Over a hundred trillion microbial organisms, mostly bacteria, inhabit the human colon and have co-evolved with their hosts to have diverse, but primarily beneficial, functions. They scavenge additional calories by fermenting non-digestible foods, secrete vitamins and ensure normal physiological development. A plethora of studies have demonstrated that microbes have the capacity to modulate host physiological homeostasis and have been linked with cognitive disorders such as anxiety, depression, Parkinson’s disease, autism spectrum disorder and schizophrenia (1, 2), in addition to the development of inflammatory bowel disease (3) and irritable bowel syndrome (IBS) (4). Several direct and indirect mechanisms of cross-barrier communication have been proposed, where microbial, endocrine or immune factors are posited as inter-kingdom signaling molecules (5–7). In this review however, we will focus on bile acids, liver-derived bioactive host molecules that exhibit an interdependency with resident intestinal bacteria.

Hepatocytes synthesize and secrete the primary bile acids, cholic acid (CA) and chenodeoxycholic acid (CDCA), into the duodenum via the biliary ductal system. Comprising about half of the total solutes in bile, their amphipathic structure facilitates emulsification and subsequent digestion and absorption of dietary lipids being emptied from the stomach (8). The enterohepatic circuit is an extremely efficient method whereby ~95% of bile acids are reabsorbed in the terminal ileum and returned via the portal vein to the liver, where they are taken up by hepatocytes and re-secreted into the bile ducts. Just 5% of bile acids escape reuptake and spill over into the colon, the intestinal site with the highest density of microbes. A dynamic, symbiotic relationship exists between microbes and bile acids ( Figure 1 ), resulting in a great diversity of microbially-modified secondary bile acids (9). Bile salt hydrolaze (BSH)-containing bacteria hydrolyze and deconjugate taurine or glycine from the sterol core of the primary bile acids, facilitating further passive reabsorption in the colon. This process also enables further microbially-mediated transformations to produce a plethora of secondary bile acids, including deoxycholic acid (DCA) and lithocholic acid (LCA). This results in an enrichment of secondary bile acids in the colon, where their chemical characteristics help shape bacterial profiles within the microbiome (10). Given that many different cell types express bile acid receptors (11–14) and both active and passive transport of bile acids across the gut barrier and subsequent uptake into the portal vein distributes bile acids to extra-intestinal peripheral organs, bile acids are classified as bioactive signaling molecules (15). We have examined the potential role of bile acids to modify host physiological homeostasis, with a focus on gut-brain axis signaling and their potential role in IBS-related bowel dysfunction.

Biliary secretions are comprised of bile salts, pigments, water, and waste products, including bilirubin and excess cholesterol. In humans, the primary bile acids, CA and CDCA are synthesized and conjugated with either glycine or taurine (16) and stored, concentrated and acidified in the gall bladder prior to being released into the duodenum, along with pancreatic enzyme secretions. Bile acids comprise a family of closely related acidic sterols with similar, but not identical chemical structures and detergent performance. Conjugation of bile acids alters their pKa meaning bile salts are almost always in a protonated form in the duodenum, thereby restricting their passive movement through the small intestinal epithelial barrier. Apical sodium-dependent bile salt (ABST) transporters in the distal ileum facilitate active transport across the gut barrier prior to their return to the liver via the portal vein. The ~ 5% of bile acids which reach the colon, are either reabsorbed via passive diffusion or lost in the feces (17).

Bile acid metabolism is influenced by bacteria with BSH activity, a property that is unique to gut-residing bacteria and may have evolved through host-driven selection (18). An incentive for bacterial participation in this interaction may be the acquisition of the glycine and taurine conjugates for their own metabolic needs, in addition to the disposal of excess electrons generated during fermentation processes (19). Moreover, tolerance of bile may confer an advantage to these microbes in terms of their ability to colonize gut regions (20). In addition to acting as a nutrient source for intestinal bacteria and providing environmental cues, bile acids are also noted for their antimicrobial properties either through direct cytotoxicity (21) or by stimulating innate immune mechanisms (22). This constrains small intestinal bacterial overgrowth (23). Diarrhea resulting from exposure to high levels of bile acids in the colon, may be part of the innate immune response to protect the intestinal epithelium from cytotoxic bile acids, such as LCA (24).

In a bi-directional arrangement, bacterial enzymes chemically modify bile acids, and in turn, bile acids modify gut bacterial profiles. Cleavage of amino acid side chains on glycine- or taurine-conjugated primary bile acids changes their physiochemical properties, such that they are more lipophilic and susceptible to further modification by bacteria, including 7α-dehydroxylation, dehydrogenation and epimerization (21, 25, 26). Secondary bile acids, such as DCA and LCA, may undergo further modification, including sulphation and glucuronidation, imparting changes in their lipophilicity and hydrophilicity. Moreover, the potency of secondary bile acids for bile acid receptors differs from primary bile acids (23) and the amphipathic nature of bile acids can directly affect the physical properties of cellular lipid membranes, thereby modifying cell signal transduction (27). This has consequences for local signaling and gut homeostasis (28).

