There is limited knowledge about the role of esophageal microbiome in Pediatric Esophageal Eosinophilia (EE). We aimed to characterize the esophageal microbiome in pediatric patients with and without EE.
In this prospective study, esophageal mucosal biopsies were obtained from 41 children. Of these, 22 had normal esophageal mucosal biopsies (‘healthy’), 6 children had reflux esophagitis (RE), 4 had proton pump inhibitor (PPI)-responsive esophageal eosinophilia (PPI-REE), and 9 had EoE. The microbiome composition was analyzed using 16S rRNA gene sequencing. The age median (range) in years for the healthy, RE, PPI-REE and EoE group were 10 (1.5-18), 6 (2-16), 6.5 (5-16), and 9 (1.5-17), respectively.
The bacterial phylum Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria were the most predominant. The Epsilonproteobacteria, Betaproteobacteria, Flavobacteria, Fusobacteria, and Sphingobacteria class were underrepresented across groups. The Vibrionales was predominant in healthy and EoE group but lower in RE and PPI-REE groups. The genus Streptococcus, Rahnella, and Leptotrichia explained 29.65% of the variation in the data with an additional 10.86% variation in the data was explained by Microbacterium, Prevotella, and Vibrio genus. The healthy group had a higher diversity and richness index compared to other groups, but this was not statistically different.
The pediatric esophagus has an abundant and diverse microbiome, both in the healthy and diseased states. The healthy group had a higher, but not significantly different, diversity and richness index compared to other groups.

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