# A bile acid–GPBAR1 network supports anti-inflammatory and anti-fibrotic benefits of probiotics in colitis

**Authors:** Michele Biagioli, Cristina Di Giorgio, Silvia Marchianò, Benedetta Sensini, Ginevra Urbani, Eleonora Giannelli, Ginevra Lachi, Carmen Massa, Maria Rosaria Sette, Francesca Paniconi, Elva Morretta, Maria Chiara Monti, Angela Zampella, Eleonora Distrutti, Stefano Fiorucci

PMC · DOI: 10.1080/19490976.2026.2645125 · 2026-03-18

## TL;DR

A 9-strain probiotic helps reduce inflammation and fibrosis in chronic colitis by influencing bile acid signaling through GPBAR1.

## Contribution

A new 9-strain probiotic formulation shows anti-inflammatory and anti-fibrotic effects via bile acid-GPBAR1 signaling in chronic colitis.

## Key findings

- The 9-strain probiotic reduces inflammation and fibrosis in chronic colitis but not in acute colitis.
- The probiotic remodels microbiota and increases GPBAR1-agonist bile acids like 3-oxo-DCA.
- The anti-inflammatory effects of the probiotic are lost in mice lacking GPBAR1.

## Abstract

Intestinal fibrosis is a severe complication of Crohn's disease for which therapy remains suboptimal. Probiotics are widely used in the treatment of intestinal inflammation, but all major guidelines do not recommend in favor of their use, with the exception of an 8-strains bacterial formula, which is recommended for the treatment of pouch inflammation in ulcerative colitis. Using this 8-strains formulation as a comparator, we characterized a 9-strains probiotic formulation enriched with Lactobacillus rhamnosus and paracasei in a mouse model of intestinal inflammation and fibrosis. Our findings demonstrated that while both formulations exerted similar protective effects in acute colitis, only the 9-strains probiotic attenuates inflammation and fibrosis in chronic colitis. Mechanistically, we found that the 9-strains formulation remodeled the microbiota composition and the structure of microbiota-derived secondary bile acids, leading to the selective enrichment of those bile acids that act as GPBAR1 agonists, including 3-oxo-DCA, which in vitro directly attenuates activation of intestinal fibroblasts. Confirming the role of this pathway, feeding Gpbar1⁻/⁻ mice with 9-strains probiotic formulation abrogates its beneficial effects on inflammation and fibrosis. These findings highlight the importance of microbial metabolites in shaping probiotic efficacy and support the development of probiotic formulations that target host–microbiota interactions through bile acid signaling.

## Linked entities

- **Genes:** GPBAR1 (G protein-coupled bile acid receptor 1) [NCBI Gene 151306]
- **Diseases:** Crohn's disease (MONDO:0005011), colitis (MONDO:0005292), ulcerative colitis (MONDO:0005101)
- **Species:** Mus musculus (taxon 10090)

