Intratumoural Microbiota: Roles in Cancer Development, Prognosis, and Therapy
Intratumoral Microbiota: Emerging Biomarkers and Therapeutic Targets in Oncology
Abstract
Breakthroughs in sequencing technologies have overturned the notion that tumor tissues are sterile, revealing that a wide array of bacteria, fungi, and viruses—collectively known as the intratumoral microbiota—inhabit tumors across diverse cancer types. These microorganisms, which can colonize tumors via mucosal barrier disruption, adjacent tissue spread, or hematogenous routes, have emerged as critical modulators of the tumor microenvironment. Mechanistic studies demonstrate that intratumoural microbiota influence cancer biology by inducing genomic instability, altering epigenetic landscapes, promoting chronic inflammation, evading immune surveillance, and reshaping tumor metabolism. The diversity and composition of these microbial communities vary by tumor type and stage, with distinct microbial signatures linked to patient prognosis and therapeutic response. As research progresses, the intratumoural microbiota are being recognized not only as biomarkers for early cancer detection and prognosis but also as promising targets for innovative therapies, particularly in the context of immunotherapy. While challenges remain in elucidating the origins, functions, and safe manipulation of these microbes, ongoing advances hold the potential to revolutionize cancer diagnosis, prognosis, and treatment through microbiota-targeted strategies. This review summarizes the characteristics and origins of intratumoural microbiota, their prognostic significance, and their emerging applications in cancer therapy.Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, et al. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018;16(7):410-22.
Nejman D, Livyatan I, Fuks G, Gavert N, Zwang Y, Geller LT, et al. The human tumor microbiome is composed of tumor type-specific intracellular bacteria. Science. 2020;368(6494):973-80.
Cao Y, Xia H, Tan X, Shi C, Ma Y, Meng D, et al. Intratumoural microbiota: a new frontier in cancer development and therapy. Signal Transduction and Targeted Therapy. 2024;9(1):15.
Moss SF. The Clinical Evidence Linking Helicobacter pylori to Gastric Cancer. Cell Mol Gastroenterol Hepatol. 2017;3(2):183-91.
Li S, Liu J, Zheng X, Ren L, Yang Y, Li W, et al. Tumorigenic bacteria in colorectal cancer: mechanisms and treatments. Cancer Biol Med. 2021;19(2):147-62.
Liu C, Fu L, Wang Y, Yang W. Influence of the gut microbiota on immune cell interactions and cancer treatment. J Transl Med. 2024;22(1):939.
Zhang S, Huang J, Jiang Z, Tong H, Ma X, Liu Y. Tumor microbiome: roles in tumor initiation, progression, and therapy. Mol Biomed. 2025;6(1):9.
Zhang S, Huang J, Jiang Z, Tong H, Ma X, Liu Y. Tumor microbiome: roles in tumor initiation, progression, and therapy. Molecular Biomedicine. 2025;6(1):9.
Tsay JJ, Wu BG, Badri MH, Clemente JC, Shen N, Meyn P, et al. Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer. Am J Respir Crit Care Med. 2018;198(9):1188-98.
Greathouse KL, White JR, Vargas AJ, Bliskovsky VV, Beck JA, von Muhlinen N, et al. Interaction between the microbiome and TP53 in human lung cancer. Genome Biol. 2018;19(1):123.
Peters BA, Hayes RB, Goparaju C, Reid C, Pass HI, Ahn J. The Microbiome in Lung Cancer Tissue and Recurrence-Free Survival. Cancer Epidemiol Biomarkers Prev. 2019;28(4):731-40.
Gong H, Zhang S, Li Q, Zuo C, Gao X, Zheng B, et al. Gut microbiota compositional profile and serum metabolic phenotype in patients with primary open-angle glaucoma. Exp Eye Res. 2020;191:107921.
Ren Z, Li A, Jiang J, Zhou L, Yu Z, Lu H, et al. Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma. Gut. 2019;68(6):1014-23.
Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe. 2013;14(2):207-15.
Dejea CM, Fathi P, Craig JM, Boleij A, Taddese R, Geis AL, et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science. 2018;359(6375):592-7.
Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat Med. 2019;25(4):679-89.
Hannigan GD, Duhaime MB, Ruffin MTt, Koumpouras CC, Schloss PD. Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome. mBio. 2018;9(6).
Zuo T, Ng SC. The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease. Front Microbiol. 2018;9:2247.
Urbaniak C, Gloor GB, Brackstone M, Scott L, Tangney M, Reid G. The Microbiota of Breast Tissue and Its Association with Breast Cancer. Appl Environ Microbiol. 2016;82(16):5039-48.
Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. Nat Rev Microbiol. 2018;16(3):143-55.
Fu A, Yao B, Dong T, Chen Y, Yao J, Liu Y, et al. Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer. Cell. 2022;185(8):1356-72.e26.
Rao VP, Poutahidis T, Ge Z, Nambiar PR, Boussahmain C, Wang YY, et al. Innate immune inflammatory response against enteric bacteria Helicobacter hepaticus induces mammary adenocarcinoma in mice. Cancer Res. 2006;66(15):7395-400.
Mitsuhashi K, Nosho K, Sukawa Y, Matsunaga Y, Ito M, Kurihara H, et al. Association of Fusobacterium species in pancreatic cancer tissues with molecular features and prognosis. Oncotarget. 2015;6(9):7209-20.
Wei MY, Shi S, Liang C, Meng QC, Hua J, Zhang YY, et al. The microbiota and microbiome in pancreatic cancer: more influential than expected. Mol Cancer. 2019;18(1):97.
Riquelme E, Zhang Y, Zhang L, Montiel M, Zoltan M, Dong W, et al. Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes. Cell. 2019;178(4):795-806.e12.
Aykut B, Pushalkar S, Chen R, Li Q, Abengozar R, Kim JI, et al. The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL. Nature. 2019;574(7777):264-7.
Perera M, Al-Hebshi NN, Speicher DJ, Perera I, Johnson NW. Emerging role of bacteria in oral carcinogenesis: a review with special reference to perio-pathogenic bacteria. J Oral Microbiol. 2016;8:32762.
Mager DL, Haffajee AD, Devlin PM, Norris CM, Posner MR, Goodson JM. The salivary microbiota as a diagnostic indicator of oral cancer: a descriptive, non-randomized study of cancer-free and oral squamous cell carcinoma subjects. J Transl Med. 2005;3:27.
Yamashita Y, Takeshita T. The oral microbiome and human health. J Oral Sci. 2017;59(2):201-6.
Guerrero-Preston R, Godoy-Vitorino F, Jedlicka A, Rodríguez-Hilario A, González H, Bondy J, et al. 16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment. Oncotarget. 2016;7(32):51320-34.
Bučević Popović V, Šitum M, Chow CT, Chan LS, Roje B, Terzić J. The urinary microbiome associated with bladder cancer. Sci Rep. 2018;8(1):12157.
Liu F, Liu A, Lu X, Zhang Z, Xue Y, Xu J, et al. Dysbiosis signatures of the microbial profile in tissue from bladder cancer. Cancer Med. 2019;8(16):6904-14.
Banerjee S, Alwine JC, Wei Z, Tian T, Shih N, Sperling C, et al. Microbiome signatures in prostate cancer. Carcinogenesis. 2019;40(6):749-64.
Mitra A, MacIntyre DA, Marchesi JR, Lee YS, Bennett PR, Kyrgiou M. The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia: what do we know and where are we going next? Microbiome. 2016;4(1):58.
Audirac-Chalifour A, Torres-Poveda K, Bahena-Román M, Téllez-Sosa J, Martínez-Barnetche J, Cortina-Ceballos B, et al. Cervical Microbiome and Cytokine Profile at Various Stages of Cervical Cancer: A Pilot Study. PLoS One. 2016;11(4):e0153274.
Łaniewski P, Ilhan ZE, Herbst-Kralovetz MM. The microbiome and gynaecological cancer development, prevention and therapy. Nat Rev Urol. 2020;17(4):232-50.
Su ZY, Siak PY, Leong CO, Cheah SC. The role of Epstein-Barr virus in nasopharyngeal carcinoma. Front Microbiol. 2023;14:1116143.
