Amelioration of Colitis by a Gut Bacterial Consortium Producing Anti-Inflammatory Secondary Bile Acids

Abstract

The Integrative Human Microbiome Project and other cohort studies have indicated that inflammatory bowel disease is accompanied by dysbiosis of gut microbiota, decreased production of secondary bile acids, and increased levels of primary bile acids. Secondary bile acids, such as ursodeoxycholic acid (UDCA) and lithocholic acid (LCA), have been reported to be anti-inflammatory, yet it remains to be studied whether introducing selected bacteria strains to restore bile acid metabolism of the gut microbiome can alleviate intestinal inflammation. In this study, we screened human gut bacterial strains for bile acid metabolism and designed a consortium of three species, including Clostridium AP sp000509125, Bacteroides ovatus, and Eubacterium limosum, and named it BAC (bile acid consortium). We showed that the three-strain gut bacterial consortium BAC is capable of converting conjugated primary bile acids taurochenodeoxycholic acid and glycochenodeoxycholic acid to secondary bile acids UDCA and LCA in vitro. Oral gavage treatment with BAC in mice resulted in protective effects against dextran sulfate sodium (DSS)-induced colitis, including reduced weight loss and increased colon length. Furthermore, BAC treatment increased the fecal level of bile acids, including UDCA and LCA. BAC treatment enhanced intestinal barrier function, which may be attributed to the increased activation of the bile acid receptor TGR5 by secondary bile acids. Finally, we examined the remodeling of gut microbiota by BAC treatment. Taken together, the three-strain gut bacterial consortium BAC restored the dysregulated bile acid metabolism and alleviated DSS-induced colitis. Our study provides a proof-of-concept demonstration that a rationally designed bacterial consortium can reshape the metabolism of the gut microbiome to treat diseases. IMPORTANCE Secondary bile acids have been reported to be anti-inflammatory, yet it remains to be studied whether introducing selected bacteria strains to restore bile acid metabolism of the gut microbiome can alleviate intestinal inflammation. To address this gap, we designed a consortium of human gut bacterial strains based on their metabolic capacity to produce secondary bile acids UDCA and LCA, and we evaluated the efficacy of single bacterial strains and the bacterial consortium in treating the murine colitis model. We found that oral gavage of the bacterial consortium to mice restored secondary bile acid metabolism to increase levels of UDCA and LCA, which induced the activation of TGR5 to improve gut-barrier integrity and reduced the inflammation in murine colitis. Overall, our study demonstrates that rationally designed bacterial consortia can reshape the metabolism of the gut microbiome and provides novel insights into the application of live biotherapeutics for treating IBD.

Keywords: bacterial consortium; colitis; gut microbiome; metabolomics; secondary bile acids; targeted metabolomics.

FIG 1

Bioinformatics analysis and experimental validation of bile acid metabolism of human gut bacterial strains. (a) Homology-based search in the whole-genome sequence of human gut bacterial strains identified genes related to bile acid metabolism, including BSH, 7α/βHSDH, and the bai operon. Red rectangles, E. limosum with 7α/βHSDH, Clostridium AP sp000509125, and Peptacetobacter with the complete bai operon. (b) B. ovatus converts TCDCA and GCDCA into CDCA. (c) E. limosum converts CDCA into UDCA. (d) Clostridium AP sp000509125 converts CDCA into LCA. (e) The three-strain consortium BAC (B. ovatus, E. limosum, and Clostridium AP sp000509125) converts TCDCA and GCDCA into UDCA and LCA. In our experimental validation, bacterial strains were incubated with TCDCA and GCDCA or CDCA for 60 h and then subjected to LC/MS description. G, glyco-; T, tauro-; UDCA, ursodeoxycholic acid; LCA, lithocholic acid; CDCA, chenodeoxycholic acid; B.O, Bacteroides ovatus; E.L, Eubacterium limosum; C.S, Clostridium AP sp000509125.

FIG 2

Three-strain consortium BAC ameliorated DSS-induced colitis. (a) Design of animal experiments. C57BL/6 mice were treated with 2% DSS (wt/vol) for 7 days before sacrifice. Bacterial strains (single strain or in consortium) were orally administered on a daily basis. For the DSS group, BHI medium was orally administered as a control. (b to f) Oral administration of BAC ameliorated weight loss during DSS treatment. (g) Animal weights on the last day of DSS treatment. (h) Representative colon images of sacrificed mice. (i) Oral administration of BAC restored colon length. (j and k) Colon inflammation and histopathology score. B.O, Bacteroides ovatus; E.L, Eubacterium limosum; C.S, Clostridium AP sp000509125. The mean and standard error of the mean (SEM) of each group are shown (n = 5 to 8 mice). Each treatment group was compared with the DSS group using a one-way ANOVA (g, i, and k) or two-way ANOVA (b, c, d, e, and f) followed by the Bonferroni post hoc test. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.

FIG 3

Treatment of three-strain consortium BAC increased secondary bile acids in mouse fecal samples. Targeted metabolomic analysis of unconjugated bile acids (a) and conjugated bile acids (b). The mean and SEM of each group are shown (n = 8 mice). Two-tailed Student's t test (or Mann-Whitney test) was used. *, P < 0.05; **, P < 0.01.

FIG 4

Three-strain consortium BAC restored gut barrier integrity in DSS-induced colitis. (a-e) Gene expression of TGR5 (a membrane receptor for bile acids), tight junction proteins ZO-1, Claudin-1, Occludin, and IL-10. Gene expression levels in colon tissue were assayed by qPCR. (f) FITC-dextran assay indicated that BAC treatment decreased intestinal paracellular permeability (i.e., restoration of gut barrier integrity). The mean and SEM of each group are shown (DSS group: n = 5 mice; DSS+BAC group: n = 7 mice). Two-tailed Student's t test (or Mann-Whitney test), *, P < 0.05, **, P < 0.01.

FIG 5

Three-strain consortium BAC reshaped gut microbiota in DSS-induced colitis mice. (a) PCoA of the murine gut microbiota of three different groups. (b) Compositional profile of murine gut microbiota at the species level. (c) Bacterial taxa identified as differentially abundant between the untreated group (DSS) and the BAC treatment group (DSS + BAC) by LEfSe. Green indicates bacterial taxa whose abundance was higher in the DSS + BAC group; red indicates otherwise. (d to g) The relative abundance of bacterial species of each group was compared with DSS group (n = 7), using a one-way ANOVA followed by the Bonferroni post hoc test. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.