Intratumoral microbiota: implications for colorectal cancer pathogenesis and therapy

CRC is the third most prevalent malignancy worldwide and the second leading cause of cancer-related mortality. According to GLOBOCAN 2022 estimates, approximately 1.93 million new CRC cases and 900,000 CRC-related deaths occur annually worldwide. Incidence rates continue to rise in developing countries, driven by the westernization of dietary patterns, sedentary lifestyles, and increasing obesity prevalence, with a notable trend toward younger-onset disease. In recent years, mounting evidence has implicated the microbiota as a critical contributor to CRC initiation and progression. Distinct from the fecal microbiome, the intratumoral microbiome constitutes an independent, low-biomass microbial community predominantly composed of bacteria, with additional fungal, viral, and archaeal components. Microbial communities within the TME promote CRC development and progression by modulating host immune responses, metabolic pathways, and tumor cell proliferation and metastasis. Fusobacterium nucleatum, ETBF, polyketide synthase genotoxicity island-harboring Escherichia coli and Parvimonas micra represent the most well-substantiated candidate oncomicrobes, whose carcinogenic activities involve multiple intertwined pathways, including chronic inflammation, genotoxic DNA damage, immune evasion, metabolic reprogramming, and non-coding RNA regulation. Furthermore, intratumoral microbiota may serve as early diagnostic biomarkers for CRC, offer novel therapeutic targets, and provide potential biological rationale for prognostic prediction. Microbiome-based diagnostic biomarkers, such as multi-bacterial fecal/tissue panels, have demonstrated sensitivity comparable to or superior to the fecal immunochemical test in select retrospective cohorts; however, large-scale, multicenter, prospective validation remains necessary. Strategies targeting intratumoral bacteria — including antibiotics, bacteriophages, phage-guided nanocarriers, and FMT — remain predominantly in the preclinical stage. Although phase I/II trials of FMT for immunotherapy sensitization have yielded encouraging results, small sample sizes and substantial heterogeneity preclude its near-term adoption as a standard-of-care recommendation. This review systematically summarizes the latest advances in understanding the relationship between intratumoral microbiota and CRC, critically appraises the strength of evidence across different hierarchical levels, evaluates the consistency and controversies surrounding major mechanistic hypotheses, addresses methodological challenges inherent to low-biomass microbiome research, and discusses the translational potential in CRC diagnosis, therapy, and prognostic prediction.