Single cell profiling pig caecum at various developmental stages

The intestinal tract has critical roles in digesting and absorbing foods, expelling remaining wastes, and defensing against microorganisms. Profiling single cell transcriptome of intestinal track has greatly enriched the understandings on the cell types and their corresponding function heterogeneity that are important for intestine track development and disease. Although single cell transcriptome of the intestine tracts was extensively investigated in human and mice, the single cell gene expression profiles of pig caecum remained unexplored. Here, we performed single-cell RNA-seq on 45,572 cells from seven caecum samples of pigs at four developmental stages at day 30, 42, 150 and 730. We uncovered 12 major cell types and 38 subtypes, and characterized their featured genes, transcription factors and regulons, many of which were conserved in humans. We showed expansion of relative proportions of CD8+ T, GZMA (low) NKT, and decreasing of epithelium stem cells, Treg, RHEX+ T and plasmacytoid dendritic cells along the four developmental stages. We noted the upregulation of mitochondrial genes COX2 and ND2, as well as genes involved immune activation in multiple cell types after weaning. Cell-cell crosstalk analysis uncovered IBP6+ fibroblasts acted as the main signal senders at D30 while at other stages the IBP6- fibroblasts took over this role. T/NK cells interacted with epithelial cells and IBP6+ fibroblasts using GZMA-F2RL1/F2RL2 pairs only in D730 caecum. The present study provided important knowledge on cell type heterogeneity and function of pig caecum along different development stages.