Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study

Area of Science:

• Microbiology
• Gastroenterology
• Human Health

Background:

• Most gut microbiome research uses stool samples, neglecting the small intestine's crucial role in digestion, nutrient absorption, and immunity.
• Characterizing small intestinal microbial populations is vital for understanding their impact on health and disease.

Purpose of the Study:

• To comprehensively characterize microbial populations across different small intestinal segments.
• To compare the small intestinal microbiome with the stool microbiome.

Main Methods:

• Prospective recruitment of subjects undergoing esophagogastroduodenoscopy.
• Collection of luminal aspirates from the duodenum, jejunum, and farthest reached distance, alongside stool samples from a subset.
• 16S rRNA sequencing and analysis using CLC Genomics Workbench.

Main Results:

• Over 2000 operational taxonomic units (OTUs) distinguished small intestinal from stool microbiomes.
• Firmicutes and Proteobacteria were dominant in the small intestine, while Bacteroidetes were less abundant.
• Distinct microbial signatures were observed between duodenal, jejunal, and farthest distance segments, with some overlap between adjacent segments.

Conclusions:

• The small bowel microbiome composition varies significantly between segments and differs markedly from the stool microbiome.
• These findings highlight the importance of segment-specific analysis of the small intestinal microbiota.
• Understanding these compositional differences is crucial for elucidating the contribution of small intestinal microbiota to human disease states.