Fig. 1: Composition and distribution of kidney bacteria in mice.
From: Cefazolin shifts the kidney microbiota to promote a lithogenic environment
A Proportion of positive regions in kidney biopsies (undiluted) exhibiting at least one bacterial colony after inoculation of kidney tissue on six different culture media. N = 18/segment. Paired, Holm’s corrected, paired chi-square tests; cortex:medulla-df=53; X2 = 5.024; p = 0.023; medulla:ureter; X2 = 5.024; p = 0.026; ureter:cortex; X2 = 10.234; p = 0.00004. B Microbial density in kidney biopsy by regions (bacterial cells/cm2), from six different culture media. N = 18/segment. Paired, Holm’s corrected, paired t-tests; cortex:medulla-df=53; t = 3.96; p = 0.0036; cortex:ureter-df=53; t = 6.47; p = 0.00002; ureter:medulla -df=53 t = 2.17; p = 0.09. C Hybridization of FISH bacterial probe in both the cortex and medulla showing proximal tubules (PT), glomeruli (GLOM), DAPI-stained nuclei (blue color), and bacteria stained with the universal, EUB probe (BAC, red dot within yellow circle). Green fluorescence is auto-flourescence. Representative image was repeated for 5 animals in the LT_abx group and 5 in the LT_noabx group. All data generated from these images is presented in Fig. 3C. D–G Comparison of bacterial diversity using 16S rRNA V4 region sequencing from animals of all the experimental groups independent of intervention. D Principle component analysis (PCoA of weighted UniFrac distance between kidney and urine samples. Statistical analysis was conducted as a PERMANOVA with 999 permutations (N = 34 kidneys, 267 urine; df=300; f = 97; p = 0.001). E Comparative phylum profile between kidney and urine samples. Statistical comparison is provided by a false discovery corrected, DESeq2 differential abundance at the phylum level. Statistical analysis was a DESeq2 differential abundance (N = 34 kidneys, 267 urine; FDR < 0.05 for phyla with *) F Alpha diversity of normalized samples using different metrics. Statistical significance is provided by Holm’s-corrected, paired t-tests (N = 34 kidneys, 267 urine; df = 300; PD_whole_tree t = 3.24, p = 0.19; Margalef t = 914, p = 0.0009; Shannon t = 2.7 × 1011, p = 6.9 × 10-12; equitability t = 4.5 × 1017, p = 5.6 × 10-18. G Differential abundance of taxa between kidney and urine. Statistical significance is provided by false discovery corrected, DESeq2 differential abundance at the ASV level. Taxa are listed to lowest assigned taxonomy. All listed taxa have FDR < 0.05. Positive log2foldchange represents ASV’s enriched in urine, negative values are ASV’s enriched in kidneys. The full set of significantly different ASVs is provided in Supplementary data 1. H Blue arrow shows the bladder, filled with methylene blue at 150 cm3 of pressure. Black arrows show the ureters with no blue dye. *p-value < 0.05, **p-value < 0.01, ***p-value < 0.001. 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.
