Profiling the urinary microbiome in men with calcium-based kidney stones

Abstract

Background: The dogma that urine is sterile in healthy individuals has been overturned by recent studies applying molecular-based methods. Mounting evidences indicate that dysbiosis of the urinary microbiota is associated with several urological diseases. In this study, we aimed to investigate the urinary microbiome of male patients with calcium-based kidney stones and compare it with those of healthy individuals.

Results: The diversity of the urinary microbiota in kidney stone patients was significantly lower than that of healthy controls based on the Shannon and Simpson index (P < 0.001 for both indices). The urinary microbiota structure also significantly differed between kidney stone patients and healthy controls (ANOSIM, R = 0.11, P < 0.001). Differential representation of inflammation associated bacteria (e.g., Acinetobacter) and several enriched functional pathways were identified in the urine of kidney stones patients. Meanwhile, we found the species diversity, overall composition of microbiota and predicted functional pathways were similar between bladder urine and renal pelvis urine in kidney stone patients.

Conclusions: A marked dysbiosis of urinary microbiota in male patients with calcium-based kidney stones was observed, which may be helpful to interpret the association between bacteria and calcium-based kidney stones.

Keywords: Calcium-based; Kidney stone; Microbiome; Renal pelvis; Urine.

Fig. 1

Venn diagram of overlapping OTUs. A total of 928 OTUs were detected with 338 OTUs in HB samples only, 92 OTUs in KB samples only, 87 OTUs in KP samples only and 212 OTUs in all urine samples

Fig. 2

Microbial α − diversity of urine samples. The α − diversity indices include observed species index, Chao 1 index, Ace index, Shannon index, Simpson index and Good’s coverage index. Shannon diversity index and Simpson’s diversity index were significantly different between HB and KB group

Fig. 3

Microbial β − diversity analysis. PCoA plot of unweighted (a) and weighted (b) UniFrac metrics for HB (red dots), KB (green dots) and KP (blue dots) groups. Samples from KB and KP groups clustered closer in proximity to each other than HB samples

Fig. 4

Bacterial average relative abundance in HB, KB and KP groups at different taxonomic levels. a phylum, b class, c order, d family, e genus. Average distribution of major taxa is represented by bar graphs. Unclassified genera or genera with a relative abundance < 1% are grouped as “Other”

Fig. 5

Cladogram (a) and LEfSe analyses (b) of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)