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Background  The farnesoid X receptor (FXR), a ligand-activated transcription factor belonging to the adopted orphan receptor, plays an important role in maintaining health of the liver and intestine. In this study, we identified individual bacterial strains that directly modulated the activation of intestinal FXR.    Methods  The FXR stimulatory potential of 38 bacterial strains was determined using a stable FXR reporter system derived from intestinal epithelial cells (IEC). The induction of FXR target genes by screened FXR stimulatory bacteria was determined by real-time PCR. In addition, a high fat diet (HFD)-induced obese mouse model was used to evaluate  in vivo  FXR stimulatory potential of bacterial metabolites screened in this study.    Results  A luciferase assay with the FXR reporter cell line demonstrated that the FXR-stimulatory activity of most bacterial cell samples was less than 2-fold. The culture supernatants of  Bacteroides dorei  and  Eubacterium limosum  induced FXR activity and selectively regulated FXR target expression in the FXR reporter system. Treatment with  B. dorei -derived metabolites strongly induced ileal bile acid binding protein ( IBABP ) (8.4-fold) and organic solute transporter ( OST ) α (3.1-fold) compared with  E. limosum -derived metabolites. Furthermore, administration of  B. dorei  derived metabolites showed significant reduction in body weight gain, and both two bacterial metabolites reduced liver weight in obese mice compared to PBS-treated controls. Administration of each bacterial metabolites improved in serum levels of obesity-related metabolic biochemical markers such as ALT, AST, total cholesterol, and triglyceride. Furthermore, two bacterial metabolites enhanced the  Fxr  gene expression in the intestine and liver, and ileal  Shp  gene expression tended to be increased by treatment with the metabolites derived from  B. dorei .    Conclusions   B. dorei  and  E. limosum  secreted the bioactive substances that directly stimulate FXR in the intestinal epithelial cells. Administration of these bacterial FXR-stimulatory metabolites improves the obesity phenotype including body weight gain, liver damage, lipid metabolism in DIO mice.    Electronic supplementary material  The online version of this article (doi:10.1186/s12986-015-0045-y) contains supplementary material, which is available to authorized users.

Bacterial metabolites directly modulate farnesoid X receptor activity