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Antibiotic exposure early in life and other practices impacting the vertical transmission and ordered assembly of a diverse and balanced gut microbiota are associated with a higher risk of immunological and metabolic disorders such as asthma and allergy, autoimmunity, obesity, and susceptibility to opportunistic infections. In this study, we used a model of perinatal exposure to the broad-spectrum antibiotic ampicillin to examine how the acquisition of a dysbiotic microbiota affects neonatal immune system development. We found that the resultant dysbiosis imprints in a manner that is irreversible after weaning, leading to specific and selective alteration of the colonic CD4⁺ T-cell compartment. In contrast, colonic granulocyte and myeloid lineages and other mucosal T-cell compartments are unaffected. Among colonic CD4⁺ T cells, we observed the most pronounced effects on neuropilin-negative, RORγt- and Foxp3 …