Author(s)

Shuyang Yu^1,2, Tingting Liang², Yuan Gao², Heng Li², Zhemin Zhou³, Xuejie Wu^1*

¹Suzhou BenQ Medical Center, Suzhou, China.
²Suzhou Key Laboratory of Geriatric Intelligent Nursing and Health Preservation, School of Nursing, Suzhou Medical College of Soochow University, Suzhou, China.
³MOE Key Laboratory of Geriatric Diseases and Immunology, Cancer Institute, Suzhou Medical College, Soochow University, Suzhou, China.

Distinct yet linked microbial ecosystems in urinary stones and urine may influence stone pathogenesis. This study characterized the microbiome of 59 paired stone and urine samples using 16S rRNA sequencing and clinical correlation analysis. Results showed that stone biofilms were enriched with environmental bacteria (e.g., Christensenella, Chromobacterium), whereas urine primarily harbored uropathogens (e.g., Klebsiella, Acinetobacter). Significant gender and pathogen-specific patterns emerged, with Mycoplasma/Ureaplasma infections showing female predominance (85.7%) and Group 2 showing the highest median crystalluria value (57.8 counts) together with the lowest median urinary pH (6.19), although these observations were interpreted descriptively and not as statistically significant pairwise associations. Distance metrics (0 - 0.88) demonstrated varying microbial similarity between samples, with closer clustering among stone-associated communities. These findings support ecological differentiation between urinary stones and paired urine, while indicating that mechanistic and causal interpretation requires further validation.

Urinary Microbiome, Urolithiasis, 16S rRNA Sequencing, Biofilm, Microbial Ecology, Diagnostic Biomarkers

Yu, S.Y., Liang, T.T., Gao, Y., Li, H., Zhou, Z.M. and Wu, X.J. (2026) Distinct Microbial Niches in Urinary Stones and Paired Urine Samples Characterized by 16S rRNA Sequencing. Journal of Biosciences and Medicines, 14, 90-104. doi: 10.4236/jbm.2026.144008.