Lee, C. H.-J.; Fawkner-Corbett, D.; Christoforidou, Z.; Sousa Geros, A.; Lentsch, V.; Sheikh, L.; Bridges, E.; Jagielowicz, M.; Deng, L.; Qin, X.; Chuang, H.-W.; Wien Lai, V.; Craddock, S.; Mazurier, A.; Siejka-Zielinska, P.; Gomez Castro, P.; Aulicino, A.; McGregor, C.; Gupta, T.; Cianci, N.; Kujawa, R.; Vargas Gutierrez, P.; Cheng, C.; Greco, M.; Fowler, D.; Buczacki, S. J. A.; Rimmer, G.; Harwood, R.; Hall, N.; Johnson, P.; Koohy, H.; Simmons, A.; Antanaviciute, A.

At birth, the intestine must rapidly adapt to enable nutritional function and immune microbial tolerance. Here, integrating single-cell multi-omics and spatial transcriptomics we define the circuits underpinning this process. We identify asynchronous developmental trajectories with postnatal epithelial reprogramming characterised by coordinated changes in metabolism, junctional structure and innate defence. At birth epithelial stem cells demonstrate dynamic enhancer remodelling, with accessibility often preceding transcription. Fetal stemness elements remain accessible despite reduced transcription across epithelial lineages, retaining plasticity potential. Post-natal epithelia experience sequential homing of myeloid cells followed by innate T cells with peri-epithelial B cells localising later in infancy. Using developmentally staged organoids, we show that epithelial responses to inflammatory stimuli are age-dependent and constrained in early life. We identify BHLHE40 as an early-life regulator that attenuates the impact of interferon- and NF-kB-driven signalling. Altogether we define the events driving epithelial licensing and barrier adaptation at birth and through infancy.