Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the single cell transcriptome

The small intestinal epithelium is composed of several defined epithelial cell lineages, which in turn exhibit marked transcriptional and functional diversity along the crypt-villus and proximal-to-distal length of the intestinal tract. While epithelial cell type and functional heterogeneity have been characterized in the adult intestinal epithelium, the temporal and spatial changes during the postanatal period, which accompany the transition from placental energy supply to enteral feeding and facilitate the establishment of the enteric microbiota and postnatal immune maturation, have not been systematically investigated. Here, we analyzed the small intestinal epithelium of 1-, 5-, 10- and 25-day-old SPF mice by single cell RNA-Seq and used differential gene expression and pathway analysis to identify age-specific expression patterns. In addition, the influence of enteric infection on the neonatal epithelium was investigated. We identify gene clusters temporally expressed in the neonatal intestine and correlate their expression with the functional changes during postnatal tissue maturation and the neonate to adult transition. To study intestinal epithelial maturation during homeostatic conditions, intestinal epithelial cells (IECs) were isolated from small intestinal tissues obtained from 1-, 5-, 10- or 25-day-old C57Bl/6J specific pathogen-free (SPF) newborn mice. In addition, IECs were isolated from 5-day-old C57Bl/6J SPF newborn mice that had been orally infected 4 days earlier with 100-200 CFUs Salmonella Typhimurium. scRNA-Seq was then performed.