{"doi":"10.1101/2025.10.13.682122","title":"Programmable conjugative CRISPR interference targeting genotoxin in the gut","abstract":"Abstract Among microbially derived metabolites that influence host disease, colibactin garners increasing attention for its roles in the rising incidence of early-onset colorectal cancer. Produced by pks ⁺ Escherichia coli , colibactin is a potent genotoxin, yet no approved therapeutics directly suppress it. Here, we engineered a self-transmissible conjugative plasmid to deliver CRISPR interference (CRISPRi) into multiple pks⁺ strains. This system silences transcription of colibactin biosynthetic genes and abolishes pks ⁺ E. coli genotoxicity without the resistance mutations associated with wild-type Cas9-mediated bacterial inhibition. In mice, conjugation-mediated CRISPRi reduces DNA damage and pks ⁺ E. coli colonization while preserving commensal diversity. Importantly, the system also lowers tumorigenesis driven by pks ⁺ E. coli and outperforms a pharmacologic inhibitor in a mouse colorectal cancer model. Finally, we extend this platform to silence a second pathogenic metabolite, establishing a translational strategy to neutralize diverse microbial metabolites and expanding the toolkit for programmable live biotherapeutics in the gut.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":577771,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9477,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1456926,"name":"Hania Timek","orcid":null,"position":1,"is_corresponding":false},{"id":1456497,"name":"Chengyuan Fang","orcid":"0000-0002-0878-5872","position":2,"is_corresponding":false},{"id":1205574,"name":"Zongqi Wang","orcid":"0000-0003-4559-3420","position":3,"is_corresponding":false},{"id":1456927,"name":"Amber E. Haley","orcid":null,"position":4,"is_corresponding":false},{"id":1456928,"name":"Maria Jennings","orcid":null,"position":5,"is_corresponding":false},{"id":1487571,"name":"Collins I. Chimezie","orcid":null,"position":6,"is_corresponding":false},{"id":878967,"name":"Noah Hutchinson","orcid":null,"position":7,"is_corresponding":false},{"id":1487241,"name":"Zhihong Dong","orcid":"0009-0006-1543-2158","position":8,"is_corresponding":false},{"id":1456930,"name":"Shannon McCollum","orcid":null,"position":9,"is_corresponding":false},{"id":1379588,"name":"Saleh Khawaled","orcid":"0000-0002-2315-3697","position":10,"is_corresponding":false},{"id":432386,"name":"Yatrik M. Shah","orcid":"0000-0002-2487-4816","position":11,"is_corresponding":false},{"id":39713,"name":"Ömer Yılmaz","orcid":"0000-0002-0962-2725","position":12,"is_corresponding":false},{"id":650010,"name":"Jiahe Li","orcid":"0000-0002-9889-8546","position":13,"is_corresponding":false},{"id":1456925,"name":"Brian Hamp","orcid":null,"position":0,"is_corresponding":true}],"reference_count":57,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:58:16.148027Z","pmid":"41278642","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}