Microbial communities drive important biochemical cycles, from the ocean to the soil to the human gut. Technological advances are revolutionizing our ability to peer into these evolving ecosystems, providing an increasingly detailed catalog of their component species, genes, and pathways. Yet a vast gap still remains in understanding the ecological and evolutionary dynamics that control their structure and function.
Our work aims to address this gap. We use tools from statistical physics, population genetics, and computational biology to understand how microscopic growth processes and genome dynamics at the single cell level give rise to the collective behaviors that can be observed at the population level. Projects range from basic theoretical investigations of non-equilibrium processes in microbial evolution and ecology, to the development of new computational tools for measuring these processes in situ in both natural and experimental microbial communities. We work closely with experimentalists, occasionally designing new experiments ourselves, and we also leverage the vast amounts of information contained in public sequencing repositories. Through these specific examples, we seek to uncover unifying theoretical principles that could help us understand, forecast, and eventually control the ecological and evolutionary dynamics that take place in these diverse scenarios.