Cavarretta I, Ferrarese R, Cazzaniga W, Saita D, Lucianò R, Ceresola ER, et al. The Microbiome of the Prostate Tumor Microenvironment. Eur Urol. 2017;72(4):625-31.
Narunsky-Haziza L, Sepich-Poore GD, Livyatan I, Asraf O, Martino C, Nejman D, et al. Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions. Cell. 2022;185(20):3789-806.e17.
Grandi N, Tramontano E. Human Endogenous Retroviruses Are Ancient Acquired Elements Still Shaping Innate Immune Responses. Front Immunol. 2018;9:2039.
Fu Y, Li J, Cai W, Huang Y, Liu X, Ma Z, et al. The emerging tumor microbe microenvironment: From delineation to multidisciplinary approach-based interventions. Acta Pharm Sin B. 2024;14(4):1560-91.
Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science. 2018;359(6371):97-103.
Baruch EN, Youngster I, Ben-Betzalel G, Ortenberg R, Lahat A, Katz L, et al. Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients. Science. 2021;371(6529):602-9.
Mafe AN, Büsselberg D. Microbiome Integrity Enhances the Efficacy and Safety of Anticancer Drug. Biomedicines. 2025;13(2).
Sammallahti H, Rezasoltani S, Pekkala S, Kokkola A, Asadzadeh Agdaei H, Azizmohammad Looha M, et al. Fecal profiling reveals a common microbial signature for pancreatic cancer in Finnish and Iranian cohorts. Gut Pathog. 2025;17(1):24.
Tanoue T, Atarashi K, Honda K. Development and maintenance of intestinal regulatory T cells. Nat Rev Immunol. 2016;16(5):295-309.
Yamamura K, Baba Y, Miyake K, Nakamura K, Shigaki H, Mima K, et al. Fusobacterium nucleatum in gastroenterological cancer: Evaluation of measurement methods using quantitative polymerase chain reaction and a literature review. Oncol Lett. 2017;14(6):6373-8.
Andrews MC, Duong CPM, Gopalakrishnan V, Iebba V, Chen WS, Derosa L, et al. Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade. Nat Med. 2021;27(8):1432-41.
Tsilimigras MC, Fodor AA. Compositional data analysis of the microbiome: fundamentals, tools, and challenges. Ann Epidemiol. 2016;26(5):330-5.
Villemin C, Six A, Neville BA, Lawley TD, Robinson MJ, Bakdash G. The heightened importance of the microbiome in cancer immunotherapy. Trends Immunol. 2023;44(1):44-59.
Lin A, Huang L, Jiang A, Zhu L, Mou W, Li Y, et al. Microbiota boost immunotherapy? A meta-analysis dives into fecal microbiota transplantation and immune checkpoint inhibitors. BMC Medicine. 2025;23(1):341.
Hadi DK, Baines KJ, Jabbarizadeh B, Miller WH, Jamal R, Ernst S, et al. Improved survival in advanced melanoma patients treated with fecal microbiota transplantation using healthy donor stool in combination with anti-PD1: final results of the MIMic phase 1 trial. J Immunother Cancer. 2025;13(8).
Zhang M, Liu J, Xia Q. Role of gut microbiome in cancer immunotherapy: from predictive biomarker to therapeutic target. Exp Hematol Oncol. 2023;12(1):84.
Faber T, Ravaud P, Riveros C, Perrodeau E, Dechartres A. Meta-analyses including non-randomized studies of therapeutic interventions: a methodological review. BMC Med Res Methodol. 2016;16:35.
Ferreira MR, Muls A, Dearnaley DP, Andreyev HJ. Microbiota and radiation-induced bowel toxicity: lessons from inflammatory bowel disease for the radiation oncologist. Lancet Oncol. 2014;15(3):e139-47.
Yu T, Guo F, Yu Y, Sun T, Ma D, Han J, et al. Fusobacterium nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy. Cell. 2017;170(3):548-63.e16.
