Scarring of the digestive tract is a particularly dangerous complication of Crohn’s disease (CD), a subtype of inflammatory bowel disease (IBD) that has no cure (1). This intestinal fibrosis often leads to intestinal narrowing, which requires emergency surgery (2). But what causes the inflammation and fibrosis in the first place remains unclear.

“We're not really treating the root cause of the inflammation in CD. We're treating the symptoms,” said Brian Coombes, a biochemist at McMaster University. “To get to the cause, we need to know mechanisms.”

Now, in a recent study, researchers led by Janelle Arthur, an immunologist at the University of North Carolina at Chapel Hill, identified a molecule produced by a specific strain of Escherichia coli  living in the gut that recruits immune cells and initiates fibrosis (3). This new finding provides researchers with a potential treatment avenue for CD.

The gastrointestinal (GI) tract is home to an extremely diverse collection of microbes including many different types of E. coli. One such type, called adherent-invasive E. coli, contributes to CD pathogenesis (4). In 2019, Arthur and her team found that this strain of E. coli releases a compound called yersiniabactin, which led to increased fibrosis in an IBD mouse model (5).

Recently, the research team noticed that macrophages were highly abundant in intestinal fibrosis tissue samples from their IBD mouse models. Knowing the previous connection between yersiniabactin and fibrosis, Arthur wondered if yersiniabactin might be influencing the macrophages in CD.

“Yersiniabactin, at the time, was thought to just be a siderophore, an iron sequestering molecule,” said Arthur. “So, when Ju-Hyun Ahn [a postdoctoral fellow and first author] joined us, she had really excellent expertise in biochemistry and molecular biology, and I asked her to try and figure out what was going on.”

Analyzing the gut microbes from healthy people and those with CD using available metagenomic and metatranscriptomic data from MetaHIT and The Human Microbiome Project 2, they found that microbes from people with CD had higher levels of yersiniabactin genes being expressed compared to the healthy group. Also, consistent with what they saw in their IBD mouse model, the team saw that there were more macrophages in colon tissue samples from people with CD compared to healthy controls. But one question remained: How were the yersiniabactin-producing E. coli influencing the flux of immune cells?

Arthur wondered, “Is there some host signaling pathway that's being activated by the yersiniabactin, almost as collateral damage?”

Is there some host signaling pathway that's being activated by the yersiniabactin, almost as collateral damage?” 
- Janelle Arthur, University of North Carolina at Chapel Hill

To investigate this relationship between macrophages and yersiniabactin-producing E. coli, the researchers took bone-derived macrophages and grew them together with the bacteria for 14 days. Using a suite of molecular techniques, they saw that the hypoxia-inducible factor 1-alpha (HIF-1α) signaling pathway proteins were more localized towards the nucleus of macrophages that were in the presence of yersiniabactin, indicating the pathway’s role in this relationship. The HIF-1α pathway triggers inflammation and profibrotic macrophage activity (6).

“We think that the immune cells are recognizing the bacteria and then telling the fibroblasts, for some reason, to lay down the scar tissue.”

As the team went on to fully dissect the genetic regulation of HIF-1α, they found that yersiniabactin was stealing away zinc from the macrophages. Zinc, like other metal ions, helps bacterial enzymes function properly, and prior work has demonstrated that yersiniabactin can also act as a zincophore (7,8). Without the intracellular zinc regulating HIF-1α, the macrophages started running rampant and activating nearby fibrotic cells. Furthermore, they saw high levels of HIF-1α expression in colon tissue samples from both CD patients and IBD mouse models.

Coombes, who was not involved in the study, stated that a translational limitation of this work was that the mice used in this study only had the one E. coli species present and not the normal microbial diversity seen in humans.  Additionally, he wished to have seen direct measurements of yersiniabactin produced, instead of the indirect measurement of HIF-1α expression.

Arthur’s team is eager to follow up on this work and explore other signaling pathways disrupted by yersiniabactin or metal sequestration in general. Ahn is developing a new fibrotic mouse model that is missing HIF-1α expression to confirm what was seen in the macrophages. Furthermore, the team is working on exploring the relationship of yersiniabactin, macrophages, and fibrosis using spatial transcriptomics.

“There're a lot of new things in here,” said Coombes. “So I think this brings us closer to understanding the mechanisms better of where this inflammation is coming from.”

References

1. Seyedian, S.S. et al. A review of the diagnosis, prevention, and treatment methods of inflammatory bowel disease. J Med Life 12, 113-122 (2019).
2. D’Alessio, S. et al. Revisiting fibrosis in inflammatory bowel disease: the gut thickens. Nat Rev Gastroenterol Hepatol 19, 169–184 (2022).
3. Ahn, J.H. et al. Intestinal E. coli-produced yersiniabactin promotes profibrotic macrophages in Crohn’s disease. Cell Host & Microbe 33, 71-88.e9 (2025).
4. Agus, A. et al. Understanding Host-Adherent-Invasive Escherichia coli Interaction in Crohn’s Disease: Opening Up New Therapeutic Strategies. Biomed Res Int  2014, 567929 (2014).
5. Ellermann, M. et al. Yersiniabactin-Producing Adherent/Invasive Escherichia coli Promotes Inflammation-Associated Fibrosis in Gnotobiotic Il10^−/− Mice. Infect Immun 87, e00587-19 (2019).
6. McGettrick, A.F. & O’Neill, L.A.J. The Role of HIF in Immunity and Inflammation. Cell Metab 32, 524–536 (2020).
7. Gammoh, N.Z. & Rink, L. Zinc in Infection and Inflammation. Nutrients 9, 624 (2017).
8. Behnsen, J. et al. Siderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut. Nat Commun 12, 7016 (2021).