Given the diversity of bile acids identified in mammals and the variety of bile acid receptors with variable binding affinities and response potencies, it is no surprise that the bioactive functions of bile acids differ significantly. Farnesoid X (FXR) is the most extensively studied nuclear bile acid receptor, for which CDCA is the most potent agonist (15), however there are also other bile acid-sensitive nuclear receptors, such as pregnane X (PXR) and vitamin D receptors (VDR), which are expressed on several different cells types (11–14, 29–31). To activate nuclear bile acid receptors, bile acids must cross cellular and nuclear lipid bilayers, a process that can occur by passive diffusion or be facilitated by active transport (15, 32, 33). FXR is translocated to the cell nucleus upon activation, where it forms a heterodimer with retinoid X receptor and binds to hormone response elements present on DNA (34), instigating changes in gene regulation. One of the primary functions of FXR activation by bile acids is the feedback inhibition of bile acid synthesis through the suppression of CYP7A1, the rate-limiting enzyme in the classical bile acid synthesis pathway. Mice lacking FXR exhibit bile acid dyshomeostasis and metabolic disorders (35).

Other nuclear receptors may also be activated by bile acids, although higher concentrations are often required, indicating that they may be more relevant under pathological conditions. PXR is a promiscuous transcription factor important in the metabolism of xenobiotics. It is stimulated by pharmacological reagents, environmental toxicants, bacterial metabolites and the secondary bile acid, LCA. Consistent with a role under pathological conditions, activation of PXR downregulates bacteria which metabolize bile acids and thereby modify bile acid homeostasis (36). In addition to 1,25-dihydroxy vitamin D₃ and certain dietary ligands, LCA acts as endogenous ligands for VDR (37), a classic nuclear receptor that mediates several biological functions mainly related to calcium homeostasis and bone maintenance. Similar to FXR, ligand-induced activation of VDR facilitates interaction with retinoid X receptor and DNA binding (37). VDR is highly expressed throughout the digestive tract, where it has been found to induce expression of CYP3A and the multidrug resistance-associated protein-3 (37, 38), two enzymes known to metabolize toxic LCA, preventing its re-uptake and ensuring excretion in the feces (39).

Bile acids also bind to membrane expressed G-Protein-Coupled Bile Acid Receptor 1 (GPBAR1), also called Takeda G-protein-coupled receptor 5 (TGR5) (40). TGR5 is a member of the G-protein-coupled receptor family, which promotes cyclic adenosine monophosphate (cAMP) synthesis by adenylate cyclase upon activation. This subsequently activates the protein kinase-A pathway, thereby inducing the expression of its target genes (40). LCA is the most potent natural agonist of TGR5, which is expressed at high levels in the liver and intestinal tissue (40), but is also found in many other tissue types. Both conjugated and unconjugated bile acids bind to TGR5, with secondary bile acids, LCA and DCA being most potent (40). Functionally, TGR5 activation is associated with glucose metabolism, neuronal function, immune system control and liver regeneration (41). Other membrane receptors such as sphingosine 1-phosphate receptor (S1PR2) (42) and fibronectin receptor (α5β1 integrin) (43) are also activated by bile acids to stimulate intracellular signaling. Cytosolic ileal lipid binding proteins bind to intracellular bile acids, shuttling them to heteromeric OSTα-OSTβ transporters, which efficiently export them to the portal circulation. To a lesser extent, multidrug resistance-associated protein-3 basolaterally exports native and modified (glucuronidated or sulphated) bile acids from the enterocyte (44).

IBS is a clinically diverse disorder, with a multifactorial etiology. Global prevalence varies from ~1% to more than 45%, with between 5-10% reported for Europe, the United States and China (45). IBS is the most widespread gastrointestinal disorder in the western world (46). Characterized by chronic, recurrent visceral pain and discomfort, individuals with IBS can be categorized according to predominant bowel habits. Subtypes include IBS with constipation (IBS-C), IBS with diarrhea (IBS-D), mixed or alternating IBS and unsubtyped phenotypes (46). In addition to genetic, epigenetic (47), immunological (48), gender differences (49) and food hypersensitivity (50, 51) being reported in individuals with IBS, an increased prevalence of adverse life events and comorbid mood disorders such as anxiety, depression and somatoform disorders (52, 53) are also common. It is generally accepted that dysfunction of the bi-directional gut-brain signaling axis contributes to symptom manifestation (54, 55). Indeed, chronic activation of the hypothalamic-pituitary-adrenal (HPA) stress axis has been identified in individuals with IBS (52, 56).

