Technical Aspects of Fecal Microbial Transplantation (FMT)

  • N. Bhutiani
  • J. E. Schucht
  • K. R. Miller
  • Stephen A. McClaveEmail author
Nutrition and Obesity (S McClave, Section Editor)
Part of the following topical collections:
  1. Topical Collection on Nutrition and Obesity


Purpose of Review

Fecal microbial transplantation (FMT) has become established as an effective therapeutic modality in the treatment of antibiotic-refractory recurrent Clostridium difficile colitis. A number of formulations and methods of delivery of FMT are currently available, each with distinct advantages. This review aims to review donor and patient selection for FMT as well as procedural aspects of FMT to help guide clinical practice.

Recent Findings

FMT can be obtained in fresh, frozen, lyophilized, and capsule-based formulations for delivery by oral ingestion, nasoenteric tube, colonoscopy, or enema (depending on the formulation used). Choosing the optimal method relies heavily on patient-related factors, including underlying pathology and severity of illness. As potential applications for FMT expand, careful donor screening and patient selection are critical to minimizing risk to patients and physicians.


FMT represents an excellent therapeutic option for treatment of recurrent Clostridium difficile colitis and holds promise as a possible treatment modality in a variety of other conditions. The wide array of delivery methods allows for its application in various disease states in both the inpatient and outpatient setting.


Fecal transplant Dysbiosis 


Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Human and Animal Rights and Informed Consent

This article does not contain any studies with human or animal subjects performed by any of the authors.


Papers of particular interest, published recently, have been highlighted as: • Of importance

