Gastric mucosal brushing enhances gastric microbiome profiling compared with conventional biopsy in gastric cancer

Gastric microbiota dysbiosis has been implicated in gastric carcinogenesis; however, the specific sampling method for assessing non-Helicobacter pylori microbiota associated with gastric cancer (GC) remains unestablished. This study compared gastric mucosal brushing with conventional biopsy for microbiota profiling in patients with GC and controls. We enrolled treatment-naïve GC patients and controls and analysed paired brushing and biopsy specimens using 16 S rRNA sequencing. Microbial analyses were compared between sampling methods and between the GC and control groups, and taxa-GC associations were assessed using age- and sex-adjusted mixed models. Overall brushing samples exhibited higher α-diversity than biopsy, including genus richness 60 ± 46.5 vs. 25.5 ± 19.5, Shannon 3.45 ± 0.71 vs. 2.80 ± 0.79, and Simpson 0.95 ± 0.03 vs. 0.92 ± 0.06 (all p < 0.0001), with different β-diversity (R² = 0.05, p < 0.001). In brushing samples, GC showed reduced α-diversity compared with controls (richness 39.5 ± 35 vs. 82 ± 51.8, p = 0.01; Shannon 3.20 ± 0.53 vs. 3.78 ± 0.52, p < 0.0001; Simpson 0.94 ± 0.05 vs. 0.96 ± 0.02, p = 0.002) and altered β-diversity (R² = 0.05, p = 0.01), whereas biopsy showed no α- and β-diversity differences. Our study demonstrates that brushing yielded higher bacterial diversity and different gastric microbiota profile compared with conventional biopsy sampling. Brushing also revealed depleted microbial diversity and altered microbial profile in gastric cancer. These findings suggest that brushing may improve the detection of certain gastric cancer-associated microbiota alterations.