Submitted:
05 August 2025
Posted:
07 August 2025
You are already at the latest version
Abstract
The gut microbiome, a complex community of microorganisms residing in the gastrointestinal tract, is increasingly recognized as a critical player in cancer pathophysiology. Its influence extends beyond local gastrointestinal disorders to systemic diseases, including breast and colorectal cancers. This review examines current evidence on the interplay between gut microbial dysbiosis and the development, progression, and treatment response in both malignancies. In colorectal cancer (CRC), pathogenic bacteria such as Fusobacterium nucleatum, Escherichia coli, and Bacteroides fragilis have been implicated in tumor initiation and progression through mechanisms involving chronic inflammation, DNA damage, and immune modulation. Meanwhile, in breast cancer, the gut microbiome may contribute indirectly via regulation of estrogen metabolism, immune signaling, and systemic inflammation. Furthermore, the gut microbiota is increasingly being explored as a source of non-invasive biomarkers for early detection and disease monitoring, as well as a modifiable factor that could enhance therapeutic efficacy. Interventions such as probiotics, prebiotics, dietary modulation, and fecal microbiota transplantation (FMT) hold promise in reprogramming the microbiome to support antitumor responses and reduce treatment-related toxicity. Despite the growing body of research, translating these findings into clinical application requires deeper mechanistic understanding and standardized methodologies. This review emphasizes the need for longitudinal and multi-omics studies to unravel causal relationships and identify therapeutic targets. Understanding gut microbiome dynamics offers exciting opportunities for developing microbiota-informed strategies for cancer prevention, diagnosis, and therapy—particularly in breast and colorectal cancers.
Keywords:
1. Introduction
2. Overview of the Gut Microbiome
2.1. Composition of the Gut Microbiome
2.2. Factors Influencing Microbiome Diversity
2.3. The Microbiome’s Function in Immune System Control and Metabolism
3. Gut Microbiome and Colon Cancer Development
3.1. Inflammation and Tumorigenesis
3.2. Inflammatory Pathways in Colon Cancer Development
Microbiota-Induced Immune Modulation
3.3. Microbial Metabolites and Carcinogenesis
Short-Chain Fatty Acids (SCFAs): Dual Roles in Colon Cancer
3.4. Bile Acid Metabolism and Genotoxic Effects
3.5. Production of Secondary Metabolites (Toxins, Reactive Oxygen Species)
3.6. Key Bacteria Implicated in Colon Cancer
3.7. Evidence from Human and Animal Studies
3.7.1. Human Studies
3.7.2. Animal Models
4. Gut Microbiome and Breast Cancer Development
4.1. Gut–Breast Axis: Systemic Effects of the Microbiome
4.2. Microbial Metabolites and Breast Cancer Risk
4.3. Short-Chain Fatty Acids (SCFAs) and Their Dual Roles
4.4. Bile Acid Metabolism and Genotoxic Effects
4.5. Obesity and Lipid Metabolism
4.6. Inflammation and Immune Dysregulation
4.7. Evidence from Human and Animal Studies
4.8. Human Studies
The Role of the Estrobolome in Estrogen Metabolism
4.9. Microbiome Signatures in Breast Cancer Patients
4.10. Faecal Microbiota and Breast Cancer Risk
4.11. Animal Models
Germ-Free Mice and Hormone-Driven Tumors
4.12. Microbial Modulation of Immune Responses in Breast Cancer
4.13. Obesity, Microbiota, and Breast Cancer Risk
5. Therapeutic and Preventive Strategies Targeting the Microbiome
5.1. Probiotics and Prebiotics
5.2. Fecal Microbiota Transplantation (FMT)
5.3. Microbiome-Based Biomarkers for Early Detection
5.4. Future Therapeutic Approaches
6. Challenges, Limitations, and Future Directions
6.1. Research Gaps
6.2. Translational Challenges
6.3. Emerging Technologies
6.4. Future Studies
7. Conclusions
References
- Afzaal, M., Saeed, F., Shah, Y. A., Hussain, M., Rabail, R., Socol, C. T., Hassoun, A., Pateiro, M., Lorenzo, J. M., Rusu, A. V., & Aadil, R. M. (2022). Human gut microbiota in health and disease: Unveiling the relationship. Frontiers in microbiology, 13, 999001. [CrossRef]
- World Health Organization (WHO), 2021. Cancer. Available at: https://www.who.int/news-room/fact-sheets/detail/cancer?