  1. 1.
    de Groot PF, Frissen MN, de Clercq NC, Nieuwdorp M. Fecal microbiota transplantation in metabolic syndrome: history, present and future. Gut Microbes. 2017;8(3):253–67.CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Krezalek MA, DeFazio J, Zaborina O, Zaborin A, Alverdy JC. The shift of an intestinal “microbiome” to a “pathobiome” governs the course and outcome of sepsis following surgical injury. Shock (Augusta, Ga.). 2016;45(5):475.CrossRefGoogle Scholar
  3. 3.
    Gopalakrishnan V, Spencer C, Nezi L, et al. Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients. Science. 2018;359(6371):97–103.CrossRefPubMedGoogle Scholar
  4. 4.
    Gopalakrishnan V, Spencer C, Reuben A, et al. Response to anti-PD-1 based therapy in metastatic melanoma patients is associated with the diversity and composition of the gut microbiome. AACR; 2017.Google Scholar
  5. 5.
    Wargo JA, Gopalakrishnan V, Spencer C, et al. Association of the diversity and composition of the gut microbiome with responses and survival (PFS) in metastatic melanoma (MM) patients (pts) on anti-PD-1 therapy. Proc Am Soc Clin Oncol; 2017.Google Scholar
  6. 6.
    Wang Z-K, Yang Y-S, Chen Y, Yuan J, Sun G, Peng L-H. Intestinal microbiota pathogenesis and fecal microbiota transplantation for inflammatory bowel disease. World J Gastroenterol: WJG. 2014;20(40):14805–20.CrossRefPubMedGoogle Scholar
  7. 7.
    Alverdy JC, Chang EB. The re-emerging role of the intestinal microflora in critical illness and inflammation: why the gut hypothesis of sepsis syndrome will not go away. J Leukoc Biol. 2008;83(3):461–6.CrossRefPubMedGoogle Scholar
  8. 8.
    Morowitz MJ, Babrowski T, Carlisle EM, Olivas A, Romanowski KS, Seal JB, et al. The human microbiome and surgical disease. Ann Surg. 2011;253(6):1094–101.Google Scholar
  9. 9.
    Morowitz MJ, Carlisle EM, Alverdy JC. Contributions of intestinal bacteria to nutrition and metabolism in the critically ill. Surgical Clinics. 2011;91(4):771–85.CrossRefPubMedGoogle Scholar
  10. 10.
    Medicine USNLo. Clinical trials: fecal microbiota transplantation. List of clinical trials involving fecal microbiota transplantation. Available at: Accessed 2/15/2018.Google Scholar
  11. 11.
    OpenBiome. Stool donation. Accessed 2/15/2018, 2018.Google Scholar
  12. 12.
    Costello SP, Tucker EC, La Brooy J, Schoeman MN, Andrews JM. Establishing a fecal microbiota transplant service for the treatment of Clostridium difficile infection. Clin Infect Dis: Off Publ Infect Dis Soc Am. 2016;62(7):908–14.CrossRefGoogle Scholar
  13. 13.
    Paramsothy S, Borody TJ, Lin E, Finlayson S, Walsh AJ, Samuel D, et al. Donor recruitment for fecal microbiota transplantation. Inflamm Bowel Dis. 2015;21(7):1600–6.Google Scholar
  14. 14.
    Tariq R, Weatherly R, Kammer P, Pardi DS, Khanna S. Donor screening experience for fecal microbiota transplantation in patients with recurrent C. difficile infection. J Clin Gastroenterol. 2018;52(2):146–50.PubMedGoogle Scholar
  15. 15.
    Hamilton MJ, Weingarden AR, Sadowsky MJ, Khoruts A. Standardized frozen preparation for transplantation of fecal microbiota for recurrent Clostridium difficile infection. Am J Gastroenterol. 2012;107(5):761–7.CrossRefPubMedGoogle Scholar
  16. 16.•
    Van Nood E, Vrieze A, Nieuwdorp M, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368(5):407–15. Excellent source for stool donor screening protocol. CrossRefPubMedGoogle Scholar
  17. 17.
    Woodworth MH, Neish EM, Miller NS, Dhere T, Burd EM, Carpentieri C, et al. Laboratory testing of donors and stool samples for fecal microbiota transplantation for recurrent Clostridium difficile infection. J Clin Microbiol. 2017;55(4):1002–10.Google Scholar
  18. 18.
    Weil AA, Hohmann EL. Fecal microbiota transplant: benefits and risks. Open Forum Infectious Diseases. 2015;2(1).Google Scholar
  19. 19.
    Center TOSUWM. Fecal microbiota transplant (FMT) for the Treatmet of Clostridium difficile infection. Accessed 2/15/2018.Google Scholar
  20. 20.
