Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut

Metagenomic sequencing and metabolomics of fecal matter have revealed the impact of the gut microbiome on health and disease. Besides microbiota, feces also contain shed or exfoliated host epithelial, secretory, and immune cells, but RNA profiling of these cells is challenging due to degradation and cross-contamination. Here, we introduce Foli-seq to profile exfoliated eukaryotic mRNAs (eRNA) originating from upper and lower gastrointestinal regions and show that this "fecal exfoliome" harbors stable RNAs that reflect intestinal and immune function. By selectively amplifying targeted transcripts, Foli-seq demonstrates robust, accurate, sensitive, and quantitative measurement of fecal eRNAs. In murine colitis models, eRNA reveals temporal processes of epithelial damage, immune response, and intestinal recovery specific to different types of gut inflammation. Simultaneous exfoliome and microbiome profiling uncovers a dense host-microbe interaction network.