Purpose of Review
Fecal microbiota transplantation (FMT) has been investigated as a potential treatment for inflammatory bowel disease (IBD). This review examines current evidence around the efficacy and safety of FMT for patients with IBD.
Randomized controlled trials (RCTs) and meta-analyses have suggested that FMT may facilitate clinical and endoscopic remission in patients with active ulcerative colitis (UC). Although the evidence for FMT in Crohn’s disease (CD) is more limited, positive outcomes have been observed in small cohort studies. Most adverse events (AEs) were mild and included transient gastrointestinal symptoms. Serious adverse events (SAEs) did not differ significantly between the FMT and control groups, and a marginal increased rate of IBD flares following FMT was observed. Microbiota analysis following FMT showed increased intestinal bacterial diversity and a shift towards the donor microbial profile in recipients’ stools.
FMT for patients with IBD is promising as RCTs have shown the benefit of FMT for UC, although the efficacy of FMT for CD is less clear. Further large and well-designed trials are necessary to resolve critical issues such as the donor selection, the ideal route of administration, duration, frequency of FMT, and the long-term sustained efficacy and safety.
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Kassam Z, Lee CH, Yuan Y, Hunt RH. Fecal microbiota transplantation for Clostridium difficile infection: systematic review and meta-analysis. Am J Gastroenterol. 2013;108(4):500–8.
van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368(5):407–15.
Lee CH, Steiner T, Petrof EO, Smieja M, Roscoe D, Nematallah A, et al. Frozen vs fresh fecal microbiota transplantation and clinical resolution of diarrhea in patients with recurrent Clostridium difficile infection: a randomized clinical trial. JAMA. 2016;315(2):142–9.
Singh P, Ananthakrishnan A, Ahuja V. Pivot to Asia: inflammatory bowel disease burden. Intest Res. 2017;15(1):138–41.
Borody TJ, Khoruts A. Fecal microbiota transplantation and emerging applications. Nat Rev Gastroenterol Hepatol. 2011;9(2):88–96.
Petersen C, Round JL. Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol. 2014;16(7):1024–33.
•• Moayyedi P, Surette MG, Kim PT, et al. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology. 2015;149(1):102–9. The RCT on FMT for IBD.
•• Rossen NG, Fuentes S, van der Spek MJ, et al. Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterology. 2015;149(1):110–8 e4. The RCT on FMT for IBD.
•• Paramsothy S, Kamm MA, Kaakoush NO, et al. Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial. Lancet. 2017;389(10075):1218–28. The RCT on FMT for IBD.
•• Costello SWBR, Katsikeros R, et al. Short duration, low intensity pooled faecal microbiota transplantation induces remission in patients with mild-moderately active ulcerative colitis: a randomised controlled trial. J Crohns Colitis. 2017;11(suppl 1):S23. The RCT on FMT for IBD.
Anderson JL, Edney RJ, Whelan K. Systematic review: faecal microbiota transplantation in the management of inflammatory bowel disease. Aliment Pharmacol Ther. 2012;36(6):503–16.
Colman RJ, Rubin DT. Fecal microbiota transplantation as therapy for inflammatory bowel disease: a systematic review and meta-analysis. J Crohns Colitis. 2014;8(12):1569–81.
• Paramsothy S, Paramsothy R, Rubin DT, et al. Faecal microbiota transplantation for inflammatory bowel disease: a systematic review and meta-analysis. J Crohns Colitis. 2017;11(10):1180–99. This article updates the current evidences on FMT in the various IBD subtypes by performing meta-analyses.
• Narula N, Kassam Z, Yuan Y, et al. Systematic review and meta-analysis: fecal microbiota transplantation for treatment of active ulcerative colitis. Inflamm Bowel Dis. 2017;23(10):1702–9. This meta-analysis using only RCTs demonstrates that the use FMT for UC is beneficial.
Chu H, Khosravi A, Kusumawardhani IP, Kwon AHK, Vasconcelos AC, Cunha LD, et al. Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Science. 2016;352(6289):1116–20.
Palm NW, de Zoete MR, Cullen TW, Barry NA, Stefanowski J, Hao L, et al. Immunoglobulin a coating identifies colitogenic bacteria in inflammatory bowel disease. Cell. 2014;158(5):1000–10.
Eckburg PB, Relman DA. The role of microbes in Crohn's disease. Clin Infect Dis. 2007;44(2):256–62.
Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, et al. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med. 2014;6(12):107.
Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology. 2008;134(2):577–94.
Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007;104(34):13780–5.
Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007;449(7164):804–10.
Chassaing B, Darfeuille-Michaud A. The commensal microbiota and enteropathogens in the pathogenesis of inflammatory bowel diseases. Gastroenterology. 2011;140(6):1720–8.
Packey CD, Sartor RB. Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Curr Opin Infect Dis. 2009;22(3):292–301.
Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014;15(3):382–92.
Gianotti RJ, Moss AC. Fecal microbiota transplantation: from Clostridium difficile to inflammatory bowel disease. Gastroenterol Hepatol (N Y). 2017;13(4):209–13.
• Allegretti J, Eysenbach LM, El-Nachef N, Fischer M, Kelly C, Kassam Z. The current landscape and lessons from fecal microbiota transplantation for inflammatory bowel disease: past, present, and future. Inflamm Bowel Dis. 2017;23(10):1710–7. This review offers the current evidences on the efficacy and safety of FMT for IBD and outline ongoing clinical trials.
Siegmund B. Is intensity the solution for FMT in ulcerative colitis? Lancet. 2017;389(10075):1170–2.
Li N, Tian H, Ma C, Ding C, Ge X, Gu L, et al. Efficacy analysis of fecal microbiota transplantation in the treatment of 406 cases with gastrointestinal disorders. Zhonghua Wei Chang Wai Ke Za Zhi. 2017;20(1):40–6.
Vaughn BP, Vatanen T, Allegretti JR, Bai A, Xavier RJ, Korzenik J, et al. Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn’s disease. Inflamm Bowel Dis. 2016;22(9):2182–90.
Cui B, Feng Q, Wang H, Wang M, Peng Z, Li P, et al. Fecal microbiota transplantation through mid-gut for refractory Crohn’s disease: safety, feasibility, and efficacy trial results. J Gastroenterol Hepatol. 2015;30(1):51–8.
Suskind DL, Brittnacher MJ, Wahbeh G, Shaffer ML, Hayden HS, Qin X, et al. Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn’s disease. Inflamm Bowel Dis. 2015;21(3):556–63.
Vermeire S, Joossens M, Verbeke K, Wang J, Machiels K, Sabino J, et al. Donor species richness determines faecal microbiota transplantation success in inflammatory bowel disease. J Crohns Colitis. 2016;10(4):387–94.
Wei Y, Zhu W, Gong J, et al. Fecal microbiota transplantation improves the quality of life in patients with inflammatory bowel disease. Gastroenterol Res Pract. 2015;2015:517597.
Melton GB, Fazio VW, Kiran RP, He J, Lavery IC, Shen B, et al. Long-term outcomes with ileal pouch-anal anastomosis and Crohn’s disease: pouch retention and implications of delayed diagnosis. Ann Surg. 2008;248(4):608–16.
Stallmach A, Lange K, Buening J, Sina C, Vital M, Pieper DH. Fecal microbiota transfer in patients with chronic antibiotic-refractory pouchitis. Am J Gastroenterol. 2016;111(3):441–3.
Zezos P, Saibil F. Inflammatory pouch disease: the spectrum of pouchitis. World J Gastroenterol. 2015;21(29):8739–52.
Batista D, Raffals L. Role of intestinal bacteria in the pathogenesis of pouchitis. Inflamm Bowel Dis. 2014;20(8):1481–6.
Shen B. Acute and chronic pouchitis—pathogenesis, diagnosis and treatment. Nat Rev Gastroenterol Hepatol. 2012;9(6):323–33.
Landy J, Walker AW, Li JV, al-Hassi HO, Ronde E, English NR, et al. Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis. Sci Rep. 2015;5:12955.
Weingarden AR, Vaughn BP. Intestinal microbiota, fecal microbiota transplantation, and inflammatory bowel disease. Gut Microbes. 2017;8(3):238–52.
Binion DG. Clostridium difficile infection in patients with inflammatory bowel disease. Gastroenterol Hepatol (N Y). 2012;8(9):615–7.
Nguyen GC, Kaplan GG, Harris ML, Brant SR. A national survey of the prevalence and impact of Clostridium difficile infection among hospitalized inflammatory bowel disease patients. Am J Gastroenterol. 2008;103(6):1443–50.
Ananthakrishnan AN, Binion DG. Impact of Clostridium difficile on inflammatory bowel disease. Expert Rev Gastroenterol Hepatol. 2010;4(5):589–600.
Kelsen JR, Kim J, Latta D, Smathers S, McGowan KL, Zaoutis T, et al. Recurrence rate of clostridium difficile infection in hospitalized pediatric patients with inflammatory bowel disease. Inflamm Bowel Dis. 2011;17(1):50–5.
Ananthakrishnan AN, McGinley EL, Binion DG. Excess hospitalisation burden associated with Clostridium difficile in patients with inflammatory bowel disease. Gut. 2008;57(2):205–10.
Tariq R, Law CCY, Khanna S, Murthy S, McCurdy JD. The impact of Clostridium difficile infection on mortality in patients with inflammatory bowel disease: a systematic review and meta-analysis. J Clin Gastroenterol. 2017. https://doi.org/10.1097/MCG.0000000000000968.
