Bile Acids, Their Receptors, and the Gut Microbiota

Abstract

Bile acids (BAs) are a family of hydroxylated steroids secreted by the liver that aid in the breakdown and absorption of dietary fats. BAs also function as nutrient and inflammatory signaling molecules, acting through cognate receptors, to coordinate host metabolism. Commensal bacteria in the gastrointestinal tract are functional modifiers of the BA pool, affecting composition and abundance. Deconjugation of host BAs creates a molecular network that inextricably links gut microtia with their host. In this review we highlight the roles of BAs in mediating this mutualistic relationship with a focus on those events that impact host physiology and metabolism.

Introduction

Bile acids (BAs) are cholesterol-derived, amphiphilic molecules that are synthesized by hepatocytes. BAs in most species are stored in the gallbladder and in response to the cholecystokinin elicited by a meal are released into the small intestine where they emulsify dietary fat and enhance lipid, sterol, and vitamin absorption before being reabsorbed in the terminal ileum and returned back to the liver via portal circulation (1, 2). BA uptake in the ileum is facilitated by apical bile salt transporter (ASBT) in the liver and by organic anion transporter polypeptide (OATPA/B) and sodium taurocholate cotransporting polypeptide (NTCP) transporter in the ileum. This process, termed enterohepatic circulation, is highly efficient, occurs 8–10 times per day, and is an important component of circadian timing (3, 4). Small amounts of BAs (<5%) that escape transporter-mediated uptake in the ileum then enter the colon. During their transit through the intestine and colon commensal gut bacteria oxidize, deconjugate, dehydroxylate, and epimerize BAs into secondary BAs with differing hydrophobicity (5). Recently, BA amide conjugations with phenylalanine, tyrosine, and leucine associated with the microbiome were also shown to exist (6).

BA Synthesis, Composition, and Interspecies Differences

The structures of BAs contribute to their functionality. BAs are composed of a sterol core consisting of three six-member carbon rings and one five-member carbon ring, typically having a 5β-hydrogen and a cis-configuration along the plane of the first two fused rings. BAs species are determined by the number and position of hydroxy, carboxy, sulfate, and amino acid groups conjugated to them (FIGURE 1). The hydroxy and carbonyl group face the same side of the sterol core, while the methyl groups face the opposite side. This renders BAs with amphiphilic properties as one side is hydrophobic while the other is hydrophilic (8) (FIGURE 1).

FIGURE 1.

Bile acid (BA) hydrophobicity is determined by the number and position of hydroxyl and sulfate groups to the sterol ring as well whether the BA is conjugated to an amino acid, which in mice is predominantly taurine and in humans is mostly glycine. Hydroxylation at carbons 3, 6, 7, and 12 on the sterol core of primary (highlighted gray) and secondary (white) BAs increases the BA hydrophobicity index (blue shaded arrow). Adapted from Heuman et al. (7).

There are major differences in BA composition between humans and mice. Cholic acid (CA) and chenodeoxycholic acid (CDCA) are the two primary BAs synthesized in human liver. There are two pathways for BA biosynthesis: the classical pathway (also referred to as the neutral pathway) and the alternative pathway (also referred to as the acidic pathway, due to the production of acidic intermediates). The classical BA biosynthetic pathway accounts for >90% of total BA production under normal physiologic conditions and is considered the major BA biosynthesis pathway. The first and rate-limiting step of CDCA synthesis via this pathway is catalyzed by the microsomal protein cholesterol 7α-hydroxylase (encoded by CYP7A1), which converts cholesterol to 7α-hydroxycholesterol (7α-HCO) (FIGURE 2). Other enzymes can prevent or stimulate BA synthesis by inhibiting or activating this enzyme. Subsequent 12α hydroxylation of 7α-HCO by 3β-hydroxy-Δ⁵-C₂₇-steroid hydroxylase (encoded by CYP8B1) generates 7α,12α-dihydroxy-4-cholesten-3-one (7α,12α-diHCO), a precursor to the more hydrophilic BA, CA. Whereas CYP7A1 regulates the overall rate of BA production, CYP8B1 regulates the ratio of CA/CDCA. Chenodeoxycholic acid (CDCA) is a BA end product in humans. In humans, the gut microbiota converts the primary BAs, cholic acid (CA) and CDCA, into deoxycholic acid (DCA) and lithocholic acid (LCA), respectively.

