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Background <p>Functional dyspepsia (FD) is a prevalent gastrointestinal disorder affecting quality of life, with recent studies suggesting a role of the duodenal microbiome in its pathogenesis via the gut-brain axis. The optimal specimen sampling collection method and the specific microbial features associated with FD remain unclear.</p> Objectives <p>This pilot study compared mucosal brushing and biopsy for duodenal microbiome sampling, with an exploratory secondary aim of assessing microbial differences between FD and non-FD controls.</p> Methods <p>Patients undergoing esophago-gastro-duodenoscopy (EGD) were recruited from February 2024 to May 2025. FD patients were identified using the Rome IV criteria, and non-FD controls without upper GI symptoms were included. Duodenal samples were collected via mucosal brushing and biopsy, followed by DNA extraction and 16&#xa0;S rRNA sequencing of the V1–V2 region. α-diversity (richness, Shannon, Simpson) and β-diversity (Bray–Curtis dissimilarity) were assessed between FD and non-FD controls and between sampling methods. Paired Wilcoxon signed-rank tests compared sampling methods, while linear regression models adjusted for age, sex, and BMI compared FD and non-FD controls within each method. Microbial associations with FD were examined using generalized linear models, adjusting for age, sex, and BMI, with Benjamini–Hochberg FDR correction.</p> Results <p>Forty participants (FD <i>n</i> = 20; non-FD controls <i>n</i> = 20) were included, yielding 80 paired samples. Brushing showed higher retention of non-chimeric reads and lower filtering losses than biopsy (all <i>p</i> &lt; 0.0001). Brushing also yielded greater alpha diversity—genus richness (81[33] vs. 19[17]), Shannon (3.68[0.46] vs. 2.60[0.89]), and Simpson (0.96[0.03] vs. 0.89[0.08]); all <i>p</i> &lt; 0.0001—and a distinct community structure (PERMANOVA R²=0.16, <i>p</i> = 0.001). Within each sampling method, FD and non-FD controls did not differ in alpha or beta diversity after adjustment. Exploratory differential abundance modeling identified <i>Streptococcus</i> as numerically higher in FD across both methods, although no genus survived FDR correction (all q &gt; 0.05).</p> Conclusion <p>Mucosal brushing collects luminal/mucus-associated microbiota and therefore yielded higher bacterial biomass and greater microbial diversity than mucosal biopsy. No significant differences in alpha or beta diversity were detected between FD and non-FD controls within either method, although the study was not powered to exclude such differences. Exploratory analyses suggested numerically higher <i>Streptococcus</i> abundance in FD that did not survive FDR correction. This hypothesis-generating finding requires validation in larger studies.</p> ClinicalTrials.gov Identifier <p>NCT06326918.</p>

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Comparative pilot study using mucosal brushing and mucosal biopsy for detecting duodenal microbiome in functional dyspepsia

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月28日

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  • Chatpol Samuthpongtorn,
  • Thanrada Vimonsuntirungsri,
  • Pisit Tangkijvanich,
  • Rapat Pittayanon

摘要

Background

Functional dyspepsia (FD) is a prevalent gastrointestinal disorder affecting quality of life, with recent studies suggesting a role of the duodenal microbiome in its pathogenesis via the gut-brain axis. The optimal specimen sampling collection method and the specific microbial features associated with FD remain unclear.

Objectives

This pilot study compared mucosal brushing and biopsy for duodenal microbiome sampling, with an exploratory secondary aim of assessing microbial differences between FD and non-FD controls.

Methods

Patients undergoing esophago-gastro-duodenoscopy (EGD) were recruited from February 2024 to May 2025. FD patients were identified using the Rome IV criteria, and non-FD controls without upper GI symptoms were included. Duodenal samples were collected via mucosal brushing and biopsy, followed by DNA extraction and 16 S rRNA sequencing of the V1–V2 region. α-diversity (richness, Shannon, Simpson) and β-diversity (Bray–Curtis dissimilarity) were assessed between FD and non-FD controls and between sampling methods. Paired Wilcoxon signed-rank tests compared sampling methods, while linear regression models adjusted for age, sex, and BMI compared FD and non-FD controls within each method. Microbial associations with FD were examined using generalized linear models, adjusting for age, sex, and BMI, with Benjamini–Hochberg FDR correction.

Results

Forty participants (FD n = 20; non-FD controls n = 20) were included, yielding 80 paired samples. Brushing showed higher retention of non-chimeric reads and lower filtering losses than biopsy (all p < 0.0001). Brushing also yielded greater alpha diversity—genus richness (81[33] vs. 19[17]), Shannon (3.68[0.46] vs. 2.60[0.89]), and Simpson (0.96[0.03] vs. 0.89[0.08]); all p < 0.0001—and a distinct community structure (PERMANOVA R²=0.16, p = 0.001). Within each sampling method, FD and non-FD controls did not differ in alpha or beta diversity after adjustment. Exploratory differential abundance modeling identified Streptococcus as numerically higher in FD across both methods, although no genus survived FDR correction (all q > 0.05).

Conclusion

Mucosal brushing collects luminal/mucus-associated microbiota and therefore yielded higher bacterial biomass and greater microbial diversity than mucosal biopsy. No significant differences in alpha or beta diversity were detected between FD and non-FD controls within either method, although the study was not powered to exclude such differences. Exploratory analyses suggested numerically higher Streptococcus abundance in FD that did not survive FDR correction. This hypothesis-generating finding requires validation in larger studies.

ClinicalTrials.gov Identifier

NCT06326918.