The human body is an ecosystem, with the human microbiome playing a crucial role in maintaining health and preventing diseases. The human microbiome can be viewed as a community of symbiotic species that interact with the host through various ecological processes, including dispersal, local diversification, environmental selection, and ecological drift. These processes influence the assembly and dynamics of the microbiome, which can vary across individuals and over time. The authors explore three key scenarios of microbiome assembly: development in infants, recovery from antibiotic use, and invasion by pathogens. They argue that applying ecological theory, particularly metacommunity theory, can help explain these dynamics and inform strategies for maintaining and restoring the microbiota. The review highlights the importance of understanding the role of the microbiome in health and disease, and suggests that an ecological approach to medicine could revolutionize the treatment of infectious diseases by focusing on ecosystem services provided by the microbiome.The human body is an ecosystem, with the human microbiome playing a crucial role in maintaining health and preventing diseases. The human microbiome can be viewed as a community of symbiotic species that interact with the host through various ecological processes, including dispersal, local diversification, environmental selection, and ecological drift. These processes influence the assembly and dynamics of the microbiome, which can vary across individuals and over time. The authors explore three key scenarios of microbiome assembly: development in infants, recovery from antibiotic use, and invasion by pathogens. They argue that applying ecological theory, particularly metacommunity theory, can help explain these dynamics and inform strategies for maintaining and restoring the microbiota. The review highlights the importance of understanding the role of the microbiome in health and disease, and suggests that an ecological approach to medicine could revolutionize the treatment of infectious diseases by focusing on ecosystem services provided by the microbiome.