Contemporary view on the microbiota of kidney stones and urine in patients with urolithiasis: a narrative review

Urolithiasis is a highly prevalent disease with a frequent recurrent course, indicating the limited effectiveness of existing preventive and therapeutic strategies. The revision of the long-standing paradigm of urinary tract sterility, enabled by the advent of high-throughput sequencing technologies, has led to the emergence of the urobiome concept as a complex ecosystem involved in the pathogenesis of urolithiasis. The present review systematizes current data on the role of the microbiota of urine and renal calculi in the pathogenesis of urolithiasis. The analysis demonstrated that urobiome dysbiosis, characterized by reduced alpha diversity and altered proportions of major taxa, represents a pathogenetic factor of lithogenesis rather than its consequence. Metagenomic studies show that the microbiome of kidney stones consists of specific bacterial consortia encapsulated within the mineral matrix. It has been established that different bacterial taxa directly influence stone formation through the production of enzymes initiating the formation of struvite stones (urease) and oxalate-degrading enzymes, with Oxalobacter formigenes being one of the principal producers. An important role in pathogenesis is played by the formation of bacterial biofilms, which serve as a scaffold for microbial colonization and subsequent crystallization. In addition, the role of the gut–kidney axis has been identified, in which intestinal dysbiosis triggers systemic inflammation, disruption of lithogenic metabolite homeostasis, and increased intestinal barrier permeability, collectively creating conditions favorable for lithogenesis. Thus, the available data provide a contemporary and in-depth understanding of the pathogenesis of urolithiasis, in which the microbiota is considered an active pathogenetic factor. Integration of data on the taxonomic and functional status of the urobiome opens new prospects for the development of innovative diagnostic, prognostic, and therapeutic strategies aimed at correcting dysbiosis for the treatment and prevention of urolithiasis recurrence.