The focus of the research paper is to analyze and investigate archaea and viruses within the gut microbiome of the PCOS mouse model. The PCOS mouse model was initially studied to investigate the association between the gut microbiome and PCOS. This study was led by Dr. Scott Kelley. The Kelley study finds that the gut microbiome is altered in a letrozole-induced mouse model of PCOS. The results showed letrozole produced hallmarks of PCOS and altered the bacteria within the gut microbiome. Archaea and viruses are less studied organisms that contain little literature about their association with PCOS. Through metagenomic analysis, we can start to understand the association between archaea, viruses, and PCOS. The results of this research showed that letrozole had little effect on the diversity of archaea and viruses. Letrozole only affected the abundance of virus families. Specifically, three virus families increased (Myoviridae ~5%, Siphoviridae ~5%, Unclassified ~2%) and one family decreased (Retroviridae ~12%). Archaea/virus identification was performed through different algorithms that identified the important species within the dataset. Three species were found for Archaea which are Methanobrevibacter smithii, Methanosarcina acetivorans, and Methanospirillum hungatei while viruses contained multiple species of bacteriophages. Future research should be undertaken to understand the role these species play in the gut and PCOS.