Christopher Smillie

Christopher Smillie

Assistant Professor
Christopher Smillie

The Smillie Lab uses systems approaches to understand the mechanisms of host-microbiome interactions. Our research interests are broad, spanning mucosal immunology, microbiome evolution and ecology, and tissue biology, while relying on a combination of computational and experimental methods.

The human microbiome has been one of the most fascinating research areas over the past two decades. Mammals and their microbiota have co-evolved for millions of years, giving rise to ancient symbioses that profoundly impact human health and disease. For example, bacterial species have been linked to epithelial cell differentiation (stem cell biology), immune system maturation and function (immunology), and the nervous system (neurobiology), whereas microbial dysbiosis is a hallmark of several diseases.

However, the extent of these interactions and their underlying mechanisms are largely unknown, due to the complexity of the host-microbiome interface. We are building an integrated research environment, where novel computational methods and high-throughput assays will generate targeted hypotheses for experimental investigation. Current research directions include:

  • Discovering bacterial strains and metabolites associated with the onset or resolution of IBD
  • Computational methods for spatial transcriptomics to understand gut inflammation and fibrosis
  • Developing methods to detect host-microbiome interactions in single-cell transcriptomic data
  • Extending droplet-based single-cell RNA-seq to bacterial cells in the human microbiome
  • Decoding microbiome functions using protein structures and representations (e.g. AlphaFold)

Contact Information

Massachusetts General Hospital
Simches Research Center, 8th Floor
185 Cambridge Street
Boston, MA 02114


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