A butyrate-producing synbiotic mitigates intestinal inflammation in a murine colitis model

Abstract

Inflammatory bowel disease (IBD) is a chronic condition characterized by intestinal inflammation and gut dysbiosis, with limited treatment options primarily focused on immune-modulating therapies. Among potential therapeutic agents, butyrate has emerged as a promising candidate due to its anti-inflammatory and gut-restorative properties. However, direct administration of butyrate poses significant challenges, including its rapid absorption, uneven distribution within the intestinal tract, and an unpleasant odor that reduces patient compliance. To address these issues, we evaluated the therapeutic potential of Bacillus subtilis BM107, a strain selected for its superior butyrate-producing capabilities and established bacterial safety. BM107 efficiently hydrolyzed tributyrin (TB), a butyrate prodrug, producing substantial butyrate levels in TB-supplemented media. In a dextran sodium sulfate-induced colitis mouse model, co-administration of BM107 and the TB diet significantly improved inflammatory indices, such as reduced disease activity index scores, increased colon length, and restored body weight. Additionally, this combination treatment markedly improved gut microbiome composition, restoring microbial diversity and balance. Furthermore, butyrate levels in the cecum contents of the TB + BM107 group were restored to levels comparable to those in healthy controls, demonstrating the ability of this approach to promote gut homeostasis and intestinal recovery. These findings highlight the therapeutic potential of BM107 combined with a TB diet as a safe, effective, and innovative strategy for addressing gut dysbiosis and inflammation in IBD, paving the way for the development of microbiome-based bacterial therapeutics to improve patient outcomes.

Keywords

Bacillus subtilis / butyrate / esterase / IBD / tributyrin

References

[1] Xavier RJ, Podolsky DK. Unravelling the pathogenesis of inflammatory bowel disease. Nature. 2007; 448: 427-434.

[2] Taleban S, Elquza E, Gower-Rousseau C, Peyrin-Biroulet L. Cancer and inflammatory bowel disease in the elderly. Dig Liver Dis. 2016; 48: 1105-1111.

[3] Singh S, Blanchard A, Walker JR, Graff LA, Miller N, Bernstein CN. Common symptoms and stressors among individuals with inflammatory bowel diseases. Clin Gastroenterol Hepatol. 2011; 9: 769-775.

[4] Barberio B, Zamani M, Black CJ, Savarino EV, Ford AC. Prevalence of symptoms of anxiety and depression in patients with inflammatory bowel disease: a systematic review and meta-analysis. Lancet Gastroenterol Hepatol. 2021; 6: 359-370.

[5] Podolsky DK. Inflammatory bowel disease. N Engl J Med. 2002; 347: 417-429.

[6] Cosnes J, Beaugerie L, Carbonnel F, Gendre JP. Smoking cessation and the course of Crohn's disease: an intervention study. Gastroenterology. 2001; 120: 1093-1099.

[7] Neuman MG. Immune dysfunction in inflammatory bowel disease. Transl Res. 2007; 149: 173-186.

[8] Galvez J, Rodríguez-Cabezas ME, Zarzuelo A. Effects of dietary fiber on inflammatory bowel disease. Mol Nutr Food Res. 2005; 49: 601-608.

[9] Ananthakrishnan AN. Epidemiology and risk factors for IBD. Nat Rev Gastroenterol Hepatol. 2015; 12: 205-217.

[10] Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, et al. Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol. 2019; 10: 277.

[11] Wong JMW, de Souza R, Kendall CWC, Emam A, Jenkins DJA. Colonic health: fermentation and short chain fatty acids. J Clin Gastroenterol. 2006; 40: 235-243.

[12] Salvi PS, Cowles RA. Butyrate and the intestinal epithelium: modulation of proliferation and inflammation in homeostasis and disease. Cells. 2021; 10: 1775.

[13] Thibault R, Blachier F, Darcy-Vrillon B, de Coppet P, Bourreille A, Segain JP. Butyrate utilization by the colonic mucosa in inflammatory bowel diseases: a transport deficiency. Inflamm Bowel Dis. 2010; 16: 684-695.

[14] Singh N, Gurav A, Sivaprakasam S, Brady E, Padia R, Shi H, et al. Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis. Immunity. 2014; 40: 128-139.

[15] Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science. 2011; 331: 337-341.

[16] Hamer HM, Jonkers D, Venema K, Vanhoutvin S, Troost FJ, Brummer RJ. Review article: the role of butyrate on colonic function. Aliment Pharmacol Ther. 2008; 27: 104-119.

[17] Donohoe DR, Collins LB, Wali A, Bigler R, Sun W, Bultman SJ. The Warburg effect dictates the mechanism of butyrate-mediated histone acetylation and cell proliferation. Mol Cell. 2012; 48: 612-626.

