Disentangling causal relationships linking the oral microbiome, metabolism, inflammation, and dental caries via Mendelian randomization.

Dental caries is a major global health burden. While observational studies suggest links between the oral microbiome, metabolism, inflammation, and caries, causal relationships remain unclear due to confounding and reverse causation. This study aimed to systematically dissect both the causal roles and the interplay between these factors in caries etiology. We employed a two-sample Mendelian randomization (MR) framework using large-scale genome-wide association study summary statistics. Univariable MR was used to assess the direct causal effects of oral microbial taxa, circulating metabolites, and inflammatory proteins on caries risk. Multivariable MR and 2-step MR were subsequently applied to perform mediation analysis and disentangle complex causal pathways. Effect sizes are reported as odds ratios (ORs) with 95% confidence intervals (CIs). Univariable MR identified protective causal effects of the genera Haemophilus (OR = 0.965, 95% CI: 0.937-0.994) and Rothia (OR = 0.965, 95% CI: 0.934-0.996) on caries risk. Genetically predicted higher levels of N4-acetylcytidine and pyrraline were associated with increased risk, whereas eicosapentaenoate showed a protective effect. The inflammatory proteins C-X-C motif chemokine 11 and signaling lymphocytic activation molecule family member 1 were causally associated with higher caries risk. Crucially, mediation analysis revealed that the protective effect of Haemophilus was partly mediated through its influence on circulating gamma-glutamylthreonine and X-11483 (an untargeted metabolomics feature ID). Our findings provide robust causal evidence for an integrated oral microbiome-metabolism-inflammation axis in caries etiology. These results highlight novel biomarkers for risk stratification and potential therapeutic targets, offering a scientific basis for developing more effective preventive strategies against this prevalent disease.