FIG 2.

C. albicans colonization altered network topology of the bacterial microbiota. Mice were pretreated with cefoperazone in drinking water for 10 days and then either colonized with C. albicans (5 × 10⁷ CFU by oral inoculation) or not. Mice were then switched back to sterile water, and the microbiota were allowed to recover for 3 weeks. 16S rRNA sequencing was used to analyze the bacterial microbiota of fecal pellets collected prior to clindamycin treatment (day −1). The sequencing data were analyzed using QIIME2 and taxonomic identification of amplicon sequence variants (ASVs) at the genus level performed by matching to the Greengenes database. Absolute abundance of each genus was determined by multiplying the relative abundance of that genus by the total quantity of bacterial DNA normalized to grams of fecal pellet material measured by qPCR using universal primers. The absolute abundance of each genus was correlated with the abundance of every other genus using Pearson correlation, and this correlation matrix was used for network analysis (A to D) using qgraph. Each node represents a genus (described in Table 1), and each edge and its thickness represent the strength (R) of the correlation between those nodes. Only statistically significant edges are shown, P < 0.05 after Benjamini-Hochberg correction. Positive correlations are shown as black edges and negative correlations are red edges. (A and B) Co-occurrence network of the uncolonized bacterial microbiota. (C and D) C. albicans-colonized microbiota network. Nodes are colored by cluster (A and C) as determined by fast-greedy cluster analysis using igraph, such that different colors indicate separate community clusters, and by taxonomic class (B and D), for which the legend is shown far right. Network analysis of the pre-clindamycin microbiota included mice from two cohorts: total uncolonized, N = 20; C. albicans colonized, N = 24.