This case study focuses on the relationship between the microbiome (the suite of species that live in or on the human body) and autoimmune and allergic diseases. At the center of the case is Amelia, a young woman living with Crohn's disease. As the case unfolds, students learn about the hygiene hypothesis that modern, "cleaner" living conditions may be linked to the rise of autoimmune disorders throughout the developed world. After students learn the basics of the hygiene hypothesis, they are asked to design an experiment to test it. They are then introduced to some of the modern experimental treatments for autoimmune disorders, including fecal transplants and worm therapy. These treatments aim to restore a more diverse microbiome to the human body. The case ends by relating the human body to an ecosystem, and asks students to think about how ecological principles are being used to treat human diseases. The case was written for a sophomore level biodiversity class and a sophomore level physiology class, but could easily be used in introductory biology or similar courses.