In a number of clinical studies, bile acid dyshomeostasis has been detected in individuals with IBS (summarized in Table 1 ). It has consistently been reported that individuals with diarrhea-predominant IBS have elevated concentrations of fecal primary bile acids (57–60, 62, 63). Changes in bile acid profiles were also linked with IBS-D symptoms, such as the defecation frequency (57, 58, 61, 62) and abdominal pain (60, 62, 63). The link with IBS-C is not as strong, although fecal LCA was decreased in this subset of individuals (58). Deconjugated bile acids can drive phylum level shifts, increasing firmicutes and decreasing bacteroidetes (64). Individuals with IBS have an altered microbiome, where the ratio of fecal firmicutes to bacteroidetes is increased (65) and changes in the gut microbiome (66, 67) are important contributors to the pathophysiology of IBS. Several studies have examined microbial profiles and bile acid pools in IBS and found that bacteria with functions in bile acid transformation were modified in IBS-D patients (57). Others detected distinct changes in bacterial profiles. In IBS-D, E. coli (60) and clostridia-rich microbiota were elevated and associated with excessive bile acid secretion (61), whereas the abundance of ruminococcaceae was decreased (62).

In health, specialized innate and adaptive immune mechanisms are important in priming the gut against possible attack from luminal pathogens. An intact epithelial barrier and primed immune response excludes both commensal and non-commensal bacteria, restricting them to the external environment of the gut lumen, although it has been reported that the presence of bacterial products in the lamina propria is actually important for maintaining homeostasis in the enteric nervous system (68). However, interoceptive signaling relating to the luminal environment of the intestines are reported to the central nervous system (CNS) (69), thus, an intrinsic cross-barrier signaling mechanism would enable signaling between luminal factors and host physiological systems.

Colonic exposure to excess bile acids, which may be due to loss of bile acid transporters in the ileum causing bile acid malabsorption (124), overproduction of bile acids, or as a secondary consequence of gastrointestinal disease, has been linked to increased intestinal secretion and motility. Bile acid malabsorption typically results in chronic watery diarrhea, a symptom also characteristic of IBS-D, although the selenium-homocholic acid taurine test (Se-HCAT) test, which detects increased colonic bile acid exposure can differentiate between the two disorders (125). Fecal bile acids are raised in ~25% of individuals with IBS-D (126) resulting in accelerated colonic transit, which is linked with diarrhea and visceral pain sensitivity. Moreover, colestipol treatment, which binds bile acids and prevents reabsorption in the ileum, improved IBS symptoms (127).

Research into the etiology of IBS recognizes the complexity of this multifactorial and heterogenous bowel disorder. There is growing evidence to support a role for bile acids in the pathophysiology of IBS, through interactions with the microbiome and host sensory and/or immune cells or through direct actions on the peripheral and central nervous system ( Figure 2 ). The perfunctory actions of bile acids as detergents in the small intestine belie the complex functions instilled in these bioactive signaling molecules. The bidirectional relationship with gut microbiota impacts on microbial profiles and on the bile acid pool itself. The striking pro-secretory and prokinetic actions of bile acids on colonic function are consistent with the manifestation of IBS-D symptoms, whereas reduction in exposure to bile acids, though less researched, is more consistent with decreased gut secretion and transit, as presented in individuals with IBS-C. Elevated levels of excreted primary bile acids have consistently been detected in individuals with IBS-D and a growing number of studies have linked changes in fecal and serum bile acids with IBS symptomology, and changes in bacterial profiles with specific links to bacteria with bile acid transformation functionality ( Table 1 ).

Mechanistically, bile acid receptors are expressed on intrinsic and extrinsic nerves, which could facilitate direct neurally-mediated changes in gut function. Moreover, when bile acids are at supraphysiological levels, they can breach the blood brain barrier to modify the HPA axis, which in turn, can modulate intestinal function and luminal microbes. However, bile acid receptors are also detected on enteroendocrine and immune cells, which could both act as signal transducing intermediaries, secreting factors which subsequently modify colonic activity either through direct actions or by modulating neural regulation of the gut. Further complexity lies in the variability of responses evoked by conjugated or unconjugated, primary or secondary bile acids. As bile acids have emerged as effectors in microbe-host signaling and can directly and indirectly modulate gut homeostasis, these bioactive molecules should not be overlooked as the pathophysiology of IBS is elucidated. Indeed, interventions to modify colonic exposure to bile acids could reveal effective therapeutic options for this functional bowel disorder.

RD, QX, and DO’M prepared this review together. All authors contributed to the article and approved the submitted version.

DO’M is a funded investigator in APC Microbiome Ireland, which is supported by Science Foundation Ireland [Grant SFI/12/RC/2273]. QX is supported by CSC, PR of China.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The reviewer VC declared a shared affiliation with the authors to the handling editor at time of review.

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