCA are also converted to deoxycholic acid (DCA) and lithocholic acid (LCA), respectively, through the multipstep Hylemon-Björkhem pathway of bile acid 7α-dehydroxylation by intestinal Clostridia (Table 1). UCA and UDCA can be directly 7β-dehydroxylated through the Hylemon-Björkhem pathway or, alternatively, epimerized back to CA and CDCA and 7α-dehydroxylated to DCA and LCA. The Hylemon-Björkhem pathway also yields A/B-ring epimers that are planar, known as ‘allo’ bile acids. We have designated both epimers of DCA and alloDCAas (allo)DCA as well as (allo)LCA and their derivatives. (allo)DCA has two hydroxyl groups that can be oxidized to 3-oxoDCA by 3α-hydroxysteroid dehydrogenase (isoA) and/or 12-oxoDCA by 12ahydroxysteroid dehydrogenase (epiA), and epimerized by 3β-hydroxysteroid dehydrogenase (isoB) and/or 12β-hydroxysteroid dehydrogenase (epiB) to iso(allo)DCA and epi(allo)DCA, respectively. (allo)LCA is monohydroxylated at C3 and can yield 3-oxo(allo)LCA and lso(allo)LCAonly. Additionally, the host sulfates lca to yield 3-sulfoLCA. It is reported that 3 sulfoLCA can be C3-dehydroxylated to the non bile acid, 5β-cholanic acid. isoDCA and isoLCA are also esterified to short-chain and long-chain fatty acids.and DCA can be polymerized through esterification between C3-OH and C24-COOH. There is some support for the C12-dehydroxylation of CA to CDCA and of DCA to LCA.

Fig. 5|. Modulation of inflammation and immune cell differentiation and function by secondary bile acid derivatives in the gastrointestinal tract.

The illustration summarizes the latest observations on the effects of rarely measured and hence understudied microbially derived secondary bile acid derivatives on host immune cells. In general, the data indicate that particular secondary bile acid derivatives exert distinct effects on the differentiation of macrophage progenitors as well as dendritic cell antigen presentation and naive CD4⁺ T cell differentiation, thereby purportedly influencing the inflammatory tone in the gastrointestinal tract. For specific details on the findings illustrated, readers are referred to the original research papers^{–,,,,,,–,}, which are summarized in the body of the present Review and subsequent review articles^,,,,. Briefly, iso-lithocholic acid (isoLCA) and 3-oxoLCA were shown to modulate macrophage polarization states, iso-deoxycholic acid (isoDCA) induced FOXP3 expression in dendritic cells to diminish their immunostimulatory properties, the planar secondary bile acid isoalloLCA enhanced regulatory T (T_reg) cell differentiation through interactions with the nuclear hormone receptor NR4A1, leading to activation of FOXP3gene transcription .and 3-oxoLCA inhibited T helper 17 (T_H17) cell differentiation^,. Similar to 3-oxoLCA, isoLCA suppressed T_H17 cell differentiation by inhibiting the canonical transcription factor retinoid-related orphan receptor γt (RORγt⁺). FXR, farnesoid X receptor; M-CSF, macrophage colony-stimulating factor. TCR, T cell receptor.