Fig. 1

Bacterial diversity and structure among the groups. a Comparison of alpha diversity (Observed species, Chao1, Shannon index, and Simpson’s index) between the urinary microbiome of the Bladder A, Bladder B, SKP, NSKP and Blood samples illustrates lower bacterial richness and diversity in Blood samples than the other groups. b PCoA shows the bacterial composition clustering of the Bladder A, Bladder B, SKP, NSKP and Blood samples based on Bray–Curtis distances, with each point corresponding to a patient and colored according to the sample type (Bladder A, Bladder B, SKP, NSKP or Blood). PERMANOVA indicated that the bacterial communities between SKP vs Bladder A/Bladder B/ NSKP were non-significantly different (p > 0.05), whereas SKP vs Blood was significantly different (p = 0.003); Bladder A/Bladder B vs NSKP were non-significantly different (p > 0.05), whereas NSKP vs Blood was significantly different (p = 0.003); Bladder A vs Bladder B was non-significantly different (p > 0.05), whereas Bladder A vs Blood was significantly difference (0.003); Bladder B vs Blood was significantly different (p = 0.003). c Venn diagram showing that the number of shared OTUs by the KP (including SKP and NSKP) and Blood samples is lower than that shared by the Bladder A/B and KP samples. In addition, the number of shared OTUs by the Bladder A/B and SKP samples is lower than those shared by the Bladder A/B samples and NSKP. Abbreviations: NSKP, non-stone kidney pelvis; OTUs, operational taxonomic units; PCoA, principal coordinates analysis; PERMANOVA, permutational multivariate analysis of variance; SKP: SKP, stone kidney pelvis