- Zhao, L. Y., Mei, J. X., Yu, G., Lei, L., Zhang, W. H., Liu, K., Chen, X. L., Kołat, D., Yang, K., & Hu, J. K. (2023). Role of the gut microbiota in anticancer therapy: from molecular mechanisms to clinical applications. Signal transduction and targeted therapy, 8(1), 201. [CrossRef]
- Sekirov, I., Russell, S. L., Antunes, L. C., & Finlay, B. B. (2010). Gut microbiota in health and disease. Physiological reviews, 90(3), 859–904. [CrossRef]
- Human Microbiome Project Consortium (2012). A framework for human microbiome research. Nature, 486(7402), 215–221. [CrossRef]
- Yang, J., & Yu, J. (2018). The association of diet, gut microbiota and colorectal cancer: what we eat may imply what we get. Protein & cell, 9(5), 474–487. [CrossRef]
- Bäckhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., Semenkovich, C. F., & Gordon, J. I. (2004). The gut microbiota as an environmental factor that regulates fat storage. Proceedings of the National Academy of Sciences of the United States of America, 101(44), 15718–15723. [CrossRef]
- David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., Biddinger, S. B., Dutton, R. J., & Turnbaugh, P. J. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), 559–563. [CrossRef]
- Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J. T., Spector, T. D., Clark, A. G., & Ley, R. E. (2014). Human genetics shape the gut microbiome. Cell, 159(4), 789–799. [CrossRef]
- Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2010). Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology (Reading, England), 156(Pt 11), 3216–3223. [CrossRef]
- Ekpunobi, N. F., Mgbedo, U. G., Okoye, L. C. and Agu, K. C. Prevalence of ESBL genes in Klebsiella pneumoniae from individuals with community-acquired urinary tract infections in Lagos state, Nigeria. Journal of RNA and Genomics, 2024; 20 (2):1-6. Doi: 10.35841/2591-7781.19.1000181.
- Yoo, J. Y., Groer, M., Dutra, S. V. O., Sarkar, A., & McSkimming, D. I. (2020). Gut Microbiota and Immune System Interactions. Microorganisms, 8(10), 1587. [CrossRef]
- Clarke, S. F., Murphy, E. F., O’Sullivan, O., Lucey, A. J., Humphreys, M., Hogan, A., Hayes, P., O’Reilly, M., Jeffery, I. B., Wood-Martin, R., Kerins, D. M., Quigley, E., Ross, R. P., O’Toole, P. W., Molloy, M. G., Falvey, E., Shanahan, F., & Cotter, P. D. (2014). Exercise and associated dietary extremes impact on gut microbial diversity. Gut, 63(12), 1913–1920. [CrossRef]
- Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., Heath, A. C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J. G., Lozupone, C. A., Lauber, C., Clemente, J. C., Knights, D., Knight, R., … Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222–227. [CrossRef]
- Ekpunobi, N. F. and Agu, K. C. (2024). Emergence and Re-Emergence of Arboviruses: When Old Enemies Rise Again. Cohesive J Microbiol Infect Dis, 7(2). CJMI. 000658. DOI: 10.31031/CJMI.2024.07.000658.
