Urinary volatilomics for biomarker discovery in kidney stone patients and healthy controls

Nephrolithiasis is a prevalent and recurrent condition with a rising incidence worldwide, largely attributed to modifiable lifestyle factors, including diet. Novel, non-invasive biomarkers are needed to improve early diagnosis, recurrence monitoring, and personalized prevention. This study aimed to identify urinary volatile organic compounds (VOCs) that differentiate healthy individuals from kidney stone formers and to explore their associations with fermented food intake. Using dynamic headspace Vacuum in-tube extraction gas chromatography-mass spectrometry (DHS-V-ITEX-GC-MS), 24-h urine samples were analyzed to identify potential volatile biomarkers related to kidney stone risk. This case-control study included 232 patients with recurrent kidney stone disease and 168 healthy controls enrolled in the Swiss Kidney Stone Cohort. Urine samples were analyzed using untargeted volatilomic profiling. Data were normalized, quality-filtered, and adjusted for relevant confounders, including study center, sex, age, body mass index, smoking status, and diabetes status. Uni- and multivariate statistical analyses were applied to identify discriminative features, followed by metabolite identification. Seventy-seven metabolites differed significantly between kidney stone formers and controls. Octane, 1,1'-oxybis- and 6-methyl-5-hepten-2-one were present at higher levels in controls, whereas acetic acid and propanoic acid were detected at higher levels in participants with kidney stones. Among these metabolites, three were associated with fermented food consumption, with 3-nonen-2-one emerging as a potential mediator of the association between coffee consumption and reduced kidney stone risk.