title: Inflammation-associated microbiota in pediatric eosinophilic esophagitis.
abstract: BACKGROUND
  Eosinophilic esophagitis (EoE) is an allergic disorder characterized by eosinophil-predominant esophageal inflammation, which can be ameliorated by food antigen restriction. Though recent studies suggest that changes in dietary composition may alter the distal gut microbiome, little is currently known about the impact of a restricted diet upon microbial communities of the oral and esophageal microenvironments in the context of EoE. We hypothesize that the oral and esophageal microbiomes of EoE patients are distinct from non-EoE controls, that these differences correspond to changes in esophageal inflammation, and that targeted therapeutic dietary intervention may influence community structure. Using 16S rRNA gene sequencing, we characterized the bacterial composition of the oral and esophageal microenvironments using oral swabs and esophageal biopsies from 35 non-EoE pediatric controls and compared this cohort to samples from 33 pediatric EoE subjects studied in a longitudinal fashion before and after defined dietary changes.
  
  
  RESULTS
  Firmicutes were more abundant in esophageal samples compared to oral. Proportions of bacterial communities were significantly different comparing all EoE esophageal microbiota to non-EoE controls, with enrichment of Proteobacteria, including Neisseria and Corynebacterium in the EoE cohort, and predominance of the Firmicutes in non-EoE control subjects. We detected a statistically significant difference between actively inflamed EoE biopsies and non-EoE controls. Overall, though targeted dietary intervention did not lead to significant differences in either oral or esophageal microbiota, reintroduction of highly allergenic foods led to enrichment in Ganulicatella and Campylobacter genera in the esophagus.
  
  
  CONCLUSIONS
  In conclusion, the esophageal microbiome in EoE is distinct from that of non-EoE controls, with maximal differences observed during active allergic inflammation.
authors.affiliation: Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA.
authors.forename: Alain J
authors.initials: AJ
authors.lastname: Benitez
authors.affiliation: Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104 USA ; Depto. de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP 05508-000 Brazil.
authors.forename: Christian
authors.initials: C
authors.lastname: Hoffmann
authors.affiliation: Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA ; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.
authors.forename: Amanda B
authors.initials: AB
authors.lastname: Muir
authors.affiliation: Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA.
authors.forename: Kara K
authors.initials: KK
authors.lastname: Dods
authors.affiliation: Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, PA USA ; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Spergel
authors.affiliation: Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104 USA.
authors.forename: Frederic D
authors.initials: FD
authors.lastname: Bushman
authors.affiliation: Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104 USA ; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.
authors.forename: Mei-Lun
authors.initials: ML
authors.lastname: Wang