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Background  The distal esophagus harbors a complex bacterial population. We hypothesized that a better understanding of bacterial communities in the esophagus would facilitate understanding of the role of bacteria in esophageal disease. Here, we investigated bacterial composition in the distal esophagus in subjects with a normal esophagus, reflux esophagitis, and Barrett’s esophagus.    Methods  Two biopsy specimens were obtained from the distal esophagus at 1 cm above the gastroesophageal junction under endoscopic examination in 18 patients (6 each with normal esophagus, reflux esophagitis, and Barrett’s esophagus) and used for histological examination and DNA extraction. Fragments of 16S rDNA genes were amplified by PCR using general bacterial primers, and bacterial populations were examined. A third biopsy specimen was taken from the patients with Barrett’s esophagus to histologically confirm the replacement of squamous epithelium with columnar epithelium in the distal esophagus.    Results  Endoscopic diagnoses of normal esophagus, esophagitis, and Barrett’s esophagus were confirmed by histological findings. The total amount of bacterial DNA detected did not significantly differ among groups (p > 0.1). On average, each of the 18 subjects yielded about 350 clones, of which 40 were randomly picked and sequenced. Analysis of 147 16S rDNA sequences from 240 clones of 6 subjects with normal esophagus yielded four phyla,  Proteobacteria  (49%),  Firmicutes  (40%),  Bacteroidetes  (8%), and  Actinobacteria  (3%). Similar analysis of 139 16S rDNA sequences from 240 clones of 6 patients with reflux esophagitis yielded 6 phyla,  Proteobacteria  (43%),  Firmicutes  (33%),  Bacteroidetes  (10%),  Fusobacteria  (10%),  Actinobacteria  (2%), and  TM7  (2%). while that of 138 16S rDNA sequences from 240 clones of 6 cases of Barrett’s esophagus yielded 5 phyla,  Firmicutes  (55%),  Proteobacteria  (20%),  Bacteroidetes  (14%),  Fusobacteria  (9%), and  Actinobacteria  (2%). Thus, microbial communities differed among patients with a normal esophagus, reflux esophagitis and Barrett’s esophagus.    Conclusions  Esophageal bacterial composition differs under conditions of normal esophagus, reflux esophagitis, and Barrett’s esophagus. Diverse bacterial communities may be associated with esophageal disease.

Characterization of bacterial biota in the distal esophagus of Japanese patients with reflux esophagitis and Barrett’s esophagus