Single cell spatial transcriptomics of the small intestine

The intestinal epithelium is a highly structured tissue composed of repeating crypt-villus units. Enterocytes perform the diverse tasks of absorbing a wide range of nutrients while protecting the body from the harsh bacterial-rich environment. Using laser-capture-microdissection and single-cell transcriptomics we uncovered broad zonation of enterocyte function along the villus. We found that enterocytes at villi bottoms express an anti-bacterial Reg gene program in a microbiome-dependent manner, reducing crypt pathogen exposure. They next shift to sequential expression of carbohydrates, peptides and fat absorption machineries in distinct villus compartments, finally inducing a Cd73 immune-modulatory programs and hundreds of additional genes at the villi tips. Spatial transcriptomics of the villus stromal compartment revealed a unique villus tip expression program that orchestrates these zonated changes. Our work highlights the spatial diversity in the gut and details the spatially-varying crosstalk between stromal and epithelial cell populations.