Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer
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Co-culture of intestinal organoids with a colibactin-producing pks + E. coli strain (EcC) revealed mutational signatures also found in colorectal cancer (CRC). E. coli Nissle 1917 (EcN) remains a commonly used probiotic, despite harboring the pks operon and inducing double strand DNA breaks. We determine the mutagenicity of EcN and three CRC-derived pks + E. coli strains with an analytical framework based on sequence characteristic of colibactin-induced mutations. All strains, including EcN, display varying levels of mutagenic activity. Furthermore, a machine learning approach attributing individual mutations to colibactin reveals that patients with colibactin-induced mutations are diagnosed at a younger age and that colibactin can induce a specific APC mutation. These approaches allow the sensitive detection of colibactin-induced mutations in ∼12% of CRC genomes and even in whole exome sequencing data, representing a crucial step toward pinpointing the mutagenic activity of distinct pks + E. coli strains.
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E. coli Nissle 1917 synthesizes and releases colibactin, a mutagenic substance that promotes colorectal polyposis and cancer and reduces cancer response to irinotecan.
“having the capability of synthetizing and releasing colibactin, a mutagenic substance described to promote colorectal polyposis and cancer, and reducing cancer response to irinotecan [26, 34–39].”
From Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces (2026) · cites this paper as [39]
The Introduction identifies E. coli Nissle 1917 as carrying the colibactin-producing pks operon, and the Abstract reports that it has mutagenic activity. The Introduction links colibactin-associated mutations to colorectal cancer, but the Discussion says in vivo evidence that those mutations lead to transformation is lacking. Our copy does not substantiate colorectal polyposis or reduced response to irinotecan (searched: polyposis, irinotecan). (LLM, conf=0.88)
Experimental — accuracy not yet measuredpks-positive CRC occurs mainly in young people.
“Indeed, pks-positive CRC occurs mainly in young people [39].”
From Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces (2026) · cites this paper as [39]
In “Colibactin-linked mutations correlate with earlier CRC onset,” the paper reports that colibactin-positive CRC patients were younger than negative patients in the HMF cohort (mean age 58.48 versus 63.51 years). This supports an earlier-onset association, but not the claim that pks-positive CRC occurs mainly in young people. (LLM, conf=0.90)
Experimental — accuracy not yet measuredThe pks genetic island is absent in E. coli 5C but present and productive in E. coli Nissle 1917.
“the pks genetic island is absent in the E. coli 5C but present and productive in the E. coli Nissle 1917 [39].”
From Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces (2026) · cites this paper as [39]
The Introduction states that E. coli Nissle 1917 (EcN) harbors the pks operon, and the Results report DNA damage from EcN exposure, supporting its presence and activity. Our copy does not identify E. coli 5C or establish that the pks island is absent from it (pages unavailable). (LLM, conf=0.88)
Experimental — accuracy not yet measuredE. coli Nissle 1917 is pks-positive.
“the most widely used E. coli-based probiotic, known as E. coli Nissle 1917 (DSM 6601), is pks-positive.”
From Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces (2026) · cites this paper as [39]
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- Authors
- Rosendahl Huber, A., Pleguezuelos-Manzano, C., Puschhof, J., Ubels, J., Boot, C., Saftien, A., Verheul, M., Trabut, L. T., Groenen, N., van Roosmalen, M., Ouyang, K. S., Wood, H., Quirke, P., Meijer, G., Cuppen, E., Clevers, H., & van Boxtel, R.
- Affiliations
- Royal Netherlands Academy of Arts and Sciences (NL)
- Oncode Institute (NL)
- German Cancer Research Center (DE)
- University of Leeds (GB)
- The Netherlands Cancer Institute (NL)
- University Medical Center Utrecht (NL)
- F. Hoffmann-La Roche AG (CH)
- Corresponding author
- Puschhof, Jens
- Clevers, Hans
- ORCID
- Venue
- Cancer Cell
- Publisher
- Elsevier BV
- Published
- 2024-03
- Volume
- 42
- Issue
- 3
- Pages
- 487-496.e6
- ISSN
- 1535-6108 (ISSN-L)
- OpenAlex
- W4392638507
- Cited by
- 106
- References
- 52
- Citations by year
- 2026: 53 · 2025: 39 · 2024: 14
- FWCI
- 32.02
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cancer Cell (publishedVersion, cc-by)
- PubMed (publishedVersion)
- KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) (publishedVersion, other-oa)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion, cc-by)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- American Association for Cancer Research (SU2C-3.1416)
- European Research Council (864499)
- Hubrecht Institute
- Cancer Research UK (C10674/A27140)
- Ministerie van Onderwijs, Cultuur en Wetenschap
- National Human Genome Research Institute
- Entertainment Industry Foundation
- Oncode Institute
- National Cancer Institute
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- New York Stem Cell Foundation
- Princess Máxima Center for Pediatric Oncology
- KWF Kankerbestrijding
- Koninklijke Nederlandse Akademie van Wetenschappen
- Energy Council of Canada (2F8, CFF16-2F8, CFF159-19H2, 19H2)
- Topics
- Health Sciences › Medicine › Pathology and Forensic Medicine › Genetic factors in colorectal cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Carcinogens and Genotoxicity Assessment
- Keywords
- colibactin, Escherichia coli, colorectal cancer, intestinal organoids, mutagenicity, genotoxicity, Escherichia coli Nissle 1917, probiotics, DNA double-strand breaks, APC mutation, mutational signatures, age at diagnosis
- MeSH terms
- DNA Damage, Escherichia coli, Humans, Mutagens, Mutation, Organoids, Peptides, Colorectal Neoplasms, Polyketides
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