ArticleScientific reports2025
Endoscopic swab sampling as a novel method for gastric Microbiome profiling: A pilot study compared with tissue biopsy.
Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Abstract
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.
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