Gluten free diet does not fully restore the faecal metabolome in paediatric coeliac disease

Abstract Background and Aims Coeliac disease (CD) is an autoimmune enteropathy triggered by gluten ingestion, with a strict gluten-free diet (GFD) as the only currently effective treatment. Despite clinical and serological improvements with dietary management, the extent to which the gut metabolic environment normalises remains poorly understood. This study aimed to characterise the faecal metabolome of children with CD across disease states and following GFD intervention. Methods Faecal samples were collected from 143 children aged 2–15 years, comprising untreated CD (UCD; n = 27), treated CD (TCD; n = 40), healthy controls (HC; n = 56), and unaffected siblings (n = 20). A prospective cohort of UCD patients (n = 12) was sampled at diagnosis and at 6 and 12 months after GFD initiation. Untargeted liquid chromatography–mass spectrometry (LC-MS) metabolomics was performed, with multivariate (OPLS-DA, PC-CVA) and univariate statistical analyses applied, alongside ROC-based biomarker evaluation. Results Three distinct metabolite patterns were identified: (1) CD-specific metabolites persistently altered in both UCD and TCD relative to HC, including bile acid derivatives, sterols, acylcarnitines, and amino acid dipeptides (combined AUC = 0.868); (2) treatment-responsive metabolites normalised by GFD, predominantly amino acid oligopeptides and microbial-derived compounds such as indole-3-lactic acid; and (3) diet-driven metabolites altered in TCD independently of disease status, reflecting GFD-related shifts in tryptophan and purine metabolism. Longitudinal analysis confirmed dynamic, time-dependent metabolic changes over 12 months of treatment. Conclusion Paediatric CD is characterised by distinct faecal metabolic signatures that only partially resolve with GFD. Persistent alterations in bile acid, sterol, and microbial metabolite pathways may reflect ongoing gut dysfunction and represent promising non-invasive biomarkers for disease monitoring.