Distinct oesophageal microbiota is associated with paediatric eosinophilic oesophagitis

Eosinophilic oesophagitis (EoE) is a chronic immune-mediated disease in which oesophageal microbiota may vary according to disease activity and treatment. We aimed to characterise oesophageal microbiota in treatment-naïve children with EoE before and after proton pump inhibitor (PPI) therapy, and to assess spatial variability along the oesophagus.

In this multicentre longitudinal study, oesophageal biopsies were obtained from proximal-mid and distal oesophagus of treatment-naïve children with newly diagnosed EoE at baseline and after standardised PPI induction therapy, and from non-EoE controls. Microbiota composition was analysed using 16S rRNA gene sequencing. Alpha and beta diversity, differential taxonomic abundance and associations with eosinophilic inflammation and treatment response were assessed.

Oesophageal microbiota profiles differed between active EoE, post-treatment EoE and non-EoE controls. Active EoE showed higher alpha diversity, particularly in the presence of moderate-to-severe eosinophilic inflammation. Microbial diversity and composition were largely consistent between proximal-mid and distal oesophageal regions. Active EoE was associated with enrichment of inflammation-related taxa, including Fusobacteriota and Bacteroidota, and genera such as Neisseria, Fusobacterium and Prevotella. PPI induction therapy was associated with reduced alpha diversity and compositional shifts characterised by increased Firmicutes and reduced inflammation-associated genera, irrespective of histological response. Specific taxa were enriched in non-responders post-treatment.

Children with EoE exhibit an oesophageal microbiota profile associated with disease activity and largely stable across oesophageal regions. PPI therapy was associated with microbiota compositional changes irrespective of histological response, supporting a dynamic interaction between treatment, inflammation and the oesophageal microbial ecosystem.