Altered gut microbiome populations are associated with a broad range of neurodevelopmental disorders. Disruption of the gut microbiome via dietary intake has been shown to influence brain function and behavior in animal models. Utilizing diffusion tensor imaging we identified global changes in white matter structural integrity occurring in a diet-dependent manner. Subsequent diet-crossover experiments demonstrate the varying permanence of these diet-induced changes and the degree of plasticity associated with these changes. These studies allow us to further explore our understanding of the gut-brain-microbiota axis by revealing possible links between altered and dysbiotic gut microbiome populations and changes in brain structure.