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

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.

哺乳动物胃肠道由多种异质性细胞类型构成，每类细胞均可响应多种源自膳食、宿主及微生物的小分子物质。这类小分子可被大量不同的受体所识别感知，而这些受体在肠道区域、空间维度与细胞间的差异化表达，是介导感知过程的核心方式。
与此同时，肠道微生物组（gut microbiome）在调控哺乳动物肠道的稳态细胞、分子与空间结构方面发挥关键作用，包括可能参与塑造肠道的受体表达谱，进而影响肠道的分子感知能力。
本研究提供了一套空间分辨单细胞基因表达图谱（spatially resolved single-cell atlas of gene expression），涵盖存在微生物组与无菌两种条件下，小鼠肠道四个区域的基因表达情况。
该数据集所产生的测量数据，为理解细胞类型特异性感知能力、细胞在不同肠道区域间如何微调其感知能力，以及更微观尺度下，细胞在肠道黏膜内的位置如何调控感知能力的微调，提供了极为丰富的研究资源。