Phenotypic characterization and complete genome of a tumorigenic pathobiont Escherichia coli LI60C3
Abstract Background Symbiotic microbes benefit the host, but the emergence of pathobionts leads to disease. An invasive Escherichia coli LI60C3, isolated from mouse colonocytes, shows colitogenic and tumorigenic properties. Despite extensive research on the role of microbiota in colorectal cancer (C...
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BMC
2025-08-01
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| Series: | Gut Pathogens |
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| Online Access: | https://doi.org/10.1186/s13099-025-00732-1 |
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| author | Linda Chia-Hui Yu Shu-Chen Wei Yi-Hsuan Li Chung-Yen Huang Yu-Chen Pai Yuan-Mao Hung Liang-Chuan Lai Yen-Hsuan Ni |
| author_facet | Linda Chia-Hui Yu Shu-Chen Wei Yi-Hsuan Li Chung-Yen Huang Yu-Chen Pai Yuan-Mao Hung Liang-Chuan Lai Yen-Hsuan Ni |
| author_sort | Linda Chia-Hui Yu |
| collection | DOAJ |
| description | Abstract Background Symbiotic microbes benefit the host, but the emergence of pathobionts leads to disease. An invasive Escherichia coli LI60C3, isolated from mouse colonocytes, shows colitogenic and tumorigenic properties. Despite extensive research on the role of microbiota in colorectal cancer (CRC) development, the genetic markers associated with this pathobiont remain elusive. The objective is to characterize the tumorigenic E. coli through whole-genome sequencing (WGS) and phenotypic assays, and validate their presence in human CRC. Methods The intracellular bacterial counts and proliferation rates of human intestinal epithelial cells were evaluated after exposure to various E. coli strains. Tumor burden was assessed in mice orally administered LI60C3. WGS of LI60C3 was performed on a PacBio Sequel II platform, and the long reads were assembled de novo for gene annotation and detection of virulence factors and antibiotic resistance. Bacteria-specific genes were assessed in CRC specimens by qPCR analysis. Results A 100-fold increase in intracellular bacterial count was observed in epithelial cells exposed to LI60C3 compared to commensal E. coli strains. LI60C3 resulted in a threefold increase in epithelial cell cycle rate and a fourfold rise in mouse tumor numbers. WGS revealed a circular chromosome of 4,863,930 bases for LI60C3, demonstrating a high sequence homology to adherent-invasive E. coli LF82 (91%) and NC101 (87%) and to uropathogenic E. coli 536 (88%). Two extrachromosomal plasmids, pTra and pCoMb, were identified. While pTra exhibits sequence homology with other commensal E. coli plasmids, pCoMb has partial matches with those found in pathogenic bacteria. LI60C3 is classified as phylogroup B2 and expresses virulence factors, including Type 1 and P fimbriae, contact-dependent growth inhibition system, iron acquisition system, and hemolysin. Unique gene clusters, named Epm and Phz islands, were identified in the LI60C3 genome. The emergence of LI60C3-specific genes was observed in mouse tumors induced by chemicals and gene mutation, and higher levels of LI60C3 markers were validated in human CRC specimens compared with healthy mucosal samples. Conclusion Genetic signatures of LI60C3 were detected in mouse and human CRC. The comparative genome analysis for LI60C3 helps identify pathobionts and may be used as cancer predictors. |
| format | Article |
| id | doaj-art-21a41d15a3214d329791d4706af0222a |
| institution | Kabale University |
| issn | 1757-4749 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
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| series | Gut Pathogens |
