This study attempted to investigate the association between changes in the intestinal environment and the brain using a model that received aerobic exercise and microbiome transplantation. All mice were fed a diet containing 60% fat. For the obesity with nonexercise microbiome transplantation group, feces from donors that did not undergo exercise were administered. For the obesity with exercise microbiome trans-plantation group, feces from donors who underwent exercise were administered. Treadmill exercise started 16 weeks after the intake of the high fat feeding and continued for 24 weeks. The short-term memory and spatial learning memory were determined by step-down avoidance test and Morris water maze task, immunohistochemistry for glial fibrillary acidic protein, western blot analysis for brain-derived neurotrophic factor and tropomyosin receptor kinase B were performed in the hippocampus. Exercise was the most effective way to reduce obesity, improve memory function, suppress inflammation, and increase brain-derived neurotrophic factor expression. Intestinal microbiota transplantation was the second most effective after exercise. However, there was no significant difference in the fecal microbiota transplant group according to whether or not exercise was performed.