Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

The microbial landscape of colorectal cancer

Subjects

Abstract

Colorectal cancer (CRC) is a substantial source of global morbidity and mortality in dire need of improved prevention and treatment strategies. As our understanding of CRC grows, it is becoming increasingly evident that the gut microbiota, consisting of trillions of microorganisms in direct interface with the colon, plays a substantial role in CRC development and progression. Understanding the roles that individual microorganisms and complex microbial communities play in CRC pathogenesis, along with their attendant mechanisms, will help yield novel preventive and therapeutic interventions for CRC. In this Review, we discuss recent evidence concerning global perturbations of the gut microbiota in CRC, associations of specific microorganisms with CRC, the underlying mechanisms by which microorganisms potentially drive CRC development and the roles of complex microbial communities in CRC pathogenesis. While our understanding of the relationship between the microbiota and CRC has improved in recent years, our findings highlight substantial gaps in current research that need to be filled before this knowledge can be used to the benefit of patients.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Associations between specific microorganisms and CRC.
Fig. 2: Microbial mechanisms of CRC pathogenesis.
Fig. 3: Microbial communities and CRC pathogenesis.

Similar content being viewed by others

References

  1. Sung, H. et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 71, 209–249 (2021).

    PubMed  Google Scholar 

  2. Siegel, R. L., Miller, K. D., Fuchs, H. E. & Jemal, A. Cancer statistics, 2022. CA Cancer J. Clin. 72, 7–33 (2022).

    PubMed  Google Scholar 

  3. Sender, R., Fuchs, S. & Milo, R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 14, e1002533 (2016).

    PubMed  PubMed Central  Google Scholar 

  4. de Martel, C et al. Global burden of cancers attributable to infections in 2008: a review and synthetic analysis. Lancet Oncol. 13, 607–615 (2012).

    PubMed  Google Scholar 

  5. Veettil, S. K. et al. Role of diet in colorectal cancer incidence. JAMA Netw. Open. 4, e2037341 (2021).

    PubMed  PubMed Central  Google Scholar 

  6. Clay, S. L., Fonseca-Pereira, D. & Garrett, W. S. Colorectal cancer: the facts in the case of the microbiota. J. Clin. Invest. 132, e155101 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Shaukat, A. & Levin, T. R. Current and future colorectal cancer screening strategies. Nat. Rev. Gastroenterol. Hepatol. 19, 521–531 (2022).

    PubMed  PubMed Central  Google Scholar 

  8. Zhang, J. et al. Oral antibiotic use and risk of colorectal cancer in the United Kingdom, 1989–2012: a matched case–control study. Gut 68, 1971 (2019).

    CAS  PubMed  Google Scholar 

  9. Lu, S. S. M. et al. Antibiotics use and subsequent risk of colorectal cancer: a Swedish nationwide population-based study. J. Natl Cancer Inst. 114, djab125 (2021).

    Google Scholar 

  10. Weng, L. et al. Antibiotics use and risk of colorectal neoplasia: an updated meta-analysis. Int. J. Colorectal Dis. 37, 2291–2301 (2022).

    PubMed  Google Scholar 

  11. Huttenhower, C. et al. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).

    ADS  CAS  Google Scholar 

  12. He, Y. et al. Regional variation limits applications of healthy gut microbiome reference ranges and disease models. Nat. Med. 24, 1532–1535 (2018).

    CAS  PubMed  Google Scholar 

  13. Keohane, D. M. et al. Microbiome and health implications for ethnic minorities after enforced lifestyle changes. Nat. Med. 26, 1089–1095 (2020).

    CAS  PubMed  Google Scholar 

  14. Zhang, J. & Sears, C. L. Antibiotic use impacts colorectal cancer: a double-edged sword by tumor location? J. Natl Cancer Inst. 114, djab126 (2021).

    Google Scholar 

  15. Bartolomaeus, T. U. P. et al. Quantifying technical confounders in microbiome studies. Cardiovasc. Res. 117, 863–875 (2020).

    Google Scholar 

  16. Thomas, A. M. et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nat. Med. 25, 667–678 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Liu, N.-N. et al. Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts. Nat. Microbiol. 7, 238–250 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Wirbel, J. et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat. Med. 25, 679–689 (2019). Together with Thomas et al. (2019) and Liu et al. (2022), this study identified associations of microbial taxa and genes with CRC across multiple populations and study designs.

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Mouradov, D. et al. Onco-microbial community profiling identifies clinico-molecular and prognostic subtypes of colorectal cancer. Gastroenterology 165, 104–120 (2023).

    CAS  PubMed  Google Scholar 

  20. Yachida, S. et al. Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer. Nat. Med. 25, 968–976 (2019).

    CAS  PubMed  Google Scholar 

  21. Gao, R. et al. Integrated analysis of colorectal cancer reveals cross-cohort gut microbial signatures and associated serum metabolites. Gastroenterology 163, 1024–1037.e9 (2022).

    CAS  PubMed  Google Scholar 

  22. Tjalsma, H., Boleij, A., Marchesi, J. R. & Dutilh, B. E. A bacterial driver–passenger model for colorectal cancer: beyond the usual suspects. Nat. Rev. Microbiol. 10, 575–582 (2012).

