FIG 4.

E. faecalis suppresses E. coli-driven inflammation in catheterized mouse bladders. Female C57BL/6NTac mice were implanted with catheters in the bladder and infected with 10⁷ CFU of E. coli UTI89 or 10⁷ CFU each of E. coli and E. faecalis in a 1:1 mixture. After 24 h, bladders were removed and RNA extracted. (A) Binary matrix showing association between differentially expressed genes (rows) and Gene Ontology biological process (GOBP) terms (columns) enriched in the differential expression analysis between E. coli-infected and polymicrobial species-infected animals. Differentially expressed genes that did not map to an enriched GOBP term are not shown. Dark cells indicate genes that are annotated with a GOBP term, and light cells indicate genes that are not. (B) Summary of differential expression in the set of 31 genes shown in panel A. Differential expression of each gene is summarized by the mean (black dot) log₂ ratio of expression between E. coli-infected and polymicrobial species-infected animals, where the line indicates the estimated standard error of the mean. (C) To examine whether the observed differential gene expression may be associated with a given ImmGen-defined cell type, we calculated the percentage of the top differentially expressed genes (upregulated in E. coli-infected compared to polymicrobial species-infected animals) that were placed within the top 1% of the distribution of the cell type-specific enrichment scores (73) (purple dots) compared to those for 100 sets of 50 expressed genes drawn at random (gray dots; the violin plot in yellow summarizes the overall distribution, and the vertical bar shows the level of the median). SP, stem and progenitor cells; B, B cells; DC, dendritic cells; MF, macrophages; MO, monocytes; GN, granulocytes; T4, CD4⁺ cells; T8, CD8⁺ cells; NKT, natural killer T cells; GDT, γδ T cells; SC, stromal cells; NK, natural killer cells. See Tables S1 and S2 in the supplemental material for related analyses. The experiment was performed twice (n = 3 mice per group per experiment). Representative data from one experiment are shown.