[18] Kuefer R, Hofer MD, Altug V, Zorn C, Genze F, Kunzi-Rapp K, et al. Sodium butyrate and tributyrin induce in vivo growth inhibition and apoptosis in human prostate cancer. Br J Cancer. 2004; 90: 535-541.

[19] Yang N, Lan T, Han Y, Zhao H, Wang C, Xu Z, et al. Tributyrin alleviates gut microbiota dysbiosis to repair intestinal damage in antibiotic-treated mice. PLoS One. 2023; 18: e0289364.

[20] Yan J, Xu YH. Tributyrin inhibits human gastric cancer SGC-7901 cell growth by inducing apoptosis and DNA synthesis arrest. World J Gastroenterol. 2003; 9: 660-664.

[21] Suva M, Sureja V, Kheni D. Novel insight on probiotic Bacillus subtilis: mechanism of action and clinical applications. J Curr Res Sci Med. 2016; 2: 65-72.

[22] Li G, Tong Y, Xiao Y, Huang S, Zhao T, Xia X. Probiotic Bacillus subtilis contributes to the modulation of gut microbiota and blood metabolic profile of hosts. Comp Biochem Physiol C Toxicol Pharmacol. 2023; 272: 109712.

[23] Saravanakumar S, Prabakaran NN, Ashokkumar R, Jamuna S. Unlocking the gut's treasure: lipase-producing Bacillus subtilis probiotic from the intestine of Microstomus kitt (lemon sole). Appl Biochem Biotechnol. 2024; 196: 4273-4286.

[24] Bornscheuer UT, Kazlauskas RJ. Hydrolases in Organic Synthesis: Regio-and Stereoselective Biotransformations. John Wiley & Sons; 2006.

[25] Brutscher LM, Borgmeier C, Garvey SM, Spears JL. Preclinical safety assessment of Bacillus subtilis BS50 for probiotic and food applications. Microorganisms. 2022; 10: 1038.

[26] Kim SH, Yehuala GA, Bang WY, Yang J, Jung YH, Park MK. Safety evaluation of Bacillus subtilis IDCC1101, newly isolated from cheonggukjang, for industrial applications. Microorganisms. 2022; 10: 2494.

[27] Ding S, Ma Y, Liu G, Yan W, Jiang H, Fang J. Lactobacillus brevis alleviates DSS-induced colitis by reprograming intestinal microbiota and influencing serum metabolome in murine model. Front Physiol. 2019; 10: 1152.

[28] Gu W, Zhang L, Han T, Huang H, Chen J. Dynamic changes in gut microbiome of ulcerative colitis: initial study from animal model. J Inflamm Res. 2022; 15: 2631-2647.

[29] Guan Q. A comprehensive review and update on the pathogenesis of inflammatory bowel disease. J Immunol Res. 2019; 2019: 7247238.

[30] Abraham C, Cho JH. Inflammatory bowel disease. N Engl J Med. 2009; 361: 2066-2078.

[31] Cai Z, Wang S, Li J. Treatment of inflammatory bowel disease: a comprehensive review. Front Med. 2021; 8: 765474.

[32] Kaplan GG. The global burden of IBD: from 2015 to 2025. Nat Rev Gastroenterol Hepatol. 2015; 12: 720-727.

[33] Rudbaek JJ, Agrawal M, Torres J, Mehandru S, Colombel JF, Jess T. Deciphering the different phases of preclinical inflammatory bowel disease. Nat Rev Gastroenterol Hepatol. 2024; 21: 86-100.

[34] Neurath MF. Strategies for targeting cytokines in inflammatory bowel disease. Nat Rev Immunol. 2024; 24: 559-576.

[35] Nielsen OH, Ainsworth MA. Tumor necrosis factor inhibitors for inflammatory bowel disease. N Engl J Med. 2013; 369: 754-762.

[36] Ungaro R, Mehandru S, Allen PB, Peyrin-Biroulet L, Colombel J-F. Ulcerative colitis. Lancet. 2017; 389: 1756-1770.

[37] Abraham BP, Quigley EMM. Probiotics in inflammatory bowel disease. Gastroenterol Clin North Am. 2017; 46: 769-782.

[38] Hu KA, Gubatan J. Gut microbiome-based therapeutics in inflammatory bowel disease. Clin Transl Discov. 2023; 3: e182.

[39] Ghosh S, van Heel D, Playford RJ. Probiotics in inflammatory bowel disease: is it all gut flora modulation? Gut. 2004; 53: 620-622.

