The many commensal microbial communities that reside on our bodies have a profound ability to modulate our health. We are interested in understanding the molecular mechanisms that mediate both the interactions between these communities and the host as well as between the many different bacterial species that make up the remarkably complex community in the gut. We are also interested in understanding the mechanisms by which the host senses microbial activity and processes this information.

To tackle these questions, we adopt a single-cell perspective with the goal of cataloging the many cell types that comprise the microbiome-gut-brain axis. However, catalogs of cell types alone offer limited insight into cellular interactions and the spatial organization of cells both within microbial communities and within the host. Thus, we are developing and utilizing state-of-the-art spatially resolved single-cell approaches that characterize genome-scale expression profiles within single cells via massively multiplexed molecular imaging within intact biological samples. These methods offer the exciting ability to not only discover cell types in any organism but to also map their spatial organization within intact tissues and infer cellular communication mechanisms from spatial correlations in gene expression between cells. By using these methods to map single-cell gene expression in both the microbiome and the host, we aim to provide new understanding of how microbial activity is sensed and shaped by the host.