Endoscopic swab sampling as a novel method for gastric Microbiome profiling: A pilot study compared with tissue biopsy.

The gastric microbiome is increasingly recognized in gastric carcinogenesis, extending beyond Helicobacter pylori to oral-associated bacteria. Tissue biopsy is the current standard but is limited in spatial coverage. This pilot study evaluated an endoscopic swab-based approach as an alternative. Paired swab and biopsy samples were obtained from the gastric antrum and body of 16 patients undergoing esophagogastroduodenoscopy (32 swabs, 32 biopsies). Microbiome profiling was performed using 16 S rRNA V3–V4 amplicon sequencing. Swabs demonstrated higher alpha diversity than biopsies (observed ASVs: 123.5 vs. 48.5, p < 0.001; Shannon index: 4.73 vs. 3.99, p = 0.003). Overall community structures did not differ significantly on robust principal component analysis based on Aitchison distance (p = 0.16 and 0.17, permutational multivariate analysis). Helicobacter was significantly enriched in tissue samples (94.0% vs. 30.7%, log₂ fold change [LFC] = 1.521, q = 0.020), whereas Fusobacterium showed higher abundance in swab samples (LFC = -1.514, q = 0.006). These findings demonstrate that gastric swabs yield microbial profiles comparable to biopsies, with greater diversity and practical advantages. The swab method may provide a less invasive and reliable alternative for gastric and gastrointestinal microbiome research.