Extended Data Fig. 3: Effects of F18-mix on pathogenic and commensal bacteria.
From: Commensal consortia decolonize Enterobacteriaceae via ecological control
a, b, GF B6 mice were monocolonized with Kp-2H7 and then treated with the indicated bacterial mix including F6 Bacteroidota-mix and F25 non-Bacteroidota-mix (n = 4 per group). Kp-2H7 faecal CFUs were counted over time (a), and full-length 16S rRNA gene sequencing was performed on longitudinally-collected faecal samples from each mouse (b). c, To examine the colonization resistance effect of F18-mix, GF B6 mice were first colonized with either F18-mix or F13-mix and then inoculated with Kp-2H7 on day 7. Kp-2H7 faecal CFUs were counted over time. d, GF B6 mice (n = 4 per group) were monocolonized with Pseudomonas aeruginosa or Campylobacter upsaliensis, followed by oral administration of the indicated bacterial mix. CFUs (P. aeruginosa) or level of bacterial DNA (C. upsaliensis) in longitudinal faecal samples was determined by culture or qPCR. e, f, GF B6 mice were colonized with Kp-2H7 along with 7 commensal strains chosen from our culture collection, then treated with F18-mix. Faecal abundance of each bacterial strain was quantified by qPCR using strain-specific primer sets. The relative abundance (e) and DNA concentration (f) of each strain is shown. g, GF B6 mice (n = 4 per group) were colonized with either I41-mix, K46-mix, or both of these consortia together along with a C. scindens strain (totaling 88 strains), followed by oral inoculation with F18-mix without prior antibiotic treatment. Full-length 16S rRNA gene sequencing was performed on faecal samples. Strains substantially reduced after F18-mix treatment are displayed in purple, including Bifidobacterium, Collinsella, and Megasphaera strains. Data are expressed as median ± IQR, representative of two independent experiments, and compared by Kruskal-Wallis test using the Benjamini-Hochberg correction for multiple comparisons at day 28 compared to F31-mix (a) or F18-mix (c).
