Infancy and early childhood represent the most dynamic phase of postnatal brain development—a period marked by rapid myelination, exuberant synaptogenesis, programmed cell death, and extensive synaptic and axonal pruning. These processes drive dramatic changes in neuroimaging phenotypes as well as in cognitive, emotional, and social abilities (Gilmore, Knickmeyer, & Gao, 2018). At the same time, the gut microbiome—a complex community of microorganisms capable of influencing the brain through the production of short-chain fatty acids, neurotransmitters, and immune-modulating metabolites—undergoes rapid assembly and maturation (Stewart et al., 2018). Although the microbiome’s ability to affect brain function and behavior is now well established (Sharon, Sampson, Geschwind, & Mazmanian, 2016), relatively little is known about how this gut-brain communication system develops during infancy and toddlerhood, despite strong evidence that early alterations in brain development can have lifelong consequences for learning and mental health.