Microbial ecosystems represent a new paradigm for ecology. Recent technological advances allow empirical studies of microbial communities across habitats, elucidating their functioning with unprecedented detail. New culturing techniques and synthetic microcosms, for instance, enable observation of increasingly realistic eco-evolutionary dynamics as they unfold. The picture that emerges is often complex and unexpected, challenging our current ecological theories and reshaping our understanding of how species interact, how energy flows through ecosystems, and why certain patterns are observed in nature. In my talk I will explain some of the models that we developed to understand these patterns in the light of multi-omics data. I will particularly focus on the mechanisms that lead to the emergence of multistability and alternative community types.