Our research goal is to understand how communities of microbes self-assemble into functional communities at the micro-scale, and to use that understanding to engineer more efficient and resilient microbiomes. In particular, we focus on biopolymer degrading communities, which play a central role in all ecosystems by digesting complex forms of organic matter originating from plant and animal tissues. In order to deconstruct such complex substrates, multiple species of bacteria with a diverse set of behaviors and functions self-assemble in dense communities to initiate a cascade of ecological and metabolic transitions that eventually lead to the decomposition of organic matter. To address this problem we take a hybrid approach, integrating synthetic ecology, computational models and genomics to measure ecological and evolutionary dynamics in natural and domesticated communities.