All statistical analysis was conducted using R and Prism 7 (GraphPad). Data are expressed as means ± SD. For each set of data, normality was determined using the Shapiro-Wilk Normality Test. For data with two treatment groups, each experimental group mean was compared pairwise against the control group mean using either Welch’s t test or Wilcoxon rank sum test with a correction for multiple comparisons using the Benjamini-Hochberg procedure. Means of parametric data with >2 treatment variables compared at a single time point were analyzed using a one-way ANOVA. Significant ANOVA results were followed by Tukey’s honestly significant difference post hoc test. Means of nonparametric data with >2 treatment variables compared at a single time were analyzed using pairwise Wilcoxon rank sum tests with P value correction for multiple testing using the Benjamini-Hochberg procedure. To compare means of two treatment groups over time, a two-way ANOVA was used, followed by Tukey’s honestly significant difference post hoc test. If the two-way ANOVA residuals were nonparametric, the Kruskal-Wallis rank sum test, followed by Dunn’s Kruskal-Wallis multiple comparison post hoc test, was used. Intergroup significance in β-diversity was computed using the Adonis test applied pairwise, using the Benjamini-Hochberg procedure for P value correction. A value of P < 0.05 was considered significant, except for the assessment of colonic tissue cytokines and chemokines, the pairwise group comparisons of observed species for α-diversity, and β-diversity comparisons between MMF- and vancomycin-treated animals, where a value P < 0.1 was considered significant.

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