Associations of gastrointestinal tract bacteriome profiles with complications of gastroesophageal reflux disease

Abstract Gastroesophageal reflux disease (GERD) and its complications – reflux esophagitis (RE), Barrett’s esophagus (BE), and esophageal adenocarcinoma (EAC) – have been associated with bacterial dysbiosis. However, comprehensive characterization of the gastrointestinal tract (GIT) bacteriome across these GERD complications is lacking. This multicenter observational study aimed to fill this gap. Biopsies from patient-matched pathological esophageal tissues, gastric body and antrum, duodenum, and oral and rectal swabs were collected from 151 patients with histologically confirmed RE, BE, or EAC, respecting their pharmacotherapy with proton pump inhibitors (PPIs) status. DNA isolates were analyzed by qPCR and 16S rRNA amplicon sequencing. Basic GIT bacteriome profiles were similar between PPI users and non-users with EAC. In PPI users, the genus Porphyromonas in oral swabs was associated with EAC ( P < 0.05). Of esophageal biopsies, EAC samples showed the highest bacterial load and alpha diversity among PPI users ( P < 0.05). In PPI users, the relative abundance of genus Streptococcus in esophageal samples was significantly higher for RE than for BE and EAC ( P < 0.05), while the opposite was observed for genus Lachnoanaerobaculum in both esophageal and duodenal samples ( P < 0.05). Interestingly, BE samples showed distinct bacteriome features deviating from the expected trend reflecting the severity of the pathology in individual groups. This study revealed significant associations of some bacteriome characteristics with GERD complications, especially in the oral swabs and esophageal biopsies.