FIGURE 2.

Bile acid (BA) biosynthesis and metabolism in the liver and intestine. The primary BAs, chenodeoxycholic acid (CDCA) and cholic acid (CA) are synthesized from cholesterol and other precursors via Cyp7a1 in the liver yielding the precursors 7α-hydroxycholesterol (7α -HCO) and (7,12-dihydroxycholesterol (7α,12α-diHCO), respectively, the latter generated via the 12α-hydroxylase activity of Cyp8b1. In mice, Cyp2c70 6-hydroxylates CDCA yielding α-muricholic acid (αMCA), which is further epimerized into βMCA and ursodeoxycholic acid (UDCA) via the same enzyme. CA and CDCA are primary BAs in humans while CA, CDCA, MCAs, and UDCA, are primary BAs in mice. After conjugation with glycine (G) or taurine (T) via hepatic BA amino transferase (BAAT), these BAs are secreted into bile which is then released into the intestines. Bacterial 7α-hydroxysteroid dehydrogenase (7α-HSDH) generates deoxycholic acid (DCA), and lithocholic acid (LCA) and 7β-hydroxysteroid dehydrogenase (7β-HSDH) render UDCA. Hepatic Cyp2a12 rehydroxylates DCA and LCA into CA and CDCA, respectively. In humans, CA, CDCA, and DCA are conjugated derivatives are predominant. In mice, CA, αMCA, and βMCA and conjugated derivates are predominant. Cyp2c70^-/- mice have increased CDCA and are void of MCAs. Cyp2a12^-/- mice have increased DCA, CDCA, and LCA. Cyp2c70^-/- and Cyp2a12^-/- [double knockout (DKO)] mice have increased DCA, CDCA, and LCA.

BAs are frequently modified by conjugation with taurine (rodents) or glycine (humans), increasing solubility and reducing lipophilicity (9). BAs can also be sulfated, which increases critical micellar concentrations and diminishes bile cytotoxicity as sulfated BAs do not solubilize cholesterol. Sulfated bile acids are shown to accumulate in patients with hepatobiliary diseases (10) and in children with constipation (11) and with cholestasis (12).

In mice, the majority of CDCA is converted to α-muricholic acid (MCA), β-MCA, and UDCA in part by 6β-hydroxylase (Cyp2c70) (13). Therefore, CDCA, CA, α-MCA, β-MCA, and UDCA are major primary BAs in mice. These are the dominant BA species in mice, yielding a BA pool that is more hydrophilic. In the alternative pathway of BA biosynthesis, cholesterol is converted to 27-hydroxycholesterol via actions of sterol 27-hydroxylase (CYP27A1). 27-Hydroxycholesterol and other oxysterols serve as substrates for a nonspecific 7α-hydroxylase (CYP7B1) rendering CDCA (14). In the acidic environment of the duodenum, the pK_a of unconjugated BAs is between 5 and 6.5, whereas at physiologic pH conjugated BAs are almost fully ionized and are termed bile salts (15).

In mice, an additional reaction occurs wherein Cyp2a12 reverts this action and converts these secondary BAs back to primary BAs. Novel mouse models deficient in Cyp2c70 (16–18), Cyp2a12 (17) or both genes [double knockout (DKO)] exhibit humanized BA compositions and varied BA pool sizes that differ in their capacity to activate BA receptors and that inhibit cytokine-mediated hepatic Cyp7a1 repression. Cyp2c70^-/- mice are deficient in MCAs, Cyp2a12^-/- cannot convert secondary BAs back to primary BAs, and DKO (lacking both Cyp2c70^-/- and Cyp2a12^-/-) mice possess both these features. These Cyp-deficient mice exhibit profoundly different BA profiles that more closely resemble humans. In addition, Cyp2c70 KO and DKO mice have a lower BA pool size (up to 50%) resulting from repressed hepatic Cyp7a1 expression. Findings with respect to the complement of enzymes catalyzing MCA formation are not entirely clear as there is evidence that some MCAs can still be produced in the absence of Cyp2c70 (16) and not all Cyp2c70-deficient lines exhibit reduced Cyp7a1 mRNA. Remarkably, none of the aforementioned mice strains exhibit altered expression of ileal Fgf15 nor do they show evidence of FXR activation. Instead, Cyp2c70 and DKO mice exhibited FXR/SHP-independent and BA/cytokine-mediated inhibition of Cyp7a1-mediated BA synthesis. Future mechanistic studies using these mice will help shed new light on how humanized BA profiles regulate metabolism.