    CAS  PubMed  Google Scholar 

  23. Zuo, W., Michail, S. & Sun, F. Metagenomic analyses of multiple gut datasets revealed the association of phage signatures in colorectal cancer. Front. Cell Infect. Microbiol. 12, 918010 (2022).

    PubMed  PubMed Central  Google Scholar 

  24. Hannigan, G. D., Duhaime, M. B., Ruffin, M. T., Koumpouras, C. C. & Schloss, P. D. Diagnostic potential and interactive dynamics of the colorectal cancer virome. mBio 9, e02248-18 (2018).

    PubMed  PubMed Central  Google Scholar 

  25. Nakatsu, G. et al. Alterations in enteric virome are associated with colorectal cancer and survival outcomes. Gastroenterology 155, 529–541.e5 (2018).

    PubMed  Google Scholar 

  26. Chen, F. et al. Meta-analysis of fecal viromes demonstrates high diagnostic potential of the gut viral signatures for colorectal cancer and adenoma risk assessment. J. Adv. Res. 49, 103–114 (2022).

    PubMed  PubMed Central  Google Scholar 

  27. Coker, O. O. et al. Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer. Gut 68, 654 (2019).

    CAS  PubMed  Google Scholar 

  28. Nejman, D. et al. The human tumor microbiome is composed of tumor type-specific intracellular bacteria. Science 368, 973–980 (2020). This study profiled intratumoural microbiota across diverse human cancer types, revealing that each tumour type has a distinct microbial composition.

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Niño, J. L. G. et al. Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer. Nature 611, 810–817 (2022). This study showed that intratumoural microbiota localize to ‘microniches’ within tumours characterized by distinctive physiological and immunological states, suggesting that intratumoural microbiota affect the biology of the tumours.

    ADS  Google Scholar 

  30. Bullman, S. et al. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Science 358, 1443–1448 (2017).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  31. Klein, R. S. et al. Association of Streptococcus bovis with carcinoma of the colon. N. Engl. J. Med. 297, 800–802 (1977).

    CAS  PubMed  Google Scholar 

  32. Pasquereau-Kotula, E., Martins, M., Aymeric, L. & Dramsi, S. Significance of Streptococcus gallolyticus subsp. gallolyticus association with colorectal cancer. Front. Microbiol. 9, 614 (2018).

    PubMed  PubMed Central  Google Scholar 

  33. Peek, R. M. & Crabtree, J. E. Helicobacter infection and gastric neoplasia. J. Pathol. 208, 233–248 (2006).

    CAS  PubMed  Google Scholar 

  34. Knippel, R. J., Drewes, J. L. & Sears, C. L. The cancer microbiome: recent highlights and knowledge gaps. Cancer Discov. 11, 2378–2395 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Swidsinski, A. et al. Association between intraepithelial Escherichia coli and colorectal cancer. Gastroenterology 115, 281–286 (1998).

    CAS  PubMed  Google Scholar 

  36. Nougayrède, J.-P. et al. Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 313, 848–851 (2006).

    ADS  PubMed  Google Scholar 

  37. Arthur, J. C. et al. Intestinal inflammation targets cancer-inducing activity of the microbiota. Science 338, 120–123 (2012).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  38. Bossuet-Greif, N. et al. The colibactin genotoxin generates DNA interstrand cross-links in infected cells. mBio 9, e02393-17 (2018).

    PubMed  PubMed Central  Google Scholar 

  39. Dziubańska-Kusibab, P. J. et al. Colibactin DNA-damage signature indicates mutational impact in colorectal cancer. Nat. Med. 26, 1063–1069 (2020).

    PubMed  Google Scholar 

  40. Pleguezuelos-Manzano, C. et al. Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli. Nature 580, 269–273 (2020). Together with Dziubańska-Kusibabh et al. (2020), this study identified a distinct mutational signature generated by colibactin in human CRC.

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  41. Iftekhar, A. et al. Genomic aberrations after short-term exposure to colibactin-producing E. coli transform primary colon epithelial cells. Nat. Commun. 12, 1003 (2021).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  42. Berger, H. & Meyer, T. F. Mechanistic dissection unmasks colibactin as a prevalent mutagenic driver of cancer. Cancer Cell 39, 1439–1441 (2021).

    CAS  PubMed  Google Scholar 

  43. Tsunematsu, Y. et al. Mother-to-infant transmission of the carcinogenic colibactin-producing bacteria. BMC Microbiol. 21, 235 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Lee-Six, H. et al. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 574, 532–537 (2019).

    ADS  CAS  PubMed  Google Scholar 

  45. Tang-Fichaux, M. et al. The polyphosphate kinase of Escherichia coli is required for full production of the genotoxin colibactin. mSphere 5, e01195-20 (2020).

    PubMed  PubMed Central  Google Scholar 

  46. Valguarnera, E. & Wardenburg, J. B. Good gone bad: one toxin away from disease for Bacteroides fragilis. J. Mol. Biol. 432, 765–785 (2019).

