Microbial communities dramatically influence human health through causing disease, protecting against pathogens, and manipulating metabolism. It is therefore of great interest to understand the forces that shape the content and dynamics of microbial communities. Such an understanding will require an integrated approach that ties the biochemistry of microbial metabolism to ecological and evolutionary processes. The first aim is to utilize systems biology tools to determine the functional basis of the cooperation that evolved in a model microbial community. Increased productivity was observed in a two-species community after Salmonella enterica evolved to secrete a metabolite necessary for the growth of the Escherichia coli. Metabolomic, transcriptomic and genomic analysis of the bacteria before and after evolution will be used to determine the functional cause of the observed evolutionary change. The second aim is to determine the extent to which evolutionary patterns observed in two-species communities can be extrapolated to more complex communities. Methylobacterium extorquens will be grown with E. coli and Salmonella to create a community in which all three species are required for growth. It will be tested whether theory about the evolution of cooperation can still predict adaptation in this more complex assemblage. Additionally, high throughput methods will be used to test the degree to which community evolution is parallel. The third aim is to test the constraints on the metabolites one bacteria will evolve to provide another. A novel implementation of flux balance analysis will be used to determine the complete set of E. coli gene functions for which Salmonella can evolve to compensate. These predictions will be tested by evolving Salmonella in the presence of 10 representative E. coli knockout lines. PUBLIC HEALTH RELEVANCE: Microbial communities dramatically influence human health. They make us sick, protect us from illness and determine how we metabolize the things we eat. It is therefore of great interest to understand the forces that shape the content and dynamics of microbial communities. This study investigates how evolution changes the properties of communities of bacteria.