FAECAL microbiota transplantation (FMT) was associated with mucosal decolonisation of adherent-invasive E. coli (AIEC) in patients with Crohn’s disease, alongside increased mucosal microbial diversity and changes in microbial pathway profiles.
An open-label pilot study investigated whether FMT could clear mucosal AIEC and alter faecal and mucosal microbiomes in patients with Crohn’s disease. Thirty adults with Crohn’s disease and seropositivity for serum anti-E. coli antibody (AEcAb) received a single colonoscopic FMT from one of two donors.
The primary outcome was adverse events within 12 weeks after FMT. Secondary outcomes included changes in mucosal AIEC, clinical measures, and faecal and mucosal microbiome profiles.
Shotgun metagenomic sequencing was performed on faecal samples, while 16S ribosomal RNA sequencing was used to assess ileal mucosal samples at baseline and after FMT.
Baseline AEcAb levels were higher in patients with mucosal AIEC colonisation: p=0.019. These antibody levels remained elevated after FMT.
No FMT-related serious adverse events were reported. Among the eight evaluable patients with mucosal AIEC colonisation at baseline, all experienced mucosal AIEC decolonisation after FMT.
Mucosal α-diversity also increased following FMT: p=0.023. This increase correlated with reduced faecal calprotectin: p=0.034.
These findings indicated an association between changes in mucosal microbial diversity and faecal calprotectin, although the pilot study was not designed to establish causality.
Microbial pathway profiles in patients with Crohn’s disease became more similar to those of their respective donors after FMT, with reduced donor-recipient dissimilarity: p=0.030. This reduction was particularly evident among recipients who experienced mucosal AIEC decolonisation: p=0.039.
The findings demonstrated the feasibility of using FMT to modulate mucosal AIEC colonisation in Crohn’s disease. They also highlighted the potential importance of assessing microbial changes directly at the disease site, as alterations in the mucosal microbiome may not be detectable in faecal samples.
Further investigation will be needed to clarify the relationship between FMT, mucosal AIEC decolonisation, microbial diversity, and clinical measures in patients with Crohn’s disease.
Reference
Xu Z et al. Fecal microbiota transplantation for the decolonization of mucosal adherent-invasive Escherichia coli in Crohn’s disease: an open-label pilot study. Nat Commun. 2026;DOI:10.1038/s41467-026-77455-7.
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