Novel ex vivo model to examine the mechanism and relationship of esophageal microbiota and disease

Samuel Cass, Catherine Hamilton, Aaron Miller, Daniel Jupiter, Kamil Khanipov, Adam Booth, Richard Pyles, Timothy Krill, Gabriel Reep, Ikenna Okereke

Research output: Contribution to journalArticlepeer-review


Rates of esophageal cancer have increased over the last 40 years. Recent clinical research has identified correlations between the esophageal microbiome and disease. However, mechanisms of action have been difficult to elucidate performing human experimentation. We propose an ex vivo model, which mimics the esophagus and is ideal for mechanistic studies on the esophageal microbiome and resultant transcriptome. To determine the microbiome and transcriptome profile of the human distal esophagus, the microbiome was assessed in 74 patients and the transcriptome profile was assessed in 37 patients with and without Barrett’s esophagus. Thereafter, an ex vivo model of the esophagus was created using an air–liquid interfaced (ALI) design. This design created a sterile apical surface and a nutrient-rich basal surface. An epithelial layer was grown on the apical surface. A normal microbiome and Barrett’s microbiome was harvested and created from patients during endoscopic examination of the esophagus. There was a distinct microbiome in patients with Barrett’s esophagus. The ex vivo model was successfully created with a squamous epithelial layer on the apical surface of the ex vivo system. Using this ex vivo model, multiple normal esophageal and Barrett’s esophageal cell lines will be created and used for experimentation. Each microbiome will be inoculated onto the sterile apical surface of each cell line. The resultant microbiome and transcriptome profile on each surface will be measured and compared to results in the human esophagus to determine the mechanism of the microbiome interaction.

Original languageEnglish (US)
Article number142
Pages (from-to)1-15
Number of pages15
Issue number2
StatePublished - Feb 2021


  • Barrett’s esophagus
  • Ex vivo
  • Microbiome

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • General Biochemistry, Genetics and Molecular Biology


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