Increased reflux secondary bile acids are associated with changes to the microbiome and transcriptome in Barrett’s esophagus

Bile acids are a major component of gastro-esophageal refluxate, thought to contribute to the development of Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). As the microbiome shifts with EAC progression and bile acids influence bacterial composition, we examined these connections in a multi-center, cross-sectional study. We analyzed biospecimens from patients undergoing endoscopy using LC-MS to quantify bile acids in gastric aspirates, 16S rRNA sequencing for tissue microbiome profiling, and RNA sequencing on BE or cardia tissue. Among 153 patients (52 controls, 101 BE: 50 no dysplasia, 10 indefinite, 17 low-grade dysplasia, 17 high-grade dysplasia, and 7 EAC), we observed increased <i>Streptococcus</i> in BE tissue; dysplasia and EAC were associated with more <i>Lactobacillus</i> and decreased <i>Actinomyces</i> and other genera. Refluxate bile acids were mainly conjugated, indicating minimal bacterial metabolism, while BE patients had elevated secondary bile acid levels. <i>Streptococcus</i> correlated with upregulation of <i>IL6</i>, <i>FGF2</i>, and <i>HGF</i>, and decreased <i>Actinomyces</i> showed the most associations with gene expression, including the oxidative phosphorylation pathway. We identified two distinct BE gene expression clusters independent of histology, bile acid, or microbiome composition. These findings suggest bile acids shape the BE microbiome and associate with gene expression changes potentially relevant to EAC development.