Gut microbiome and metabolome signatures in calcium oxalate stone recurrence: a multi-omics study

The incidence and recurrence rate of nephrolithiasis have been increasing annually. Recent evidence highlights a close association between the composition and function of the gut microbiome and the occurrence and recurrence of kidney stones. We performed a multi-omic study to investigate changes in gut microbiota and their metabolites during nephrolithiasis development and recurrence, and to explore the underlying molecular mechanisms. Stool samples from 37 recurrent stone patients, 38 first-episode stone patients, and 39 healthy controls were collected for 16S rDNA amplicon sequencing and liquid chromatography-mass spectrometry. Ten samples from each group were randomly selected for metagenomic sequencing. Compared to incident cases, recurrent stone patients exhibited further reduced gut microbial richness and diversity, with enrichment of Enterobacterales, Pseudomonadota, Gammaproteobacteria, Enterobacteraceae, Escherichia-Shigella, and Bacillia. In the recurrent kidney stone group, 9 metabolites were upregulated and 86 downregulated, with enrichment of genes in purine and caffeine metabolism pathways. We identified 10 metabolites as recurrence biomarkers and significant correlations between Escherichia-Shigella and Asn-Tyr, Leu-Ala-Ile, Tyrosyl-Alanine, or 3'-hydroxyhexobarbital. Additionally, gender-specific gut microbiota signatures were observed. Oxalate decarboxylase and short-chain fatty acid-related enzymes decreased during stone formation but rebounded with recurrence. Caffeine and its metabolites were significantly downregulated in recurrent patients, suggesting a potential association with stone formation and recurrence that merits further investigation. Our study comprehensively characterizes gut microbiome and metabolome signatures associated with nephrolithiasis recurrence. The findings reveal that recurrent nephrolithiasis is characterized by impaired gut microbial evenness, enrichment of specific taxa including Escherichia-Shigella, and dysregulated metabolic pathways such as purine metabolism and caffeine metabolism. The 10 identified metabolites show promise as potential recurrence biomarkers, with notable correlations between Escherichia-Shigella and key metabolites. These results highlight the critical association of the gut microbiome-metabolome axis with renal stone recurrence, providing novel microbial and metabolic targets for early prediction, with potential implications for prevention and personalized treatment that require further validation.