Intestinal Epithelial Cells and the Microbiome Undergo Swift Reprogramming at the Inception of Colonic Citrobacter rodentium Infection

Abstract

We used the mouse attaching and effacing (A/E) pathogen Citrobacter rodentium, which models the human A/E pathogens enteropathogenic Escherichia coli and enterohemorrhagic E. coli (EPEC and EHEC), to temporally resolve intestinal epithelial cell (IEC) responses and changes to the microbiome during in vivo infection. We found the host to be unresponsive during the first 3 days postinfection (DPI), when C. rodentium resides in the caecum. In contrast, at 4 DPI, the day of colonic colonization, despite only sporadic adhesion to the apex of the crypt, we observed robust upregulation of cell cycle and DNA repair processes, which were associated with expansion of the crypt Ki67-positive replicative zone, and downregulation of multiple metabolic processes (including the tricarboxylic acid [TCA] cycle and oxidative phosphorylation). Moreover, we observed dramatic depletion of goblet and deep crypt secretory cells and an atypical regulation of cholesterol homeostasis in IECs during early infection, with simultaneous upregulation of cholesterol biogenesis (e.g., 3-hydroxy-3-methylglutaryl–coenzyme A reductase [Hmgcr]), import (e.g., low-density lipoprotein receptor [Ldlr]), and efflux (e.g., AbcA1). We also detected interleukin 22 (IL-22) responses in IECs (e.g., Reg3γ) on the day of colonic colonization, which occurred concomitantly with a bloom of commensal Enterobacteriaceae on the mucosal surface. These results unravel a new paradigm in host-pathogen-microbiome interactions, showing for the first time that sensing a small number of pathogenic bacteria triggers swift intrinsic changes to the IEC composition and function, in tandem with significant changes to the mucosa-associated microbiome, which parallel innate immune responses. IMPORTANCE The mouse pathogen C. rodentium is a widely used model for colonic infection and has been a major tool in fundamental discoveries in the fields of bacterial pathogenesis and mucosal immunology. Despite extensive studies probing acute C. rodentium infection, our understanding of the early stages preceding the infection climax remains relatively undetailed. To this end, we apply a multiomics approach to resolve temporal changes to the host and microbiome during early infection. Unexpectedly, we found immediate and dramatic responses occurring on the day of colonic infection, both in the host intestinal epithelial cells and in the microbiome. Our study suggests changes in cholesterol and carbon metabolism in epithelial cells are instantly induced upon pathogen detection in the colon, corresponding with a shift to primarily facultative anaerobes constituting the microbiome. This study contributes to our knowledge of disease pathogenesis and mechanisms of barrier regulation, which is required for development of novel therapeutics targeting the intestinal epithelium.

Faecal neutrophil elastase-antiprotease balance reflects colitis severity

“…S6). 8 This suggests similar temporal neutrophil recruitment irrespective of mouse strain. We therefore hypothesised that the differences between the two mouse strains is due degranulation.…”

“…3 Moreover, shortly after mucosal colonisation C. rodentium triggers extensive reprogramming of cell proliferation and metabolic processes in IECs. [7][8][9] Importantly, the severity of colitis differs depending on the mouse strain. While some strains (e.g.…”

Characterization of the intestinal microbiota during Citrobacter rodentium infection in a mouse model of infection-triggered Parkinson’s disease

“…C. rodentium infection induces temporal shifts in the mouse intestinal microbiota including an expansion of Enterobacteriaceae. 32,33 As described above, gut microbiota alterations, such as an expansion in Enterobacteriaceae and Verrucomicrobia, have been implicated in PD. 25 This raises the possibility that microbiota differences between wild-type (WT) and Pink1 −/mice, either before, during, or after infection could be implicated in the infection-induced PD-like phenotypes observed.…”

Intestinal epithelial cells: at the interface of the microbiota and mucosal immunity

“…Microbes also induce a number of non‐barrier functions in IECs, including changes in metabolism and the biosynthesis of signalling molecules. For example, early during Citrobacter rodentium infection, IECs have been shown to exhibit changes in cholesterol and carbon metabolic pathways, suggesting that IEC metabolism is reprogrammed to meet increased cellular energetic demands during tissue repair . Some enterochromaffin cells, a subtype of enteroendocrine cell, have been shown to secrete serotonin (5‐hydroxytryptamine, 5‐HT) in response to mechanosensing via the mechanotransducer Piezo2, and 5‐HT is an important regulator of enteric nervous system development, and gastrointestinal tract motility and inflammation .…”