Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study



This pilot study assessed the efficacy, safety, and microbiome dynamics of fecal microbiota transplantation (FMT) for patients with chronic pouchitis.


A prospective open-label pilot study was performed at an academic center among pouchitis patients undergoing FMT. Patients received a minimum of a single FMT by pouchoscopy from healthy, screened donors. The primary outcome was clinical improvement in pouchitis assessed by patient survey at week 4. Secondary outcomes included decrease in total Pouchitis Disease Activity Index (PDAI) Score ≥ 3 at week 4, bowel movement frequency, ESR, CRP, fecal calprotectin, abdominal pain, and PDAI subscores including endoscopic and histologic changes. Stool samples were collected at baseline and 4 weeks post-FMT to assess bacterial microbiota using V4 16S rRNA sequencing.


Nineteen patients were enrolled; however, 1 patient was lost to follow-up. No patients had a major adverse event or escalation of therapy related to FMT. Total PDAI scores, endoscopic scores, and histologic scores did not decrease significantly post-FMT. However, there was a statistically significant improvement in bowel movement (BM) frequency (9.25–7.25 BM/day, p = 0.03) and trend for improvement in abdominal pain to improve post-FMT (p = 0.05). Bacterial microbiota profiling revealed no distinct community-level changes post-FMT, though a small number of specific bacterial taxa significantly differed in relative abundance.


A single FMT has a tolerable short-term safety profile and may be associated with a decrease in bowel movements in patients with chronic pouchitis; however, no robust endoscopic or histologic changes were observed.

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Philanthropic Gift. The study design, data collection, analysis, and interpretation were performed independently of the funding source.

Author information




DS contributed to analysis and interpretation of the data, drafting of the manuscript, and critical revision of the manuscript. YP contributed to microbial sample processing and analysis, drafting of the manuscript, analysis and interpretation of the data. DF, KL, and BL contributed to microbial sequencing. MZ contributed to study supervision, data collection, and regulatory submissions. KB and SL provided blinded endoscopy scores. SU and DB provided blinded histology scores. TL contributed to data collection, regulatory submission, and intervention operations. ZK and JT contributed to study concept and design, and critical revision of the manuscript. AM conceived and designed the study. MS analyzed and interpreted the data. SL contributed to microbial analysis and critical revision of the manuscript. NE-N contributed to study concept and design, principal investigator, and critical revision of the manuscript.

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Correspondence to Najwa El-Nachef.

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Conflict of interest

ZK is currently an employee and shareholder of Finch Therapeutics Group. ZK and TL were employees of the nonprofit stool bank, OpenBiome, at the time of the study. SVL co-founded, is a shareholder, is on the board of directors and acts as a consultant for Siolta Therapeutics, and is a scientific advisory board member for Bloom Science.

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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Declaration of Helsinki and its later amendments or comparable ethical standards.

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Selvig, D., Piceno, Y., Terdiman, J. et al. Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study. Dig Dis Sci 65, 1099–1106 (2020). https://doi.org/10.1007/s10620-019-05715-2

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  • Pouchitis
  • IBD
  • Microbiome
  • Dysbiosis
  • FMT
  • Fecal microbiota transplantation
  • IPAA