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.
Highlights
Recent studies of the human microbiome have provided robust support for the important role of the microbiome in health and disease [1,2]
Five subjects were on proton pump inhibitor (PPI) for heartburn at the time of the study, two were on inhaled steroids for asthma or rhinitis, three were on food elimination diet, and one was on inhaled steroid in addition to PPI and food elimination diet
Bacterial ribosomal RNA gene amplification products from mucosal biopsies and from the nasal cavity, oral cavity and Esophageal String Test’’ (EST) were visualized by gel electrophoresis (Figure S2)
Summary
Recent studies of the human microbiome have provided robust support for the important role of the microbiome in health and disease [1,2]. Whereas a significant body of work defines the intestinal microbiology, few studies have investigated the esophageal microbiome To date, these studies utilized mucosal biopsy samples that were obtained at the time of endoscopic procedures [3,4,5,6,7,8]. Repeated and frequent sampling following therapeutic interventions are impractical and the full characterization of esophageal mucosal microbiome is limited to a ,3 mm section of procured tissue. To address this issue, we utilized the proximal section of a minimally invasive device, the EnterotestTM, to sample the esophageal mucosal microbial microenvironment. We hypothesized that analogous to fecal sampling, the intraluminal contents in the esophagus would be reflective of the mucosal microbial environment present on esophageal mucosal tissue
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