in situ single-cell transcriptomic techniques offer the exciting ability to characterize gene expression within single cells in their native tissue context. With these technologies, it is possible to discover different types and states of cells in essentially any tissue in any organism while simultaneously mapping the spatial and functional organization of these cells. Our laboratory adopts, improves, and innovates new approaches to in situ single-cell 'omics, and we use these novel approaches to understand a range of biological systems. Our primary focus is to understand the spatial organization of the gut microbiome and the host gut and, in turn, to understand how this spatial organization modulates the mechanisms by which the host senses and shapes the composition and activity of the microbiome and by which the microbiome remodels many different aspects of host physiology.