The gut microbiome has been implicated in the development of metabolic disorders, and recently polycystic ovary syndrome (PCOS). PCOS is a disorder with reproductive, endocrine and metabolic irregularities, and several studies report that PCOS causes a decrease in microbial diversity and composition. Diet is an important regulator of the gut microbiome, as alterations in macronutrient balance impact gut microbial communities which correlate with different metabolic health outcomes (1). We identified that macronutrient balance impacts the development of PCOS traits. Therefore, to investigate the interplay between macronutrient balance and PCOS on the gut microbiome, we analyzed the intestinal microbiome from fecal pellets of control and DHT-induced PCOS mice exposed to 10 different diets that varied in protein (P), carbohydrate (C) and fat (F) content. The amount of dietary P, C and F consumed significantly altered alpha and beta diversity of the gut microbiota of pooled control and PCOS mice (P<0.0001). Alpha diversity between control and PCOS mice on the same diet did not differ significantly, hence was only affected by diet composition. However, beta diversity was significantly altered between control and PCOS mice (P<0.05). DESeq2 analysis identified an operational taxonomic unit (OTU) within Bacteroides (OTU3) to be the most differentially abundant OTU between control and PCOS mice, with a significant decrease in PCOS mice (P<0.0001). The consensus sequence of Bacteroides OTU3 shares 99.2% similarity to Bacteroides acidifaciens, which is associated with obesity as it has been reported to protect its host against obesity and improve insulin sensitivity (2). Overall, these findings demonstrate that diet exerts a stronger influence over the gut microbiome than PCOS pathology. However, PCOS did lead to a specific decrease in an obesity-associated Bacteroides species in PCOS mice and supports further exploration of the potential preventative role of Bacteroides acidifaciens in the development of PCOS traits.