The vertebrate microbiome consists of the bacteria, fungi, archaea, protozoans, and viruses that inhabit the body at diverse locations including the skin, mouth, upper airways, urogenital tract, and digestive tract. These microorganisms are known to synthesize vitamins, interact with and tone the immune system, and dramatically affect human health. A long list of diseases has been associated with imbalances in commensal microbiome communities. The work presented in this dissertation aims to characterize the microeukaryotic and archaeal components of the gut microbiome through development of wet lab techniques and in silico methods, and apply them to the study of response to antibiotics. These methods provided a picture of the healthy fungal and archaeal communities in the gut, with high prevalence of the yeast Saccharomyces and the archaeon Methanobrevibactor, along with several other species. These new tools were then used to investigate the longitudinal changes that the microbiome undergoes when treated with heavy antibiotics. Using an antibiotic cocktail containing ampicillin, neomycin, vancomycin, and metronidazole in a mouse model, we found that bacterial communities were effectively suppressed and fungi grew out by one to two orders of magnitude. After we discontinued antibiotics, bacterial and fungal cell counts returned to baseline levels within one week, but community composition was still significantly altered. Eight weeks after cessation of antibiotics, fungal community composition was not significantly different from non-treated controls, but several mice continued to have elevated levels of yeasts that had grown out during antibiotic treatment. The bacterial community composition was still significantly different from non-treated controls. Ultimately, this work demonstrated potentially deleterious long term effects of antibiotic use, and emphasizes how strong cage effects can be in mouse studies. The research performed in this dissertation will aid researchers looking to study all three domains of life and take into account the effects of commonly used antibiotics in future microbiome studies.