Jiang SS, Xie YL, Xiao XY, Kang ZR, Lin XL, Zhang L, et al. Fusobacterium nucleatum-derived succinic acid induces tumor resistance to immunotherapy in colorectal cancer. Cell Host Microbe. 2023;31(5):781-97.e9.
Zeiders SM, Chmielewski J. Antibiotic-cell-penetrating peptide conjugates targeting challenging drug-resistant and intracellular pathogenic bacteria. Chem Biol Drug Des. 2021;98(5):762-78.
Aranaga C, Pantoja LD, Martínez EA, Falco A. Phage Therapy in the Era of Multidrug Resistance in Bacteria: A Systematic Review. Int J Mol Sci. 2022;23(9).
Zheng JH, Nguyen VH, Jiang SN, Park SH, Tan W, Hong SH, et al. Two-step enhanced cancer immunotherapy with engineered Salmonella typhimurium secreting heterologous flagellin. Sci Transl Med. 2017;9(376).
Fukuhara H, Ino Y, Todo T. Oncolytic virus therapy: A new era of cancer treatment at dawn. Cancer Sci. 2016;107(10):1373-9.
Helmink BA, Khan MAW, Hermann A, Gopalakrishnan V, Wargo JA. The microbiome, cancer, and cancer therapy. Nat Med. 2019;25(3):377-88.
Gurbatri CR, Lia I, Vincent R, Coker C, Castro S, Treuting PM, et al. Engineered probiotics for local tumor delivery of checkpoint blockade nanobodies. Sci Transl Med. 2020;12(530).
Duggan WP, Kisakol B, Woods I, Azimi M, Dussmann H, Fay J, et al. Spatial transcriptomic analysis reveals local effects of intratumoral fusobacterial infection on DNA damage and immune signaling in rectal cancer. Gut Microbes. 2024;16(1):2350149.
Schorr L, Mathies M, Elinav E, Puschhof J. Intracellular bacteria in cancer-prospects and debates. NPJ Biofilms Microbiomes. 2023;9(1):76.
D'Antonio DL, Zenoniani A, Umme S, Piattelli A, Curia MC. Intratumoral Fusobacterium nucleatum in Pancreatic Cancer: Current and Future Perspectives. Pathogens. 2024;14(1).
Dohlman AB, Arguijo Mendoza D, Ding S, Gao M, Dressman H, Iliev ID, et al. The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants. Cell Host Microbe. 2021;29(2):281-98.e5.
Zitvogel L, Daillère R, Roberti MP, Routy B, Kroemer G. Anticancer effects of the microbiome and its products. Nat Rev Microbiol. 2017;15(8):465-78.
Long J, Wang J, Xiao C, You F, Jiang Y, Li X. Intratumoral microbiota in colorectal cancer: focus on specific distribution and potential mechanisms. Cell Commun Signal. 2024;22(1):455.
Wang N, Wu S, Huang L, Hu Y, He X, He J, et al. Intratumoral microbiome: implications for immune modulation and innovative therapeutic strategies in cancer. J Biomed Sci. 2025;32(1):23.
Ma C, Han M, Heinrich B, Fu Q, Zhang Q, Sandhu M, et al. Gut microbiome-mediated bile acid metabolism regulates liver cancer via NKT cells. Science. 2018;360(6391).
Fong W, Li Q, Yu J. Gut microbiota modulation: a novel strategy for prevention and treatment of colorectal cancer. Oncogene. 2020;39(26):4925-43.
Zheng DW, Dong X, Pan P, Chen KW, Fan JX, Cheng SX, et al. Phage-guided modulation of the gut microbiota of mouse models of colorectal cancer augments their responses to chemotherapy. Nat Biomed Eng. 2019;3(9):717-28.
Bernardes N, Seruca R, Chakrabarty AM, Fialho AM. Microbial-based therapy of cancer: current progress and future prospects. Bioeng Bugs. 2010;1(3):178-90.
| Files | ||
| Issue | Vol 16 No 4 (2024) | |
| Section | Reviews | |
| Keywords | ||
| Intratumoral microbiota Tumor microenvironment Cancer progression Microbial biomarkers Immunotherapy Microbiome-based therapy | ||
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