The gut microbiota limits systemic inflammation during neurotrophic viral CNS infection by priming tonic type I interferon signaling

Neurotropic viruses, such as Japanese encephalitis virus (JEV), trigger central nervous system (CNS) inflammation primarily through disruption of the blood–brain barrier (BBB) and infiltration of peripheral immune cells. Although the gut microbiota is known to regulate diverse immunopathological processes, its contribution to CNS neuroinflammation and systemic immune responses during neurotropic viral infection remains poorly understood. Here, we show that depletion of gut microbiota by antibiotic cocktail treatment markedly increases susceptibility to CNS neuroinflammation following JEV infection. Loss of microbiota promoted viral dissemination into extraneural tissues, aggravated systemic inflammation and organ damage, and impaired tonic type I interferon (IFN-I) responses and hematopoietic differentiation during disease progression. Remarkably, fecal microbiota transplantation (FMT) restored resistance to CNS neuroinflammation, highlighting the protective role of the microbiota. Moreover, ampicillin-mediated depletion of specific gram-positive bacteria—including Bifidobacterium, Faecalibaculum, Ligilactobacillus, and Turicibacter—was associated with enhanced viral spread, systemic inflammation, and organ injury, accompanied by distinct shifts in fecal metabolites. Collectively, these findings demonstrate that gut microbiota–driven tonic IFN-I responses limit viral dissemination in extraneural tissues, thereby attenuating systemic inflammation and protecting against CNS neuroinflammation, particularly viral encephalitis.