Bioinformatic Analysis of Oxalate-Degrading Enzymes in Probiotics: A Systematic Genome-Scale and Structural Survey

This bioinformatic study provides a comprehensive theoretical assessment of oxalate-degrading enzymes in probiotics. Kidney stone disease is a common urological disorder with rising global incidence, largely driven by the precipitation of insoluble calcium oxalate salts. Current treatments-including thiazides, lithotripsy, or ultrasound fragmentation-often show variable outcomes and high recurrence rates. Here, we systematically assessed the oxalate-degrading potential of 38 probiotic species listed in the List of Cultures Available in Food (China National Health Commission) along with selected next-generation probiotics. Using BLASTp homology searches, we identified seven strains carrying both <i>oxalyl-CoA decarboxylase</i> (<i>OXC</i>) and <i>formyl-CoA transferase</i> (<i>FRC</i>) genes, one encoding <i>oxalate decarboxylase</i> (<i>OXDC</i>), and three harboring subunits of <i>oxalate oxidoreductase</i> (<i>OOR</i>). Additionally, seven species from international probiotic lists (<i>EFSA QPS</i> and <i>AEProbio</i>) were analyzed, among which two carry both <i>OXC</i> and <i>FRC</i> genes. We prioritized strains with the coupled OXC-FRC pathway or OOR enzymes, examined catalytic site conservation by multiple sequence alignment, and performed AlphaFold-based structural prediction with Template Modeling (TM)-align scoring. Species with TM-scores >0.8 exhibited highly conserved folds, suggesting functional oxalate degradation capacity. These findings provide theoretical guidance for identifying probiotic candidates with oxalate-degrading activity and establish a framework for developing next-generation functional probiotics to alleviate kidney stone disease.