The role of pks -positive bacteria in colorectal cancer

The gut epithelium is a dynamic environment engaged in constant crosstalk with trillions of microbes, including bacteria, viruses, fungi, and archaea, that collectively shape host health and disease. Among these are Enterobacteriaceae that carry the polyketide synthase ( pks ) pathogenicity island, which encodes colibactin, a genotoxin that induces DNA damage and genomic instability in human cells. pks -positive bacteria are enriched in inflammatory bowel disease and colorectal cancer (CRC), and colibactin-associated mutational signatures are present in key CRC driver genes, including APC . These signatures are disproportionately elevated in early-onset CRC (eoCRC; diagnosis <50 years) and have been detected in histologically normal colonic crypts, including in children. Despite this growing evidence, pks presence alone is insufficient to predict colibactin-associated mutagenesis or cancer risk, indicating strong context dependence shaped by host, microbial, and environmental factors, as well as timing of exposure. We hypothesize that colibactin-driven mutagenesis relevant to CRC is governed by three interacting determinants: (i) population- and life stage-specific variability in the prevalence and diversity of pks -positive bacteria, and (ii) host-microbe-environmental configurations that permit or suppress functional colibactin activity despite pks presence, and (iii) the heightened vulnerability during infancy, where ecological imbalances create opportunities for early colonization and mutagenesis. To investigate these determinants, we developed pks Profiler, a scalable Nextflow-based framework integrating alignment-based and hidden Markov model approaches for gene-level profiling of the pks biosynthetic island. Application to 259 TCGA CRC samples revealed pronounced sequencing modality-dependent variability, with pks detected in 32.2% of whole-genome sequenced tumors, 14.9% of whole-exome sequenced tumors, and 2.0% of RNA-seq samples. In contrast, analysis of 376 stool metagenomes showed substantially higher pks prevalence (54.0% positive) and more uniform island-wide coverage. To support systematic investigation of contexts in which pks presence does or does not result in colibactin-associated mutagenesis, we constructed an LLM-augmented knowledge graph integrating multimodal genomic, microbial, immune, dietary, lifestyle, and epidemiologic data from 900 colorectal cancer cases, providing a resource for hypothesis generation by highlighting candidate host, microbial, and environmental factors that may modulate functional colibactin exposure in colorectal cancer. Finally, analysis of a globally diverse infant metagenome compendium (~18,000 samples, including ~300 infant-mother dyads) demonstrated that pks -positive bacteria are detectable early in life, with prevalence increasing during early infancy, peaking at approximately six months of age, and declining thereafter. Dyad-level analyses showed increasing infant-mother discordance over time, with infants frequently pks -positive despite pks -negative mothers. Together, these findings establish a cancer-relevant framework in which the timing and context of pks-positive bacterial exposure, rather than presence alone, shape colibactin-associated mutational risk relevant to CRC.