The gut microbiome is recognized as playing a key role in infant health. Alessio Fasano, MD, world-renowned for his research on the gut microbiome focuses on the ways in which the gut microbiome influences allergy and autoimmunity. The effects of infant nutrition on the composition of the microbiome are also discussed, including the impact of feeding mode and probiotic and prebiotic supplementation. Dr. Fasano highlights the most recent clinical evidence supporting the use of key probiotic strains, including Lactobacillus rhamnosus GG (LGG), Bifidobacterium animalis subsp. Lactis (BB-12), and others, to inform clinicians about the current and emerging roles of probiotics for allergy management.