Biogeography of microbial bile acid transformations along the murine gut

Bile acids, which are synthesized from cholesterol by the liver, are chemically transformed along the intestinal tract by the gut microbiota, and the products of these transformations signal through host receptors, affecting overall host health. These transformations include bile acid deconjugation, oxidation, and 7 alpha-dehydroxylation. An understanding of the biogeography of bile acid transformations in the gut is critical because deconjugation is a prerequisite for 7 alpha-dehydroxylation and because most gut microorganisms harbor bile acid transformation capacity. Here, we used a coupled metabolomic and metaproteomic approach to probe in vivo activity of the gut microbial community in a gnotobiotic mouse model. Results revealed the involvement of Clostridium scindens in 7 alpha-dehydroxylation, of the genera Muribaculum and Bacteroides in deconjugation, and of six additional organisms in oxidation (the genera Clostridium, Muribaculum, Bacteroides, Bifidobacterium, Acutalibacter, and Akkermansia). Furthermore, the bile acid profile in mice with a more complex microbiota, a dysbiosed microbiota, or no microbiota was considered. For instance, conventional mice harbor a large diversity of bile acids, but treatment with an antibiotic such as clindamycin results in the complete inhibition of 7 alpha-dehydroxylation, underscoring the strong inhibition of organisms that are capable of carrying out this process by this compound. Finally, a comparison of the hepatic bile acid pool size as a function of microbiota revealed that a reduced microbiota affects host signaling but not necessarily bile acid synthesis. In this study, bile acid transformations were mapped to the associated active microorganisms, offering a systematic characterization of the relationship between microbiota and bile acid composition.

Functional intestinal bile acid 7-alpha-dehydroxylation by Clostridium scindens associated with protection from C. difficile infection in a gnotobiotic mouse model

Rizlan Bernier-Latmani, Lyne Desharnais, Laure Menin

Bile acids, important mediators of lipid absorption, also act as hormone-like regulators and as antimicrobial molecules. In all these functions their potency is modulated by a variety of chemical modifications catalyzed by bacteria of the healthy gut microbiota, generating a complex variety of secondary bile acids. Intestinal commensal organisms are well adapted to normal concentrations of bile acids in the gut. In contrast, physiological concentrations of the various intestinal bile acid species play an important role in the resistance to intestinal colonization by pathogens such as Clostridium difficile. Antibiotic therapy can perturb the gut microbiota and thereby impair the production of protective secondary bile acids. The most important bile acid transformation is 7 alpha-dehydroxylation, producing deoxycholic acid (DCA) and lithocholic acid (LCA). The enzymatic pathway carrying out 7 alpha-dehydroxylation is restricted to a narrow phylogenetic group of commensal bacteria, the best-characterized of which is Clostridium scindens. Like many other intestinal commensal species, 7 alpha-dehydroxylating bacteria are understudied in vivo. Conventional animals contain variable and uncharacterized indigenous 7 alpha-dehydroxylating organisms that cannot be selectively removed, making controlled colonization with a specific strain in the context of an undisturbed microbiota unfeasible. In the present study, we used a recently established, standardized gnotobiotic mouse model that is stably associated with a simplified murine 12-species "oligo-mouse microbiota" (Oligo-MM12). It is representative of the major murine intestinal bacterial phyla, but is deficient for 7 alpha-dehydroxylation. We find that the Oligo-MM12 consortium carries out bile acid deconjugation, a prerequisite for 7 alpha-dehydroxylation, and confers no resistance to C. difficile infection (CDI). Amendment of Oligo-MM12 with C. scindens normalized the large intestinal bile acid composition by reconstituting Ty-dehydroxylation. These changes had only minor effects on the composition of the native Oligo-MM12, but significantly decreased early large intestinal C. difficile colonization and pathogenesis. The delayed pathogenesis of C. difficile in C. scindens-colonized mice was associated with breakdown of cecal microbial bile acid transformation.