Bacterial Transformation of Bile Salts

Bacteria colonize all surfaces of the body, but nowhere are they more abundant than the gastrointestinal tract. In mammals, the gut microbiome is made up of four major bacterial phyla: Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. In the human gastrointestinal tract, there are more than 100 trillion (10¹⁴) microorganisms (19), including over 100,000 (10⁴) bacterial species (19). This variety is established early in neonatal life with BAs serving as potent drivers of microbial diversity (20). Bacterial enzymes modify BAs in the small intestine, changing the structure and hydrophobicity and increasing BA diversity in enterohepatic circulation. Bacterial deconjugation of BAs via bile salt hydrolase (BSH) hydrolyzes and deconjugates taurine (rodents) or glycine (humans) from the BA sterol core, preventing active reuptake from the small intestine via ASBT (21). Metagenomic analyses demonstrated that functional BSH is present in all major bacterial divisions and archaeal species in the human gut including members of Lactobacilli, Bifidobacteria, Clostridium, and Bacteroides (21, 22). It is thought that BSH is associated with increased resistance to bile toxicity (22, 23). Novel mechanisms have been proposed for how bacteria may exploit BSH activity. For example, the enzyme 7α-HSDH converts CDCA to 7-oxo-LCA. This metabolite acts as a competitive inhibitor for 11β-HSDH-1, an enzyme responsible for the conversion of cortisone to cortisol. It is believed that the cortisol/cortisone ratio may alter the environment into one more favorable for bacteria that produce 7α-HSDH (24). A growing body of literature emerged implicating gut microbes and the abundance of bile-salt hydrolase (BSH) genes as pathologic determinants of intestinal inflammation (25, 26) and consequently metabolic (e.g., obesity and type 2 diabetes) and cardiovascular disease (27, 28). We and others have demonstrated that the gut microbiota-mediated biotransformation of the BA pool also regulates host BA signaling (by primary and secondary BAs) by affecting the activation of intestinal FXR. Recent studies showed the antioxidant Tempol alters the gut microbiome by preferentially reducing the genus Lactobacillus and its BSH activity leading to the accumulation of intestinal TβMCA with weight-lowering effects in mice (29).

Unconjugated BAs are subject to bacterial biotransformations including dehydroxylation, dehydrogenation, and epimerization leading to the formation of secondary BAs. BA oxidation and epimerization are mediated by 3α-, 7α-, 7β-, and 12α-hydroxysteroid dehydrogenase (HDSH) activities of several gut bacteria (5, 30, 31). These reactions serve to dramatically diversify the BA pool and render BA species that may serve as signaling molecules among bacteria or between bacteria and host (5). The 7α-dehydroxylation reaction is, quantitatively speaking, the most important reaction performed by gut bacteria. Deoxycholic acid (DCA) and lithocholic acid (LCA) comprise the majority of secondary bile acids and are formed from CA and CDCA, respectively, via 7α-dehydroxylation (32). This dehydroxylation, carried out mainly by Clostridium cluster XIV bacteria (5), leads to an increase in the BA hydrophobicity index, which impacts intestinal permeability (33), pathogen resistance, bacterial antibiotic secretion (34), and importantly, FXR activation (35, 36). The genes facilitating 7α-dehydroxylation are encoded by elements of the bile acid inducible (bai) operon, best described in high-activity strains of Clostridia such as Clostridium hiranonis and C. scindens. The bai operon encodes proteins needed to uptake unconjugated BAs (baiG), with additional transformation facilitated by enzymes with CoA-ligase (baiB), 3α-dehydroxylase (baiA), 7α-dehydroxylase (baiCD and baiE with different stereospecificities), 7β-dehydroxylase (baiH and baiI), and presumed BA-CoA hydrolase (baiF) activity (5). Ketohydroxyl BAs, formed by oxidoreduction, are also the result of bacterial dehydrogenation that can be produced in certain physiologic scenarios, the formation of which is influenced by oxygen and cofactor availability as well as pH.