    PubMed  Google Scholar 

  47. Sears, C. L. Enterotoxigenic Bacteroides fragilis: a rogue among symbiotes. Clin. Microbiol. Rev. 22, 349–369 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Boleij, A. et al. The Bacteroides fragilis toxin gene is prevalent in the colon mucosa of colorectal cancer patients. Clin. Infect. Dis. 60, 208–215 (2015).

    CAS  PubMed  Google Scholar 

  49. Wu, S., Lim, K.-C., Huang, J., Saidi, R. F. & Sears, C. L. Bacteroides fragilis enterotoxin cleaves the zonula adherens protein, E-cadherin. Proc. Natl Acad. Sci. USA 95, 14979–14984 (1998).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  50. Wu, S., Morin, P. J., Maouyo, D. & Sears, C. L. Bacteroides fragilis enterotoxin induces c-Myc expression and cellular proliferation. Gastroenterology 12f4, 392–400 (2003).

    Google Scholar 

  51. Wu, S. et al. A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Nat. Med. 15, 1016–1022 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Rhee, K.-J. et al. Induction of persistent colitis by a human commensal, enterotoxigenic Bacteroides fragilis, in wild-type C57BL/6 mice. Infect. Immun. 77, 1708–1718 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Chung, L. et al. Bacteroides fragilis toxin coordinates a pro-carcinogenic inflammatory cascade via targeting of colonic epithelial cells. Cell Host Microbe 23, 203–214.e5 (2018). This study elucidated the immunological mechanism of enterotoxigenic B. fragilis-induced colon tumorigenesis in ApcMin mice.

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Zhang, L. & Shay, J. W. Multiple roles of APC and its therapeutic implications in colorectal cancer.J. Natl Cancer Inst. 109, djw332 (2017).

    PubMed  PubMed Central  Google Scholar 

  55. Purcell, R. V. et al. Colonization with enterotoxigenic Bacteroides fragilis is associated with early-stage colorectal neoplasia. PLoS ONE 12, e0171602 (2017).

    PubMed  PubMed Central  Google Scholar 

  56. Périchon, B. et al. Detection of Streptococcus gallolyticus and four other CRC-associated bacteria in patient stools reveals a potential “driver” role for enterotoxigenic Bacteroides fragilis. Front. Cell Infect. Microbiol. 12, 794391 (2022).

    PubMed  PubMed Central  Google Scholar 

  57. Zamani, S. et al. Enterotoxigenic Bacteroides fragilis: a possible etiological candidate for bacterially-induced colorectal precancerous and cancerous lesions. Front. Cell Infect. Microbiol. 9, 449 (2020).

    PubMed  PubMed Central  Google Scholar 

  58. Aitchison, A., Pearson, J. F., Purcell, R. V., Frizelle, F. A. & Keenan, J. I. Detection of Fusobacterium nucleatum DNA in primary care patient stool samples does not predict progression of colorectal neoplasia. PLoS ONE 17, e0269541 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Han, Y. W. Fusobacterium nucleatum: a commensal-turned pathogen. Curr. Opin. Microbiol. 23, 141–147 (2015).

    CAS  PubMed  Google Scholar 

  60. Kostic, A. D. et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 22, 292–298 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Castellarin, M. et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res. 22, 299–306 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Rubinstein, M. R. et al. Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-Cadherin/β-Catenin signaling via its FadA adhesin. Cell Host Microbe 14, 195–206 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Kostic, A. D. et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14, 207–215 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Abed, J. et al. Fap2 mediates Fusobacterium nucleatum colorectal adenocarcinoma enrichment by binding to tumor-expressed Gal-GalNAc. Cell Host Microbe 20, 215–225 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Komiya, Y. et al. Patients with colorectal cancer have identical strains of Fusobacterium nucleatum in their colorectal cancer and oral cavity. Gut 68, 1335 (2019).

    PubMed  Google Scholar 

  66. Abed, J. et al. Colon cancer-associated Fusobacterium nucleatum may originate from the oral cavity and reach colon tumors via the circulatory system. Front. Cell Infect. Microbiol. 10, 400 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Yu, T. et al. Fusobacterium nucleatum promotes chemoresistance to colorectal cancer by modulating autophagy. Cell 170, 548–563.e16 (2017). This study showed that F. nucleatum increases chemoresistance of CRC cells by stimulating autophagy.

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Queen, J. et al. Comparative analysis of colon cancer-derived Fusobacterium nucleatum subspecies: inflammation and colon tumorigenesis in murine models. mBio 13, e02991-21 (2022).

    PubMed Central  Google Scholar 

  69. Brennan, C. A. et al. Fusobacterium nucleatum drives a pro-inflammatory intestinal microenvironment through metabolite receptor-dependent modulation of IL-17 expression. Gut Microbes 13, 1987780 (2021).

    PubMed  PubMed Central  Google Scholar 

  70. Rubinstein, M. R. et al. Fusobacterium nucleatum promotes colorectal cancer by inducing Wnt/β‐catenin modulator Annexin A1. EMBO Rep. 20, e47638 (2019).

    PubMed  PubMed Central  Google Scholar 

  71. Kumar, R. et al. Streptococcus gallolyticus subsp. gallolyticus promotes colorectal tumor development. PLoS Pathog. 13, e1006440 (2017).

