People spend most of their time in spaces and structures designed, built, and managed by humans. The factors that affect the environments within buildings, the ways in which building characteristics influence the composition and function of indoor microbial communities, and the ways in which these microbial communities relate to human health and well-being are extraordinarily complex and can be explored only as a dynamic, interconnected ecosystem. This report examines how to advance understanding of the ecosystem of built environments, indoor microbiomes, and effects on human health and well-being.