Figure 1

Antibiotic-pretreated FMT-responsive patients are depleted of transcriptionally active bacteria on the colonic mucosa. (A) Schematic of the study design, clinical arms, and biospecimen collections. Participants were randomized to one of four arms: (1) antibiotic-pretreated with capsule delivery; (2) non-antibiotic-pretreated with capsule delivery; (3) antibiotic-pretreated with enema delivery; (4) non-antibiotic-pretreated with enema delivery. Initial FMT was delivered by colonoscopy, followed by weekly FMTs over the subsequent 6 weeks. (B) Bacterial burden based on 16S rRNA copy number measured by qPCR for four antibiotic response groups: antibiotic-pretreated non-responders (Abx+ NR), non-antibiotic-pretreated non-responders (Abx− NR), antibiotic-pretreated responders (Abx+ R), and non-antibiotic-pretreated responders (Abx− R). (C) Absolute abundance plots of the 16S rRNA read counts for the top 10 genera are displayed for the four antibiotic/response groups. Columns indicate individual patients (with unique study ID) with the pre-FMT (after antibiotic pretreatment) sample displayed on the left and the post-FMT sample on the right. (D) The number of microbial-encoded antimicrobial resistance (AMR) genes expressed by mucosal-associated microbiota in NR and R patients (One-sided Wilcoxon rank sum test).