The present disclosure a method and nutritional composition for improving the microbiome and metabolic profile of a pediatric subject, which includes administering to a pediatric subject a composition having up to about 7 g/100 kCal of a protein or protein equivalent source； up to about 7 g/100 kCal of a fat or lipid source； at least about 5 g/100 kCal of a carbohydrate； at least about 0.05 mg/100 kCal of bacterial metabolites； and either a probiotic or a prebiotic composition, or both.