    PubMed  PubMed Central  Google Scholar 

  72. Andres-Franch, M. et al. Streptococcus gallolyticus infection in colorectal cancer and association with biological and clinical factors. PLoS ONE 12, e0174305 (2017).

    PubMed  PubMed Central  Google Scholar 

  73. Aymeric, L. et al. Colorectal cancer specific conditions promote Streptococcus gallolyticus gut colonization. Proc. Natl Acad. Sci. USA 115, E283–E291 (2018).

    CAS  PubMed  Google Scholar 

  74. Long, X. et al. Peptostreptococcus anaerobius promotes colorectal carcinogenesis and modulates tumour immunity. Nat. Microbiol. 4, 2319–2330 (2019).

    PubMed  Google Scholar 

  75. Wang, X. et al. Porphyromonas gingivalis promotes colorectal carcinoma by activating the hematopoietic NLRP3 inflammasome. Cancer Res. 81, 2745–2759 (2021).

    CAS  PubMed  Google Scholar 

  76. Zhao, L. et al. Parvimonas micra promotes colorectal tumorigenesis and is associated with prognosis of colorectal cancer patients. Oncogene 41, 4200–4210 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Nagaraja, V. & Eslick, G. D. Systematic review with meta‐analysis: the relationship between chronic Salmonella typhi carrier status and gall‐bladder cancer. Aliment. Pharm. Ther. 39, 745–750 (2014).

    CAS  Google Scholar 

  78. Scanu, T. et al. Salmonella manipulation of host signaling pathways provokes cellular transformation associated with gallbladder carcinoma. Cell Host Microbe 17, 763–774 (2015).

    CAS  PubMed  Google Scholar 

  79. Mughini-Gras, L. et al. Increased colon cancer risk after severe Salmonella infection. PLoS ONE 13, e0189721 (2018).

    PubMed  PubMed Central  Google Scholar 

  80. Duijster, J. W. et al. Association between Salmonella infection and colon cancer: a nationwide registry-based cohort study. Epidemiol. Infect. 149, e56 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Drewes, J. L. et al. Human colon cancer-derived Clostridioides difficile strains drive colonic tumorigenesis in mice. Cancer Discov. 12, 1873–1885 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. He, Z. et al. Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin. Gut 68, 289–300 (2019).

    CAS  PubMed  Google Scholar 

  83. Wu, N. et al. Dysbiosis signature of fecal microbiota in colorectal cancer patients. Microb. Ecol. 66, 462–470 (2013).

    ADS  CAS  PubMed  Google Scholar 

  84. Okuda, S. et al. Profiling of host genetic alterations and intra-tumor microbiomes in colorectal cancer. Comput. Struct. Biotechnol. J. 19, 3330–3338 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Li, Y. et al. Gut microbiota signatures in tumor, para-cancerous, normal mucosa, and feces in colorectal cancer patients. Front. Cell Dev. Biol. 10, 916961 (2022).

    ADS  PubMed  PubMed Central  Google Scholar 

  86. Crobach, M. J. T. et al. Understanding Clostridium difficile colonization.Clin. Microbiol. Rev. 31, e00021-17 (2018).

    PubMed  PubMed Central  Google Scholar 

  87. Fearon, E. R. & Vogelstein, B. A genetic model for colorectal tumorigenesis. Cell 61, 759–767 (1990).

    CAS  PubMed  Google Scholar 

  88. Nguyen, L. H., Goel, A. & Chung, D. C. Pathways of colorectal carcinogenesis. Gastroenterology 158, 291–302 (2020).

    CAS  PubMed  Google Scholar 

  89. Cao, Y. et al. Commensal microbiota from patients with inflammatory bowel disease produce genotoxic metabolites. Science 378, eabm3233 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Wilson, M. R. et al. The human gut bacterial genotoxin colibactin alkylates DNA. Science 363, eaar7785 (2019).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  91. Xue, M. et al. Structure elucidation of colibactin and its DNA cross-links. Science 365, eaax2685 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Xue, M., Wernke, K. M. & Herzon, S. B. Depurination of colibactin-derived interstrand cross-links. Biochemistry 59, 892–900 (2020).

    CAS  PubMed  Google Scholar 

  93. Scuron, M. D., Boesze-Battaglia, K., Dlakić, M. & Shenker, B. J. The cytolethal distending toxin contributes to microbial virulence and disease pathogenesis by acting as a tri-perditious toxin. Front. Cell Infect. Microbiol. 6, 168 (2016).

    PubMed  PubMed Central  Google Scholar 

  94. Buc, E. et al. High prevalence of mucosa-associated E. coli producing cyclomodulin and genotoxin in colon cancer. PLoS ONE 8, e56964 (2013).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  95. Greten, F. R. & Grivennikov, S. I. Inflammation and cancer: triggers, mechanisms, and consequences. Immunity 51, 27–41 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  96. Eaden, J. A., Abrams, K. R. & Mayberry, J. F. The risk of colorectal cancer in ulcerative colitis: a meta-analysis. Gut 48, 526 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Raskov, H., Orhan, A., Christensen, J. P. & Gögenur, I. Cytotoxic CD8+ T cells in cancer and cancer immunotherapy. Br. J. Cancer 124, 359–367 (2021).

