DescriptionThe gut microbiota has recently been acknowledged as having an impact on overall systemic health and obesity. To date, research has primarily focused on male mice due to the unknown effects of the menstrual cycle in females. Exercise is a known mediator of obesity related diseases, and the literature demonstrates an effect on the microbiome in males thus far. As post-menopausal obesity continues to rise, there is a need to explore the relationship between estrogen and the microbiome, with exercise as a possible moderator. In this study, female mice either had an ovariectomy, to simulate estrogen deficiency, or a sham procedure. Mice were placed into either a continuous exercise group, high intensity, or sedentary control group for six weeks. Microbial analysis was completed to view differences between groups. The estrogen deficient group had higher body weight and body fat percentages, regardless of exercise. Microbial analysis indicated a decrease in diversity in the estrogen deficient group, as well as a higher Firmicutes/Bacteriodetes ratio. These results are similar to obesity studies, suggesting that changes in the microbiome may be one mechanism that promotes obesity in the estrogen deficient state. Exercise interventions increased microbial diversity, with a higher percent of Bacteroidetes compared to Firmicutes.