BA Receptors

Along with being physiological detergents that aid in lipophilic molecule metabolism, BAs regulate a wide array of bioenergetic and cell signaling pathways through both nuclear and G protein-coupled receptors with different potencies (37).

The farnesoid X receptor (FXR) is a nuclear receptor that acts as a BA sensor critical in regulating BA synthesis and transport. FXR is highly expressed in the liver, intestine, and kidneys and the adrenal gland (38, 39). In the intestine, FXR controls BA availability by regulating expression of apical bile salt transporter (ASBT) and basolateral organic solute transporters-α and -β (OSTA/OSTB) (40). FXR activation also regulates intestinal secretion of FGF 15/19 (41, 42), a circulating enterokine that inhibits expression of hepatic CYP7A1. Whole body FXR KO mice exhibit worsened oral glucose tolerance (OGT) and lower glucose disposal than the wild type (WT) (43–45). Surprisingly, both agonism and antagonism of intestinal FXR in mice show beneficial effects. The gut-restricted FXR agonist fexaramine improved glycemia and reduced weight gain in mice (46, 47) while TβMCA and glycine-β-muricholate (Gly-MCA) antagonize FXR activity to improve insulin tolerance, and reduce OGT and fasting insulin levels (48). Furthermore, the antioxidant Tempol (4-hydroxy-2, 2, 6, 6-tetramethylpiperidine 1-oxyl) altered gut microbiota and BA composition, increased levels of TβMCA, and decreased FXR signaling (29). Fexaramine treatment increases LCA-producing Acetatifactor and Bacteroides, while Tempol decreases Lactobacillus and BSH activity (49). In liver, FXR activation stimulates expression of the canalicular bile salt export pump (BSEP, ACBC11). Hepatic FXR activation results in stimulation of glycogen synthesis (50) and triglyceride clearance (51–53) and inhibition of gluconeogenesis (44, 54, 55) and lipogenesis (45). This FXR signaling spans several pathways that include enhanced transintestinal cholesterol excretion via enhanced increased expression of ATP binding cassette subfamily G member 5/8 (ABCG5/8) (56); released inhibition of glucagon-like peptide-1 (GLP-1; encoded by proglucagon; Gcg) expression in enteroendocrine cells (57); and decreased hepatic glucose production resulting from the muricholic acid-induced depletions of ceramides (58). CDCA is the most efficacious endogenous FXR ligand (CDCA > DCA > LCA > CA) (59), whereas hydrophilic bile acids, such as UDCA and MCAs, do not activate FXR (35).

FXR function is modulated by phosphorylation (60), acetylation (61), sumoylation (62), O-GlcNAcylation (63), and alternative splicing (64, 65). In humans and rodents, the FXR gene encodes four isoforms (FXRα1-α4) (64–66) that are differentially expressed in tissues. Isoform pairs Fxrα1/α2 are transcribed from a common promoter but differ in that Fxrα1 contains an extra 12 nucleotides (encoding MYTG, orange) resulting from splicing events at exon 5. Splicing events skipping exon 3 encoding the longer activation function (AF-1) domain (teal) generate Fxrα3 and Fxrα4. Human livers primarily express Fxrα1/α2 isoforms, whereas intestines express Fxrα3/α4 (64). Expression of these isoforms is somehow altered in pathophysiologic states. For example, the Fxrα2/Fxrα1 ratio is decreased in human livers and tumors of hepatocellular carcinoma patients (67), while it is upregulated upon fasting and exercise in mice (68). More importantly, FXR isoforms regulate transcription of target genes in an isoform-specific manner (65, 69). Stable expression of Fxrα2 and Fxrα4 by liver-specific adeno-associated viral vectors revealed Fxrα2-specific reductions in high-density lipoprotein, increased neutral sterol expression, and trans-repressed Cyp8b1, which greatly decreased thehydrophobicity of the BA pool (70). Future studies are needed to examine the relationships between FXR isoform expression, host physiology, and the gut microbiome.