    Brandt LJ, Aroniadis OC, Mellow M, Kanatzar A, Kelly C, Park T, et al. Long-term follow-up of colonoscopic fecal microbiota transplant for recurrent Clostridium difficile infection. Am J Gastroenterol. 2012;107(7):1079–87.Google Scholar
  21. 21.
    Aroniadis OC, Brandt LJ, Greenberg A, Borody T, Kelly CR, Mellow M, et al. Long-term follow-up study of fecal microbiota transplantation for severe and/or complicated Clostridium difficile infection: a multicenter experience. J Clin Gastroenterol. 2016;50(5):398–402.Google Scholar
  22. 22.
    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.CrossRefPubMedGoogle Scholar
  23. 23.
    OpenBiome. Welcome to OpenBiome. Scholar
  24. 24.
    Kelly CR, de Leon L, Jasutkar N. Fecal microbiota transplantation for relapsing Clostridium difficile infection in 26 patients: methodology and results. J Clin Gastroenterol. 2012;46(2):145–9.CrossRefPubMedGoogle Scholar
  25. 25.•
    Rohlke F, Stollman N. Fecal microbiota transplantation in relapsing Clostridium difficile infection. Ther Adv Gastroenterol. 2012;5(6):403–20. Well-written overview of methodologic aspects of FMT for Clostridium difficile infection. CrossRefGoogle Scholar
  26. 26.
    Lohsiriwat V. Colonoscopic perforation: incidence, risk factors, management and outcome. World J Gastroenterol: WJG. 2010;16(4):425–30.CrossRefPubMedGoogle Scholar
  27. 27.
    Borody TJ, Paramsothy S, Agrawal G. Fecal microbiota transplantation: indications, methods, evidence, and future directions. Curr Gastroenterol Rep. 2013;15(8):337.CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.•
    Borody TJ, Campbell J. Fecal microbiota transplantation: techniques, applications, and issues. Gastroenterol Clin N Am. 2012;41(4):781–803. This report is an excellent review of many of the technical aspects of FMT.Google Scholar
  29. 29.•
    Borody TJ, Khoruts A. Fecal microbiota transplantation and emerging applications. Nat Rev Gastroenterol Hepatol. 2012;9(2):88. Review article detailing history of FMT, evidence supporting its use in recurrent Clostridium difficile infection, and potential application in patients with ulcerative colitis. CrossRefGoogle Scholar
  30. 30.
    Brandt LJ, Aroniadis OC. An overview of fecal microbiota transplantation: techniques, indications, and outcomes. Gastrointest Endosc. 2013;78(2):240–9.CrossRefPubMedGoogle Scholar
  31. 31.
    Kronman MP, Nielson HJ, Adler AL, Giefer MJ, Wahbeh G, Singh N, et al. Fecal microbiota transplantation via nasogastric tube for recurrent clostridium difficile infection in pediatric patients. J Pediatr Gastroenterol Nutr. 2015;60(1):23–6.Google Scholar
  32. 32.
    Postigo R, Kim JH. Colonoscopic versus nasogastric fecal transplantation for the treatment of Clostridium difficile infection: a review and pooled analysis. Infection. 2012;40(6):643–8.CrossRefPubMedGoogle Scholar
  33. 33.
    Jeon YD, Hong N, Kim JH, Park SH, Kim SB, Song IJ, et al. Fecal transplantation using a nasoenteric tube during an initial episode of severe Clostridium difficile infection. Inf Chemother. 2016;48(1):31–5.Google Scholar
  34. 34.•
    Kao D, Roach B, Silva M, et al. Effect of oral capsule– vs colonoscopy-delivered fecal microbiota transplantation on recurrent clostridium difficile infection: a randomized clinical trial. JAMA, 1993. 2017;318(20):1985. Randomized controlled trial demonstrating the non-inferiority of oral capsule-based FMT to standard colonoscopy-based FMT in treatment of recurrent Clostridium difficile infection. Google Scholar
  35. 35.
    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.Google Scholar
  36. 36.
    Youngster I, Russell GH, Pindar C, Ziv-Baran T, Sauk J, Hohmann EL. Oral, capsulized, frozen fecal microbiota transplantation for relapsing Clostridium difficile infection. JAMA. 2014;312(17):1772–8.CrossRefPubMedGoogle Scholar
  37. 37.
    Jiang ZD, Alexander A, Ke S, Valilis EM, Hu S, Li B, et al. Stability and efficacy of frozen and lyophilized fecal microbiota transplant (FMT) product in a mouse model of Clostridium difficile infection (CDI). Anaerobe. 2017;48:110–4.Google Scholar
  38. 38.•
