Microbial communities (normal indigenous microbiota) inhabit those regions of the human body that are exposed to the external environment, including the skin, eyes, oral cavity and the respiratory, urinary, reproductive and gastrointestinal tracts. Consequently, the key anatomical and physiological characteristics of each body site are described throughout this book to reveal why particular organisms are able to colonize an anatomical region. The crucial roles of the indigenous microbiota in protecting against exogenous pathogens, regulating the development of our immune system and mucosae, and providing nutrients are also discussed.