Fig. 5: Clindamycin treatment alters the bacteriome composition across donors, but no specific profile predicts Candida albicans colonization success.

Relative microbiome profiling from the simulated proximal colonic compartments inoculated with the faecal-derived microbiome from donors C to J (A), from donors K to N (B) and their resulting β-diversity (C, D), from samples collected during the baseline, antibiotic, and recovery periods. A Samples were collected in Experiment 3, specifically during the baseline period (days 16 and 19) during which C. albicans strain SC5314 was inoculated at days 0 and 2, during the clindamycin treatment (days 21, 24, and 26), which started with the re-inoculation of C. albicans on day 20, and during the recovery period (days 28 and 33). B Samples were collected in Experiment 4, specifically during the baseline period (days 12 and 14) during which a GFP reporter strain of C. albicans SC5314 was inoculated at days 0 and 2, and during the clindamycin treatment (days 16, 19, and 21), which started with the re-inoculation of C. albicans on day 15. C, D Nonmetric multidimensional scaling (Bray–Curtis dissimilarity) of the genus-level relative microbiome profiling, with a focus on either the donors (C), or the range of concentrations in C. albicans, expressed in log₁₀(26S rRNA gene copy/mL) (D), with ellipses representing 95% confidence intervals.