About Our Research

Microbes are the most abundant and diverse group of organisms in nature, forming intricate and dynamic ecosystems that evolve over time. Yet, it is often difficult to untangle the myriad of complex interactions that occur in a heterogeneous microbial community.

We are interested in understanding the key principles that drive the formation, maintenance, and evolution of genomes within and across microbial populations. We apply new approaches in systems biology and synthetic biology to address important questions that lie at the intersection of molecular biology, genomics, and evolution. We utilize genome engineering, DNA synthesis, and next-generation sequencing methods to better understand genome evolution and population dynamics of a variety of model organisms and microbial communities under different environments. Furthermore, we aim to develop synthetic approaches in ecological engineering to manipulate disease-relevant microbial ecosystems such as those found on the human body and in the human gut towards ultimately improving health.

We are focused on these general areas of basic and applied research:

Genome-scale (cellular-level)

  • Transcription, translation, & protein perturbations

  • Metabolism & metabolic interactions

  • Reconstructing evolution

  • Alternative genetic codes

  • Genetic interactions

Ecological-scale (population-level)

  • Human-microbiome engineering

  • Temporal & spatial population dynamics

  • Cooperativity & competition

  • Horizontal gene transfer

  • Functional metagenomics

Our repertoire of cutting-edge techniques include:

  • Multiplex automated genome engineering (MAGE)

  • Conjugative Assemby Genome Engineering (CAGE)

  • High-throughput DNA synthesis & sequencing

  • Engineered self-transmissible replicons & CRISPRs

  • Non-natural amino acid incorporation

  • Hyperactive transposons

  • Novel transformation methods

  • DNA-based cellular recording (TRACE)

We use a variety of model organisms and systems including:

  • Bacteria: E. coli, Pseudomonas, Bacillus, Lactobacillus,
    Bacteroides, Streptomycetes, etc    .

  • Eukarya: yeast, fungi, mammalian cells

  • Synthetic communities: engineering microbial consortia

  • Natural communities: human-associated microbiota

  • Animal models: conventional and gnotobiotic mice

Funding

We are very grateful for the generous support of our research by the following agencies and foundations: NIH-OD, NIGMS, NIAID, NIDDK, NCI, ONR, DARPA, NSF, Burroughs Wellcome Fund, Sloan Foundation.