DNA sequencing has revealed hundreds to thousands of microbial species coexisting in all natural habitats, including inside human hosts. However, resource-competition models predict that the number of species in steady coexistence cannot exceed the number of resources - the so-called “paradox of the plankton”. To address this puzzle, we model how trade-offs in metabolic abilities level the playing field among competing microbes. Our model spontaneously reproduces several notable features of natural ecosystems, including high diversity, keystone species, and population dynamics.