The Microbiome at Other Mucosal Sites

Culture-independent studies of the microbiome of mucosal sites other than the intestine are at an early and exciting stage. Mucosal surfaces are universally warm and moist and often contiguous with or adjacent to each other and the upper or lower gastrointestinal tract. The microbiome at different sites may share common elements as well as possessing distinct and characteristic members. The impression from the limited number of studies currently available is that each site may possess a surprisingly consistent core microbiome that is shared by most individuals. This consistency is likely to reflect almost completely unexplored host factors that actively manage the microbiome. In the place of a simplistic model that pathogens cause disease, microbial-induced injuries may now be understood in terms of complex changes in a dynamic and innately homeostatic community. Therefore, in this review, we discuss what is known about the normal microbiome at each site, before exploring changes in the microbiome that accompany or cause disease. The emphasis of the review is on the bacterial microbiome only because of the limited nature of investigation into normal viral and fungal communities at human mucosal sites.