Estrogens are a group of steroid hormones involved in regulating physiological processes including metabolism. Decreases in estrogen levels, such as observed in post- menopausal women, are often accompanied by symptoms of metabolic dysregulation. Symptoms of post-menopausal metabolic dysregulation can include weight gain, increased abdominal fat, and insulin resistance. To investigate the role decreased estrogen levels play in metabolism, ovariectomized (OVX) female mice have been used as a model of estrogen deficiency. Previous studies indicate that estrogen in combination with gut microbe composition may offer protection against metabolic dysregulation in the presence of a high- fat diet (HFD). In order to further investigate the role of the gut microbiome on estrogen deficient metabolic dysregulation, we analyzed fecal bacterial composition following OVX in female mice independent of diet. Bacterial 16S rRNA sequencing analysis did not indicate differences in alpha diversity (a measure of species richness) between the two treatment groups. However, differences in between sample diversity (beta diversity) were demonstrated using unweighted UniFrac analysis. Furthermore, differential abundance analysis revealed a shift in taxa abundance beginning 3 weeks post-surgery in OVX mice relative to SHAM mice. Increased weight gain was observed in OVX mice beginning 2 weeks post-surgery, suggesting that the shift in differential abundance was a consequence rather than the cause of metabolic dysregulation in OVX mice. In addition, a cohousing study was performed to investigate whether exposure to a healthy microbiome would offer protection from developing metabolic dysregulation in OVX mice. In contrast to previous studies, cohousing did not prevent development of the phenotype observed in OVX mice, supporting the idea that alterations in microbiome composition did not lead to the metabolic dysregulation observed in OVX mice.