Association of gastric microbiota with gastric cancer in patients infected with helicobacter pylori

Background: The association between Helicobacter pylori and the resident gastric microbiota plays a critical role in gastric carcinogenesis; however, the specific microbial alterations accompanying the transition from chronic inflammation to malignancy remain to be fully elucidated. This study aimed to characterize the distinct bacterial signatures associated with gastric cancer (GC) and non-ulcer dyspepsia (NUD) within a Turkish cohort, evaluating these structural shifts in the context of the “hit-and-run” hypothesis. Methods: Genomic DNA was isolated from 158 gastric biopsy specimens obtained from 96 individuals stratified into four homogeneous groups based on clinical H. pylori status and histopathological presentation: H. pylori-positive GC (Hp+GC, n = 37), H. pylori-negative GC (Hp-GC, n = 25), H. pylori-positive NUD (Hp+NUD, n = 17), and H. pylori-negative NUD (Hp-NUD, n = 17). Next-generation amplicon sequencing targeting the V3–V4 hypervariable regions of the 16S rRNA gene was executed, followed by strict quality filtering via the DADA2 pipeline and taxonomic classification against the SILVA database. Results: Alpha diversity analysis demonstrated a significant reduction in microbial richness and evenness within the Hp+GC group compared with all other cohorts (FDR-adjusted q < 0.001). Beta diversity metrics revealed distinct ecological trajectories, with the overall microbial community structure of the Hp+GC group diverging sharply from non-malignant controls. Taxonomic profiling unveiled a profound dysbiotic shift in the Hp+GC microenvironment, characterized by a massive depletion of the Firmicutes phylum and a concomitant overrepresentation of Proteobacteria (66.56%). While the Helicobacter genus predominated in the non-malignant Hp+NUD group, its relative abundance declined to negligible levels (<0.01%) in biopsy samples of gastric cancer patients, despite clinical positivity. This malignant niche was instead robustly invaded by potentially pathogenic bacteria belonging to the Enterobacteriaceae family, showing highly significant enrichment of Morganella (11.14% mean relative abundance; FDR-adjusted q < 0.001), Providencia (3.43%; FDR-adjusted q < 0.001), and Klebsiella (2.03%; FDR-adjusted q < 0.001). Conclusions: These findings support the “hit-and-run” model, indicating that H. pylori acts as an initiator of carcinogenesis but is progressively outcompeted by an aggressive, nitrate-reducing, and pro-inflammatory Enterobacteriaceae-dominated dysbiotic bacterial community as mucosal atrophy and hypochlorhydria neutralize the typical acidic gastric barrier.