In humans, microbial organisms known as the microbiota, normally colonize airway passages, skin, the oral cavity, the gastrointestinal tract, and the vagina. There is a growing body of evidence linking the gut microbiota with the overall health of its host. Normally, the microbes that make up the microbiota coexist with a human or animal host without any noticeable difficulty. However, if the symbiotic balance is altered as a result of illness, stress, dietary changes, antibiotic treatment, or other disturbances, the result may be a disruption of normal interactions known as dysbiosis. As a result, the body may become more susceptible to disease. This article examines the most common means by which the microbiota are identified, the process by which the microbiome is acquired, fecal microbial transplantation, and the association of the gut microbiome with specific illnesses such as diabetes and autism. The utility of these applications in developing a teaching module that incorporates the microbiome into courses in physiology or pathophysiology is also reviewed.