AUTHOR=Gong Jiayin , Lin Mingxing , Chen Lizhen , Xiong Wenting , Zhang Yuying , Liu Changyun , Chen Shenggen , Lin Wanhui , Zhu Chaofeng , Huang Huapin 

TITLE=Microbiota–sphingolipid pathway in generalized epilepsy: evidence from Mendelian randomization and clinical metabolomics

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 16 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1662050

DOI=10.3389/fmicb.2025.1662050

ISSN=1664-302X

ABSTRACT=ObjectiveEpilepsy is a complex disorder with growing evidence linking gut microbiota and metabolism, though causal relationships unclear. This study investigated causal effects of gut microbiota on three epilepsy types via metabolic pathways, using Mediation Mendelian randomization (MR), evaluated directional consistency metabolomics of refractory epilepsy (RE) patients before and after medium-chain triglyceride (MCT) diet intervention.MethodsTwo-step MR was applied to summary statistics for 207 species (Dutch Microbiome Project) and 196 species (MiBioGen consortium), evaluating 871 serum metabolites as mediators of three epilepsy types. For validation, directional consistency in metabolomics was conducted on serum samples from 9 RE patients before and after MCT diet intervention.ResultsOnly sphingomyelin (SM; d18:0/20:0, d16:0/22:0) and Glycocholate glucuronide (1) were the metabolites significantly associated with three epilepsy types. Mediation MR analysis revealed Mollicutes RF9 had a unidirectional effect via sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1) modulation (P = 0.009). In contrast, Gamma-proteobacteria and Oxalobacter demonstrated bidirectional mediation: via glutamine conjugate of C6H10O2(2) and cerotoylcarnitine (C26) (P = 0.026 and P = 0.033, respectively); while these pathways were protective in mediation, higher abundances were associated with increased risk of generalized epilepsy. Notably, no significant mediators were identified for epilepsy or focal epilepsy. Metabolomics further confirmed MCT diet-induced elevations in 7 specific SM species. Among these, SM (d18:1/36:8) remained statistically significant after Benjamini–Hochberg false discovery rate (BH-FDR) correction. Notably, changes in SM (d18:1/36:8) and SM (d18:1/14:3) were positively correlated with seizure control rates.ConclusionThis study identifies both unidirectional and bidirectional microbiota–metabolite pathways modulating generalized epilepsy risk, with converging evidence pointing to sphingomyelin as a potential lipid biomarker and therapeutic target.