Fecal and colonic microbiota differ in composition, function, diagnostic utility and correlation with inflammatory...

Area of Science:

• Gastroenterology
• Microbiome Research
• Immunology

Background:

• Fecal microbiota is commonly studied in ulcerative colitis (UC) due to ease of access.
• The accuracy of fecal microbiota as a proxy for colonic mucosal microbiome in UC remains uncertain.

Purpose of the Study:

• To compare gut microbiota composition and function between fecal and colonic tissue samples in UC patients.
• To determine if fecal microbiota can fully represent the colonic tissue microbiome in UC.

Main Methods:

• 16S rRNA sequencing of fecal and colonic tissue samples from 12 UC patients and 16 controls.
• ELISA, functional analysis, and machine learning (SHAP, random forest) were integrated.

Main Results:

• Colonic tissue showed higher microbial diversity than feces; some taxa were unique to tissue.
• UC patients had higher colonic tissue α-diversity but lower fecal α-diversity compared to controls.
• Only Ligilactobacillus and Intestinimonas showed consistent differential abundance in both sample types.
• Colonic microbiota linked to immune pathways (e.g., NOD-like receptor signaling); fecal microbiota primarily linked to metabolic pathways.
• UC tissues overexpressed IL-1β, IL-17, and IL-22; fecal microbes mostly negatively correlated with these cytokines.
• UC classification model based on tissue markers was more stable than fecal marker-based model.

Conclusions:

• Fecal microbiota profiles inadequately represent the colonic tissue microbiome in UC patients.
• Colonic tissue is the preferred sample type for investigating UC disease mechanisms.
• Fecal samples are valuable for microbial biomarker discovery and diagnostic model development due to accessibility.