It strongly modulates overall host physiology, including the ability of pathogenic microbes to establish themselves in or on host surfaces.¹

The sheer numbers of these microbes and their genomic variability often exceed the numbers of host cells and the variability of host genes in a typical animal.

Changes and differences in microbiomes within and between individuals impact such diverse conditions as obesity; type 1 diabetes; cognition; neurologic states; autoimmune diseases; skin, gastrointestinal, respiratory, and vaginal infectious diseases; and development and control of the immune system.

It has been difficult to directly associate specific types of microbiomes with pathophysiologic states, and our understanding of the degree to which microbial species are conserved or variable within human and other animal microbiotas is evolving. Experimental studies in laboratory animals, particularly in germ-free mammals, show the potent ability of changes in the microbiota to manipulate health status and outcomes. One of the clearest functions of the microbiota is to influence and mature the cells of the immune system, thereby exerting a major effect on susceptibility and resistance to microbial infection. The degree to which studies of the microbiome will translate into strategies for the management of human health and disease (e.g., the use of fecal transplants to treat and prevent recurrences of serious Clostridium difficileinfection) is still an open question. For the moment, defining clusters of organisms associated with diseases may be more feasible than identifying single organisms or microbial molecules. Results from the Human Microbiome Project suggest a high level of variability among individuals in microbiome components, although many individuals appear to maintain a fairly conserved microbiome throughout their lives. In the context of infectious diseases, changes and disruptions of the indigenous microbiome—i.e., alterations of the normal flora due to antibiotic and immunosuppressive drug use, environmental changes, and the effects of microbial virulence factors used to displace the indigenous microbial flora and thus to facilitate pathogen colonization—have a strong and often fundamental impact on the progression of infection. While the technology for defining and understanding the microbiome is still quite young, there is little doubt that the resulting data will markedly affect our concepts of and approaches to microbial pathogenesis and infectious disease treatment.