Frontiers Media Sa2016

Biogeography and biochemistry of bile acid 7-dehydroxylation in the mammalian gut

Solenne Anne Marie Marion

Bile acids (BAs) are small molecules synthesized by the host and chemically modified by the microorganisms inhabiting the intestinal tract. The microbial transformation of BAs in the gut is critical to BA-mediated signaling as it modifies their amount and affinity for specific BA receptors. Bile acid 7-dehydroxylating bacteria are intestinal commensals of particular importance as they catalyze the dehydroxylation of liver-derived (primary) bile acids at the C7 position (i.e., 7-dehydroxylation) and produce secondary bile acids. One of the major receptors for secondary BAs is Takeda G-protein receptor 5 (TGR5), and it is associated with regulation of energy expenditure and glucose management, protection from liver steatosis and inflammation. In addition, 7-dehydroxylated bile acids are also associated with protection from infection by specific intestinal pathogens (i.e., Clostridioides difficile). Thus, through their action on primary BAs, 7-dehydroxylating (7-DH-ing) bacteria play an important role in health promotion and in the functioning of major physiological processes in the body such as insulin secretion, thermogenesis and immune responses. Despite these potentially important roles in the mammalian host, bile acid 7-dehydroxylating bacteria are poorly studied and much remains to be deciphered regarding their metabolism, diversity, abundance in the gut, and colonization dynamics in the host. Here, we use Clostridium scindens, as model organism to study bile acid 7-dehydroxylation in vitro and in gnotobiotic mice. We found that C. scindens metabolize only human primary bile acids (CA and CDCA). We uncovered the formation of a novel intermediate during CA 7-dehydroxylation by C. scindens in vitro: 12-oxoLCA. In vivo, using NanoSIMS and metabolomic analysis, we demonstrated that the large intestine constitutes C. scindens primary ecological niche in gnotobiotic mice. Following up on the discovery of the 12oxoLCA, we hypothesized the existence of another 7-dehydroxylation pathway for cholic acid. We postulated that it may involve the B and C rings of the steroid structure and may entail the oxidation/reduction of the C12- hydroxyl group. Thus, it was dubbed the putative vertical pathway. Conducting in vitro enzymatic assays with purified enzymes, we confirmed the existence of this novel vertical biosynthetic 7-dehydroxylation pathway for cholic acid, the most abundant primary bile acid in humans, and identified the core of enzymes necessary and sufficient for CA 7-dehydroxylation. Furthermore, we used a coupled metabolomic and metaproteomic approach to probe in vivo activity of the gut microbial community in a gnotobiotic mouse model. Additionnally, we also considered the bile acid profile in mice with more complex microbiota or with no microbiota. By comparing the bile acid profile of the different mice models along with expression of key genes of bile acid synthesis, we emphasized the profound influence of the gut microbial community on BA pool homeostasis. Altogether, our data provides a significant contribution to our collective understanding of the microbiology of bile acid 7-dehydroxylating bacteria, a group of gut commensals highly relevant to host health but that remains poorly characterized. The discovery of a novel 7-dehydroxylation pathway is a major scientific achievement of this thesis.

EPFL2020

Impaired expression of peroxisome proliferator-activated receptor gamma in ulcerative colitis

Johan Auwerx, Mehdi Karoui

BACKGROUND & AIMS: The peroxisome proliferator-activated receptor gamma (PPAR gamma) has been proposed as a key inhibitor of colitis through attenuation of nuclear factor kappa B (NF-kappa B) activity. In inflammatory bowel disease, activators of NF-kappa B, including the bacterial receptor toll-like receptor (TLR)4, are elevated. We aimed to determine the role of bacteria and their signaling effects on PPAR gamma regulation during inflammatory bowel disease (IBD). METHODS: TLR4-transfected Caco-2 cells, germ-free mice, and mice devoid of functional TLR4 (Lps(d)/Lps(d) mice) were assessed for their expression of PPAR gamma in colonic tissues in the presence or absence of bacteria. This nuclear receptor expression and the polymorphisms of gene also were assessed in patients with Crohn's disease (CD) and ulcerative colitis (UC), 2 inflammatory bowel diseases resulting from an abnormal immune response to bacterial antigens. RESULTS: TLR4-transfected Caco-2 cells showed that the TLR4 signaling pathway elevated PPAR gamma expression and a PPAR gamma-dependent reporter in an I kappa kappa beta dependent fashion. Murine and human intestinal flora induced PPAR gamma expression in colonic epithelial cells of control mice. PPAR gamma expression was significantly higher in the colon of control compared with Lps(d)/Lps(d) mice. Although PPAR gamma levels appeared normal in patients with CD and controls, UC patients displayed a reduced expression of PPAR gamma confined to colonic epithelial cells, without any mutation in the PPAR gamma gene. CONCLUSIONS: These data showed that the commensal intestinal flora affects the expression of PPAR gamma and that PPAR gamma expression is considerably impaired in patients with UC.