research

Microbes rarely live in isolation. They form complex multi-species communities that drive a wide range of biogeochemical processes. Advances in DNA sequencing now allow us to measure the composition, function, and dynamics of these communities at scale, opening the door to extending microbial engineering from single strains to entire microbiomes. Yet we still lack the tools to genetically manipulate and interrogate most microbes and the communities they form. This limits our ability to control microbiome composition and function, and to understand how individual genes and species give rise to community-level behavior and emergent ecological principles.

To address this challenge, we develop foundational technologies in systems and synthetic biology for the scalable characterization and engineering of microbial ecosystems. We combine experimental and computational approaches, including high-throughput DNA synthesis and sequencing, massively parallel phenotyping, cell-free expression, molecular recording, directed evolution, and bioinformatics, to uncover the genetic basis of complex microbiome processes and to develop new applications of microbiome engineering. With greater control over how microbial communities assemble and function, programmable microbiomes could transform medicine, agriculture, and bioproduction, in settings ranging from the human gut and soil to industrial bioreactors.