Metabolic rules of microbial community assembly
Microbes form complex multi-species communities that play important roles across the biosphere. Metabolism is a major determinant of microbial community assembly, but a quantitative and predictive connection between nutrient composition and microbiome composition (and function) is lacking. Can we possibly predict which communities will form in a given, known environment? We have addressed this question through a combination of metabolic modeling and quantitative experiments. Experimentally, we have followed a high-throughput "enrichment-culture" approach to cultivate large numbers of natural communities in synthetic environments with a defined nutrient composition. Our experiments indicate that community assembly in replicate environments follows simple and reproducible metabolic rules, despite substantial species-level variability. Explicit, quantitative metabolic models allow us to predict the assembly of communities in novel nutrients, suggesting that the relationship between nutrient composition and microbiome assembly can be explained from first principles.