## Full-text entities

- **Genes:** Mrc1 (mannose receptor, C type 1) [NCBI Gene 17533] {aka CD206, MR}, S100a9 (S100 calcium binding protein A9 (calgranulin B)) [NCBI Gene 20202] {aka 60B8Ag, BEE22, Cagb, GAGB, L1Ag, MRP14}, CCL2 (C-C motif chemokine ligand 2) [NCBI Gene 6347] {aka GDCF-2, HC11, HSMCR30, MCAF, MCP-1, MCP1}, CDH1 (cadherin 1) [NCBI Gene 999] {aka Arc-1, BCDS1, CD324, CDHE, ECAD, LCAM}, Itgam (integrin alpha M) [NCBI Gene 16409] {aka CD11b/CD18, CR3, CR3A, Cd11b, F730045J24Rik, Ly-40}, Itga2 (integrin alpha 2) [NCBI Gene 16398] {aka CD49B, DX5, GPIa}, Ccl2 (C-C motif chemokine ligand 2) [NCBI Gene 20296] {aka HC11, JE, MCAF, MCP-1, MCP1, SMC-CF}, Osm (oncostatin M) [NCBI Gene 18413] {aka OncoM}, Ccl5 (C-C motif chemokine ligand 5) [NCBI Gene 20304] {aka MuRantes, RANTES, SISd, Scya5, TCP228}, Cnot7 (CCR4-NOT transcription complex, subunit 7) [NCBI Gene 18983] {aka CAF-1, Caf1, Pop2}, D9Mgc45e (DNA segment, Chr 9, MRC UK Mouse Genome Centre 45 expressed) [NCBI Gene 28134] {aka CD3}, Col3a1 (collagen, type III, alpha 1) [NCBI Gene 12825] {aka Col3a-1, Tsk-2, Tsk2}, Ahr (aryl-hydrocarbon receptor) [NCBI Gene 11622] {aka Ah, Ahh, Ahre, In, bHLHe76}, Col1a1 (collagen, type I, alpha 1) [NCBI Gene 12842] {aka Col1a-1, Cola-1, Cola1, Mov-13, Mov13}, Cd38 (CD38 antigen) [NCBI Gene 12494] {aka ADPRC 1, Cd38-rs1, I-19}, Il17a (interleukin 17A) [NCBI Gene 16171] {aka Ctla-8, Ctla8, IL-17, IL-17A, Il17}, Ptprc (protein tyrosine phosphatase receptor type C) [NCBI Gene 19264] {aka B220, CD45R, Cd45, L-CA, Ly-5, Lyt-4}, Cdh1 (cadherin 1) [NCBI Gene 12550] {aka ARC-1, E-cad, Ecad, L-CAM, UVO, Um}, Hprt1 (hypoxanthine phosphoribosyltransferase 1) [NCBI Gene 15452] {aka HPGRT, Hprt}, Tbp (TATA box binding protein) [NCBI Gene 21374] {aka GTF2D1, Gtf2d, SCA17, TFIID}, Nos2 (nitric oxide synthase 2, inducible) [NCBI Gene 18126] {aka MAC-NOS, NOS-II, Nos-2, Nos2a, i-NOS, iNOS}, HPRT1 (hypoxanthine phosphoribosyltransferase 1) [NCBI Gene 3251] {aka HGPRT, HPRT}, POLR2A (RNA polymerase II subunit A) [NCBI Gene 5430] {aka NEDHIB, POLR2, POLRA, RPB1, RPBh1, RPO2}, ACTA1 (actin alpha 1, skeletal muscle) [NCBI Gene 58] {aka ACTA, ASMA, CFTD, CFTD1, CFTDM, CMYO2A}, Ctbp1 (C-terminal binding protein 1) [NCBI Gene 13016] {aka BARS, CtBP3/BARS, D4S115h, D5H4S115, D5H4S115E}, S100a8 (S100 calcium binding protein A8 (calgranulin A)) [NCBI Gene 20201] {aka 60B8Ag, B8Ag, CFAg, CP-10, Caga, MRP8}, Acta2 (actin alpha 2, smooth muscle, aorta) [NCBI Gene 11475] {aka 0610041G09Rik, Actvs, SMAalpha, SMalphaA, a-SMA, alphaSMA}, RXRA (retinoid X receptor alpha) [NCBI Gene 6256] {aka NR2B1, RXR-alpha, RXRalpha}, Cd4 (CD4 antigen) [NCBI Gene 12504] {aka L3T4, Ly-4}, Cxcl1 (C-X-C motif chemokine ligand 1) [NCBI Gene 14825] {aka Fsp, Gro1, KC, Mgsa, N51, Scyb1}, Ly6g (lymphocyte antigen 6 family member G) [NCBI Gene 546644] {aka Gr-1, Gr1, Ly-6G}, ISYNA1 (inositol-3-phosphate synthase 1) [NCBI Gene 51477] {aka INO1, INOS, IPS, IPS 1, IPS-1}, Polr2a (polymerase (RNA) II (DNA directed) polypeptide A) [NCBI Gene 20020] {aka 220kDa, Rpb1, Rpo2-1}, COL1A1 (collagen type I alpha 1 chain) [NCBI Gene 1277] {aka CAFYD, EDSARTH1, EDSC, OI1, OI2, OI3}, Il1b (interleukin 1 beta) [NCBI Gene 16176] {aka IL-1beta, Il-1b}, Gpbar1 (G protein-coupled bile acid receptor 1) [NCBI Gene 227289] {aka BG37, GPCR, GPR131, M-BAR, TGR5}, GPBAR1 (G protein-coupled bile acid receptor 1) [NCBI Gene 151306] {aka BG37, GPCR19, GPR131, M-BAR, TGR5}, PTPRC (protein tyrosine phosphatase receptor type C) [NCBI Gene 5788] {aka B220, CD45, CD45R, GP180, IMD105, L-CA}, Vdr (vitamin D (1,25-dihydroxyvitamin D3) receptor) [NCBI Gene 22337] {aka Nr1i1}, IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, COL3A1 (collagen type III alpha 1 chain) [NCBI Gene 1281] {aka EDS4A, EDSVASC, PMGEDSV}, Il6 (interleukin 6) [NCBI Gene 16193] {aka Il-6}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, HSPB2 (heat shock protein family B (small) member 2) [NCBI Gene 3316] {aka HSP27, Hs.78846, LOH11CR1K, MKBP}, NR1H4 (nuclear receptor subfamily 1 group H member 4) [NCBI Gene 9971] {aka BAR, FXR, HRR-1, HRR1, PFIC5, RIP14}, Tnf (tumor necrosis factor) [NCBI Gene 21926] {aka DIF, TNF-a, TNF-alpha, TNFSF2, TNFalpha, Tnfa}
