Background: Inducible nitric oxide synthase (iNOS) has emerged as a crucial regulator of host metabolism and gut microbiota activity. The present study examines the role of the gut microbiome in determining host metabolic functions in absence of iNOS.Results: Insulin resistant and dyslipidemic iNOS-/- mice displayed reduced microbial diversity, with a higher relative abundance of the gram-positive bacteria, Allobaculum and Bifidobacterium, and altered serum metabolites linked with the metabolic dysregulation. Vancomycin, which largely depletes gram-positive bacteria, reversed the insulin resistance (IR), dyslipidemia, and related metabolic abnormalities in iNOS-/- mice. Such correction in metabolic markers was accompanied by reduced the expression of genes involved in fatty acid synthesis in liver and adipose tissue, decreased lipid uptake by adipose tissue and enhanced lipid efflux by liver and intestine. Rescue of IR in vancomycin treated iNOS-/- mice was associated with the alterations in the select serum metabolites such as 10-hydroxydecanoate, indole-3-ethanol, allantoin, hippurate, sebacic acid, aminoadipate, and ophthalmate, along with improvement in phosphatidylethanolamine to phosphatidylcholine (PE/PC) ratio.Conclusions: Vancomycin-mediated depletion of gram-positive bacteria negates the detrimental metabolic effect, dyslipidemia and IR, observed in iNOS-/- mice.