Key gut microbes shape intestinal epithelial lineage development, differentiation and metabolic function

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PROJECT SUMMARY The intestinal epithelium perpetually self-renews and differentiates into specialized progenies. This process is often viewed as a hard-wired genetic program under the control of host-derived factors. The organizing principal of my proposal is that specification, differentiation and functional specialization of these epithelial lineages are modulated by members of the gut microbiota and their metabolic products. Our groups' studies of healthy and undernourished Bangladeshi children revealed that Prevotella copri is a key species whose abundance in the developing microbiota is positively associated with ponderal growth. My current work in the Gordon lab has established a gnotobiotic mouse model of mother-to-infant transmission of defined collections of human gut bacterial strains that represent different stages in the postnatal assembly of gut microbiota. I performed single-nucleus RNA-seq to test the effects of including or excluding P copri from these defined communities. A prominent epithelial response to the presence of P. copri is enhanced enterocytic fatty acid oxidation. Pseudotime analysis of snRNA-seq datasets disclosed that expression of fatty acid oxidation genes was spatially regulated by P. copri as enterocytes differentiate/migrate from crypts up villi and that nuclear receptor PPAR appears to be a top candidate regulator of these genes. I hypothesize that i) exposure to the P. copri-containing community broadly alters the epigenetic landscape as well as chromatin accessibility to transcription factor binding as enterocytes execute their differentiation program up the villus, and (ii) PPAR functions as a key transcription factor that mediates the effects of P. copri on fatty acid oxidation with additional regulatory inputs from other transcription factors. I propose two aims to test these hypotheses. In Aim 1, I will characterize, at single-cell resolution, changes in the epigenetic landscape and the transcription factors that comprise the signaling pathways that P. copri-containing community uses to regulate enterocyte differentiation/function along the length of the intestine. In Aim 2, I will characterize how the P. copri-containing defined bacterial community modulates PPAR signaling to control enterocytic fatty acid oxidation along the crypt-to-villus axis, by using a combination of liquid-chromatography mass spectrometry, 2-dimensional organoid culture system, and gnotobiotic mouse models. This research will provide (i) mechanistic insights on how gut microbiota modulates host signaling to control epithelial lineage development, metabolic function, and functional specialization, and (ii) novel metabolites that have therapeutic potential to benefit intestinal physiology and function.