ABSTRACT

The small intestinal epithelial barrier inputs signals from the gut microbiota in order to balance physiological inflammation and tolerance, and to promote homeostasis. Understanding the dynamic relationship between microbes and intestinal epithelial cells has been a challenge given the cellular heterogeneity associated with the epithelium and the inherent difficulty of isolating and identifying individual cell types. Here, we used single-cell RNA sequencing of small intestinal epithelial cells from germ-free and specific pathogen-free mice to study microbe-epithelium crosstalk at the single-cell resolution. The presence of microbiota did not impact overall cellular composition of the epithelium, except for an increase in Paneth cell numbers. Contrary to expectations, pattern recognition receptors and their adaptors were not induced by the microbiota but showed concentrated expression in a small proportion of epithelial cell subsets. The presence of the microbiota induced the expression of host defense- and glycosylation-associated genes in distinct epithelial cell compartments. Moreover, the microbiota altered the metabolic gene expression profile of epithelial cells, consequently inducing mTOR signaling thereby suggesting microbe-derived metabolites directly activate and regulate mTOR signaling. Altogether, these findings present a resource of the homeostatic transcriptional and cellular impact of the microbiota on the small intestinal epithelium.

摘要

小肠上皮屏障输入来自肠道微生物群的信号，以平衡生理炎症和耐受性，并促进体内平衡。鉴于与上皮相关的细胞异质性以及分离和鉴定单个细胞类型的固有困难，了解微生物和肠上皮细胞之间的动态关系一直是一项挑战。在这里，我们使用来自无菌和无特定病原体小鼠的小肠上皮细胞的单细胞 RNA 测序来研究单细胞分辨率下的微生物-上皮细胞串扰。除了潘氏细胞数量的增加外，微生物群的存在并不影响上皮的整体细胞组成。与预期相反，模式识别受体及其接头不是由微生物群诱导的，而是在一小部分上皮细胞亚群中集中表达。微生物群的存在诱导了宿主防御和糖基化相关基因在不同的上皮细胞区室中的表达。此外，微生物群改变了上皮细胞的代谢基因表达谱，从而诱导 mTOR 信号传导，从而表明微生物衍生的代谢物直接激活和调节 mTOR 信号传导。总之，这些发现提供了微生物群对小肠上皮细胞的稳态转录和细胞影响的资源。微生物群的存在诱导了宿主防御和糖基化相关基因在不同的上皮细胞区室中的表达。此外，微生物群改变了上皮细胞的代谢基因表达谱，从而诱导 mTOR 信号传导，从而表明微生物衍生的代谢物直接激活和调节 mTOR 信号传导。总之，这些发现提供了微生物群对小肠上皮细胞的稳态转录和细胞影响的资源。微生物群的存在诱导了宿主防御和糖基化相关基因在不同的上皮细胞区室中的表达。此外，微生物群改变了上皮细胞的代谢基因表达谱，从而诱导 mTOR 信号传导，从而表明微生物衍生的代谢物直接激活和调节 mTOR 信号传导。总之，这些发现提供了微生物群对小肠上皮细胞的稳态转录和细胞影响的资源。