FXR plays a critical role in intestinal bacterial growth (40). WT and FXR-deficient mice raised in conventional or germ-free conditions showed differential accumulation of BAs and an abolishment of FXR signaling in the ileum (71). Fecal microbial transfer (FMT) of human or mouse feces into germ-free mice showed that mice with human bacteria produced relatively less TβMCA in both the liver and gall bladder, as well as the portal and caval veins. In addition, fewer secondary BAs were observed from MCA than mice who received mouse feces (72). In mice, FXR deficiency enriched Desulfovibrionaceae, Deferribacteraceae, and Helicobacteraceae and increased hepatic taurine-conjugated CA and β-MCA as well as hepatic and serum lipids (73). Treatment of mice with VSL#3, a commercial mixture of Lactobacilli (L. casei, L. plantarum, L. acidophilus, and L. delbrueckii), Bifidobacteria (B. longum, B. breve, and B. infantis), and Streptococcus (S. salivarius), promoted BA deconjugation and enhanced fecal BA excretion (74). In mice with mucosal injury caused by bile duct ligation FXR deficiency, intestinal FXR activation inhibited bacterial overgrowth and blocked bacteria-induced mucosal injury (75). In humans, administration of obeticholic acid, a BA analog and potent FXR agonist, led to a reversible induction of gram-positive bacteria and suppression of endogenous BA synthesis (76).

The vitamin D receptor (VDR) is involved in immunity, cellular growth, insulin secretion, and detoxification of secondary bile acids (77). VDR has an affinity for the following BAs: dehydro-LCA > LCA > CDCA > DCA (59). VDR is more sensitive than other receptors to LCA and 3-oxo-LCA and upon activation induces expression CYP3A genes, cytochrome P450 enzymes responsible for detoxifying LCA in the liver and intestine (78). Genome-wide association studies of gut microbiota from 1,812 individuals identified differences in beta-diversity that associated with the VDR gene (79). In the same study, VDR-deficient mice exhibit shifts in microbial flora that associated with changes in serum BAs, fatty acids. These studies supported earlier findings where Lactobacillus were depleted and Clostridium and Bacteroidetes species were enriched in Vdr-/- mice (80). Schmidt et al. (81) reported that Vdr-/- mice have an enlarged (∼30%) BA pool at 3 mo old and more than twice the amount at 6 mo of age. In addition, increased expression of FGF15 was linked with VDR activation. Highlighting its role in tumorigenesis, intestinal deletion of VDR resulted in shifts in bacterial taxa abundance that correlated with increased intestinal tumor burden and secondary BAs and activated JAK/STAT signaling (82).

Pregnane X receptor (PXR) is a well-known orphan nuclear receptor that regulates gene expression in response to xenobiotic and BA exposure (83, 84). PXR also plays important roles in counteracting inflammation (85). PXR has an affinity for the following BAs: LCA > DCA > CA (86). As FXR is unresponsive to LCA, LCA signaling through PXR provides an important sensory role in catabolism of BAs, particularly in a setting of LCA accumulation (87) or cholestasis (88). In clinical studies, it was revealed that patients with inflammatory bowel disease (IBD) had downregulated PXR in inflamed tissue (59). In germ-free mice versus conventionally housed mice, PXR was among those genes most differentially expressed, being lower in GF mice then conventionally housed mice (89). When adequately expressed, PXR acts as a sensor for both BA dysregulation and bacterial derived metabolites such indole 3-propionic acid (90), thereby potentiating immune responses in the host.

Takeda G-protein receptor 5 (TGR5), also known as G protein-coupled bile acid receptor (Gpbar1) is cell surface BA receptor that imparts the nongenomic actions of BAs. TGR5 has an affinity for the following BAs: DCA > LCA > CDCA > CA (86). TGR5 is expressed in monocytes, enteroendocrine cells, adipose tissue, smooth and skeletal muscle, pancreas, and the central nervous system (91–99). Through kinase signaling pathways, TGR5 activation stimulates gallbladder filling (100), modulates energy expenditure (99), stimulates GLP-1 release from intestinal L cells (91, 98, 101), suppresses hepatic glycogenolysis (102), and reduces inflammation and macrophage activation (92, 103–106). TGR5-/- mice have mildly reduced BA pools (107, 108), impaired glucose tolerance (98), and exacerbated inflammatory responses (109). TGR5 has an anti-inflammatory function in the intestine by inhibiting proinflammatory cytokine production in macrophages and modifying innate immune responses (110).

