Faecal microbiota transplantation (FMT) in ulcerative colitis (UC) is associated with specific bacterial changes: Stool and colonic mucosa 16s microbiota analysis from the randomised controlled focus study

Abstract

Introduction: In a randomised placebo-controlled trial, intensive FMT therapy for active ulcerative colitis (UC) was significantly superior to placebo, producing a clinical response in >50% and clinical remission with endoscopic remission or response in 27% of patients (ECCO 2016 & DDW 2016)1. This part of the FOCUS study aimed to characterise the microbial changes underlying FMT in UC, and identify those predictive of, and associated with, response and lack of response. Aims & Methods: Active UC patients were randomised to intensive FMT or placebo enemas 5 days/week for 8 weeks, with placebo-treated patients subsequently offered 8 weeks of open label FMT. Each FMT enema was derived from 3-7 unrelated donors. Faecal samples were collected from patients at week 0, 4 and 8, open label mid and end of treatment (if applicable), and 8 weeks after FMT; colonic biopsies were collected at week 0 and 8, and end of open label treatment (if applicable). Faecal samples were also collected from individual donors and donor batches. DNA was extracted from faecal samples and 16S ribosomal RNA gene sequencing performed using 2x300 bp Illumina Miseq chemistry (F27 & 519R). Raw sequences were analysed using MOTHUR, and statistical tests performed on counts and relative abundances. Results: Faecal and colonic samples were collected from 70 study patients. 14 donors contributed to 21 donor batches. 314 patient and 113 donor (individual + batch) faecal samples along with 160 patient colonic samples were analysed. 26976 ± 540 clean sequences per faecal sample and 28093±881 per colonic biopsy were obtained with rarefaction curves suggesting sampling had reached saturation. In both faecal and colonic samples α-diversity significantly increased at all FMT treatment time points relative to baseline (p<0.005); this persisted 8 weeks after FMT in the faecal samples. On PCA, Cluster, and PERMANOVA analyses FMT significantly influenced patient microbial profiles, with the shift towards healthy donor microbiota most notable at the genus and OTU levels. LEfSe analysis of both faecal and colonic samples showed a decrease in patient Bacteroides and an increase in donor Prevotella with FMT, independent of clinical outcome. A range of other microbial taxa were identified as transplanted or displaced with FMT across all taxanomic levels. Patients receiving FMT who achieved remission had greater baseline faecal and colonic mucosal α-diversity than those who did not achieve remission, and also had greater resultant diversity with and after FMT treatment. Specific taxa were consistently significantly associated with FMT remission across both faecal and colonic samples: taxa within Barnesiella were associated with remission, while OTUs within Fusobacterium and Sutterella were associated with lack of remission. Conclusion: Baseline patient microbial diversity in UC appears to be predictive of therapeutic response to FMT. Intensive FMT is associated with increased microbial diversity, with the greatest diversity noted in patients achieving remission. Increased diversity persists 8 weeks after cessation of therapy. Specific bacterial taxa are transplanted or displaced by FMT, some of which are associated with treatment outcome. A high level of concordance was observed between the faecal and colonic mucosal microbiota. These findings may be important in both understanding the pathophysiology of the microbiota in UC and shaping future bacterial therapy.L619935735 <br />