Single Delivery of High-Diversity Fecal Microbiota Preparation by Colonoscopy Is Safe and Effective in Increasing Microbial Diversity in Active Ulcerative Colitis

Abstract

Background: Recent trials suggest fecal microbiota transplantation (FMT) with repeated enemas and high-diversity FMT donors is a promising treatment to induce remission in ulcerative colitis.

Methods: We designed a prospective, open-label pilot study to assess the safety, clinical efficacy, and microbial engraftment of single FMT delivery by colonoscopy for active ulcerative colitis using a 2-donor fecal microbiota preparation (FMP). Safety and clinical endpoints of response, remission, and mucosal healing at week 4 were assessed. Fecal DNA and rectal biopsies were used to characterize the microbiome and mucosal CD4 T cells, respectively, before and after FMT.

Results: Of the 20 patients enrolled in this study, 7 patients (35%) achieved a clinical response by week 4. Three patients (15%) were in remission at week 4 and 2 of these patients (10%) achieved mucosal healing. Three patients (15%) required escalation of care. No serious adverse events were observed. Microbiome analysis revealed that restricted diversity of recipients pre-FMT was significantly increased by high-diversity 2-donor FMP. The microbiome of recipients post-transplant was more similar to the donor FMP than the pretransplant recipient sample in both responders and nonresponders. Notably, donor composition correlated with clinical response. Mucosal CD4 T-cell analysis revealed a reduction in both Th1 and regulatory T-cells post-FMT.

Conclusions: High-diversity, 2-donor FMP delivery by colonoscopy seems safe and effective in increasing fecal microbial diversity in patients with active ulcerative colitis. Donor composition correlated with clinical response and further characterization of immunological parameters may provide insight into factors influencing clinical outcome.

Figure 1.. Two donor FMP improved Mayo score and endoscopic subscore at week 4 post-FMT.

A. Complete Mayo score at baseline and 4 weeks post-FMT. Red dots indicate subjects requiring escalation of care. Wilcoxon matched-pairs signed rank test of subjects not requiring escalation of care is indicated by asterisk. B. Endoscopic subscore score at baseline and 4 weeks post-FMT. Wilcoxon matched-pairs signed rank test, p-value < 0.05 is indicated.

Figure 2.. Two donor FMP increases recipient diversity.

Fecal DNA samples were sequenced by 16S rRNA sequencing. A. Alpha diversity metrics of observed OTUs (left panel) and Shannon index (right panel) are compared for donor and recipient pre-transplant (pre). B. Alpha diversity metrics of observed OTUs (left panel) and Shannon index (right panel) are compared for recipient pre-transplant (pre) and at week 2 (W2) and 4 (W4) following FMT. C. Alpha diversity of samples faceted by the primary endpoint of clinical response (No, left panel; Yes, right panel). For all panels P-values are shown, Kruskal-Wallis.

Figure 3.. Two donor FMP engrafts effectively in active UC recipient.

A. Principal coordinate analysis plot is shown using Bray-Curtis dissimilarity matrix and stratified by recipient pre-transplant (pre, orange) and at week 2 (W2, blue) and 4 (W4, green) following FMT. P-values are shown, Monte-Carlo, PERMANOVA. B. Unweighted UniFrac distance to donor is shown for the recipient before FMT and at 4 weeks post-FMT. P-values are indicated, Wilcoxon signed rank.

Figure 4.. Donor composition correlates with clinical response.

A. Principal coordinate analysis plot is shown using Bray-Curtis dissimilarity matrix and stratified by donor (blue) and recipient pre-transplant (pre, red). P-values are shown, Monte-Carlo, PERMANOVA. B. Boxplot displays the top 10 differential abundant bacteria by genus between donor and recipient pre-transplant (Pre). P-values indicated by *<0.05, Mann-Whitney, FDR-adjusted. C. Principal coordinate analysis of donor composition by Bray-Curtis dissimilarity matrix stratified by clinical response. P-values indicated, Monte Carlo, PERMANOVA. D. Hierarchical clustering of a heatmap representation of donor composition by genus colored by clinical remission as indicated. Scale represents the normalized relative abundance.

Figure 5.. Two donor FMP alters mucosal T cell responses.

Lamina propria mononuclear cells (LPMCs) were isolated from rectal endoscopic biopsies taken before (Pre) and 4 weeks after FMT (Post). A. LPMCs were stimulated with PMA/ionomycin for 4 hours and intracellular cytokine staining was performed. The percentage of total CD4+ T cells producing the designated cytokine is indicated. P-values reflect paired T-test. B. LPMCs were stained for Foxp3 and RORγt expression. The percentage of total CD4+ T cells expressing the designated transcription factor is indicated. P-values reflect paired T-test.