It has been noted that the diseased esophagus associated with healthy controls is home to a bacterial population unusually rich in gram-negative species. Insights into the esophageal microbiome could help guide further analysis of new therapeutic tools.

Dysbiosis is a term that encompasses changes in the composition of the combined microbiota compared to that found in healthy individuals. When distinguishing the microbiota of a normal healthy esophagus from dysbiotic disease states such as reflux esophagitis, esophagitis, Barrett's esophagus, or esophageal adenocarcinoma, it is clear that dysbiosis may precede inflammation.

Age influences the gastroesophageal microbiome, although the full significance remains to be determined. During early life, the human colonic microbiome varies widely. Analysis of colonic microbiome composition in patients from infancy to 80 years of age and across three different geographic locations (United States, Venezuela, and Malawi) found that phylogenetic composition fluctuated significantly during the first 3 years of life.