    CAS  PubMed  Google Scholar 

  98. Schmitt, M. & Greten, F. R. The inflammatory pathogenesis of colorectal cancer. Nat. Rev. Immunol. 21, 653–667 (2021).

    CAS  PubMed  Google Scholar 

  99. Ellulu, M. S., Patimah, I., Khaza’ai, H., Rahmat, A. & Abed, Y. Obesity and inflammation: the linking mechanism and the complications. Arch. Med. Sci. 13, 851–863 (2017).

    CAS  PubMed  Google Scholar 

  100. Tabung, F. K. et al. Association of dietary inflammatory potential with colorectal cancer risk in men and women. JAMA Oncol. 4, 366 (2018).

    PubMed  PubMed Central  Google Scholar 

  101. Geis, A. L. et al. Regulatory T-cell response to enterotoxigenic Bacteroides fragilis colonization triggers IL17-dependent colon carcinogenesis. Cancer Discov. 5, 1098–1109 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  102. Canli, Ö. et al. Myeloid cell-derived reactive oxygen species induce epithelial mutagenesis. Cancer Cell 32, 869–883.e5 (2017).

    ADS  CAS  PubMed  Google Scholar 

  103. Irrazabal, T. et al. Limiting oxidative DNA damage reduces microbe-induced colitis-associated colorectal cancer. Nat. Commun. 11, 1802 (2020).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  104. Zea, A. H. et al. Arginase-producing myeloid suppressor cells in renal cell carcinoma patients: a mechanism of tumor evasion. Cancer Res. 65, 3044–3048 (2005).

    CAS  PubMed  Google Scholar 

  105. Huang, B. et al. Gr-1+ CD115+ immature myeloid suppressor cells mediate the development of tumor-induced T regulatory cells and T-cell anergy in tumor-bearing host. Cancer Res. 66, 1123–1131 (2006).

    CAS  PubMed  Google Scholar 

  106. Wang, K. et al. Interleukin-17 receptor a signaling in transformed enterocytes promotes early colorectal tumorigenesis. Immunity 41, 1052–1063 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Gur, C. et al. Binding of the Fap2 protein of Fusobacterium nucleatum to human inhibitory receptor TIGIT protects tumors from immune cell attack. Immunity 42, 344–355 (2015). This study showed that F. nucleatum inhibits antitumor immunity by binding its Fap2 adhesin to the TIGIT receptor expressed on natural killer cells and T cells.

    CAS  PubMed  PubMed Central  Google Scholar 

  108. Galaski, J. et al. Fusobacterium nucleatum CbpF mediates inhibition of T cell function through CEACAM1 activation. Front. Cell Infect. Microbiol. 11, 692544 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. Peuker, K. et al. Microbiota-dependent activation of the myeloid calcineurin-NFAT pathway inhibits B7H3- and B7H4-dependent anti-tumor immunity in colorectal cancer. Immunity 55, 701–717.e7 (2022).

    CAS  PubMed  Google Scholar 

  110. Zhang, X. et al. Tissue-resident Lachnospiraceae family bacteria protect against colorectal carcinogenesis by promoting tumor immune surveillance. Cell Host Microbe 31, 418–432.e8 (2023).

    CAS  PubMed  Google Scholar 

  111. Tanoue, T. et al. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature 565, 600–605 (2019).

    ADS  CAS  PubMed  Google Scholar 

  112. Kim, J. M. et al. Mitogen‐activated protein kinase and activator protein‐1 dependent signals are essential for Bacteroides fragilis enterotoxin‐induced enteritis. Eur. J. Immunol. 35, 2648–2657 (2005).

    CAS  PubMed  Google Scholar 

  113. Wu, S. et al. Bacteroides fragilis enterotoxin induces intestinal epithelial cell secretion of interleukin-8 through mitogen-activated protein kinases and a tyrosine kinase-regulated nuclear factor-κB pathway. Infect. Immun. 72, 5832–5839 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  114. Bao, Y. et al. Long noncoding RNA BFAL1 mediates enterotoxigenic Bacteroides fragilis-related carcinogenesis in colorectal cancer via the RHEB/mTOR pathway. Cell Death Dis. 10, 675 (2019).

    PubMed  PubMed Central  Google Scholar 

  115. Cao, Y. et al. Enterotoxigenic Bacteroides fragilis promotes intestinal inflammation and malignancy by inhibiting exosome-packaged miR-149-3p. Gastroenterology 161, 1552–1566.e12 (2021).

    CAS  PubMed  Google Scholar 

  116. Goodwin, A. C. et al. Polyamine catabolism contributes to enterotoxigenic Bacteroides fragilis-induced colon tumorigenesis. Proc. Natl Acad. Sci. USA 108, 15354–15359 (2011).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  117. Allen, J. et al. Colon tumors in enterotoxigenic Bacteroides fragilis (ETBF)-colonized mice do not display a unique mutational signature but instead possess host-dependent alterations in the APC gene. Microbiol. Spectr. 10, e01055-22 (2022).

