Statistical analysis

Statistical analyses were performed in JMP Pro version 15 (SAS). Survival curves were calculated using the Kaplan–Meier method. We used the log-rank test to determine if the survival functions of two or more groups were equal. We used analysis of variance (ANOVA) to determine whether the fold-change in gene expression of specific gene sets and of all genes were equal. We used ANOVA for GFP expression comparisons and, in cases where more than two groups were compared, used the Tukey HSD post hoc test to determine which pairs of groups in the sample differed. We used the Cell chi-square test to determine if a cell in a table differed from its expected value in the overall table. We used ordinal linear regression to determine whether the proportions of dead animals after treatment with E. faecium supernatant were equal across groups and to quantify interactions between groups using the following linear model: data = intercept + group 1 + group 2 + group 1 × group 2 + ε. The second to last term in this model quantifies the existence, magnitude, and type (synergistic or antagonistic) of interaction between groups. We used the Bonferroni correction to adjust p values when performing multiple comparisons.