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  • Review Article
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Harnessing the microbiome for cancer therapy

Abstract

The microbiome is increasingly recognized as a key player in cancer pathogenesis and treatment response, acting through both local and systemic mechanisms. Microbial communities and their metabolites can directly influence drug metabolism, shape the immune landscape, and alter transcriptional and epigenetic programmes in the gut, systemically and in the tumour microenvironment. Emerging data support the potential of microbiome-targeted interventions (such as faecal microbiota transplantation, diet, prebiotics and probiotics) as adjuncts to conventional cancer therapies, with the goal of enhancing efficacy and reducing toxicity. This Review highlights the promise of the microbiome as a prognostic and predictive biomarker, a modifiable factor in cancer care and prevention, and a therapeutic target. We also discuss major knowledge gaps, limitations in current study designs, and the need for mechanism-guided, personalized strategies to advance clinical translation.

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Fig. 1: Mechanisms underlying microbiome-driven cancer pathogenesis.
Fig. 2: Progressive degradation of microbiome health might contribute to cancer development across the human lifespan.
Fig. 3: Microorganism-mediated mechanisms that affect cancer treatment outcomes.
Fig. 4: Conceptual framework for AI-driven precision oncology using multi-omics integration.

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References

  1. McCallum, G. & Tropini, C. The gut microbiota and its biogeography. Nat. Rev. Microbiol. 22, 105–118 (2024).

    Article  CAS  PubMed  Google Scholar 

  2. Verdegaal, A. A. & Goodman, A. L. Integrating the gut microbiome and pharmacology. Sci. Transl. Med. 16, eadg8357 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Yang, L., Li, A., Wang, Y. & Zhang, Y. Intratumoral microbiota: roles in cancer initiation, development and therapeutic efficacy. Signal Transduct. Target. Ther. 8, 35 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Domzaridou, E. et al. The impact of oral antibiotics prior to cancer diagnosis on overall patient survival: findings from an English population-based cohort study. Curr. Oncol. 30, 8434–8443 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Yuan, L. et al. The influence of gut microbiota dysbiosis to the efficacy of 5-fluorouracil treatment on colorectal cancer. Biomed. Pharmacother. 108, 184–193 (2018).

    Article  CAS  PubMed  Google Scholar 

  6. Routy, B. et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 359, 91–97 (2018). This groundbreaking translational study demonstrates that the microbiome can enhance the efficacy of ICIs by modulating antitumour immune responses in both human cohorts and animal models.

    Article  CAS  PubMed  Google Scholar 

  7. Elkrief, A. et al. Antibiotics are associated with worse outcomes in lung cancer patients treated with chemotherapy and immunotherapy. NPJ Precis. Oncol. 8, 143 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Ransohoff, J. D. et al. Antimicrobial exposure is associated with decreased survival in triple-negative breast cancer. Nat. Commun. 14, 2053 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Cong, J. et al. Bile acids modified by the intestinal microbiota promote colorectal cancer growth by suppressing CD8+ T cell effector functions. Immunity 57, 876–889.e11 (2024).

    Article  CAS  PubMed  Google Scholar 

  10. Tintelnot, J. et al. Microbiota-derived 3-IAA influences chemotherapy efficacy in pancreatic cancer. Nature 615, 168–174 (2023). Using human cohorts and animal models, this translational study uncovers a microbial metabolite that might enhance treatment outcomes for notoriously difficult-to-treat pancreatic cancer.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Bender, M. J. et al. Dietary tryptophan metabolite released by intratumoral Lactobacillus reuteri facilitates immune checkpoint inhibitor treatment. Cell 186, 1846–1862.e26 (2023). This mechanistic preclinical study unveils how a conventional probiotic translocates to melanoma tumours and promotes antitumour immunity through production of the tryptophan catabolite indole-3-aldehyde.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Salminen, S. et al. The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics. Nat. Rev. Gastroenterol. Hepatol. 18, 649–667 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Battaglia, T. W. et al. A pan-cancer analysis of the microbiome in metastatic cancer. Cell 187, 2324–2335.e19 (2024). This is a large exploration of human metastatic tumour biopsy-associated bacteria using metagenomics, genomics and transcriptomics and their association with immune infiltration and resistance to therapy.

    Article  CAS  PubMed  Google Scholar 

  14. Ghaddar, B. et al. Tumor microbiome links cellular programs and immunity in pancreatic cancer. Cancer Cell 40, 1240–1253.e5 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Riquelme, E. et al. Tumor microbiome diversity and composition influence pancreatic cancer outcomes. Cell 178, 795–806.e12 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Nejman, D. et al. The human tumor microbiome is composed of tumor type-specific intracellular bacteria. Science 368, 973–980 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Perez Escriva, P., Correia Tavares Bernardino, C. & Letellier, E. De-coding the complex role of microbial metabolites in cancer. Cell Rep. 44, 115358 (2025).