- Round, J. L., & Mazmanian, S. K. (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nature reviews. Immunology, 9(5), 313–323. [CrossRef]
- Belkaid, Y., & Hand, T. W. (2014). Role of the microbiota in immunity and inflammation. Cell, 157(1), 121–141. [CrossRef]
- Liu, X. F., Shao, J. H., Liao, Y. T., Wang, L. N., Jia, Y., Dong, P. J., Liu, Z. Z., He, D. D., Li, C., & Zhang, X. (2023). Regulation of short-chain fatty acids in the immune system. Frontiers in immunology, 14, 1186892. [CrossRef]
- Dinan, T. G., & Cryan, J. F. (2017). The Microbiome-Gut-Brain Axis in Health and Disease. Gastroenterology clinics of North America, 46(1), 77–89. [CrossRef]
- Gagnière, J., Raisch, J., Veziant, J., Barnich, N., Bonnet, R., Buc, E., Bringer, M. A., Pezet, D., & Bonnet, M. (2016). Gut microbiota imbalance and colorectal cancer. World journal of gastroenterology, 22(2), 501–518. [CrossRef]
- Louis, P., Hold, G. L., & Flint, H. J. (2014). The gut microbiota, bacterial metabolites and colorectal cancer. Nature reviews. Microbiology, 12(10), 661–672. [CrossRef]
- Schwabe, R. F., & Jobin, C. (2013). The microbiome and cancer. Nature reviews. Cancer, 13(11), 800–812. [CrossRef]
- Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., Ojesina, A. I., Jung, J., Bass, A. J., Tabernero, J., Baselga, J., Liu, C., Shivdasani, R. A., Ogino, S., Birren, B. W., Huttenhower, C., Garrett, W. S., & Meyerson, M. (2012). Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome research, 22(2), 292–298. [CrossRef]
- Donohoe, D. R., Holley, D., Collins, L. B., Montgomery, S. A., Whitmore, A. C., Hillhouse, A., Curry, K. P., Renner, S. W., Greenwalt, A., Ryan, E. P., Godfrey, V., Heise, M. T., Threadgill, D. S., Han, A., Swenberg, J. A., Threadgill, D. W., & Bultman, S. J. (2014). A gnotobiotic mouse model demonstrates that dietary fiber protects against colorectal tumorigenesis in a microbiota- and butyrate-dependent manner. Cancer discovery, 4(12), 1387–1397. [CrossRef]
- O’Keefe S. J. (2016). Diet, microorganisms and their metabolites, and colon cancer. Nature reviews. Gastroenterology & hepatology, 13(12), 691–706. [CrossRef]
- Ridlon, J. M., Harris, S. C., Bhowmik, S., Kang, D. J., & Hylemon, P. B. (2016). Consequences of bile salt biotransformations by intestinal bacteria. Gut microbes, 7(1), 22–39. [CrossRef]
- Nougayrède, J. P., Homburg, S., Taieb, F., Boury, M., Brzuszkiewicz, E., Gottschalk, G., Buchrieser, C., Hacker, J., Dobrindt, U., & Oswald, E. (2006). Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science (New York, N.Y.), 313(5788), 848–851. [CrossRef]
- Chung, L., Thiele Orberg, E., Geis, A. L., Chan, J. L., Fu, K., DeStefano Shields, C. E., Dejea, C. M., Fathi, P., Chen, J., Finard, B. B., Tam, A. J., McAllister, F., Fan, H., Wu, X., Ganguly, S., Lebid, A., Metz, P., Van Meerbeke, S. W., Huso, D. L., Wick, E. C., … Housseau, F. (2018). Bacteroides fragilis Toxin Coordinates a Pro-carcinogenic Inflammatory Cascade via Targeting of Colonic Epithelial Cells. Cell host & microbe, 23(2), 203–214.e5. [CrossRef]
- Jones, R. M., Mercante, J. W., & Neish, A. S. (2012). Reactive oxygen production induced by the gut microbiota: pharmacotherapeutic implications. Current medicinal chemistry, 19(10), 1519–1529. [CrossRef]
- Shang, F. M., & Liu, H. L. (2018). Fusobacterium nucleatum and colorectal cancer: A review. World journal of gastrointestinal oncology, 10(3), 71–81. [CrossRef]
- Sadeghi, M., Mestivier, D., & Sobhani, I. (2024). Contribution of pks+ Escherichia coli (E. coli) to Colon Carcinogenesis. Microorganisms, 12(6), 1111. [CrossRef]
