title: Novel device to sample the esophageal microbiome--the esophageal string test.
abstract: A growing number of studies implicate the microbiome in the pathogenesis of intestinal inflammation. Previous work has shown that adults with esophagitis related to gastroesophageal reflux disease have altered esophageal microbiota compared to those who do not have esophagitis. In these studies, sampling of the esophageal microbiome was accomplished by isolating DNA from esophageal biopsies obtained at the time of upper endoscopy. The aim of the current study was to identify the esophageal microbiome in pediatric individuals with normal esophageal mucosa using a minimally invasive, capsule-based string technology, the Enterotest™. We used the proximal segment of the Enterotest string to sample the esophagus, and term this the "Esophageal String Test" (EST). We hypothesized that the less invasive EST would capture mucosal adherent bacteria present in the esophagus in a similar fashion as mucosal biopsy. EST samples and mucosal biopsies were collected from children with no esophageal inflammation (n = 15) and their microbiome composition determined by 16S rRNA gene sequencing. Microbiota from esophageal biopsies and ESTs produced nearly identical profiles of bacterial genera and were different from the bacterial contents of samples collected from the nasal and oral cavity. We conclude that the minimally invasive EST can serve as a useful device for study of the esophageal microbiome.
authors.affiliation: Department of Pediatrics, Section of Gastroenterology, Hepatology and Nutrition, Digestive Health Institute, Children's Hospital Colorado, University of Colorado Denver, School of Medicine, Aurora, Colorado, United States of America. sophie.fillon@ucdenver.edu
authors.forename: Sophie A
authors.initials: SA
authors.lastname: Fillon
authors.forename: J Kirk
authors.initials: JK
authors.lastname: Harris
authors.forename: Brandie D
authors.initials: BD
authors.lastname: Wagner
authors.forename: Caleb J
authors.initials: CJ
authors.lastname: Kelly
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Stevens
authors.forename: Wendy
authors.initials: W
authors.lastname: Moore
authors.forename: Rui
authors.initials: R
authors.lastname: Fang
authors.forename: Shauna
authors.initials: S
authors.lastname: Schroeder
authors.forename: Joanne C
authors.initials: JC
authors.lastname: Masterson
authors.forename: Charles E
authors.initials: CE
authors.lastname: Robertson
authors.forename: Norman R
authors.initials: NR
authors.lastname: Pace
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Ackerman
authors.forename: Glenn T
authors.initials: GT
authors.lastname: Furuta
mesh_terms: D000293:Adolescent; D000328:Adult; D001706:Biopsy / Q000379:methods; D002648:Child; D004724:Endoscopy / Q000379:methods; D004867:Equipment Design; D004947:Esophagus / Q000382:microbiology*; D020224:Expressed Sequence Tags; D005260:Female; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D007249:Inflammation; D008297:Male; D054892:Metagenome; D008957:Models, Genetic; D012336:RNA, Ribosomal, 16S / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S