When we think about bacteria, we often think first about disease. While there are many bacteria that cause diseases, there are also many other bacteria that are useful for human health. The human body has an enormous number of these good bacteria, which work together and with the immune system to protect us against diseases. In this article, we will discuss this relationship between the good bacteria living inside us and the immune system. We will explain how we can study these helpful bacteria, and describe the tools and methods at our disposal, such as special mice whose bodies do not contain any bacteria. Finally, we will describe how we can use the good bacteria living in the human body to advance medicine and drug development.