Microbiota and mucosal gene expression of fecal microbiota transplantation or placebo treated patients with chronic pouchitis

Figures & data

Figure 1. Luminal microbiota characteristics in chronic pouchitis patients, and comparison to the healthy fecal donor.

a: Genus-level Principal Coordinates Analysis (PCoA) plot at baseline showing separation of patients and the donor. b: Diversity index (inverse Simpson) in the donor samples and patients at baseline and follow-up time points. nr = non-relapsed, r = relapsed. Statistically significant difference indicated with an asterisk (p < .05). c: Phylum-level mean relative abundance in the donor and patients at baseline (BL) and follow-up time points (4 wk, 12 wk, 26 wk and 52 wk) based on study group and relapse status. nr = non-relapsed, r = relapsed. d: Genera with a statistically significant (q < 0.05) difference in relative abundance at baseline between pouchitis patients and the healthy donor. Selected 20 genera with the highest and lowest log2 fold change. Color of the points indicates the phylum.

Figure 2. Chronic pouchitis patients had significant differences in the luminal microbiota composition at baseline, based on the pattern of the antibiotic use and type of antibiotics used.

a:Principal Coordinates Analysis (PCoA) plot at baseline. Patients are grouped by repeated or continuous antibiotic usage and by the type of antibiotic. b: Genera with a significant (q < 0.05) difference in the relative abundance at baseline between patients using metronidazole or ciprofloxacin. Different colors of the points correspond to different phyla. c: Genera with a significant (q < 0.05) difference in the relative abundance at baseline between patients using antibiotics repeatedly or continuously. Different color of the points corresponds to different phyla.

Figure 3. The effect of FMT on microbiota composition.

a: Average Bray-Curtis dissimilarity index between the non-relapsed FMT-treated patients and placebo groups compared to the donor. Non-relapsed FMT-treated patients had lower microbiota dissimilarity with the donor at week four (4 wk) than patients in the placebo group (p = .02, Wilcoxon signed rank test). b: Principal Coordinates Analysis (PCoA) plot for the non-relapsed FMT-treated patients and placebo groups at week four (4 wk), showing a grouping of some FMT-treated patients with the donor. c: Percentage of OTUs that were present in the donor’s and patients’ post-FMT sample but absent in the patients’ pre-FMT sample, indicating the donor-like OTUs appearing after baseline in the FMT group. d: PCoA plot for the four FMT-treated patients who did not relapse during the one-year follow-up. The microbiota composition of two patients showed a shift toward the donor microbiota. Non-relapsed (nr) and relapsed (r) patients.

Figure 4. Post-FMT change in genus-level relative abundance.

Selected genera Prevotella (a) and Feacalibacterium (b) had at baseline a significant difference in abundance between patients who would receive FMT and the donor, but no significant difference was found post-FMT. Patients in the placebo group had a significantly lower abundance of selected genera compared to the donor at all time points. Significant difference (q < 0.05) as compared to the donor is indicated with an asterisk. D = donor, nr = non-relapsed.

Figure 5. Average relative abundance of phylum-level taxa in the mucosal microbiota and difference between mucosal and luminal microbiota.

a: Phylum-level average relative abundance in pouch mucosa at baseline (BL) and at week 52 (52 wk). b: Phylum-level average relative abundance in ileal mucosa at baseline and at week. 52. nr = non-relapsed, r = relapsed. c: Principal Coordinates Analysis (PCoA) plot for the luminal and mucosal microbiota at genus-level with Bray-Curtis dissimilarity in the patients and the healthy donor showing separation of the mucosal and luminal microbiota in the patients at baseline.

Figure 6. Baseline characteristics of mucosal gene expression.

a: Schematic representation of the differential gene expression analysis comparisons at baseline and the number of differentially expressed genes (DEGs). Comparison of pouch (n = 26) and ileum (n = 26), patients with high PDAI (≥7, n = 8) versus low PDAI values (<7, n = 18), patients who would eventually relapse (n = 17), independent of treatment group, and who would not relapse (n = 9), and patients who used continuous antibiotics (AB) before the trial (n = 12) and who used repeated antibiotics before the trial (n = 14). b: Volcano plot showing genes from the comparison of ileal and pouch mucosal gene expression with q-value >0.05 in black, q-value <0.05 in gray (q-value <0.05, log2FC < -1.0), in green and (q-value <0.05, log2FC >1.0) in red. c: The 15 most significant canonical pathways associated with upregulated genes in the pouch as compared to the ileum at baseline. d: The 15 most significant canonical pathways associated with downregulated genes in the pouch as compared to the ileum at baseline.

Data availability statement

The datasets generated and/or analyzed during the current study are available in the European Nucleotide Archive (ENA) repository with the accession number PRJEB52304 or by request.