Comparison of sampling methods in assessing the microbiome from patients with ulcerative colitis

Area of Science:

• Gastroenterology
• Microbiome Research
• Inflammatory Bowel Disease

Background:

• Ulcerative colitis (UC) dysbiosis is often studied using stool samples, which may not accurately reflect the mucosal microbiome.
• Luminal contents, including loosely adherent bacteria, are hypothesized to be more representative of the gut environment in UC.
• Bowel preparation may influence the composition of luminal content samples.

Purpose of the Study:

• To investigate the suitability of luminal content analysis for diagnosing UC dysbiosis.
• To compare the microbiome composition of stool, luminal contents, and endoscopic biopsies.
• To determine if luminal content microbiome can predict UC.

Main Methods:

• 16S rRNA gene sequencing was used to analyze microbiome composition.
• Samples included stool, luminal contents, and biopsies from 16 UC patients and 15 healthy controls.
• Statistical analyses included Procrustes and Mantel tests for correlation and AUC for prediction.

Main Results:

• Significant differences in alpha and beta diversity were observed between stool, luminal contents, and biopsy microbiomes.
• A correlation was found between stool and luminal content microbiomes (p < 0.001).
• While stool microbiome differed between UC patients and controls, luminal content and biopsy microbiomes did not show significant differences. Stool and lavage predicted UC with AUCs of 0.85 and 0.81, respectively.

Conclusions:

• The microbiome composition varies significantly across stool, luminal contents, and biopsy samples.
• Luminal content analysis during colonoscopy can predict UC with an AUC of 0.81.
• Endoscopic luminal content aspiration is a valuable method for identifying UC-associated microbiome differences and screening for dysbiosis.