Clinical Focus

  • Gastroenterology

Academic Appointments

Professional Education

  • Fellowship: UCSF Gastroenterology Fellowship (2019) CA
  • Board Certification: American Board of Internal Medicine, Gastroenterology (2018)
  • Board Certification: American Board of Internal Medicine, Internal Medicine (2015)
  • Residency: Massachusetts General Hospital Internal Medicine Residency (2015) MA
  • Medical Education: Pritzker School of Medicine University of Chicago Registrar (2012) IL

Current Research and Scholarly Interests

My research involves high throughput anaerobic culture of gut microbes to generate complex defined microbial communities. These synthetic microbiomes have genetic content, metabolic output, and immunologic effect that is comparable to existing native human gut microbiomes. Moreover these synthetic communities allow for precise control of species and abundance and the opportunity for disease-specific research and therapy.

Currently I am designing and investigating the biological effects of various synthetic communities on recurrent C. difficile colitis, inflammatory bowel disease (IBD), and nonalcoholic fatty liver disease (NAFLD). My research entails engraftment of various synthetic communities in germ free mouse models of IBD (IL 10 deficient and DSS) and NAFLD (FDD fibrosis) to identify microbes that are important for disease modification.

All Publications

  • Design, construction, and invivo augmentation of a complex gut microbiome. Cell Cheng, A. G., Ho, P., Aranda-Diaz, A., Jain, S., Yu, F. B., Meng, X., Wang, M., Iakiviak, M., Nagashima, K., Zhao, A., Murugkar, P., Patil, A., Atabakhsh, K., Weakley, A., Yan, J., Brumbaugh, A. R., Higginbottom, S., Dimas, A., Shiver, A. L., Deutschbauer, A., Neff, N., Sonnenburg, J. L., Huang, K. C., Fischbach, M. A. 2022


    Efforts to model the human gut microbiome in mice have led to important insights into the mechanisms of host-microbe interactions. However, the model communities studied to date have been defined or complex, but not both, limiting their utility. Here, we construct and characterize invitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2. In gnotobiotic mice, hCom2 exhibited increased stability to fecal challenge and robust colonization resistance against pathogenic Escherichia coli. Mice colonized by either hCom2 or a human fecal community are phenotypically similar, suggesting that this consortium will enable a mechanistic interrogation of species and genes on microbiome-associated phenotypes.

    View details for DOI 10.1016/j.cell.2022.08.003

    View details for PubMedID 36070752