Fig. 5

Antibiotic treatments alter fungal microbiota before and during colitis. a Fungal levels on day 0 in the fecal microbiota of mice treated with vancomycin, colistin, and vehicle were quantified using 18S rRNA qRT-PCR and were normalized to the bacterial population and quantity of DNA (μg of DNA). Data are presented as the mean ± s.e.m. b Shannon index describing the alpha diversity of the fungal microbiota (ITS2) in the fecal microbiota of mice treated with vancomycin (V), colistin (C), and vehicle (H₂O). c Beta diversity. Principal coordinate analysis of Bray–Curtis distance with each sample colored according to the disease phenotype. PC1, PC2, and PC3 represent the top three principal coordinates that, together, captured most of the diversity. The fraction of diversity captured by the coordinate is given as a percentage. Groups were compared using PERMANOVA. d Specific bacterial-fungal correlation pattern in mice treated with vancomycin, colistin, and vehicle. Distance correlation plots of the relative abundance of fungal and bacterial families and genera. Statistical significance was determined for all pairwise comparisons; only significant correlations (P value < 0.05) are displayed and “*” means that correlations remained statistically significant after correction for false discovery rate. Positive values (blue squares) indicate positive correlations, and negative values (red squares) indicate negative correlations. The shading of the square indicates the magnitude of the association; darker shades are more strongly associated than lighter shades. The sign of the correlation was determined using Spearman’s method. Throughout, data are mean ± s.e.m. *P < 0.05 and **P < 0.01 by one-way ANOVA with a post hoc Tukey test; n = 5 mice per group