The foregut harbours a complex microbiome that potentially play an important role in the development of dental/periodontal diseases, gastroesophageal reflux diseases (GERD), and Helicobacter pylori gastritis.The microbiota in the distal esophagus is represented by nine phyla, 70 genera, or >200 species.Samples of the esophageal biota obtained by mucosal biopsy can be classified into two metagenotypes, based on 16S rDNA-based phylogenetie distance between samples and a reference range of the distance between normal samples.The type Ⅰ biota is dominated by the genus Streptococcus and concentrated in the normal esophagus.Conversely, the type Ⅱ biota is more abundant in Gram-negative anaerobic/microaerophilic bacteria and primarily correlated with esophagitis (Odds ratio: 15.4) and Barretts esophagus (Odds ratio: 16.5).By population, the normal oral microbiota is similar to the type Ⅰ biota, while the normal gastric biota resembles the type Ⅱ biota.By lineage, however, the two metagenotypes are closely related each other and statistically indistinguishable from the oral or gastric biota.The oral biota differs from the gastric biota by both population and phylogeny.The type Ⅱ biota may represent an altered metagenotype Ⅰ biota or an ectopic gastric biota.These findings make plausible design of further studies to directly examine causal roles of the metagenotype Ⅱ biota in GERD development.If GERD represents a microecological disease, a new type of treatment for reflux might become possible, for example, by converting the type Ⅱ to type Ⅰ biota through use of antibiotics, probiotics, or prebiotics.