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Background <p>Kidney stones represent a common urological disorder affecting approximately 14.8% of the global population, with calcium oxalate (CaOx) stones constituting nearly 80% of all cases. Recent studies have revealed a potential association between the gut microbiome and the risk of forming CaOx stones. Additionally, urinary microbiota has been implicated to influence stone development, although the relationship between urinary microbiota and urinary metabolites in patients with calcium oxalate kidney stones remains incompletely characterized.</p> Methods <p>In this pilot cross-sectional study, we used 2bRAD sequencing for microbiome profiling (2bRAD-M) and liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to characterize urinary microbial and metabolic features. We analyzed urine samples from a pilot cohort of 12 patients with calcium oxalate kidney stones and 10 healthy controls. Statistical analyses of microbial diversity and metabolomic profiles were conducted to explore between-group differences. To explore microbiome–metabolite associations, we performed Spearman correlation analysis with multiple-testing correction and provided stratified correlation heatmaps as supplementary analyses. This study is registered in the National Medical Research Registry filing system of China (<a href="https://www.medicalresearch.org.cn">https://www.medicalresearch.org.cn</a>) (No. MR-37-23-016317).</p> Results <p>Compared with healthy controls, patients with calcium oxalate kidney stones showed exploratory differences in urinary microbial diversity and community composition. Shannon and Simpson diversity were nominally higher in the CaOx group but did not remain significant after multiple-testing correction. At the genus level, <i>Lactobacillus</i> showed a nominally lower relative abundance in the CaOx group, whereas <i>Escherichia</i> showed a nominally higher relative abundance; however, no genus remained significant after BH-FDR correction. Untargeted metabolomics identified 131 candidate metabolites using exploratory screening criteria of VIP &gt; 1 and nominal <i>P</i> &lt; 0.05, including 33 higher-abundance and 98 lower-abundance candidates in the CaOx group; however, no metabolite remained significant after BH-FDR correction. Microbiome–metabolome correlation analyses suggested exploratory association patterns but did not establish direct biological interactions.</p> Conclusions <p>This pilot cross-sectional study describes exploratory voided urine-associated microbiome and metabolome profiles in patients with calcium oxalate kidney stones. The findings are hypothesis-generating and require validation in larger, multicenter, longitudinal studies with rigorous contamination-control strategies and paired urine, stone, and fecal sampling.</p>

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Exploratory urinary microbiome and metabolome profiles in patients with calcium oxalate kidney stones: a pilot cross-sectional study

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月6日

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  • Jianchao Zhang,
  • Heng Zhang,
  • Yang Xu,
  • Changjuan Wang,
  • Xiaopeng Li,
  • Yongliang Ni

摘要

Background

Kidney stones represent a common urological disorder affecting approximately 14.8% of the global population, with calcium oxalate (CaOx) stones constituting nearly 80% of all cases. Recent studies have revealed a potential association between the gut microbiome and the risk of forming CaOx stones. Additionally, urinary microbiota has been implicated to influence stone development, although the relationship between urinary microbiota and urinary metabolites in patients with calcium oxalate kidney stones remains incompletely characterized.

Methods

In this pilot cross-sectional study, we used 2bRAD sequencing for microbiome profiling (2bRAD-M) and liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to characterize urinary microbial and metabolic features. We analyzed urine samples from a pilot cohort of 12 patients with calcium oxalate kidney stones and 10 healthy controls. Statistical analyses of microbial diversity and metabolomic profiles were conducted to explore between-group differences. To explore microbiome–metabolite associations, we performed Spearman correlation analysis with multiple-testing correction and provided stratified correlation heatmaps as supplementary analyses. This study is registered in the National Medical Research Registry filing system of China (https://www.medicalresearch.org.cn) (No. MR-37-23-016317).

Results

Compared with healthy controls, patients with calcium oxalate kidney stones showed exploratory differences in urinary microbial diversity and community composition. Shannon and Simpson diversity were nominally higher in the CaOx group but did not remain significant after multiple-testing correction. At the genus level, Lactobacillus showed a nominally lower relative abundance in the CaOx group, whereas Escherichia showed a nominally higher relative abundance; however, no genus remained significant after BH-FDR correction. Untargeted metabolomics identified 131 candidate metabolites using exploratory screening criteria of VIP > 1 and nominal P < 0.05, including 33 higher-abundance and 98 lower-abundance candidates in the CaOx group; however, no metabolite remained significant after BH-FDR correction. Microbiome–metabolome correlation analyses suggested exploratory association patterns but did not establish direct biological interactions.

Conclusions

This pilot cross-sectional study describes exploratory voided urine-associated microbiome and metabolome profiles in patients with calcium oxalate kidney stones. The findings are hypothesis-generating and require validation in larger, multicenter, longitudinal studies with rigorous contamination-control strategies and paired urine, stone, and fecal sampling.