Oral contraceptives are used by a significant population of women with mood disorders being a common side effect of the diurnal drug. They are an essential part of regulating hormones, particularly for women and can provide more than just preventing pregnancy like reducing the intensity and frequency of cramps, stopping heavy menstruation, and diminishing hormonally induced acne. In recent years, scientists have correlated the gut microbiome to mood changes due to interactions by the gut-brain-axis. This leads us to postulate an interaction between the gut microbiota, oral contraceptives, and the brain. To study the effect of oral contraceptives on the gut microbiome, a simple model was set up using Bacteroides fragilis, a common gut bacterium involved in increasing gut permeability while also being an opportunistic pathogen and Lactobacillus rhamnosus, a common probiotic that has been known to be involved in sex steroid hormone metabolism. We perturbed these bacteria and grew them separately and together with ethinyl estradiol at 0.7 μM, levonorgestrel at 3 μM, levonorgestrel at 50 μM, and ethinyl estradiol at 0.7 μM with levonorgestrel at 3 μM along with respective bacterial controls and a media control until their late log phase. Intercellular metabolites were extracted using a 2:2:1 acetonitrile:methanol:water mixture and analyzed using high resolution tandem mass spectrometry in an untargeted metabolomics workflow. Resulting data indicates that amino acid concentrations were significantly decreased in B. fragilis while they increased in L. rhamnosus. In particular, the regulation of amino acids: tryptophan, phenylalanine, aspartic acid, histidine, lysine, and glutamate that are involved in neurotransmission were significantly altered and could be a potential source of mood changes in oral contraceptive users.