Fig. 2: Impact of cefazolin on urine microbiota.

A Alpha diversity (Margalef’s species richness) over the course of the experiment for animals given cefazolin long-term and controls with no antibiotic treatment. Two-way ANOVA results are shown. Means are plotted +/- SEM. (N = 3-5 per group/timepoint; df=61; f = 12.6, 15.67, and 2,55 for group, timepoint, and interaction; p = 0.0007, 0.0002, and 0.11, respectively. B Alpha diversity over the course of the experiment for animals given cefazolin long-term and controls with no treatment, and with recovery following antibiotic cessation. Two-way ANOVA results are shown. Means are plotted +/- SEM. (N = 3-5 per group/timepoint; df=99; f = 8.5; p = 0.021. #Indicates when antibiotics started. ^Indicates the point at which antibiotics ceased. C PCoA of weighted UniFrac distance between the last timepoint for urine specimens with long-term antibiotic use (LT_abx) and controls without antibiotics (LT_noabx). Statistical comparison was conducted as a PERMANOVA with 999 permutations (N = 5/group; df=7, f = 3.94,p = 0.018). D Differential abundance taxa between the first and the last timepoints in urine specimens with or without antibiotic exposure. Negative values are the number of taxa lost over the course of the trial, while positive values are those that increased in abundance. Statistical significance is provided by false discovery corrected, DESEQ2 differential abundance at the ASV level. Taxa are listed to lowest assigned taxonomy. N = 5/group. Full set of significant results and statistics is provided in Supplementary data 2. E Impact of cefazolin on the abundance of Lactobacillus and Enterobacteriaceae, based on 16S rRNA sequencing of all animals. 2-way ANOVA results are shown (N = 132/group; df=342, f = 1.088, 2.097, and 4.281 for abx, taxa, and interaction; p = 0.29, 0.04, and 0.04, respectively. F Urinary cytokine concentrations (by ELISA) in response to long-term antibiotic use. Two-way ANOVA results are shown with post-hoc paired, Holm’s-corrected t-tests. (N = 3/group; df = 17, f = 16.49, 72.51, and 11.87 for abx, cytokine, and interaction; p = 0.0016, 1.99 × 10^-7, and 0.001, respectively. *p-value < 0.05, **p-value < 0.01, ***p-value < 0.001 for post-hoc t-tests. # indicates start of antibiotics; ^ indicates antibiotic cessation. For box and whisker plots; the center is the data mean, minima and maxima are the 25th and 75th percentiles; whiskers extend 1.5 interquartile range from minima and maxima. Source data are provided as a Source Data file.