Comparative gastric microbiota profiles in non-ulcer dyspepsia and peptic ulcer patients

Background Recent evidence suggests that the human stomach hosts a diverse microbiota beyond Helicobacter pylori, and that shifts in microbial composition may influence gastric health. In particular, oral-origin bacteria may dominate the gastric niche in the absence of H. pylori, yet their specific roles in different gastroduodenal disorders remain unclear. This study aimed to profile and compare the gastric microbiota composition in Turkish patients with non-ulcer dyspepsia (NUD) and peptic ulcer disease (PUD), in order to better understand microbial profiles potentially associated with gastroduodenal disease. Methods Ninety-eight patients underwent endoscopic evaluation and were divided into two groups according to the presence or absence of ulcers. Group 1 (n=52) included individuals with NUD, while Group 2 (n=46) comprised patients with PUD. Gastric biopsy samples from both groups were analyzed for the relative abundance of H. pylori using quantitative real-time PCR (qPCR), and next-generation sequencing was employed for a comprehensive analysis of the gastric microbiota. Results In total, H. pylori DNA was detected in 71.4% (70/98) of the samples, with a significantly higher prevalence in PUD patients (82.6%) compared to NUD patients (61.5%) (p=0.02). Distinct microbial profiles were observed based on H. pylori status. In NUD patients, Alloprevotella showed significantly higher relative abundance in H. pylori negative samples (p<0.05). Among PUD patients, the absence of H. pylori was associated with increased levels of Porphyromonas and Neisseria compared to NUD patients without H. pylori (p<0.05). These genera, typically associated with the oral cavity, appeared to expand opportunistically when H. pylori was absent. Conclusions The absence of H. pylori in gastric disorders was linked to a notable shift in microbiota composition, with increased representation of oral-origin bacteria such as Alloprevotella, Porphyromonas, and Neisseria. These findings, observed in a Turkish patient cohort, may reflect a potentially compensatory or opportunistic microbial shift in H. pylori-negative gastroduodenal disease. As exploratory findings, this study represents the first analysis from Türkiye comparing gastric microbiota profiles in NUD and PUD patients and provides novel regional insight into gastric microbial ecology.