Description:This study prospectively enrolled 56 patients with acute phase chikungunya virus infection and 51 healthy controls, integrating metagenomics and metabolomics to systematically characterize the structural, functional and metabolic network remodeling of the gut microbiome induced by virus infection. Metabolomic analysis revealed that chikungunya virus infection significantly perturbed the composition and pathways of the gut metabolome. It established associations between specific metabolites and the abundance of key bacterial species. This study elucidates the molecular mechanisms by which the gut microbiota influences inflammation through specific metabolites. These findings not only provide a novel perspective for understanding the pathophysiology of viral arthritis but also offer crucial theoretical evidence for developing microbiota-targeted interventions to alleviate chronic joint symptoms.