A Cross-Sectional Dual-Site Analysis of the Gastric Antral and Duodenal Mucosa-Associated Microbiome Across Gastroesophageal Reflux Disease Phenotypes

Background/Objectives: Despite increasing GERD prevalence worldwide, the role of gastroduodenal microbiota in GERD phenotypes and symptom severity remains poorly understood. This study profiled mucosa-associated microbiota from the gastric antrum and duodenum across phenotypes and examined site-specific associations with symptom severity. Methods: In this cross-sectional study, forty individuals, including 26 with erosive reflux disease (ERD), 10 with non-erosive reflux disease (NERD), and 4 participants in the endoscopically normal comparator group, underwent 16S rRNA gene sequencing. Community differences were assessed using Bray–Curtis dissimilarity, differential taxa were explored by linear discriminant analysis effect size (LEfSe), and correlations with validated symptom questionnaires were evaluated. Results: Microbial community structure differed significantly between the antrum and duodenum, with Proteobacteria and Firmicutes predominating at both sites. LEfSe suggested enrichment of Streptococcus, Haemophilus, and Enterobacter in the duodenum, whereas Sphingobium, Acinetobacter, and Aquabacterium were more abundant in the antrum. The genus Helicobacter was relatively enriched in the antrum of ERD samples, whereas Streptococcus-dominant signatures were more prominent in the duodenum. Symptom severity showed stronger associations with duodenal taxa, including Fusobacterium with odynophagia, early satiety, and globus; Aquabacterium with postnatal drip and dyspnea, whereas gastric associations were fewer. Conclusions: In this small exploratory cross-sectional cohort, gastroduodenal microbiota exhibited both site-specific and phenotype-associated differences, with phenotype-related microbial variation being more evident in the duodenum than in the antrum. These hypothesis-generating findings highlight the importance of considering both anatomical context and GERD phenotype in upper gastrointestinal host–microbe interactions, and require confirmation in larger, phenotypically well-characterized cohorts.