    Lee CH, Steiner T, Petrof EO, 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. Randomized controlled trial establishing clinical equivalence of fresh and frozen FMT in treatment of recurrent Clostridium difficile infection. CrossRefPubMedGoogle Scholar
  39. 39.
    Tang G, Yin W, Liu W. Is frozen fecal microbiota transplantation as effective as fresh fecal microbiota transplantation in patients with recurrent or refractory Clostridium difficile infection: a meta-analysis? Diagn Microbiol Infect Dis. 2017;88(4):322–9.CrossRefPubMedGoogle Scholar
  40. 40.
    Perez E, Lee CH, Petrof EOA. Practical method for preparation of fecal microbiota transplantation. Methods Mol Biol (Clifton, NJ). 2016;1476:259–67.CrossRefGoogle Scholar
  41. 41.
    OpenBiome. PersonalBiome. Accessed 2/15/2018.Google Scholar
  42. 42.
    OpenBiome. TREATMENT INFORMATION.Google Scholar
  43. 43.
    OpenBiome. FMT Capsule G3. Accessed 2/15/2018.Google Scholar
  44. 44.
    Ott SJ, Waetzig GH, Rehman A, Moltzau-Anderson J, Bharti R, Grasis JA, et al. Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium difficile infection. Gastroenterology. 2017;152(4):799–811.e797.Google Scholar
  45. 45.
    Defazio J, Fleming ID, Shakhsheer B, Zaborina O, Alverdy JC. The opposing forces of the intestinal microbiome and the emerging pathobiome. Surg Clin. 2014;94(6):1151–61.CrossRefGoogle Scholar
  46. 46.
    Banerjee S, Sindberg G, Wang F, Meng J, Sharma U, Zhang L, et al. Opioid-induced gut microbial disruption and bile dysregulation leads to gut barrier compromise and sustained systemic inflammation. Mucosal Immunol. 2016;9(6):1418–28.Google Scholar
  47. 47.
    Shakhsheer BA, Versten LA, Luo JN, Defazio JR, Klabbers R, Christley S, et al. Morphine promotes colonization of anastomotic tissues with collagenase-producing Enterococcus faecalis and causes leak. J Gastrointest Surg. 2016;20(10):1744–51.Google Scholar
  48. 48.
    Schuijt T, van der Poll T, Wiersinga W. Gut microbiome and host defense interactions during critical illness. Annual Update in Intensive Care and Emergency Medicine 2012: Springer; 2012:29–40.Google Scholar
  49. 49.
    Schuijt TJ, van der Poll T, de Vos WM, Wiersinga WJ. The intestinal microbiota and host immune interactions in the critically ill. Trends Microbiol. 2013;21(5):221–9.CrossRefPubMedGoogle Scholar
  50. 50.
    OpenBiome. Staying healthy after your fecal transplant. Accessed 2/15/2018.Google Scholar
  51. 51.•
    Wang S, Xu M, Wang W, et al. Systematic review: adverse events of fecal microbiota transplantation. PloS One. 2016;11(8):e0161174. Systematic review of adverse events in patients undergoing FMT. CrossRefPubMedPubMedCentralGoogle Scholar
  52. 52.
    Kelly CR, Kahn S, Kashyap P, Laine L, Rubin D, Atreja A, et al. Update on FMT 2015: indications, methodologies, mechanisms and outlook. Gastroenterology. 2015;149(1):223–37.Google Scholar
  53. 53.
    Jiang ZD, Ajami NJ, Petrosino JF, Jun G, Hanis CL, Shah M, et al. Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection—fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy. Aliment Pharmacol Ther. 2017;45(7):899–908.Google Scholar
  54. 54.
    Hecker MT, Obrenovich ME, Cadnum JL, Jencson AL, Jain AK, Ho E, et al. Fecal microbiota transplantation by freeze-dried oral capsules for recurrent Clostridium difficile infection. Open Forum Infect Dis. 2016;3(2)Google Scholar
  55. 55.
    Staley C, Hamilton MJ, Vaughn BP, Graiziger CT, Newman KM, Kabage AJ, et al. Successful resolution of recurrent Clostridium difficile infection using freeze-dried, encapsulated fecal microbiota; pragmatic cohort study. Am J Gastroenterol. 2017;112(6):940–7.Google Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • N. Bhutiani
    • 1
  • J. E. Schucht
    • 1
  • K. R. Miller
    • 1
  • Stephen A. McClave
    • 2
    Email author
  1. 1.Department of Surgery, Division of Trauma and Critical CareUniversity of LouisvilleLouisvilleUSA
  2. 2.Department of Medicine, Division of GastroenterologyUniversity of LouisvilleLouisvilleUSA

Personalised recommendations