Antibiotic-induced microbial disruption drives metabolic rewiring in pulmonary macrophages and a dysregulated type 2 response in the lung

Background: We previously demonstrated repopulation of the gut microbiota (recolonization) following antibiotic use in mice causes macrophage-mediated intestinal inflammation. Strong epidemiological evidence links antibiotic use with inflammatory disease in lung but the cellular mechanisms by which this occurs are unknown. Methods: We analysed effects of antibiotic treatment in mice and subsequent recolonization on pulmonary immune responses by flow cytometry. Results: Intestinal recolonization following antibiotic treatment increased levels of circulating metabolites (amino acids and energy related products) indicating systemic effects of recolonization. Alongside, alveolar macrophages demonstrated increased expression of MHC class II and CD86, with RNAseq analysis indicating increased immune activation, inflammasome activation, and enhanced expression of the IL-13 receptor suggesting enhanced responsiveness to type 2 cytokines. There was a dramatic increase in genes involved in cellular metabolism, in particular oxidative phosphorylation which is associated with alternative activation of macrophages. These alterations in pulmonary macrophages preceded the gradual development of a heightened type 2 response in the lung, indicated by increased numbers of Th2 cells, eosinophils and enhanced IL-13 production by ILC2s. During allergy challenge, recolonized mice showed heightened ILC2 activation and exacerbation of macrophage dysfunction. Conclusions: Oral antibiotics disrupt pulmonary immune homeostasis to promote susceptibility to type 2 inflammation. These data provide a direct link between the microbiota and pulmonary macrophage metabolism and function.