Bacteria ‘Rewire’ Epithelial Cells and Drive Disease in the Gut

A bacterial pathogen that causes colitis and colorectal cancer creates a nutrient-rich niche and “rewires” epithelial cell signaling in the inflamed gut, which promotes bacterial colonization and disease, mechanisms that may be promising therapeutic targets, according to a recent study published in the journal Cell.

Alexandra Grote, PhD, assistant professor of Medicine in the Division of Infectious Diseases, was a co-author of the study.

Anaerobic pathogens are strains of bacteria that grow in oxygen-poor environments, including the human colon. One of these pathogens, Enterotoxigenic Bacteroides fragilis (ETBF), has been implicated in colitis and colorectal cancer and causes disease in the gut microbiome by secreting a single virulence factor, B. fragilis toxin (BFT).

How anaerobic pathogens create nutrient-dense environments to then colonize and spread disease, however, has remained a longstanding question in the field, Grote said.

“ETBF triggers gut inflammation, which raises oxygen levels, so how does a classically anaerobic bacterium survive, and even flourish, in the increasingly oxygenated environment it creates? That was the central question conceived by Wenhan Zhu at Vanderbilt University and our collaborative team set out to answer it,” Grote said.

In the current study, the investigators used a wide range of approaches to study ETBF, including genomics, metabolomics and mouse models of disease, as well as hybrid-selection RNA sequencing, a technique that uses custom capture probes to selectively isolate ETBF gene transcripts from complex mixtures of host and microbial RNA in gut tissue.

These genomic and transcriptomic profiles were then integrated with genome-scale metabolic modeling, allowing the scientists to better identify which metabolic pathways ETBF was modulating inside a host. The scientists also generated engineered bacterial mutants, profiled colonocyte metabolism using a flow cytometry-based assay, measured oxygen and lactate levels in the gut, performed untargeted metabolomics, and tested several therapeutic interventions in mouse models of colitis and colorectal cancer.

Using myriad approaches, the scientists discovered that ETBF employs BFT, which internally rewires epithelial cells in the colon, shifting these cells from demonstrating a normal oxygen-consuming metabolism to glycolysis, or the breakdown of glucose into energy.

“This has two consequences: oxygen accumulates in the gut lumen, and lactate is secreted as a byproduct. The bacterium is well-positioned to exploit both, expressing enzymes for a complete TCA cycle and coupling lactate oxidation to oxygen respiration, generating energy far more efficiently than competing gut microbes that rely solely on anaerobic fermentation,” Grote said.

BFT also hijacks the gut’s bile acid recycling machinery by depleting compounds that normally suppress inflammatory IL-17-producing immune cells, which drives further metabolic reprogramming of colonocytes and sustains ETBF colonization.

In mouse models, restoring normal colonocyte metabolism with tributyrin, a dietary compound that has been shown to help repair the intestinal barrier and reduce inflammation, reduced infection and tumor burden. Mice that were given maralixibat, a drug currently prescribed to treat liver disease, also demonstrated blocked bile acid recycling and reduced disease.

“This work reframes how we think about anaerobic pathogens: rather than merely tolerating the inflammation they cause, ETBF appears to actively engineer an oxidative niche that it can exploit. The specific enzymes powering ETBF’s oxygen-based metabolism are potential drug targets,” Grote said. “Together, these findings suggest metabolic and immune-modulatory approaches to preventing or treating ETBF-associated colorectal cancer.”

According to Grote, next steps for this work include identifying the mechanisms by which BFT promotes the bacterium’s own tolerance of oxygen and further validating potential therapeutic approaches.

“Our team also aims to develop more physiologically realistic infection models and to explore whether the therapeutic strategies identified here, particularly tributyrin and targeted inhibition of ETBF’s oxidative metabolism, can be translated toward clinical use,” Grote said.

This work was supported in part by a Jane Coffin Childs Memorial Fund for Medical Research postdoctoral fellowship.