Treatment of eosinophilic oesophagitis with an elemental diet is associated with changes in the microbial communities of the upper gastrointestinal tract

Objective: Eosinophilic oesophagitis (EoE) is an allergic disease characterized by oesophageal dysfunction and eosinophil-predominant inflammation. The course of disease can be ameliorated by elimination diets or total restriction of food antigens through an elemental diet. Our knowledge for the role of oesophageal microbiota upon EoE is limited to two studies, both of which reported altered microbiota communities from EoE patients. Therefore, this study aimed to examine the GI-microbiota composition from EoE subjects with active disease and study their response to an elemental diet intervention and, compare with healthy subjects.Design: We used 16S rRNA gene amplicons to profile the microbial composition of the gastrointestinal tract of adult EoE participants (n=17) from the IMAGE study (trial nr. NTR4892). Biopsies from oesophagus and duodenum along with samples from saliva and faeces from EoE patients at baseline and at four weeks post intervention were sequenced. Healthy controls (n=8) were also recruited and sampled once. Clinical symptoms and dietary intake were used to assess correlations with the microbiota data. Results: The microbial composition of the upper GI tract of EoE patients was distinct at baseline and became more similar with healthy control after the elemental diet intervention. A significant reduction of the genera Streptococcus in saliva and Vellionella in oesophagus was observed after the intervention. Streptococcus was negatively correlated with iron and calcium intake and Vellionella positively with protein intake. The mucolytic bacterium Ruminococcus torques was enriched in patients with active EoE in duodenal biopsies and decreased after the intervention. No significant changes were observed for the faecal microbiota which remained different from healthy controls after 4 weeks of dietary intervention.Conclusion: These results reinforce previous findings supporting the statement that composition of oesophageal microbiota of active EoE patients is distinct and becomes mmore similar with healthy subjects after an elemental diet treatment.