Comprehensive Gastrointestinal Bacteriome Profiling Across GERD Complications

Gastroesophageal reflux disease (GERD) and its progressive complications—reflux esophagitis (RE), Barrett's esophagus (BE), and esophageal adenocarcinoma (EAC)—have been linked to shifts in gastrointestinal microbial composition. This multicenter observational study investigated bacterial load and community structure across the gastrointestinal tract (GIT) to identify microbiome signatures associated with GERD severity and to explore potential non-invasive biomarkers. A total of 923 samples were collected from 158 patients with histologically confirmed RE, BE, or EAC, including biopsies from patient-matched pathological esophageal sites, gastric compartments, duodenum, and oral and rectal swabs. DNA extracts were analyzed using qPCR and 16S rRNA gene amplicon sequencing. We quantified bacteriome richness, evenness, and taxonomic composition, comparing anaerobe/aerobe and gram-negative/gram-positive ratios among tissue sites and disease groups. Esophageal bacterial richness and evenness increased with GERD severity. Streptococcus was significantly enriched in RE compared to BE and EAC, whereas BE exhibited bacteriome characteristics that diverged from the RE–EAC progression pattern. Cross-site microbial correlations were observed throughout the GIT. Specific genera, including Porphyromonas in oral samples and Faecalibacterium in rectal samples, were associated with EAC, demonstrating potential as non-invasive microbial biomarkers for disease risk stratification. This comprehensive analysis reveals systematic alterations of the microbiome across GERD-associated disease stages and highlights candidate taxa for biomarker development.