Jeffrey Moffitt

My laboratory is interested in the role of spatial organization in host-microbe interactions in the mammalian gut. We develop, extend, and utilize image-based approaches to spatial genomics, including a massively multiplexed single-molecule RNA imaging technology known as MERFISH.

With this and other techniques we profile gene expression within single cells across large tissue sections and then use advanced image analysis and single-cell omics statistical tools to define, discover, and map cell types and states across these slices.

By leveraging these genomic-microscopy tools, we are providing a new window into a series of questions, including how commensal microbial communities are organized and how this organization shapes the bacterial response to micron-scale gradients in nutrients, oxygen, and antimicrobials; how bacterial activity shapes the organization and activity of cells in the healthy gut; how bacterial biogeography shapes dysregulated immune responses and inflammatory bowel disorder; and how the mammalian gut is remodeled when the barrier between host and microbe is disrupted, triggering broad inflammation.

We pair these biological efforts with technical efforts to improve the quality and analysis of these novel datasets. These efforts include new microscopy platforms that improve resolution and throughput, new statistical methods to identify molecules and cells from these images, genome-wide tissue modeling efforts to quantify molecular interactions, and a range of new spatial statistics that provide robust quantification to the biological insights we extract from these data. In short, we aim to build and leverage new tools to build a better quantitative understanding of interactions at the microbe-host interface.