ABSTRACTThepksisland is one of the most prevalent pathogenicity islands among theEscherichia colistrains that colonize the colon of colorectal carcinoma (CRC) patients. This pathogenic island encodes the production of a nonribosomal polyketide-peptide named colibactin, which induces double-strand breaks in DNA molecules. Detection or even depletion of thispks-producing bacteria could help to understand the role of these strains in the context of CRC. In this work, we performed a large-scalein silicoscreening of thepkscluster in more than 6,000 isolates ofE. coli. The results obtained reveal that not all thepks-detected strains could produce a functional genotoxin and, using antibodies againstpks-specific peptides from surface cell proteins, a methodology for detection and depletion ofpks+ bacteria in gut microbiotas was proposed. With our method, we were able to deplete a human gut microbiota of thispks+ strains, opening the door to strain-directed microbiota modification and intervention studies that allow us to understand the relation between these genotoxic strains and some gastrointestinal diseases.IMPORTANCEThe human gut microbiome has also been hypothesized to play a crucial role in the development and progression of colorectal carcinoma (CRC). Between the microorganisms of this community, theEscherichia colistrains carrying thepksgenomic island were shown to be capable of promoting colon tumorigenesis in a colorectal cancer mouse model, and their presence seems to be directly related to a distinct mutational signature in patients suffering CRC. This work proposes a novel method for the detection and depletion ofpks-carrying bacteria in human gut microbiotas. In contrast to methods based on probes, this methodology allows the depletion of low-abundance bacterial strains maintaining the viability of both targeted and non-targeted fractions of the microbiota, allowing the study of the contribution of thesepks-carrying strains to different diseases, such as CRC, and their role in other physiological, metabolic or immune processes.