In a groundbreaking study that could revolutionize cancer prevention linked to gut microbiota, researchers have engineered bacteria with the ability to neutralize colibactin, a potent genotoxin produced by certain strains of Escherichia coli. Colibactin, synthesized by bacteria harboring the polyketide synthase (pks) genomic island, has been strongly associated with DNA damage and colorectal tumorigenesis in humans. Despite its critical role in promoting colorectal cancer, there has been no targeted therapeutic strategy approved by the Food and Drug Administration to mitigate colibactin’s deleterious effects—until now.
The team of scientists devised a novel approach by leveraging the natural self-defense mechanism bacteria utilize against their own toxins. They identified and utilized ClbS, an intracellular protein that confers resistance to colibactin. Typically, ClbS operates inside bacteria to neutralize colibactin internally, protecting the producing bacteria from self-inflicted DNA damage. The innovation here was to engineer E. coli to display ClbS not just intracellularly but on their outer surface by fusing it with outer membrane protein A (OmpA). This fusion enabled the bacteria to act as a living shield within the gut environment, directly intercepting and neutralizing colibactin before it damages host DNA.
Extensive in vitro experiments demonstrated the efficacy of these engineered bacteria in preventing colibactin-induced genotoxicity. Human cell lines and organoid models exposed to pks-positive E. coli suffered significant DNA double-strand breaks and cell cycle arrest—hallmarks of genotoxic stress—when not shielded by the ClbS–OmpA expressing bacteria. Remarkably, the engineered strains exhibited superior protective effects compared to D-serine, a small molecule previously known for its inhibitory effects on colibactin synthesis but limited in its effectiveness and specificity.
Delving deeper, the research showed that the surface-displayed ClbS protein binds directly to colibactin or its reactive intermediates in the extracellular environment, effectively detoxifying these genotoxins before they can penetrate host cells. This mode of action contrasts with systemic pharmacological inhibitors and provides an elegant, microbiome-compatible method of protection. It also opens the door to tailored microbial therapies that can be delivered orally and modulate the gut microenvironment dynamically.
Moving from cell culture models to physiological relevance, the study evaluated the engineered bacteria in mouse models of colitis and colorectal cancer triggered by pks-positive E. coli. Administration of the ClbS–OmpA expressing strains significantly reduced intestinal inflammation and epithelial damage in mice, which are precursors to oncogenic transformation. Even more striking was the observed suppression of tumorigenesis in these models, signifying not only symptomatic relief but also a profound impact on colorectal cancer prevention.
The implications of this research are manifold. First, it provides compelling proof-of-concept that the gut microbiota’s harmful genotoxins can be neutralized in situ without broad-spectrum antibiotics or chemical inhibitors, which often disrupt beneficial microbiota and engender resistance. Second, given the diversity of bacterial metabolites implicated in various chronic diseases and cancers, this strategy sets a precedent for engineering bacteria to neutralize other pathological microbial products selectively.
Moreover, the engineered bacteria’s safety profile, although requiring further in-depth clinical testing, is promising. The researchers confirmed that expressing ClbS on the bacterial surface did not impair the bacteria’s viability or normal physiological functions, suggesting that these therapeutic strains could be stable and safe for long-term use in the gut ecosystem. This aspect is crucial for advancing live biotherapeutic products that must balance efficacy with microbiome homeostasis.
The study’s findings ignite interest in the development of next-generation microbiome therapeutics that harness synthetic biology principles. By designing bacteria that can directly counteract microbial metabolites implicated in diseases, scientists pave the way for highly specific interventions. These could one day complement, or even replace, existing chemoprevention strategies and provide personalized modulation of gut health.
Another remarkable facet of this research lies in overcoming one of the key challenges in targeting colibactin: its unstable and reactive nature. Due to the transient life of colibactin and its DNA-adduct interactions, direct chemical targeting has been notoriously difficult. Surface-displayed ClbS proteins act as a readily available, local scavenger, neutralizing these fleeting molecules before they can exert genotoxic damage. This insight underscores the power of molecular mimicry and bioengineering in therapeutic innovation.
Anticipated next steps involve optimizing delivery mechanisms for these engineered bacteria in human subjects and expanding the spectrum of microbial toxins targeted. Researchers are keen to investigate synergistic effects when combined with other microbiota-targeted strategies, including diet modulation and immune potentiation. The versatility of the ClbS–OmpA fusion concept also encourages exploration into similar resistance protein displays for combating other bacterial toxins beyond colibactin.
This pioneering approach may also spark broader interest in the nexus between microbial metabolism and carcinogenesis. As the catalog of cancer-associated bacterial metabolites expands, strategies that engineer protective microbiota to neutralize such metabolites could constitute a new frontier in cancer prevention. Importantly, this research elucidates how microbiome engineering transcends traditional probiotic concepts, moving towards precisely programmed microbial therapies capable of intervening in host-pathogen interactions at a molecular level.
The therapeutic potential extends beyond oncology. Given colibactin’s link to inflammatory bowel diseases and gut barrier dysfunction, the ability to quench its genotoxic effects may foster new treatments that address inflammatory and degenerative gut pathologies. Thus, engineered bacteria expressing self-resistance proteins may become multipurpose agents for restoring gut integrity and preventing chronic disease progression.
In sum, this study embodies a monumental leap in microbiome-based therapeutic design. By transforming a bacterial self-protection mechanism into a protective shield against a genotoxic bacterial metabolite, the research provides a promising biologic intervention with profound implications for cancer prevention and gut health maintenance. These engineered bacterial strains herald a future where live microbial therapies can be custom-crafted to mitigate the pathological impact of our complex microbiome.
As the scientific community continues to unravel the multifaceted relationships between microbes and human health, innovations like surface-displayed ClbS open exciting avenues for translational medicine. Precision bacteriotherapy could emerge as a cornerstone in combating microbiota-associated diseases, reinforcing the age-old adage that sometimes the best medicine lies within nature itself—now enhanced through cutting-edge synthetic biology.
Subject of Research: Neutralization of genotoxic colibactin produced by pks+ gut bacteria through surface expression of antitoxin proteins on engineered Escherichia coli.
Article Title: Surface expression of antitoxin on engineered bacteria neutralizes genotoxic colibactin in the gut.
Article References:
Yang, S., Wang, Z., Fang, C. et al. Surface expression of antitoxin on engineered bacteria neutralizes genotoxic colibactin in the gut. Nat Microbiol (2025). https://doi.org/10.1038/s41564-025-02177-3
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