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. 2012;7(9):e42938.
doi: 10.1371/journal.pone.0042938. Epub 2012 Sep 5.

Novel Device to Sample the Esophageal Microbiome--The Esophageal String Test

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Free PMC article

Novel Device to Sample the Esophageal Microbiome--The Esophageal String Test

Sophie A Fillon et al. PLoS One. .
Free PMC article

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.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Microbiome phylum-level diversity is similar in esophageal, oral and nasal microenvironments.
Microbiome diversity was measured from DNA samples taken from the esophageal mucosa, oral and nasal samples as identified using 454 pyrosequencing. Each point represents the number of Taxa present in each sample. The mean ± standard error of the mean are presented.
Figure 2
Figure 2. Esophageal genera captured on mucosal biopsies and ESTs are similar.
Bacterial taxa were compared from 15 matched biopsy and EST samples, the negative log p-value from this comparison is displayed for each taxa. The gray horizontal lines indicate significant differences (p<0.05 and p<0.01). The phyla are represented in different colors as in the key. Genera that were significantly different are numbered. Numbers represent: 1, Actinomyces; 2, Pasteurella. 2, had higher relative abundance in EST versus biopsy.
Figure 3
Figure 3. Esophageal phyla captured on mucosal biopsies and ESTs are similar.
A. Bar graphs indicate phylum detected in 15 matched biopsy (B) and EST samples (E) with each line corresponding to one subject sample. Each phylum is indicated in a different color. The width of the bar corresponds to the relative phylum abundance. B. Bar graphs present the aggregate of all subjects (1–15) of the relative phylum abundance detected in biopsies (B) and ESTs (E).
Figure 4
Figure 4. Similar genera in the esophageal biopsy and EST microbiomes.
A. Bar graphs indicate genera detected in 15 matched biopsy (B) and EST samples (E) with each line corresponding to one subject sample. Each genus is indicated in a different color. The width of the bar corresponds to the relative genus abundance. B. Pie chart composed of the 10 most prevalent genera in biopsies (n = 15). C. Pie chart composed of the 10 most prevalent genera in ESTs (n = 15). The average percentage of each genus is indicated based on the total bacterial population measured.
Figure 5
Figure 5. Percentage of common genera captured on mucosal biopsies and ESTs.
Venn diagram indicating the overlap between biopsies and ESTs for the common genera identified (≥1% relative abundance).
Figure 6
Figure 6. Oral and nasal microbiomes differ from the esophageal microbiome.
DNA samples were taken from the oral, nasal and EST and the microbiome identified using 454 pyrosequencing. Bacterial phyla are compared between biopsy and EST samples and results displayed using Manhattan plot as follows. A. Esophagus (EST) compared to the oral cavity, Genera that were significantly different are numbered. Numbers represent: 1, Prevotella; 2, Neisseria. 1, had higher relative abundance in EST. B. Esophagus (EST) compared to the nasal cavity. Numbers represent 1, Corynebacterium; 2, Propionibacterium; 3 Porphyromonas; 4, Prevotella; 5, Staphylococcus; 6, Streptococcus; 7, Veillonella; 8, Fusobacterium; 9, Haemophilus; 10, Pasteurella. Numbers 3, 4, 6–10 were higher in EST. C. Nasal cavity compared to the oral cavity. Numbers represent: 1, Corynebacterium; 2, Propionibacterium; 3, Porphyromonas; 4, Prevotella; 5, Staphylococcus; 6, Streptococcus; 7, Veillonella; 8, Fusobacterium; 9, Aggregatibacterium; 10, Haemophilus; 11, Pasteurella. Numbers 3, 4, 6–11 were higher in oral samples. Gray horizontal lines indicate significant differences (p<0.05 and p<0.01). Phyla are represented on the X-axis as different colors as in the key.

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