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Here, we used laser capture microdissection and bulk RNA-Seq, proteomics, and single cell RNA-Seq to analyze the total, organ site, crypt- and villus-specific intestinal epithelium of specific pathogen-free, germ-free, and\n                    <jats:italic>Salmonella<\/jats:italic>\n                    -infected mice during the postnatal period. We identified key temporal and organ-site specific expression patterns that revealed a weak effect of the microbiota but strong influence of developmental regulators during early life. We also determined age-dependent signaling pathway and transcription factor activity and characterized age- and cell type-specific developmental trajectories revealing a distinct compartmentalized maturation process along the proximal-to-distal length and crypt-villus axis and a discontinuous appearance of goblet\/Paneth cell and absorptive enterocyte transcriptional profiles. Finally, we described the cell type-specific response to neonatal enteric infection. Taken together, our findings identify the epithelium as an integral element in the maturation of postnatal mucosal tissues and in the establishment of host-microbe homeostasis.\n                  <\/jats:p>","DOI":"10.1371\/journal.pbio.3003212","type":"journal-article","created":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T17:41:19Z","timestamp":1785778879000},"page":"e3003212","update-policy":"https:\/\/doi.org\/10.1371\/journal.pbio.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Developmental factors drive the compartmentalized and discontinuous maturation of the small intestinal epithelium during the early postnatal 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