Comparative pilot study using mucosal brushing and mucosal biopsy for detecting duodenal microbiome in functional dyspepsia
- 1Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- 2Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- 3Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
Abstract
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.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s13099-026-00863-z.
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BibTeX
@article{samuthpongtorn2026comparative,
title = {{Comparative pilot study using mucosal brushing and mucosal biopsy for detecting duodenal microbiome in functional dyspepsia}},
author = {Chatpol Samuthpongtorn and Thanrada Vimonsuntirungsri and Pisit Tangkijvanich and Rapat Pittayanon},
journal = {Gut Pathogens},
year = {2026},
month = jul,
doi = {10.1186/s13099-026-00863-z},
url = {https://doi.org/10.1186/s13099-026-00863-z},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Comparative pilot study using mucosal brushing and mucosal biopsy for detecting duodenal microbiome in functional dyspepsia
AU - Chatpol Samuthpongtorn
AU - Thanrada Vimonsuntirungsri
AU - Pisit Tangkijvanich
AU - Rapat Pittayanon
PY - 2026
DA - 2026/07/28
JO - Gut Pathogens
DO - 10.1186/s13099-026-00863-z
UR - https://doi.org/10.1186/s13099-026-00863-z
AB - 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. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s13099-026-00863-z.
SN - 1757-4749
ER -