Who wants seconds? The gut bacteria-derived secondary bile acid isoDCA induces regulatory T cells

Our intestinal (or gut) microbiome—which consists of trillions of microorganisms living within our intestines, their “functional gene capacity”, and the metabolites they produce—has been shown to influence health and disease, and of particular interest to us here, the immune system1.

Previous studies* have focused on the effect of microbial metabolites on two immune cell types, dendritic cells (DCs) and regulatory T cells (Tregs). Tregs are a type of CD4+ T cell especially important in regulating immune responses. Defects in Treg responses have serious implications in immune tolerance and autoimmunity. Tregs can’t recognize potentially harmful material on their own, however. This is the job of DCs that process different substances encountered in the body and present them to the Tregs. Better understanding these interactions might help us fine-tune the immune system to fight disease.

A newly published paperfrom the Rudensky group2at the Sloan Kettering Institute shows that a new group of microbial metabolites, secondary bile acids, influences DCs and Tregs. Bile acids, synthesized from cholesterol, help with lipid digestion and absorption3. The liver makes primary bile acids, which are further converted by gut bacteria to secondary bile acids. In this paper, the authors asked whether secondary bile acids were able to modulate immune cell responses. They took a two-pronged approach: an in vitroassay and an in vivocolonization model. The assay—a DC-T cell co-culture—is used to test activation, proliferation, and cytokine production of T cells in different experimental conditions. To address the limitations of the in vitroapproach, they also colonized germ-free (microbe-free) mice with lab-engineered bacterial strains to test the effects of secondary bile acid production on gut immune cells. 

The DC-T cell assay they used involves combining mouse DCs and naïve CD4+ T cells. The authors added anti-CD3, TGF‑β, and IL-2 to create suboptimal Treg-inducing conditions and then tested, one-by-one, the effects of selected secondary bile acids most commonly found in either the human or mouse gut. They found that two secondary bile acids, isoDCA and ω-MCA, were able to induce Tregs in vitro. The authors focus on isoDCA for its well-studied biosynthesis and its abundant presence in the gut. Using cells from mutant mice with cell-specific deletions in the bile acid-sensing farnesoid X receptor (FXR), they found that isoDCA binds to FXR on DCs—but not CD4+ T cells—to induce Tregs in culture. DCs exposed to isoDCA showed transcriptional downregulation of genes involved in antigen processing and presentation, as well as those involved in production of pro-inflammatory cytokines. However, they did note that isoDCA could potentially trigger other signaling pathways in the cell outside of FXR.

The authors then focused on the role of isoDCA production by gut microbes in vivo. They took the enzymatic machinery for conversion of isoDCA normally found in bacteria such as Ruminococcus gnavusand put it into a more genetically-tractable bacteria, Bacteroides thetaiotaomicron(B. theta). The authors also engineered a strain that has a mutation in the enzyme, so that it won’t function. They then colonized mice raised in germ-free conditions with either isoDCA-producing or non isoDCA-producing B. thetaand found that both strains resulted in similar increases of Tregs in the large intestine. However, the proportion of those Tregs that express the transcription factor RORγtis increased significantly with isoDCA-producing B. theta. RORγt+ Tregs are especially important in regulating intestinal inflammation4. This phenotype is conserved regardless of the three different Bacteroides species used and activity is dependent on the presence of another bacteria, Clostridium scindens, which catalyzes the first step of bile acid conversion. Finally, by using mice with known defects in peripheral (but not thymic) Treg induction, the authors found that Tregs were generated de novoin local tissue by the presence of isoDCA.

One interesting future direction is whether combinatorial effects of different secondary bile acids from the pool they studied would skew the Treg phenotype one way or another, as the in vivodata from the study focused on colonization with one strain that expresses only isoDCA. The gut environment, after all, is teeming with diverse groups of microbes. These may render the role of Treg-promoting secondary bile acids trivial in the context of a more complex immune response. It will also be interesting to see whether isoDCA could directly change the transcriptional landscape of the gut Tregs themselves and whether or not these had increased suppressive capacity or could produce more IL-10 in the context of gut inflammation. 

In summary, the authors found a novel mechanism in which the secondary bile acid isoDCA contributes to the generation of Tregs. They were able to show that isoDCA promotes this phenotype in culture through engagement of DC-specific farnesoid X receptor and that DCs exposed to isoDCA had a more “anti-inflammatory” phenotype. The authors also showed that isoDCA-producingBacteroidesincreased induction of the RORγt+ subset of Tregs in the large intestine.The finding that a gut bacteria-derived secondary bile acid plays a role in Treg induction is exciting, as this may have implications in the resolution of gut inflammation in conditions such as IBD, for which alterations in bile acid levels have been discovered3. 

 By Geil Merana

*Relevant previous studies

·      The microbial surface molecule, polysaccharide A (PSA) from Bacteroidesfragilis, promotes induction of gut Tregs5. 

·      Bacterial-derived metabolites or products, such as short chain fatty acids made by Clostridia species, suppress pathways involved in production of pro-inflammatory cytokines in dendritic cells (DCs), leading to gut Treg induction6. 

References

1.     Durack J, Lynch SV. The gut microbiome: Relationships with disease and opportunities for therapy. J Exp Med. 2019;216(1):20–40. doi:10.1084/jem.20180448

2.     Campbell, C., McKenney, P.T., Konstantinovsky, D. et al. Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells. Nature (2020). https://doi.org/10.1038/s41586-020-2193-0

3.     Lavelle, A., Sokol, H. Gut microbiota-derived metabolites as key actors in inflammatory bowel disease. Nat Rev Gastroenterol Hepatol 17, 223–237 (2020). https://doi.org/10.1038/s41575-019-0258-z

4.     Sefik E, Geva-Zatorsky N, Oh S, et al. MUCOSAL IMMUNOLOGY. Individual intestinal symbionts induce a distinct population of RORγ⁺regulatory T cells. Science. 2015;349(6251):993‐997. doi:10.1126/science.aaa9420

5.     Round JL, Mazmanian SK. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A. 2010;107(27):12204–12209. doi:10.1073/pnas.0909122107

6.    Arpaia N, Campbell C, Fan X, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 2013;504(7480):451–455. doi:10.1038/nature12726