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The revolution in sequencing technologies offers an exciting new perspective on full microbial communities - and on both microbial effects on plant health and microbial responses to climate. Components of plant health and plant productivity can be considered part of the extended phenotype or phenome of environmental microbial communities. Progress in plant genomics supports new levels of characterization of plant responses to microbial communities, which have potential for construction of a more nuanced understanding of the extended phenome in the context of epidemics. Two types of network models may prove useful for conceptualizing the roles of microbial communities in disease ecology. In one type, nodes of the network represent individual taxa. Approaches for modeling the interactions of these communities may be analogous to genetic networks and food webs. In another type, nodes of the network represent physical locations. This case includes epidemic network models of the movement of pathogens, and may be extended to include the movement of communities of microbes. When such models treat the host as habitat for within-host modeling, they may also include the movement of forms of information associated with microbes, such as microbial and plant signaling molecules.<p><p>Keywords: