A novel method for precise endoscopic sampling of duodenal microbiota

Previous studies have established a relationship between duodenal mucosa-associated microbiota and overall health. However, sampling duodenal microbiota is technically challenging. Mucosal biopsies collected via endoscopy are the most common approach, but this method risks contamination of the working channel with gastrointestinal contents or extraneous microorganisms.

This study designed a novel accessory, an endoscopic channel plug, to improve the sampling process by ensuring a clean and sterile working channel, thereby providing more accurate microbiota results.

Microbiome analysis of samples collected from the oral cavity, traditional duodenal sampling, and the modified method with the channel plug revealed that samples obtained with the plug exhibited higher PCR product concentrations and a greater number of operational taxonomic units (335). Additionally, 16S rRNA sequencing showed significant differences in the taxonomic composition at both the phylum and genus levels among the different sampling methods. Notably, the novel method group (using the channel plug) contained a higher abundance of Veillonella, whereas this genus was less abundant in oral cavity and traditional duodenal samples. Furthermore, the abundance of specific bacterial strains varied significantly between sampling methods. These findings suggest that the use of the channel plug enables more comprehensive microbiota sampling, providing data to support clinical diagnosis of gastrointestinal diseases.