The human gastrointestinal tract is populated by a vast and diverse community of microbes. This gut microbiota participates in host metabolism, protects from invading microbes, and facilitates immune system development and function. In this review, we consider the contributions of intestinal microbes to the pathogenesis of infectious diseases. Key concepts of colonization resistance, host-commensal microbe interaction in immunity, antibiotics and gut bacterial communities, viral-gut bacterial interactions, and evolving methods for studying commensal microbes are explored.