title: Esophageal microbiome in eosinophilic esophagitis.
abstract: OBJECTIVE
  The microbiome has been implicated in the pathogenesis of a number of allergic and inflammatory diseases. The mucosa affected by eosinophilic esophagitis (EoE) is composed of a stratified squamous epithelia and contains intraepithelial eosinophils. To date, no studies have identified the esophageal microbiome in patients with EoE or the impact of treatment on these organisms. The aim of this study was to identify the esophageal microbiome in EoE and determine whether treatments change this profile. We hypothesized that clinically relevant alterations in bacterial populations are present in different forms of esophagitis.
  
  
  METHODS
  In this prospective study, secretions from the esophageal mucosa were collected from children and adults with EoE, Gastroesophageal Reflux Disease (GERD) and normal mucosa using the Esophageal String Test (EST). Bacterial load was determined using quantitative PCR. Bacterial communities, determined by 16S rRNA gene amplification and 454 pyrosequencing, were compared between health and disease.
  
  
  RESULTS
  Samples from a total of 70 children and adult subjects were examined. Bacterial load was increased in both EoE and GERD relative to normal subjects. In subjects with EoE, load was increased regardless of treatment status or degree of mucosal eosinophilia compared with normal. Haemophilus was significantly increased in untreated EoE subjects as compared with normal subjects. Streptococcus was decreased in GERD subjects on proton pump inhibition as compared with normal subjects.
  
  
  CONCLUSIONS
  Diseases associated with mucosal eosinophilia are characterized by a different microbiome from that found in the normal mucosa. Microbiota may contribute to esophageal inflammation in EoE and GERD.
authors.affiliation: Division of Pulmonology, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: J Kirk
authors.initials: JK
authors.lastname: Harris
authors.affiliation: Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, United States of America.
authors.forename: Rui
authors.initials: R
authors.lastname: Fang
authors.affiliation: Division of Pulmonology, University of Colorado School of Medicine, Aurora, CO, United States of America; Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, United States of America.
authors.forename: Brandie D
authors.initials: BD
authors.lastname: Wagner
authors.affiliation: Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Ha Na
authors.initials: HN
authors.lastname: Choe
authors.affiliation: Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Caleb J
authors.initials: CJ
authors.lastname: Kelly
authors.affiliation: Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Shauna
authors.initials: S
authors.lastname: Schroeder
authors.affiliation: Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Wendy
authors.initials: W
authors.lastname: Moore
authors.affiliation: Division of Pulmonology, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Stevens
authors.affiliation: Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Alyson
authors.initials: A
authors.lastname: Yeckes
authors.affiliation: Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University, Chicago, IL, United States of America; Department of Pediatrics, John H. Stroger Hospital of Cook County, Chicago, IL, United States of America.
authors.forename: Katie
authors.initials: K
authors.lastname: Amsden
authors.affiliation: Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University, Chicago, IL, United States of America; Department of Pediatrics, John H. Stroger Hospital of Cook County, Chicago, IL, United States of America.
authors.forename: Amir F
authors.initials: AF
authors.lastname: Kagalwalla
authors.affiliation: Department of Medicine, Division of Gastroenterology & Hepatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, United States of America.
authors.forename: Angelika
authors.initials: A
authors.lastname: Zalewski
authors.affiliation: Department of Medicine, Division of Gastroenterology & Hepatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, United States of America.
authors.forename: Ikuo
authors.initials: I
authors.lastname: Hirano
authors.affiliation: Department of Medicine, Division of Gastroenterology & Hepatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, United States of America.
authors.forename: Nirmala
authors.initials: N
authors.lastname: Gonsalves
authors.affiliation: Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Lauren N
authors.initials: LN
authors.lastname: Henry
authors.affiliation: Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Joanne C
authors.initials: JC
authors.lastname: Masterson
authors.affiliation: Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America.
authors.forename: Charles E
authors.initials: CE
authors.lastname: Robertson
authors.affiliation: Department of Pediatrics, National Jewish Health, Denver, CO, United States of America.
authors.forename: Donald Y
authors.initials: DY
authors.lastname: Leung
authors.affiliation: Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America.
authors.forename: Norman R
authors.initials: NR
authors.lastname: Pace
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, United States of America.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Ackerman
authors.affiliation: Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Glenn T
authors.initials: GT
authors.lastname: Furuta
authors.affiliation: Digestive Health Institute, Section of Pediatric Gastroenterology, Hepatology and Nutrition, Children's Hospital Colorado, Gastrointestinal Eosinophilic Diseases Program, Mucosal Inflammation Program, University of Colorado School of Medicine, Aurora, CO, United States of America.
authors.forename: Sophie A
authors.initials: SA
authors.lastname: Fillon
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D057765:Eosinophilic Esophagitis / Q000382:microbiology*; D005260:Female; D005764:Gastroesophageal Reflux / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D064307:Microbiota; D008875:Middle Aged; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S