Researchers have developed Foli-seq, a new noninvasive sequencing method that captures host messenger RNA from cells naturally shed into stool. This technique overcomes historical obstacles like RNA degradation and high bacterial interference to provide a detailed map of intestinal and immune function. Testing in murine colitis models demonstrated that the tool can track epithelial damage and recovery while identifying specific biomarkers that predict disease severity. By combining this data with microbiome profiling, the authors uncovered complex host–microbe interaction networks that were previously difficult to observe. Finally, the study successfully applied Foli-seq to human IBD patients, stratifying them into subgroups that correlate with clinical symptoms and inflammatory activity. This approach offers a powerful, longitudinal alternative to invasive biopsies for monitoring chronic gastrointestinal diseases.

References:

• Huang Y, Sun Y, Ronda C, et al. Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut[J]. Nature Biotechnology, 2025: 1-11.