Early-Life Commensal Lung Bacteria Modulate Immune Responses and Susceptibility to RSV Infection in Neonatal Mice

The lung mucosa during the neonatal period and early infancy is especially susceptible to respiratory syncytial virus (RSV) infection. Respiratory disease severity is strongly influenced by the age at first exposure, which may also affect the trajectory of airway function. Early life represents a critical window for lung development and initial microbiota colonization, both of which shape mucosal immune responses to RSV. The contribution of early lung-colonizing bacterial strains to the establishment of the lung microbiota and susceptibility to RSV infection in neonatal mice remains poorly characterized. In the present study, we showed that early-life primo-colonizing bacterial strains in the mouse lung differentially induce innate immune responses and influence RSV susceptibility in ex vivo models using lung explants and alveolar macrophages (AMs). We identified a specific bacterial strain (strain 17) whose prior exposure enhances type I interferon (IFN-I) responses in AMs upon RSV infection and reduces viral replication both ex vivo and in vivo in lung tissues. Intranasal administration of this strain during early life prevented the development of immunopathological responses upon RSV reinfection in adult mice. Finally, using a translational human airway epithelium model, we demonstrated that pre-exposure to strain 17 restricts RSV spread without cytotoxicity, likely via enhanced β-defensin 2 production. These findings highlight the potential of early-life microbiota modulation as a promising intervention for preventing RSV disease and its long-term respiratory consequences. Author summary Respiratory syncytial virus (RSV) is a major cause of severe respiratory infections in newborns and infants, a period during which the lungs and immune system are still maturing. Simultaneously, the respiratory tract undergoes its first microbial colonization by so-called primo-colonizing bacteria — the first bacterial species to establish themselves on neonatal lower respiratory mucosal surfaces. These early microbial pioneers may play an unsuspected role in shaping how the immature immune system responds to viral threats. In this study, we investigated whether these early lung-colonizing strains influence RSV susceptibility. Using neonatal mouse models, lung explants, and alveolar macrophages, we found that distinct bacterial strains trigger markedly different innate immune responses. Prior exposure to one strain in particular, strain 17, was associated with enhanced type I interferon responses, reduced viral replication, and protection against harmful inflammation upon RSV reinfection later in life. In a human airway epithelium model, pre-exposure to strain 17 also restricted RSV spread without tissue damage, potentially through increased β-defensin 2 production. These findings provide proof-of-concept that the bacterial strains establishing in the neonatal lung can influence future immune reactivity and antiviral responses, and suggest that early-life respiratory microbiota modulation could represent a promising strategy to prevent severe RSV disease.