Humans have coevolved over time to not only tolerate but also rely on trillions of microbes that aid in the development of our immune system, provide nutrients, break down potentially noxious substances, and act as a barrier against potentially pathogenic organisms. These microbes, collectively known as the microbiota, live in relatively stable communities on mucosal surfaces such as the respiratory tract and gastrointestinal tract. Changes to the microbiota are often transient, due to changes in diet, antibiotic exposure, and psychological stressor exposure. This chapter will discuss how psychological stressors can shape the intestinal microbial community and how these perturbations can contribute to stressor-induced changes in immune function, neurodevelopment, and behavioral deficits.