[40] Zhang Z, Zhang H, Chen T, Shi L, Wang D, Tang D. Regulatory role of short-chain fatty acids in inflammatory bowel disease. Cell Commun Signaling. 2022; 20: 64.

[41] Recharla N, Geesala R, Shi XZ. Gut microbial metabolite butyrate and its therapeutic role in inflammatory bowel disease: a literature review. Nutrients. 2023; 15: 2275.

[42] De Sabatino A, Morera R, Ciccocioppo R, Cazzola P, Gotti S, Tinozzi FP, et al. Oral butyrate for mildly to moderately active Crohn's disease. Aliment Pharmacol Ther. 2005; 22: 789-794.

[43] Deleu S, Machiels K, Raes J, Verbeke K, Vermeire S. Short chain fatty acids and its producing organisms: an overlooked therapy for IBD? EBioMedicine. 2021; 66: 103293.

[44] Egorin MJ, Yuan ZM, Sentz DL, Plaisance K, Eiseman JL. Plasma pharmacokinetics of butyrate after intravenous administration of sodium butyrate or oral administration of tributyrin or sodium butyrate to mice and rats. Cancer Chemother Pharmacol. 1999; 43: 445-453.

[45] Zhuang X, Li T, Li M, Huang S, Qiu Y, Feng R, et al. Systematic review and meta-analysis: short-chain fatty acid characterization in patients with inflammatory bowel disease. Inflamm Bowel Dis. 2019; 25: 1751-1763.

[46] Hetta HF, Ramadan YN, Alharbi AA, Alsharef S, Alkindy TT, Alkhamali A, et al. Gut microbiome as a target of intervention in inflammatory bowel disease pathogenesis and therapy. Immuno. 2024; 4: 400-425.

[47] Bridgeman SC, Northrop W, Melton PE, Ellison GC, Newsholme P, Mamotte CDS. Butyrate generated by gut microbiota and its therapeutic role in metabolic syndrome. Pharmacol Res. 2020; 160: 105174.

[48] Steinhart AH, Hiruki T, Brzezinski A, Baker JP. Treatment of left-sided ulcerative colitis with butyrate enemas: a controlled trial. Aliment Pharmacol Ther. 1996; 10: 729-736.

[49] Singh V, Lee G, Son H, Koh H, Kim ES, Unno T, et al. Butyrate producers, “the sentinel of gut”: their intestinal significance with and beyond butyrate, and prospective use as microbial therapeutics. Front Microbiol. 2023; 13: 1103836.

[50] Brame JE, Liddicoat C, Abbott CA, Edwards RA, Robinson JM, Gauthier NE, et al. The macroecology of butyrate-producing bacteria via metagenomic assessment of butyrate production capacity. Ecol Evol. 2024; 14: e11239.

[51] Xiao Y, Wang Y, Tong B, Gu Y, Zhou X, Zhu N, et al. Eubacterium rectale is a potential marker of altered gut microbiota in psoriasis and psoriatic arthritis. Microbiol Spectr. 2024; 12: e01154-01123.

[52] McOrist AL, Miller RB, Bird AR, Keogh JB, Noakes M, Topping DL, et al. Fecal butyrate levels vary widely among individuals but are usually increased by a diet high in resistant starch. J Nutr. 2011; 141: 883-889.

[53] Hodgkinson K, El Abbar F, Dobranowski P, Manoogian J, Butcher J, Figeys D, et al. Butyrate's role in human health and the current progress towards its clinical application to treat gastrointestinal disease. Clin Nutr. 2023; 42: 61-75.

[54] Lopez-Siles M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. ISME J. 2017; 11: 841-852.

[55] Roselli M, Finamore A. Use of synbiotics for ulcerative colitis treatment. Curr Clin Pharmacol. 2020; 15: 174-182.

[56] Jung DH, Yong JH, Hwang W, Yoon MY, Yoon SS. An efficient system for intestinal on-site butyrate production using novel microbiome-derived esterases. J Biol Eng. 2021; 15: 9.

[57] Quinn DM, Shirai K, Jackson RL, Harmony JAK. Lipoprotein lipase catalyzed hydrolysis of water-soluble p-nitrophenyl esters. Inhibition by apolipoprotein C-II. Biochemistry. 1982; 21: 6872-6879.

[58] Chen Y, Si J, Liu W, Cai J, Du Q, Wang L, et al. Induction of experimental acute ulcerative colitis in rats by administration of dextran sulfate sodium at low concentration followed by intracolonic administration of 30% ethanol. J Zhejiang Univ Sci B. 2007; 8: 632-637.

RIGHTS & PERMISSIONS

2025 The Author(s). mLife published by John Wiley & Sons Australia, Ltd on behalf of Institute of Microbiology, Chinese Academy of Sciences.