The“eco-evolutionary feedback viewpoint is reorganizing our understanding of how ecological and evolutionary processes interdependently structure the contemporary dynamics of the biosphere. However, our knowledge still depends largely on findings from simple empirical systems representing limited spatial scales and involving a small number of species. I review recent conceptual developments for the understanding of multispecies coevolutionary processes and then present an empirical research workflow based on network science and high-throughput sequencing in order to accelerate the integration of community ecology and evolutionary biology. I focus on the roles of“metacommunity hub”species, to which large parts of metacommunity-level ecological and evolutionary phenomena are potentially attributed. I then illustrate a DNA-sequencing-based workflow for searching those topological hubs within metacommunity-level network of host–symbiont (or prey–predator) associations. As large amounts of network topology data are becoming available with high-throughput sequencing analysis of various host–symbiont, prey–predator, and symbiont-symbiont systems, it is now time to promote empirical studies that test the eco-evolutionary feedback concept in species-rich metacommunities.