Chin SM, Sauk J, Mahabamunuge J, Kaplan JL, Hohmann EL, Khalili H. Fecal microbiota transplantation for recurrent Clostridium difficile infection in patients with inflammatory bowel disease: a single-center experience. Clin Gastroenterol Hepatol. 2017;15(4):597–9.
Fischer M, Kao D, Kelly C, Kuchipudi A, Jafri SM, Blumenkehl M, et al. Fecal microbiota transplantation is safe and efficacious for recurrent or refractory Clostridium difficile infection in patients with inflammatory bowel disease. Inflamm Bowel Dis. 2016;22(10):2402–9.
Khoruts A, Rank KM, Newman KM, Viskocil K, Vaughn BP, Hamilton MJ, et al. Inflammatory bowel disease affects the outcome of fecal microbiota transplantation for recurrent Clostridium difficile infection. Clin Gastroenterol Hepatol. 2016;14(10):1433–8.
Newman KM, Rank KM, Vaughn BP, Khoruts A. Treatment of recurrent Clostridium difficile infection using fecal microbiota transplantation in patients with inflammatory bowel disease. Gut Microbes. 2017;8(3):303–9.
• Qazi T, Amaratunga T, Barnes EL, Fischer M, Kassam Z, Allegretti JR. The risk of inflammatory bowel disease flares after fecal microbiota transplantation: systematic review and meta-analysis. Gut Microbes. 2017;8(6):1–15. This article provides a detailed systematic review and meta-analysis on the rate of worsening in IBD following alteration of the host microbiota.
Fischer M, Sipe BW, Rogers NA, Cook GK, Robb BW, Vuppalanchi R, et al. Vancomycin for severe-complicated Clostridium difficile infection: description of a protocol with high success rate. Aliment Pharmacol Ther. 2015;42(4):470–6.
Trial of antimicrobials versus placebo in addition to fecal transplant therapy in ulcerative colitis (FMT). ClinicalTrials Web site. https://clinicaltrials.gov/ct2/show/NCT02606032. Updated December 18, 2017. Accessed January 30, 2018.
Choi CH, Moon W, Kim YS, Kim ES, Lee BI, Jung Y, et al. Second Korean guidelines for the management of ulcerative colitis. Intest Res. 2017;15(1):7–37.
Park JJ, Yang SK, Ye BD, Kim JW, Park DI, Yoon H, et al. Second Korean guidelines for the management of Crohn’s disease. Intest Res. 2017;15(1):38–67.
Youngster I, Mahabamunuge J, Systrom HK, Sauk J, Khalili H, Levin J, et al. Oral, frozen fecal microbiota transplant (FMT) capsules for recurrent Clostridium difficile infection. BMC Med. 2016;14(1):134.
Allegretti JFMPE, Elliott RJ, et al. Fecal microbiota transplantation delivered via oral capsules achieves microbial engraftment similar to traitional delivery modalities: safety, efficacy and engraftment results from a multi-center cluster randomized dose-finding study. Gastroenterology. 2016;150:S540.
Baxter M, Colville A. Adverse events in faecal microbiota transplant: a review of the literature. J Hosp Infect. 2016;92(2):117–27.
Wang S, Xu M, Wang W, Cao X, Piao M, Khan S, et al. Systematic review: adverse events of fecal microbiota transplantation. PLoS One. 2016;11(8):e0161174.
Hohmann EL, Ananthakrishnan AN, Deshpande V. A 37-year-old man with ulcerative colitis and bloody diarrhea. N Engl J Med. 2014;371(7):668–75.
Swaminath A. The power of poop: patients getting ahead of their doctors using self-administered fecal transplants. Am J Gastroenterol. 2014;109(5):777–8.
Fuentes S, Rossen NG, van der Spek MJ, Hartman JHA, Huuskonen L, Korpela K, et al. Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation. ISME J. 2017;11(8):1877–89.
Mizuno S, Nanki K, Matsuoka K, Saigusa K, Ono K, Arai M, et al. Single fecal microbiota transplantation failed to change intestinal microbiota and had limited effectiveness against ulcerative colitis in Japanese patients. Intest Res. 2017;15(1):68–74.
Conflict of Interest
Seong Ran Jeon, Jocelyn Chai, Christiana Kim, and Christine H. Lee declare that they have no conflict of interest.
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This article does not contain any studies with human or animal subjects performed by any of the authors.
This article is part of the Topical Collection on Intra-abdominal Infections, Hepatitis, and Gastroenteritis
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Jeon, S.R., Chai, J., Kim, C. et al. Current Evidence for the Management of Inflammatory Bowel Diseases Using Fecal Microbiota Transplantation. Curr Infect Dis Rep 20, 21 (2018). https://doi.org/10.1007/s11908-018-0627-8