Gestational Environment Captured by the Neonatal Metabolome is not Predictive of Later Inflammatory Bowel Disease

BackgroundGestational exposures may contribute to the newborns lifetime risk of inflammatory bowel disease (IBD). While gestational influences are associated with IBD onset, the causality and confounding of such exposures are difficult to ascertain. The neonatal metabolome provides a metabolic snapshot of gestational influences. ObjectiveWe tested the neonatal metabolomes ability to predict future IBD, to assess whether gestational exposures are reflected in early molecular precursors of the disease. MethodsWe profiled dried blood spots from 520 newborns who later developed IBD and matched controls using high-resolution untargeted mass spectrometry metabolomics (1,350 QC-passing metabolites). Genotyping was available for 1,009 of these individuals. PERMANOVA confirmed assay sensitivity to gestational exposures, gradient boosting was used for prediction. ResultsThe neonatal metabolome significantly captured maternal smoking, birth weight, and gestational age (p < 0.001), but explained minimal variance in IBD status (R2 = 0.09%, p = 0.390) and showed no predictive power for IBD (AUC = 0.51, 95% CI 0.50-0.52, p = 0.585). Stratifying by disease subtype and age of onset did not improve performance. In contrast, genetic risk scores were modestly predictive (CD: AUC = 0.64, p < 5.11x10-14; UC: AUC = 0.63, p < 7.65x10-{superscript 1}{superscript 2}), but uncorrelated with neonatal metabolomic profiles (CD: p = 0.650; UC: p = 0.970), suggesting a later-age effect. ConclusionsUsing a large, comprehensively profiled cohort, we demonstrate that neonatal metabolomic profiles sensitively capture gestational signatures, but not the overall future IBD risk. Our findings suggest that most IBD risk accumulates later in life, beyond gestational molecular imprints.