Bile Salts as Modulators of Microbiome-Host Interactions

Alterations in gut microbiota and bile acids are associated with diet, age, antibiotic exposure, as well as the onset and remission of disease. Below are vignettes highlighting the interactions among BAs, microbiota, and host metabolism.

Diet

High-fat diet determines the composition of the murine gut microbiome independently of obesity and is an important determinant of gut microbiota composition (111). In turn, the gut microbiota drives the impact of dietary fat and bile acids on metabolism (112). Western diets composed of highly refined carbohydrate (113) and fat (114) have been attributed to the prevalence of obesity and metabolic inflammation (115). Certain dietary fats present in Western diets have a greater capacity to precipitate intestinal inflammation through their actions on the enteric microbiota of genetically susceptible hosts (115). In particular, studies in mice have shown that milk fat promotes colonic inflammation by promoting taurine conjugation with bile acids and increases the availability of organic sulfur used by the bacteria. This form of fat, when coadministered with high sugar, particularly highly refined sugars such as fructose and glucose (116), represents a Westernized diet that is a potent mediator of metabolic derangement (117). Transplantation of gut communities from obese mice fed a Western diet into germ-free mice induced adiposity in recipient mice within 2 wk (118). These conventionalization (i.e., microbiota transfer by feeding fecal material) experiments have shown that the pathogenesis of obesity can be transferred from obese mice or humans to healthy mice (119, 120).

Nonalcoholic Fatty Liver Disease

Nonalcoholic fatty liver disease (NAFLD) is one of the most prevalent forms of chronic liver disease in the United States (121). The spectrum of NAFLD ranges from simple steatosis alone to nonalcoholic steatohepatitis (NASH) to cirrhosis and occurs frequently in the setting of obesity, dyslipidemia, hyperinsulinemia, and insulin resistance (122–125). Gut dysbiosis has been ascribed often to NAFLD (126, 127) and may afford predictive power in identifying NAFLD-cirrhosis (128). Altered BA profiles including increased total primary BAs and decreased secondary BAs characterize NASH; a higher ratio of total secondary to primary BA ratio decreased the odds of fibrosis (129). Similarly, BA derivatives and compounds that influence BA-related signaling have emerged as potentially useful therapeutic agents for NAFLD and NASH (130, 131). For more information on the role of gut microbiota in liver disease we refer readers to an excellent recent review (132).

Diabetes and Diabetes Resolution after Bariatric Surgery

Gut microbiota and BAs exert considerable influence over insulin sensitivity (57, 133, 134) and enteroendocrine cell hormone release (135). We (135–137) and others have shown that many of the metabolic improvements after bariatric surgery in humans (136, 138–141) and rodents (135, 137, 142, 143) can be attributed to the prevailing bile acid (BA) profile. Surgeries including ileal transposition (144), Roux-en Y gastric bypass (RYGB) (145, 146), vertical sleeve gastrectomy (VSG) (147, 148), and biliary diversion (135, 137) markedly change the gut microbiome. We recently employed fecal metagenomics and metabolomics to understand the impact of bariatric surgery on gastrointestinal microbiota (149). In 21 RYGB and VSG patients assessed at 1 wk, 1 mo, and/or months postoperative, the alpha-diversity and abundance of bacteria with aero-tolerant, probiotic, or inflammatory/anti-diabetic properties (e.g., A. muciniphila) were increased, while Bacteroidetes were decreased. Beta-diversity and fecal metabolites, including indoles, butyrate, and secondary BAs, were also changed. These findings support our earlier work reporting longitudinal increases in secondary BAs in humans after RYGB (136). The postoperative increases in A. muciniphila are also consistent with those we observed in mice where TβMCA was increased after surgical diversion of gallbladder bile to the terminal ileum (135, 137) and in humans where A. muciniphila and GUDCA were increased after treatment with the insulin-sensitizer metformin (150).

