The lung microbiome regulates brain microglia. Intratracheal neomycin administration shifts the lung microbiota towards LPS-enriched types. The released LPS can cross the blood-brain barrier and target the brain, where the increased LPS in neomycin-treated rats induces a microglial type I interferon response within the CNS, resulting in the alleviation of EAE. Several intriguing questions arise and are worth further investigation, including the role of the lung microbiome in regulating the microglial response, the long-term astrocyte response, microglial pruning, and microglial phagocytosis in other brain disorders.