The Microbiome and Esophageal Disease: Where Are We Now?

PURPOSE OF REVIEW

The microbiome in the esophagus has been an area of early active investigation. In the past 5 years, advancements in next-generation sequencing and computational analysis have provided a more detailed picture of the esophageal microbiome. This review will examine the most recent advances in the past 5 years on the study of microbiome changes in healthy and diseased esophagus to better understand the link between microbiome and esophageal diseases, potentially leading to new prevention or treatment strategies.

RECENT FINDINGS

The microbiome has a key set of baseline parameters in the usual or non-diseased esophageal lumen. There are measurable changes in the baseline microbiome species of different disease phenotypes including eosinophilic esophagitis, gastroesophageal reflux disease, Barrett's esophagus and achalasia. Some studies suggest that certain microbiome features may even be associated with worse outcomes. Dysbiosis of esophageal microbiome is implicated in various esophageal disorders, including GERD, Barrett's esophagus, EoE, and achalasia. However, confounding factors such as antibiotic use, PPI use, dietary habits, and geographic location influence microbiome variability and make the standardized study of this field challenging. The next phase of research will need to include more focus on larger scale studies with reproducible parameters. As some features of the microbiome are associated with disease progression, there are multiple new avenues of intervention potentially available with an improved understanding of the human esophageal microbiome.

© 2026. The Author(s).