- Nouri, R., Hasani, A., Shirazi, K. M., Alivand, M. R., Sepehri, B., Sotoodeh, S., Hemmati, F., & Rezaee, M. A. (2022). Escherichia coli and Colorectal Cancer: Unfolding the Enigmatic Relationship. Current pharmaceutical biotechnology, 23(10), 1257–1268. [CrossRef]
- Blander, J. M., Longman, R. S., Iliev, I. D., Sonnenberg, G. F., & Artis, D. (2017). Regulation of inflammation by microbiota interactions with the host. Nature immunology, 18(8), 851–860. [CrossRef]
- Yu, T., Guo, F., Yu, Y., Sun, T., Ma, D., Han, J., Qian, Y., Kryczek, I., Sun, D., Nagarsheth, N., Chen, Y., Chen, H., Hong, J., Zou, W., & Fang, J. Y. (2017). Fusobacterium nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy. Cell, 170(3), 548–563.e16. [CrossRef]
- Zackular, J. P., Rogers, M. A., Ruffin, M. T., 4th, & Schloss, P. D. (2014). The human gut microbiome as a screening tool for colorectal cancer. Cancer prevention research (Philadelphia, Pa.), 7(11), 1112–1121. [CrossRef]
- Arthur, J. C., Perez-Chanona, E., Mühlbauer, M., Tomkovich, S., Uronis, J. M., Fan, T. J., Campbell, B. J., Abujamel, T., Dogan, B., Rogers, A. B., Rhodes, J. M., Stintzi, A., Simpson, K. W., Hansen, J. J., Keku, T. O., Fodor, A. A., & Jobin, C. (2012). Intestinal inflammation targets cancer-inducing activity of the microbiota. Science (New York, N.Y.), 338(6103), 120–123. [CrossRef]
- Pandey, H., Tang, D. W. T., Wong, S. H., & Lal, D. (2023). Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities. Cancers, 15(3), 866. [CrossRef]
- Goedert, J. J., Jones, G., Hua, X., Xu, X., Yu, G., Flores, R., Falk, R. T., Gail, M. H., Shi, J., Ravel, J., & Feigelson, H. S. (2015). Investigation of the association between the fecal microbiota and breast cancer in postmenopausal women: a population-based case-control pilot study. Journal of the National Cancer Institute, 107(8), djv147. [CrossRef]
- Hu, S., Ding, Q., Zhang, W., Kang, M., Ma, J., & Zhao, L. (2023). Gut microbial beta-glucuronidase: a vital regulator in female estrogen metabolism. Gut microbes, 15(1), 2236749. [CrossRef]
- Kwa, M., Plottel, C. S., Blaser, M. J., & Adams, S. (2016). The Intestinal Microbiome and Estrogen Receptor-Positive Female Breast Cancer. Journal of the National Cancer Institute, 108(8), djw029. [CrossRef]
- Baker, J. M., Al-Nakkash, L., & Herbst-Kralovetz, M. M. (2017). Estrogen-gut microbiome axis: Physiological and clinical implications. Maturitas, 103, 45–53. [CrossRef]
- Zarrinpar, A., Chaix, A., Yooseph, S., & Panda, S. (2014). Diet and feeding pattern affect the diurnal dynamics of the gut microbiome. Cell metabolism, 20(6), 1006–1017. [CrossRef]
- Fernández, M. F., Reina-Pérez, I., Astorga, J. M., Rodríguez-Carrillo, A., Plaza-Díaz, J., & Fontana, L. (2018). Breast Cancer and Its Relationship with the Microbiota. International journal of environmental research and public health, 15(8), 1747. [CrossRef]
- Gopalakrishnan, V., Spencer, C. N., Nezi, L., Reuben, A., Andrews, M. C., Karpinets, T. V., Prieto, P. A., Vicente, D., Hoffman, K., Wei, S. C., Cogdill, A. P., Zhao, L., Hudgens, C. W., Hutchinson, D. S., Manzo, T., Petaccia de Macedo, M., Cotechini, T., Kumar, T., Chen, W. S., Reddy, S. M., … Wargo, J. A. (2018). Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science (New York, N.Y.), 359(6371), 97–103. [CrossRef]
- Yang, Q., Ouyang, J., Sun, F., & Yang, J. (2020). Short-Chain Fatty Acids: A Soldier Fighting Against Inflammation and Protecting From Tumorigenesis in People With Diabetes. Frontiers in immunology, 11, 590685. [CrossRef]
- Banerjee, S., Tian, T., Wei, Z., Shih, N., Feldman, M. D., Peck, K. N., DeMichele, A. M., Alwine, J. C., & Robertson, E. S. (2018). Distinct Microbial Signatures Associated With Different Breast Cancer Types. Frontiers in microbiology, 9, 951. [CrossRef]