- **Diseases:** pouchitis (MESH:D019449), CDAI (MESH:D003092), systemic (MESH:D015619), colorectal adenocarcinoma (MESH:D003110), immune dysregulation (OMIM:614878), intestinal dysbiosis (MESH:D064806), stenosis (MESH:D003251), immune dysfunction (MESH:D007154), proinflammatory cytokines (MESH:D000080424), inflammation (MESH:D007249), fistulas (MESH:D005402), colon damage (MESH:D003108), primary sclerosing cholangitis (MESH:D015209), epithelial adenocarcinoma (MESH:D009375), IBD (MESH:D015212), CD (MESH:D003424), weight loss (MESH:D015431), intestinal enterocolitis (MESH:D004760), UC (MESH:D003093), fibrosis (MESH:D005355), tissue (MESH:D017695), Intestinal fibrosis (MESH:D007410), fibrotic diseases (MESH:D004194)
- **Chemicals:** hematoxylin (MESH:D006416), CO2 (MESH:D002245), Tween 20 (MESH:D011136), pentadecanoic acid (MESH:C117025), CA (MESH:D019826), dextran sulfate sodium (MESH:D016264), LPS (MESH:D008070), steroids (MESH:D013256), alpha-muricholic acid (MESH:C004821), taurine (MESH:D013654), HCA (MESH:C010471), HCl (MESH:D006851), sodium citrate (MESH:D000077559), UDCA (MESH:D014580), SDS (MESH:D012967), eosin (MESH:D004801), bromophenol blue (MESH:D001978), DAPI (MESH:C007293), 3-oxo-CA (MESH:C017234), butyrate (MESH:D002087), PMA (MESH:D013755), lipids (MESH:D008055), oxo (MESH:C489337), SCFA (MESH:D005232), lithocholic acid (MESH:D008095), indoleacrylic acid (MESH:C001446), ammonium acetate (MESH:C018824), polyacrylamide (MESH:C016679), glycine (MESH:D005998), glycerol (MESH:D005990), tCA (MESH:D014238), H2O (MESH:D014867), 3-oxo-UDCA (-), paraffin (MESH:D010232), agarose (MESH:D012685), FA (MESH:D005492), cholesterol (MESH:D002784), DCA (MESH:D003840), sodium thiopental (MESH:D013874), CH3CN (MESH:C032159), formalin (MESH:D005557), streptomycin (MESH:D013307), BA (MESH:D001464), cysteine (MESH:D003545), CDCA (MESH:D002635), SYBR  Green (MESH:C098022), Bile acid (MESH:D001647), L-glutamine (MESH:D005973), PBS (MESH:D007854), amino acid (MESH:D000596), tDCA (MESH:D013657), H&amp;E (MESH:D006371), tHDCA (MESH:C083510), penicillin (MESH:D010406), methanol (MESH:D000432), methionine (MESH:D008715), fatty acid (MESH:D005227)
- **Species:** Bacteroides acidifaciens (species) [taxon 85831], Bifidobacterium animalis subsp. lactis (subspecies) [taxon 302911], Limosilactobacillus vaginalis (species) [taxon 1633], Bifidobacterium animalis (species) [taxon 28025], Lactococcus garvieae (species) [taxon 1363], Bifidobacterium pseudolongum (species) [taxon 1694], Homo sapiens (human, species) [taxon 9606], Streptococcus thermophilus (species) [taxon 1308], Ligilactobacillus murinus (species) [taxon 1622], Lactobacillus acidophilus (species) [taxon 1579], Lacticaseibacillus paracasei subsp. paracasei (subspecies) [taxon 47714], Clostridium (genus) [taxon 1485], Mediterraneibacter gnavus (species) [taxon 33038], Akkermansia muciniphila (species) [taxon 239935], Mus musculus (house mouse, species) [taxon 10090], Lactococcus lactis subsp. lactis (subspecies) [taxon 1360], Lacticaseibacillus rhamnosus (species) [taxon 47715], Eshraghiella crossota (species) [taxon 45851], Lactobacillus johnsonii (species) [taxon 33959], Lacticaseibacillus paracasei (species) [taxon 1597], Bifidobacterium breve (species) [taxon 1685], Lactiplantibacillus plantarum (species) [taxon 1590], Lactococcus lactis (species) [taxon 1358], Bacteria Latreille et al. 1825 (Bacteria stick insect, genus) [taxon 629395]
- **Cell lines:** C57BL/6J — Mus musculus (Mouse), Transformed cell line (CVCL_C0MW), HT29 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0320), HEPG2 — Homo sapiens (Human), Hepatoblastoma, Cancer cell line (CVCL_0027), /6 — Homo sapiens (Human), Tongue squamous cell carcinoma, Cancer cell line (CVCL_5985), IM-HSIF — Homo sapiens (Human), Ovarian serous cystadenocarcinoma, Cancer cell line (CVCL_W444), HEK293T — Homo sapiens (Human), Transformed cell line (CVCL_0063), U937 — Homo sapiens (Human), Adult acute monocytic leukemia, Cancer cell line (CVCL_0007), C57BL/6 — Mus musculus (Mouse), Transformed cell line (CVCL_C0MU), fibroblasts — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0594)

## Figures

13 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13003854/full.md

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Source: https://tomesphere.com/paper/PMC13003854