Polycystic ovary syndrome (PCOS) is the most common endocrine disorder affecting 6-12% of women world-wide. It is characterized by reproductive, metabolic, and endocrine abnormalities such as anovulation, hyperandrogenism and polycystic ovaries. Metabolic phenotypes associated with PCOS include obesity, insulin resistance and hyperinsulinemia. Studies have suggested that PCOS is linked to shifts in gut bacteria diversity in women and in both letrozole-induced and dihydrotestosterone (DHT)-induced mouse models of PCOS. In this longitudinal study, we studied the effects of DHT (high testosterone) and ovariectomy (OVX) (no estrogen) both alone and in combination on the female mouse gut microbiome. There were observed changes in the gut microbiome over time in this study. While we did not observe an effect of treatment on alpha diversity, we did detect a significant time dependent effect of treatment on beta diversity. It was observed that the largest increase in differentiation for all treatments occurred from week four to week five. Statistical analysis of beta diversity at each week demonstrated treatment groups were all statistically different except for week one. This suggests that the different treatments resulted in unique microbiome compositions. The random forest classifier was used to identify bacterial taxa associated with treatment, and the relative abundances of the fifty bacterial features identified as most important for classification were further investigated. A linear mixed-effects model was used to analyze how relative abundance was affected for each individual bacteria by treatment over time. It was observed that well known families of bacteria showed significance in our study including S24-7, Rikenelleceae and Lachnospiraceae. Our study also identified M. schaedleri as a significant bacteria based on treatment. This species is of interest because it does not appear in other PCOS mouse model studies.