- Álvarez-Mercado, A. I., Del Valle Cano, A., Fernández, M. F., & Fontana, L. (2023). Gut Microbiota and Breast Cancer: The Dual Role of Microbes. Cancers, 15(2), 443. [CrossRef]
- Śliżewska, K., Markowiak-Kopeć, P., & Śliżewska, W. (2020). The Role of Probiotics in Cancer Prevention. Cancers, 13(1), 20. [CrossRef]
- Mishra, R., Rajsiglová, L., Lukáč, P., Tenti, P., Šima, P., Čaja, F., & Vannucci, L. (2021). Spontaneous and Induced Tumors in Germ-Free Animals: A General Review. Medicina (Kaunas, Lithuania), 57(3), 260. [CrossRef]
- Matson, V., Chervin, C. S., & Gajewski, T. F. (2021). Cancer and the Microbiome-Influence of the Commensal Microbiota on Cancer, Immune Responses, and Immunotherapy. Gastroenterology, 160(2), 600–613. [CrossRef]
- Chukwunwejim, C.R., Ekpunobi, N.F., Ogunmola, T., Obidi, N., Ajasa, O. S. & Obidi, N. L. (2025). Molecular identification of multidrug-resistant bacteria from eggshell surfaces in Nigeria: A growing threat to public health. Magna Scientia Advanced Biology and Pharmacy, 2025, 15(01), 021-028. [CrossRef]
- Ekpunobi, N. F. & Adeleye, I. A. (2020). Phenotypic characterization of biofilm formation and efflux pump activity in multidrug-resistant Staphylococcus species isolated from asymptomatic students. Journal of Microbiology and Experimentation 8(6): 223-229. [CrossRef]
- Ekpunobi, N. F., Obidi, N. O., Idowu, O., Okoye, L. C., Agu, C. K., Ogunsanya, T., ... & Uwanta, L. I. (2025b). Knowledge and awareness of breast cancer symptoms, risk factors, and early detection methods among Nigerian university students. World Journal of Advanced Research and Reviews, 25(2), 1129-1138. [CrossRef]
- Ekpunobi, N., Adesanoye, S., Orababa, O., Adinnu, C., Okorie, C., & Akinsuyi, O. (2024b). Public health perspective of public abattoirs in Nigeria, challenges and solutions. GSC Biological and Pharmaceutical Sciences, 26. 115-127. [CrossRef]
- Ekpunobi, N., Markjonathan, I., Olanrewaju, O. & Olanihun, D. (2020). Idiosyncrasies of COVID- 19;A Review. Iranian Journal of Medical Microbiology 14(3): 290-296. http://dx.doi.org/10.30699/ijmm.14.3.290.
- Liu, B. N., Liu, X. T., Liang, Z. H., & Wang, J. H. (2021). Gut microbiota in obesity. World journal of gastroenterology, 27(25), 3837–3850. [CrossRef]
- Wang, S., Huang, J., & Li, L. (2022). Effects of fecal microbiota transplantation on tumor progression in colorectal cancer: Evidence from animal models. Gut Microbes, 14(1), 2059812.
- Davar, D., Dzutsev, A. K., McCulloch, J. A., Rodrigues, R. R., Chauvin, J.-M., Morrison, R. M., Deblasio, R. N., Menna, C., Ding, Q., Cox, A. L., Chang, C.-W., Fernandez, K. C., Sidlow, R., & Trinchieri, G. (2021). Fecal microbiota transplant overcomes resistance to anti–PD-1 therapy in melanoma patients. Science, 371(6529), 595–602. [CrossRef]
- Obidi, N., Chukwunwejim, C. R., Ekpunobi, N. F., Obiajulu, A. C., Obidi, N. L., & Mirabelle, O. (2025). Parasitic diseases and coinfections: Unraveling the complex web of host-pathogen interactions, challenges and opportunities. IJMPR 2025, 9(6), 01-15.
- Obidi, N.O. & Ekpunobi, N. F. (2025). A narrative review exploring phage therapy as a sustainable alternative solution to combat antimicrobial resistance in Africa: Applications, challenges, and future directions. Afr. J. Clin. Exper. Microbiol. 26 (2): 106-113.
- Sunmonu, A. & Ekpunobi, N. (2023). Larvicidal potential of silver nanoparticles synthesized from Ocimum gratissimum leaf extracts against anopheles’ mosquito. GSC Biological and Pharmaceutical Sciences. 25. 41-48. [CrossRef]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).