Effect of antibiotic pretreatment on bacterial engraftment after Fecal Microbiota Transplant (FMT) in IBS-D

Gut Microbes. Jan-Dec 2022;14(1):2020067.doi: 10.1080/19490976.2021.2020067.


Prashant Singh 1Eric J Alm 2John M Kelley 3 4Vivian Cheng 5Mark Smith 6Zain Kassam 6Judy Nee 5Johanna Iturrino 5Anthony Lembo 5


Author information

1Division of Gastroenterology, Department of Medicine, University of Michigan, Ann, Arbor, Michigan.

2Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.

3Department of Psychology, Endicott College, Beverly, MA, USA.

4Harvard Medical School, Boston, MA.

5Division of Gastroenterology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.

6Finch Therapeutics, Somerville, MA, USA.


Fecal microbiota transplantation (FMT) is an attractive strategy to correct microbial dysbiosis in diarrhea-predominant irritable bowel syndrome (IBS-D). Although the mechanism of FMT is thought to be bacterial engraftment, the best approach to achieve engraftment after FMT in IBS-D (and other diseases) is not clear. We evaluated the effect of FMT (with or without pretreatment with antibiotics) on gut microbiome and symptoms in patients with IBS-D. In this randomized, placebo-controlled, single-center study, 44 patients with IBS-D with a least moderate severity (IBS severity scoring system, i.e., IBS-SSS, ≥175) were randomly assigned to one of four groups: single-dose oral FMT alone, single-dose oral FMT following a 7-day pretreatment course of Ciprofloxacin and Metronidazole (CM-FMT) or Rifaximin (R-FMT), or Placebo FMT. Primary endpoint was engraftment post-FMT and secondary endpoints were changes in IBS-SSS, and IBS-quality of life (IBS-QOL) at week 10. Median engraftment was significantly different among the three FMT groups (P = .013). Engraftment post-FMT was significantly higher in the FMT alone arm (15.5%) compared to that in R-FMT group (5%, P = .04) and CM-FMT group (2.4%, P = .002). The mean change in IBS-SSS and IBS-QOL from baseline were not significantly different among the four groups or between the three FMT groups combined vs. placebo at week 10. In summary, antibiotic pretreatment significantly reduced bacterial engraftment after FMT in patients with IBS-D.

Trial registration: ClinicalTrials.gov NCT02847481.

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