The human gut microbiota has been associated with health and disease and is made up of microorganisms that coexist as a stable community. The process of establishing this complex community begins in infancy and is a dynamic process that is poorly understood. We know that maternal, perinatal and infant factors contribute to taxonomic differences in infant gut communities, however, taxonomy alone cannot provide the resolution needed to identify the processes taking place during this formative time. Human cohort studies are an invaluable resource for gut microbiome research and can be used for innovative research methods and new insights into the dynamic processes happening in the infant gut microbiota.
