Our Research

Our research focuses on two primary objectives: first, to reliably introduce beneficial bacteria into gut ecosystems, and second, to uncover the genetic and metabolic determinants that facilitate microbe-microbe and host-microbe interactions. Leveraging high-throughput technologies in spatial metagenomics (MaPS-Seq) and functional genomics (DropSynth), we aim to decode the complex mechanisms underlying these activities in the gut microbiome. Ultimately, we will develop methods to precisely control the composition and metabolic activities of gut microbial communities, paving the way for personalized bacterial therapeutics.

Probiotics are promising therapies for ameliorating gastrointestinal disorders but are ineffective due to their inconsistency in colonizing gut environments across individuals. We will use high-throughput gene synthesis and screening with spatiotemporal readouts to explore the molecular mechanisms controlling how probiotic microbes access niches within the mammalian gut. This work will enable the construction of more robust probiotics that can be rapidly personalized to individuals.

FMT is an effective but imprecise therapy, which provides few insights when it fails. Our approach will leverage culturomics, metabolic modeling, and metagenomics to craft communities with defined properties for FMT. We will design transplant communities that exploit vacant nutritional niches within recipients and possess metabolic properties to address specific gastrointestinal issues. This research will lay the groundwork for creating personalized FMT therapies tailored to an individual's unique gut environment.