The present disclosure generally relates to pediatric nutritional compositions including a human milk oligosaccharide or a precursor thereof. Further, the nutritional compositions may include a prebiotic mixture of galacto-oligosaccharide and/or polydextrose, a probiotic, such as Lactobacillus rhamnosus GG, and human milk oligosaccharides. The disclosed nutritional compositions advantageously modify gut microbiome and improve select markers of immunity, brain structure, and gut function.