BACKGROUND & AIMS. The gut microbiome is implicated in the pathogenesis of colorectal cancer (CRC). While a robust body of research has identified several different CRC-associated bacterial species, the full scope of the host-microbial dialogue in CRC is unknown. Here we aimed to define the scale and membership of the body of CRC-associated and health-associated gut bacteria in global populations.
METHODS. We perform a microbiome-CRC correlation analysis of deep shotgun metagenomic sequencing data from published global microbiome surveys, utilizing a de novo (reference-agnostic) gene-level clustering approach to identify protein-coding co-abundant gene (CAGs) clusters significantly enriched in either CRC or in health. We validate predicted microbiome effects in preclinical CRC models and interrogate mechanism via colonic gene expression profiling (including through single-cell RNAseq) and using organoid co-culture systems.
RESULTS. Here we link an unprecedented ~40% of gut bacteria to CRC (split nearly evenly as CRC-associated or health-associated). These microbes encode 2,319 co-abundant genes (CAGs) encompassing 427,261 bacterial genes significantly enriched or depleted in CRC. We validate tumorigenicity of previously unimplicated bacteria in preclinical models. Single-cell RNA sequencing disclosed microbiome-induced senescence in discrete colonic populations including fibroblasts. In organoid co-cultures, primary colon fibroblasts from mice with microbiomes promoted significantly greater growth than fibroblasts from microbiome-depleted mice.
CONCLUSIONS. Our findings suggest that an astounding ~40% of gut bacteria may be carcinogenic or chemoprotective. Many of these had not previously been linked to CRC, thus expanding the scope of “known unknowns” of CRC-associated microbes. These results offer proof-of-principle for gene-level metagenomic analysis enabling wide-ranging discovery of microbiome-induced precancerous effects and cancer prevention opportunities.