Inflammation

Importantly, bacterial BA metabolism also plays a key role in modulating T-cell innate immunity by controlling the balance of proinflammatory T-helper cells and anti-inflammatory Treg cells in both the intestine (151, 152) and periphery (153, 154). Derivatives of lithocholic acid (LCA), 3-oxoLCA and isoalloLCA, induce peripheral Tregs by increasing FoxP3 expression (155). They also inhibit the differentiation of T-helper cells that express IL-17a (T_H17) cells by directly binding to the retinoid-related orphan receptor-γt (RORγt) transcription factor (156). IsoalloLCA also increased the differentiation of T_reg cells by increasing expression of FoxP3 and binding at an intronic enhancer, CNS3. It has also been reported that another secondary bile acid, 3β-hydroxydeoxycholic acid, increased FoxP3 induction by acting on dendritic cells, probably via interaction with FXR (155).

Inflammatory Bowel Disease

IBD-associated dysbiosis was characterized by a decrease in the ratio of Faecalibacterium prausntizii and Escherichia coli. BA deconjugation, transformation, and desulfation are reportedly impaired in fecal bacteria such that conjugated BAs levels are significantly higher and secondary BAs are lower in active IBD patients (157). These BA differences were recently demonstrated to impact PXR and FXR activation consequently reducing CYP3A4 activity and reducing FGF19 expression (158). Differences in the ratio of primary to secondary BAs have also been observed in subjects with ulcerative colitis versus non-IBD controls (159). Likewise, patients with Crohn’s disease exhibited significantly higher bile UDCA and decreased BA pool sizes (160).

Cancer

Colorectal cancer (CRC) is the third most common cancer diagnosis and the fourth leading cause of cancer-related death worldwide (161). Obesity, and in particular the increased intake of dietary fat (162) and the decreased intake of fiber (163), is associated with increased risk of CRC. Gut dysbiosis and secondary BAs appear to drive proinflammatory responses and epithelial cell transformation, leading to cancer or may be permissive for engraftment of opportunistic allogenic species that are keystone pathogens. In support of this, genetically predisposed mice developed fewer tumors under germ-free conditions than conventionally raised mice (164). Alterations in both fecal microbiota (165, 166) and fecal BAs (167, 168) are associated with CRC. While enhanced DCA and LCA as well as increased levels of Fusobacterium and Campylobacter species are elevated in CRC (169, 170) and in some studies with resistance to CRC chemotherapy (171), it remains unclear if such associations are causal or of consequence. Recent evidence showing that intestinal FXR knockout (KO) mice have increased susceptibility to intestinal cancer (172), particularly those cancers associated with inflammation (173), and that BAs promote protumorigenic phenotypes (174) provides fertile ground for further examining the contributions of BAs to CRC.

Neurologic Disorders

The emergence of gut bacteria and bacterial metabolites as functional modifiers of the central nervous system suggest an equally important role for endosymbiotic bacteria and bile acids in host regulation at a higher level. Gut dysbiosis in a 5xFAD mouse model of Alzheimer’s disease increased C/EBPβ/AEP signaling in the brain concomitant with age-related progression of disease severity and antibiotic treatment diminished this signaling, attenuated amyloidogenic processes, and improved cognitive functions (175). These effects were reversed with antibiotic administration. Autistic individuals exhibit maldigestion and malabsorption disorders with symptoms suggesting impaired carbohydrate digestion. Here, restoring the relative deficiency of Prevotella (176) or conjugated BAs (177) may afford therapeutic relief. Finally, dysregulated bile acid metabolism is also a component of multiple sclerosis (MS) and supplementation with tauroursodeoxycholic acid prevents astrocyte and microglia polarization and ameliorated neuropathology in animal models of MS.

Conclusions and Perspectives

The evidence reviewed here indicates that BA composition and gut bacteria are tightly coupled and together play key etiologic roles in regulating host metabolism. Experiments in rodent model systems offer important mechanistic clues about the metabolic interplay between BAs and receptors; however, major differences in enzyme activity and therefore BA species between humans and mice often complicate clinical translations. The recent development of mice with humanized BA metabolism provides new opportunities to reexamine earlier findings where observations in rats and mice occurred in tandem with changes in rodent-specific BAs, such as MCAs, complicating clinical translation. Underscoring this are recent findings in mice with a humanized BA profile showing that despite very different BA compositions, the build of the commensal microbiome was largely the same (16). While additional functional studies are needed to better understand such differences, these observations suggest that BA composition and gut bacteria may not be inextricably linked.