    PubMed  PubMed Central  Google Scholar 

  118. Allen, J., Hao, S., Sears, C. L. & Timp, W. Epigenetic changes induced by Bacteroides fragilis toxin (BFT). Infect. Immun. 87, e00447-18 (2019).

    PubMed  PubMed Central  Google Scholar 

  119. Liu, Q.-Q. et al. Enterotoxigenic Bacteroides fragilis induces the stemness in colorectal cancer via upregulating histone demethylase JMJD2B. Gut Microbes 12, 1788900 (2020).

    PubMed  PubMed Central  Google Scholar 

  120. Meng, Q. et al. Fusobacterium nucleatum secretes amyloid‐like FadA to enhance pathogenicity. EMBO Rep. 22, e52891 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  121. Zhang, Y. et al. Fusobacterium nucleatum promotes colorectal cancer cells adhesion to endothelial cells and facilitates extravasation and metastasis by inducing ALPK1/NF-κB/ICAM1 axis. Gut Microbes 14, 2038852 (2022).

    PubMed  PubMed Central  Google Scholar 

  122. Lu, X. et al. Long non-coding RNA EVADR induced by Fusobacterium nucleatum infection promotes colorectal cancer metastasis. Cell Rep. 40, 111127 (2022).

    CAS  PubMed  Google Scholar 

  123. Chen, S. et al. Fusobacterium nucleatum promotes colorectal cancer metastasis by modulating KRT7-AS/KRT7. Gut Microbes 11, 511–521 (2020).

    PubMed  PubMed Central  Google Scholar 

  124. Hong, J. et al. F. nucleatum targets lncRNA ENO1-IT1 to promote glycolysis and oncogenesis in colorectal cancer. Gut 70, 2123–2137 (2021).

    CAS  PubMed  Google Scholar 

  125. Liu, J. et al. Proteomic characterization of outer membrane vesicles from gut mucosa-derived Fusobacterium nucleatum. J. Proteom. 195, 125–137 (2019).

    CAS  Google Scholar 

  126. Engevik, M. A. et al. Fusobacterium nucleatum secretes outer membrane vesicles and promotes intestinal inflammation. mBio 12, e02706-20 (2021).

    PubMed  PubMed Central  Google Scholar 

  127. Zakharzhevskaya, N. B. et al. Interaction of Bacteroides fragilis toxin with outer membrane vesicles reveals new mechanism of its secretion and delivery. Front. Cell Infect. Microbiol. 7, 2 (2017).

    PubMed  PubMed Central  Google Scholar 

  128. Vestby, L. K., Grønseth, T., Simm, R. & Nesse, L. L. Bacterial biofilm and its role in the pathogenesis of disease. Antibiotics 9, 59 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  129. Dejea, C. M. et al. Microbiota organization is a distinct feature of proximal colorectal cancers. Proc. Natl Acad. Sci. USA 111, 18321–18326 (2014).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  130. Drewes, J. L. et al. High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia. NPJ Biofilms Microbiomes 3, 34 (2017).

    PubMed  PubMed Central  Google Scholar 

  131. Johnson, C. H. et al. Metabolism links bacterial biofilms and colon carcinogenesis. Cell Metab. 21, 891–897 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  132. Tomkovich, S. et al. Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic. J. Clin. Invest. 129, 1699–1712 (2019).

    PubMed  PubMed Central  Google Scholar 

  133. Dejea, C. M. et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science 359, 592–597 (2018).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  134. Baran, B. et al. Difference between left-sided and right-sided colorectal cancer: a focused review of literature. Gastroenterol. Res. 11, 264–273 (2018).

    ADS  CAS  Google Scholar 

  135. Mangone, L. et al. Colon cancer survival differs from right side to left side and lymph node harvest number matter. BMC Public Health 21, 906 (2021).

    PubMed  PubMed Central  Google Scholar 

  136. Cai, J., Sun, L. & Gonzalez, F. J. Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis. Cell Host Microbe 30, 289–300 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  137. Ajouz, H., Mukherji, D. & Shamseddine, A. Secondary bile acids: an underrecognized cause of colon cancer. World J. Surg. Oncol. 12, 164 (2014).

    PubMed  PubMed Central  Google Scholar 

  138. Fu, T. et al. FXR regulates intestinal cancer stem cell proliferation. Cell 176, 1098–1112.e18 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  139. Sorrentino, G. et al. Bile acids signal via TGR5 to activate intestinal stem cells and epithelial regeneration. Gastroenterology 159, 956–968.e8 (2020).

    CAS  PubMed  Google Scholar 

  140. Booth, L. A., Gilmore, I. T. & Bilton, R. F. Secondary bile acid induced DNA damage in HT29 cells: are free radicals involved? Free Radic. Res. 26, 135–144 (2009).

    Google Scholar 

  141. Zhang, H., Xu, H., Zhang, C., Tang, Q. & Bi, F. Ursodeoxycholic acid suppresses the malignant progression of colorectal cancer through TGR5-YAP axis. Cell Death Discov. 7, 207 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  142. Alberts, D. S. et al. Phase III trial of ursodeoxycholic acid to prevent colorectal adenoma recurrence. J. Natl Cancer Inst. 97, 846–853 (2005).

