Fig. 2

Compositional analysis of urine and stone microbiota. A PCA was performed on CLR-transformed Aitchison distances of all urine and stone samples. Each coloured point represents a sample. Distance between samples on the plot represents differences in microbial community composition, with 17.6% of total variance being explained by the first two components shown. Strength and association for genera are depicted by the length and direction of the grey arrows, respectively. Points are coloured by sample type and ellipses represent the 95% confidence intervals of sample types. Samples significantly differed by type and time (envfit P value < 0.05). B Shannon’s Index of alpha diversity was compared between sample groups. OR urine samples from stone patients had the lowest diversity (Kruskall-Wallis test with Dunn’s multiple comparisons, * P < 0.05, ** P < 0.01, *** P < 0.001). Data represent the median (line in box), IQR (box), and minimum/maximum (whiskers). C SVs were significantly distinct between stone former pre-operative urine compared to healthy control urine, stone former OR urine, and stones (Benjamini–Hochberg corrected Wilcoxon test P < 0.05, ANCOM W value > 0.7 threshold, ALDEx2 GLM effect size >|0.5|). Data represent the median and IQR; HC (n = 25), SF (n = 83), SF-OR (n = 59), Stone (n = 34)