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MERFISH measurements of the mouse gastrointestinal tract in the presence and absence of the microbiome

Moffitt, Jeffrey1; Xu, Rosalind1

Published Aug 05, 2025 on Dryad. https://doi.org/10.5061/dryad.p5hqbzm0z

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Abstract

The mammalian gastrointestinal tract is comprised of a diverse set of cell types, each responsive to a diversity of diet-, host-, and microbe-derived small molecules. These small molecules are sensed by a massive diversity of receptors and differential regional, spatial, and cellular expression of these receptors is a critical mode by which sensation is mediated. In parallel, the gut microbiome plays critical roles in modulating the homeostatic cellular, molecular, and spatial structure of the mammalian gut, including potential roles in shaping the receptors that are expressed and, thus, the molecular sensing capabilities of the gut. Here we provide a spatially resolved, single-cell atlas of gene expression across four regions of the murine gut in the presence and absence of the microbiome. These measurements provide a rich resource for understanding cell-type specific sensation capabilities, the way in which cells fine tune these capabilities across gut regions, and, on a smaller scale, how these capabilities are fine tuned along based on cellular location within the gut mucosa.