    CAS  PubMed  Google Scholar 

  143. Campbell, C. et al. Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells. Nature 581, 475–479 (2020).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  144. Li, W. et al. A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1. Cell Host Microbe 29, 1366–1377.e9 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  145. Song, X. et al. Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis. Nature 577, 410–415 (2020). This study determined that microbial secondary bile acid production regulates regulatory T cell differentiation in the gut.

    CAS  PubMed  Google Scholar 

  146. Sato, Y. et al. Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians. Nature 599, 458–464 (2021).

    ADS  CAS  PubMed  Google Scholar 

  147. Paik, D. et al. Human gut bacteria produce ΤΗ17-modulating bile acid metabolites. Nature 603, 907–912 (2022). This study identified the bacterial species and enzymes that produce two prominent secondary bile acids, 3-oxolithocholic acid and isolithocholic acid, which inhibit TH17 cell differentiation in the gut.

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  148. Lavoie, S. et al. Expression of free fatty acid receptor 2 by dendritic cells prevents their expression of interleukin 27 and is required for maintenance of mucosal barrier and immune response against colorectal tumors in mice. Gastroenterology 158, 1359–1372.e9 (2020).

    CAS  PubMed  Google Scholar 

  149. Singh, N. et al. Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis. Immunity 40, 128–139 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  150. Donohoe, D. R. et al. A gnotobiotic mouse model demonstrates that dietary fiber protects against colorectal tumorigenesis in a microbiota- and butyrate-dependent manner. Cancer Discov. 4, 1387–1397 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  151. Wang, T. et al. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J. 6, 320–329 (2012).

    CAS  PubMed  Google Scholar 

  152. O’Keefe, S. J. D. et al. Fat, fibre and cancer risk in African Americans and rural Africans. Nat. Commun. 6, 6342 (2015).

    ADS  PubMed  Google Scholar 

  153. Chen, D. et al. Clostridium butyricum, a butyrate-producing probiotic, inhibits intestinal tumor development through modulating Wnt signaling and gut microbiota. Cancer Lett. 469, 456–467 (2020). This study showed that administration of Clostridium butyricum could reduce high-fat diet-induced colorectal tumorigenesis in ApcMin mice.

    CAS  PubMed  Google Scholar 

  154. Deehan, E. C. et al. Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid production. Cell Host Microbe 27, 389–404.e6 (2020).

    CAS  PubMed  Google Scholar 

  155. Belcheva, A. et al. Gut microbial metabolism drives transformation of msh2-deficient colon epithelial cells. Cell 158, 288–299 (2014).

    CAS  PubMed  Google Scholar 

  156. Okumura, S. et al. Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion. Nat. Commun. 12, 5674 (2021). Together with Belcheva et al. (2014), this study demonstrated that certain bacteria in the gut can potentiate colorectal tumorigenesis through butyrate production, highlighting the context-dependent and incompletely understood role of butyrate in CRC development.

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  157. Bultman, S. J. & Jobin, C. Microbial-derived butyrate: an oncometabolite or tumor-suppressive metabolite? Cell Host Microbe 16, 143–145 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  158. Donohoe, D. R. et al. The Warburg effect dictates the mechanism of butyrate-mediated histone acetylation and cell proliferation. Mol. Cell 48, 612–626 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  159. Sinicrope, F. A. Increasing incidence of early-onset colorectal cancer. N. Engl. J. Med. 386, 1547–1558 (2022).

    CAS  PubMed  Google Scholar 

  160. Han, J.-X. et al. Microbiota-derived tryptophan catabolites mediate the chemopreventive effects of statins on colorectal cancer. Nat. Microbiol. 8, 919–933 (2023).

    CAS  PubMed  Google Scholar 

  161. Bell, H. N. et al. Reuterin in the healthy gut microbiome suppresses colorectal cancer growth through altering redox balance. Cancer Cell 40, 185–200.e6 (2022).

    CAS  PubMed  Google Scholar 

  162. Montalban-Arques, A. et al. Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors. Cell Host Microbe 29, 1573–1588.e7 (2021).

    CAS  PubMed  Google Scholar 

  163. Ryu, S. W. et al. Gut microbiota Eubacterium callanderi exerts anti-colorectal cancer activity. Microbiol. Spectr. 10, e02531-22 (2022).

    PubMed  PubMed Central  Google Scholar 

  164. Xu, H., Luo, H., Zhang, J., Li, K. & Lee, M.-H. Therapeutic potential of Clostridium butyricum anticancer effects in colorectal cancer. Gut Microbes 15, 2186114 (2023).

    PubMed  PubMed Central  Google Scholar 

  165. Dikeocha, I. J., Al-Kabsi, A. M., Chiu, H.-T. & Alshawsh, M. A. Faecalibacterium prausnitzii ameliorates colorectal tumorigenesis and suppresses proliferation of HCT116 colorectal cancer cells. Biomedicines 10, 1128 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  166. Kim, O. Y. et al. Bacterial outer membrane vesicles suppress tumor by interferon-γ-mediated antitumor response. Nat. Commun. 8, 626 (2017).

