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Research into the neonatal microbiome is beginning to unearth substantial information, particularly with regard to immune programming. Infant microbial exposures profoundly influence the development of the microbiome and major diseases including allergy, autoimmunity and infection in large populations. In this podcast episode of FX Medicine Dr Mark Donohoe and Andrew Whitfield-Cook discuss recent important findings relating to the complex symbiotic nature of the microbiome and host in early life and the factors that influence this relationship.