Polarization of microbial communities between competitive and cooperative metabolism

Resource competition and metabolic cross-feeding are among the main drivers of microbial community assembly. Yet, the degree to which these two conflicting forces are reflected in the composition of natural communities has not been systematically investigated. Here we use genome-scale metabolic modeling to assess resource competition and metabolic cooperation potential in large co-occurring groups (up to 40 members) across thousands of habitats. Our analysis revealed two distinct community types, clustering at opposite ends in a trade-off between competition and cooperation. On one end, lie highly cooperative communities, characterized by smaller genomes and multiple auxotrophies. At the other end, lie highly competitive communities, featuring larger genomes, overlapping nutritional requirements, and harboring more genes related to antimicrobial activity. While the latter are mainly present in soils, the former are found both in free-living and host-associated habitats. Community-scale flux simulations showed that, while the competitive communities can better resist species invasion but not nutrient shift, the cooperative communities are susceptible to species invasion but resilient to nutrient change. In accord, we show, through analyzing an additional dataset, that colonization by probiotic species is positively associated with the presence of cooperative species in the recipient microbiome. Together, our analysis highlights the bifurcation between competitive and cooperative metabolism in the assembly of natural communities and its implications for community modulation.