    ADS  PubMed  PubMed Central  Google Scholar 

  167. Qing, S. et al. Biomineralized bacterial outer membrane vesicles potentiate safe and efficient tumor microenvironment reprogramming for anticancer therapy. Adv. Mater. 32, 2002085 (2020).

    CAS  Google Scholar 

  168. Zheng, D.-W. et al. Phage-guided modulation of the gut microbiota of mouse models of colorectal cancer augments their responses to chemotherapy. Nat. Biomed. Eng. 3, 717–728 (2019).

    ADS  CAS  PubMed  Google Scholar 

  169. Jia, F. et al. Optimized antimicrobial peptide jelleine-I derivative Br-J-I inhibits Fusobacterium nucleatum to suppress colorectal cancer progression. Int. J. Mol. Sci. 24, 1469 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  170. Holt, R. A. Oncomicrobial vaccines: the potential for a Fusobacterium nucleatum vaccine to improve colorectal cancer outcomes. Cell Host Microbe 31, 141–145 (2023).

    CAS  PubMed  Google Scholar 

  171. Baruch, E. N. et al. Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients. Science 371, 602–609 (2021).

    ADS  CAS  PubMed  Google Scholar 

  172. Davar, D. et al. Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Science 371, 595–602 (2021). Together with Baruch et al. (2021), this study demonstrated the efficacy of faecal microbiota transplant therapy in overcoming immunotherapy resistance in melanoma, serving as a goal for future microbiome-directed therapeutics in CRC.

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  173. Walter, J. & Shanahan, F. Fecal microbiota-based treatment for recurrent Clostridioides difficile infection. Cell 186, 1087 (2023).

    CAS  PubMed  Google Scholar 

  174. Mullard, A. FDA approves second microbiome-based C. difficile therapy. Nat. Rev. Drug Discov. 22, 436 (2023).

    PubMed  Google Scholar 

  175. Tomkovich, S. et al. Locoregional effects of microbiota in a preclinical model of colon carcinogenesis. Cancer Res. 77, 2620–2632 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  176. Hwang, S. et al. Enterotoxigenic Bacteroides fragilis infection exacerbates tumorigenesis in AOM/DSS mouse model. Int. J. Med. Sci. 17, 145–152 (2020).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  177. Xi, Y. & Xu, P. Global colorectal cancer burden in 2020 and projections to 2040. Transl Oncol. 14, 101174 (2021).

    PubMed  PubMed Central  Google Scholar 

  178. Jasperson, K. W., Tuohy, T. M., Neklason, D. W. & Burt, R. W. Hereditary and familial colon cancer. Gastroenterology 138, 2044–2058 (2010).

    CAS  PubMed  Google Scholar 

  179. Jiao, S. et al. Estimating the heritability of colorectal cancer. Hum. Mol. Genet. 23, 3898–3905 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  180. Hossain, M. S. et al. Colorectal cancer: a review of carcinogenesis, global epidemiology, current challenges, risk factors, preventive and treatment strategies. Cancers 14, 1732 (2022).

    PubMed  PubMed Central  Google Scholar 

  181. Helsingen, L. M. & Kalager, M. Colorectal cancer screening — approach, evidence, and future directions. NEJM Evid. https://doi.org/10.1056/EVIDra2100035 (2022).

  182. Benson, A. B. et al. Colon cancer, version 2.2021, NCCN clinical practice guidelines in oncology. J. Natl Compr. Canc. Netw. 19, 329–359 (2021).

    PubMed  Google Scholar 

  183. Ooki, A., Shinozaki, E. & Yamaguchi, K. Immunotherapy in colorectal cancer: current and future strategies. J. Anus Rectum Colon. 5, 11–24 (2021).

    PubMed  PubMed Central  Google Scholar 

  184. Dow, L. E. et al. Apc restoration promotes cellular differentiation and reestablishes crypt homeostasis in colorectal cancer. Cell 161, 1539–1552 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was funded by the US National Institutes of Health (R01CA196845 and U2CCA233291), Cancer Research UK (Cancer Grand Challenges OPTIMISTICC team grant A27140) and Janssen. The authors are grateful for the contributions of members of the Sears Laboratory over time.

Author information

Authors and Affiliations

Authors

Contributions

The authors contributed equally to the design of the manuscript. M.T.W. wrote most of the manuscript and created all display items. C.L.S. wrote the Conclusions and clinical applications section and edited the manuscript.

Corresponding author

Correspondence to Cynthia L. Sears.

Ethics declarations

Competing interests

The Sears Laboratory receives research support through Johns Hopkins University School of Medicine from Janssen and Bristol Myers Squibb.

Peer review

Peer review information

Nature Reviews Microbiology thanks Andrew Chan, Subbaya Subramanian, Yiqing Wang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

White, M.T., Sears, C.L. The microbial landscape of colorectal cancer. Nat Rev Microbiol 22, 240–254 (2024). https://doi.org/10.1038/s41579-023-00973-4

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41579-023-00973-4

This article is cited by

Search

Quick links

Nature Briefing: Cancer

Sign up for the Nature Briefing: Cancer newsletter — what matters in cancer research, free to your inbox weekly.

Get what matters in cancer research, free to your inbox weekly. Sign up for Nature Briefing: Cancer