| spelling | doaj-art-21a41d15a3214d329791d4706af0222a2025-08-24T11:32:01ZengBMCGut Pathogens1757-47492025-08-0117112310.1186/s13099-025-00732-1Phenotypic characterization and complete genome of a tumorigenic pathobiont Escherichia coli LI60C3Linda Chia-Hui Yu0Shu-Chen Wei1Yi-Hsuan Li2Chung-Yen Huang3Yu-Chen Pai4Yuan-Mao Hung5Liang-Chuan Lai6Yen-Hsuan Ni7Graduate Institute of Physiology, National Taiwan University College of MedicineDepartment of Internal Medicine, National Taiwan University HospitalGraduate Institute of Physiology, National Taiwan University College of MedicineDepartment of Pathology, National Taiwan University HospitalGraduate Institute of Physiology, National Taiwan University College of MedicineBioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan UniversityGraduate Institute of Physiology, National Taiwan University College of MedicineDepartment of Pediatrics, National Taiwan University HospitalAbstract Background Symbiotic microbes benefit the host, but the emergence of pathobionts leads to disease. An invasive Escherichia coli LI60C3, isolated from mouse colonocytes, shows colitogenic and tumorigenic properties. Despite extensive research on the role of microbiota in colorectal cancer (CRC) development, the genetic markers associated with this pathobiont remain elusive. The objective is to characterize the tumorigenic E. coli through whole-genome sequencing (WGS) and phenotypic assays, and validate their presence in human CRC. Methods The intracellular bacterial counts and proliferation rates of human intestinal epithelial cells were evaluated after exposure to various E. coli strains. Tumor burden was assessed in mice orally administered LI60C3. WGS of LI60C3 was performed on a PacBio Sequel II platform, and the long reads were assembled de novo for gene annotation and detection of virulence factors and antibiotic resistance. Bacteria-specific genes were assessed in CRC specimens by qPCR analysis. Results A 100-fold increase in intracellular bacterial count was observed in epithelial cells exposed to LI60C3 compared to commensal E. coli strains. LI60C3 resulted in a threefold increase in epithelial cell cycle rate and a fourfold rise in mouse tumor numbers. WGS revealed a circular chromosome of 4,863,930 bases for LI60C3, demonstrating a high sequence homology to adherent-invasive E. coli LF82 (91%) and NC101 (87%) and to uropathogenic E. coli 536 (88%). Two extrachromosomal plasmids, pTra and pCoMb, were identified. While pTra exhibits sequence homology with other commensal E. coli plasmids, pCoMb has partial matches with those found in pathogenic bacteria. LI60C3 is classified as phylogroup B2 and expresses virulence factors, including Type 1 and P fimbriae, contact-dependent growth inhibition system, iron acquisition system, and hemolysin. Unique gene clusters, named Epm and Phz islands, were identified in the LI60C3 genome. The emergence of LI60C3-specific genes was observed in mouse tumors induced by chemicals and gene mutation, and higher levels of LI60C3 markers were validated in human CRC specimens compared with healthy mucosal samples. Conclusion Genetic signatures of LI60C3 were detected in mouse and human CRC. The comparative genome analysis for LI60C3 helps identify pathobionts and may be used as cancer predictors.https://doi.org/10.1186/s13099-025-00732-1Colorectal cancer microbiomeTumorigenic E. coliInvasive pathobiontsComparative genomicsComplete genome sequencingIntestinal epithelial cells |
| spellingShingle | Linda Chia-Hui Yu Shu-Chen Wei Yi-Hsuan Li Chung-Yen Huang Yu-Chen Pai Yuan-Mao Hung Liang-Chuan Lai Yen-Hsuan Ni Phenotypic characterization and complete genome of a tumorigenic pathobiont Escherichia coli LI60C3 Gut Pathogens Colorectal cancer microbiome Tumorigenic E. coli Invasive pathobionts Comparative genomics Complete genome sequencing Intestinal epithelial cells |
| title | Phenotypic characterization and complete genome of a tumorigenic pathobiont Escherichia coli LI60C3 |
| title_full | Phenotypic characterization and complete genome of a tumorigenic pathobiont Escherichia coli LI60C3 |
| title_fullStr | Phenotypic characterization and complete genome of a tumorigenic pathobiont Escherichia coli LI60C3 |
| title_full_unstemmed | Phenotypic characterization and complete genome of a tumorigenic pathobiont Escherichia coli LI60C3 |
| title_short | Phenotypic characterization and complete genome of a tumorigenic pathobiont Escherichia coli LI60C3 |
| title_sort | phenotypic characterization and complete genome of a tumorigenic pathobiont escherichia coli li60c3 |
| topic | Colorectal cancer microbiome Tumorigenic E. coli Invasive pathobionts Comparative genomics Complete genome sequencing Intestinal epithelial cells |
| url | https://doi.org/10.1186/s13099-025-00732-1 |
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