Emerging infectious diseases' hotspots have been identified as multi-host and multi-pathogen systems often characterized in tropical ecosystems by an extensive wildlife/domestic/human interface. The pathogen communities shared by the wild and domestic populations at this interface reflect the historical epidemiological interactions between them. In a research framework using recent community ecology, evolutionary biology and molecular biology advances, this information can be used to identify potential pathways for future pathogen spill-over initiating the emergence process. In other words, an understanding of the mechanisms of pathogen transmission in a specific ecosystem can provide an interaction network between host populations defined by nodes and edges and characterized by the frequency, intensity and direction of the interactions with a direct input for targeted disease surveillance.