research

Microbes rarely exist in isolation, but form intricate multi-species microbial communities, participating in a variety of biogeochemical processes. Recent advances in DNA sequencing have substantially improved our ability to quantify composition, function, and dynamics of microbial communities on a large scale, and we are poised to expand microbial engineering to microbiomes in nature, which is of great interest for both basic science and engineering applications. However, we currently lack technologies to genetically manipulate and interrogate diverse microbes and microbial communities. This greatly limits our ability to manipulate microbiome composition and function, and thus our understanding of the individual genetic and microbial factors that drive overall function and emergent ecological principles in microbial communities.

To address this challenge, we focus on developing foundational technologies for systems and synthetic biology to enable scalable characterization and engineering of microbial ecosystems. Using a diverse set of experimental and computational methodologies, including high-throughput DNA synthesis and sequencing, massively parallel phenotyping, cell-free expression, molecular recording, directed evolution, bioinformatics, and systems-level profiling, we seek to understand the genetic basis and biological mechanisms underlying complex microbiome processes and develop new applications of microbiome engineering. With a greater control on microbial community assembly and function, programmable microbiomes in diverse environments, ranging from natural habitats, such as human gut or soil, to industrial bioreactors, will have the potential to impact numerous emerging biotechnological applications spanning medicine, agriculture, and bioproduction.