Background/Question/Methods Classic studies of infections focus on the role of a single taxon as the cause of disease, even though its ultimate expression results from a complex interplay of host and environmental factors. While this conceptualization has been extremely productive for many important infections, its shortcomings are increasingly evident, leading to a new classification, diseases of disrupted biota such as Crohn's disease or bacterial vaginosis. New molecular tools make it possible to characterize healthy and diseased microbiota in ways that allow the application of ecological theories and methods to microbial communities. We explore patterns in the structure and function of microbial communities in diseased and healthy states, and how ecological factors can modify these states. For example, are microbial communities in diseased states typically more or less diverse? Is turnover in species composition and abundance greater among diseased hosts than health hosts? To what extent does geographic versus ecological distance influence turnover in community structure? How important are particular species versus functional groups in explaining diseased and healthy states? What kinds of diseases might show one or another of these patterns? Results/Conclusions To address these questions, we present results from a meta-analysis and from more in-depth studies of two systems of human microbiota: oral microbiota across multiple spatial scales, and skin microbiota as a function of disturbance and time.