Fig. 4: Characterization of bacteria in fecal samples with high and low levels of pathogenic Candida species.

a, Alignment of fecal samples according to the relative abundance of pathogenic Candida species (1^st row), bacterial burden (by 16S rDNA qPCR; 2^nd row), bacterial diversity (by Inverse Simpson Index; 3^rd row), and relative abundance of Lachnospiraceae and Bacteroidetes (4^th row). * indicates failed 16S qPCR reaction. Each bar in the bacterial diversity graph (3^rd row) is colored to indicate the anti-anaerobic antibiotic load index prior to sample collection; this index reflects the sum of administered anti-anaerobic antibiotics (metronidazole, clindamycin, carbapenems, piperacillin/tazobactam, and oral vancomycin) multiplied by the number of treatment days⁴⁰. b, Comparison of bacterial burden in samples with high (> 50%, n = 22) or low (≤ 50%, n = 71) Candida relative abundance. ***: Two-sided Wilcoxon rank sum test p = 0.00073. c, Comparison of bacterial diversity in samples with high (> 50%, n = 26) or low (≤ 50%, n = 77) Candida relative abundance. ****: Two-sided Wilcoxon rank sum test p = 1.9 × 10⁻⁵. The box plots in b and c represent the median, interquartile range (IQR) and range. d, LEfSe analysis of bacteria taxa (at family level) present in samples with high (> 50%, n = 26) or low (≤ 50%, n = 77) relative Candida abundance. The effect size corresponds to the linear discriminant analysis (LDA) score. U.C.: unclassified. A subset of the 16S rDNA sequencing data has been previously reported^7,20.