Spatially restricted immune and microbiota-driven adaptation of the gut [scRNA-seq]

The intestine is characterized by an environment where host requirements for efficient nutrient and water absorption are consequently paired with the requirement to establish and maintain tolerance to the outside environment. The organ is anatomically organized into the small intestine (SI) which specializes in nutrient absorption and the colon which specializes in water resorption. The transcriptional and cellular circuits that define intestinal regionalization and their robustness, adaptability, and resilience to changes in the local environment are not well characterized. Here, we generated a comprehensive survey of the spatial and cellular landscape of the murine intestine to demonstrate the steady state transcriptional landscape of the murine intestine is robust, adaptable, and resilient to perturbation. We characterized the transcriptional landscape of the full length of the intestine and show it is established independently of the microbiota and is not under circadian regulation. In the colon, these regional circuits were characterized by unique subsets of structural cells. Moreover, we identified a spatial adaptation to the microbiota in the colon characterized by the emergence of unique structural cell subsets including an enterocyte, fibroblast, and goblet cell, with the later two co-occurring in space. Employing a model of acute spatiotemporal damage allowed us to show the spatial landscape and adaptations we identified are both resilient to inflammation. Our results demonstrate that intestinal circuits are under host control and spatial adaptations in the steady state as well as in the process of recovery from tissue damage in the inflamed state are primarily characterized by changes to structural cell types such as epithelial and stromal cells. Single cell suspensions were generated for single cell RNA sequencing from 4 different segments (A-D) of mouse colon from WT SPF and GF mice and 2 segments (B-C) from WT FMT mice. 3 biological replicates were generated for each segment for both SPF and GF mice. 2 biological replicates were generated for each segment for FMT mice. Samples were compared within SPF mice to establish the cellular complexity of different regions in the steady state and subsequently compared to GF mice and FMT mice to establish those that are dependent on the microbiota.