The intestine is the most critical digestive organ and the largest immune organ in mammals, playing a central role in nutrient absorption, endocrine secretion, and defense against microorganisms. Domestic pigs were domesticated from wild boars through long-term artificial selection, resulting in substantial differences in body size, growth performance, and environmental adaptability, which may also be reflected in intestinal immune function and nutrient absorption. Moreover, pigs undergo key postnatal developmental stages, including pre-weaning, post-weaning, growth peak, and adulthood, during which the cellular composition and functions of the intestine undergo continuous dynamic changes. However, systematic studies on intestinal features of domestic pigs and wild boars across different developmental stages remain limited, particularly at single-cell resolution.
Researchers performed single-nucleus RNA sequencing (snRNA-seq) on the ileum and cecum of domestic pigs and wild boars at four key postnatal developmental stages: pre-weaning (30 days), post-weaning (42 days), growth peak (150 days), and adulthood (730 days). They generated the most comprehensive single-nucleus transcriptomic atlas of the pig intestine to date, identifying 19 major cell types and 58 cellular subtypes. This included previously uncharacterized rare subtypes, such as EBF1+ fibroblasts, TMEM163+ macrophages, and neuron subtypes expressing FCAMR, which were further validated by immunofluorescence experiments.
Comparative analysis of the ileum and cecum uncovered significant differences in cellular composition and gene expression. Ileum cells showed higher expression of immune-related genes, while ileum neurons exhibited elevated expression of genes involved in regulating inflammatory responses. Further cell–cell interaction analysis revealed that ileum neurons communicate with dendritic cells and lymphatic endothelial cells through the NAMPT–INSR ligand–receptor pair to regulate intestinal inflammatory response. These interactions were further validated by spatial transcriptomic data. Appropriate inflammatory responses can help the body combat infections and facilitate tissue repair, but persistent chronic inflammation may result in DNA damage, cell mutations and tumor formation. Therefore, the discovery of the mechanisms by which neurons regulate inflammatory responses is crucial for maintaining intestinal health and for the prevention and treatment of intestinal cancer.
Comparative analysis of domestic pigs and wild boars found that wild boars exhibit stronger immune functions, particularly humoral immunity mediated by plasma cells. Integration with gut metabolomic data revealed that short-chain fatty acids, such as propionic acid and acetic acid, can induce XBP1 and SDC1 expression in B cells, promoting their differentiation into plasma cells. This increases plasma cell proportions and enhances the expression of genes associated with humoral immunity, providing a molecular basis for the stronger immune response in wild boars. Furthermore, wild boars displayed superior nutrient absorption capacity, with gene regulatory network analysis identifying NR1H4 and FOXO1 as key regulators of intestinal nutrient absorption.
Development is a complex and dynamic process. Through temporal analysis, the researchers identified genes that change continuously during postnatal development, along with their associated functional pathways, including multiple genes linked to inflammatory bowel disease and cystic fibrosis. The results showed that as development progresses after birth, intestinal digestive and absorptive functions, as well as T cell–mediated immunity, gradually increase. Additionally, the study revealed cell type–specific developmental patterns, with different cell types exhibiting distinct features throughout development. Plasma cells, in particular, displayed the most pronounced developmental changes.
By comparing the human and pig intestines, researchers found that the two species share highly conserved cell types and cell type–specific genes, including key transcription factors and multiple genes associated with inflammatory bowel disease.
This study generated single-nucleus transcriptomic maps of the intestines of domestic pigs and wild boars across multiple postnatal developmental stages, providing a systematic characterization of differences and patterns in cellular composition, molecular features, and developmental dynamics. These findings provide a scientific basis for improving feed efficiency and promoting healthier pig production, while also offering important insights into the mechanisms and potential treatments of human intestinal diseases.
Journal
Science China Life Sciences