This book provides an accessible and authoritative guide to the fundamental principles of microbiome science, an exciting and fast-emerging new discipline that is reshaping many aspects of the life sciences. Resident microbes in healthy animals--including humans--can dictate many traits of the animal host. This animal microbiome is a second immune system conferring protection against pathogens, it can structure host metabolism in animals as diverse as reef corals and hibernating mammals, and it may influence animal behavior, from social recognition to emotional states. These microbial partners can also drive ecologically important traits, from thermal tolerance to diet, and have contributed to animal diversification over long evolutionary timescales.