Urine microbiome profiles in patients with different types of kidney stones.

Abstract

Kidney stone disease (KSD) is a multifactorial condition influenced by systemic and extrinsic factors, including diet, genetics, metabolic disorders, and microbial and environmental factors. Although preliminary evidence links the urinary microbiome (UMB) to stone formation, its role in different stone types remains unclear. We analysed UMB in patients with four distinct types of kidney stones (calcium oxalate, struvite, uric acid, and mixed composition). Urine samples from patients with KSD and controls were analysed using 16S rRNA gene sequencing. Patients with KSD exhibited distinct microbiota compositions, with increased abundances of Corynebacterium, Prevotella, and Staphylococcus than controls. The abundance of Dongia and Stenotrophomonas was higher in pure-stone formers than in mixed-stone formers (p < 0.05). Calcium oxalate stone formers had elevated levels of Pseudomonas and Dongia and reduced levels of Peptoniphilus than controls (p < 0.05). No significant differences in microbial diversity were observed between groups. Microbial composition correlated with blood and urine parameters, suggesting a potential influence on metabolic health and stone formation. These findings underscore the important role of UMB in KSD and provide valuable insights into its involvement in disease development and new opportunities for microbiome-based therapeutic strategies.