    Article  CAS  PubMed  Google Scholar 

  18. El Tekle, G. & Garrett, W. S. Bacteria in cancer initiation, promotion and progression. Nat. Rev. Cancer 23, 600–618 (2023).

    Article  CAS  PubMed  Google Scholar 

  19. Narunsky-Haziza, L. et al. Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions. Cell 185, 3789–3806.e17 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Dohlman, A. B., Pan, X., Zitvogel, L. & Iliev, I. D. The multi-kingdom cancer microbiome. Nat. Microbiol. 10, 2369–2383 (2025).

    Article  CAS  PubMed  Google Scholar 

  21. Chagneau, C. V. et al. Uropathogenic E. coli induces DNA damage in the bladder. PLoS Pathog. 17, e1009310 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Dejea, C. M. et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science 359, 592–597 (2018). This study demonstrates that colonic biofilms of some patients with cancer often contain E. coli (producing colibactin) and enterotoxigenic. B. fragilis (producing BFT), whose genotoxins synergistically induce DNA damage and promote colorectal tumorigenesis in animal models.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Greathouse, K. L. et al. Interaction between the microbiome and TP53 in human lung cancer. Genome Biol. 19, 123 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  24. Cullin, N., Azevedo Antunes, C., Straussman, R., Stein-Thoeringer, C. K. & Elinav, E. Microbiome and cancer. Cancer Cell 39, 1317–1341 (2021).

    Article  CAS  PubMed  Google Scholar 

  25. Shrestha, E. et al. Oncogenic gene fusions in nonneoplastic precursors as evidence that bacterial infection can initiate prostate cancer. Proc. Natl Acad. Sci. USA 118, e2018976118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Maklin, T. et al. Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli. Lancet Microbe 6, 101015 (2025).

    Article  PubMed  Google Scholar 

  27. Kienesberger, S. et al. Enterotoxin tilimycin from gut-resident Klebsiella promotes mutational evolution and antibiotic resistance in mice. Nat. Microbiol. 7, 1834–1848 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Unterhauser, K. et al. Klebsiella oxytoca enterotoxins tilimycin and tilivalline have distinct host DNA-damaging and microtubule-stabilizing activities. Proc. Natl Acad. Sci. USA 116, 3774–3783 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Diaz-Gay, M. et al. Geographic and age variations in mutational processes in colorectal cancer. Nature https://doi.org/10.1038/s41586-025-09025-8 (2025). This study reports how mutational patterns in colorectal cancer vary by geographical and age variations, and it also highlights the role of colibactin in early-onset colorectal cancer.

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Oliero, M. et al. Prevalence of pks + bacteria and enterotoxigenic Bacteroides fragilis in patients with colorectal cancer. Gut Pathog. 14, 51 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Pleguezuelos-Manzano, C. et al. Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli. Nature 580, 269–273 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Rosendahl Huber, A. et al. Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer. Cancer Cell 42, 487–496.e6 (2024).

    Article  CAS  PubMed  Google Scholar 

  35. Uemura, N. et al. Helicobacter pylori infection and the development of gastric cancer. N. Engl. J. Med. 345, 784–789 (2001).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  37. Niwa, T. et al. Inflammatory processes triggered by Helicobacter pylori infection cause aberrant DNA methylation in gastric epithelial cells. Cancer Res. 70, 1430–1440 (2010).

    Article  CAS  PubMed  Google Scholar 

  38. Wiklund, A. K. et al. Risk of gastric adenocarcinoma after eradication of Helicobacter pylori. Gastroenterology 169, 244–250.e1 (2025).

    Article  CAS  PubMed  Google Scholar 

  39. Jung, Y. S., Tran, M. T. X., Park, B. & Moon, C. M. Preventive effect of Helicobacter pylori treatment on gastric cancer incidence and mortality: a Korean population study. Gastroenterology 169, 251–260.e4 (2025).

    Article  CAS  PubMed  Google Scholar 

  40. Galeano Nino, J. L. et al. Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer. Nature 611, 810–817 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  41. Zepeda-Rivera, M. et al. A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche. Nature 628, 424–432 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Zhou, R. W., Harpaz, N., Itzkowitz, S. H. & Parsons, R. E. Molecular mechanisms in colitis-associated colorectal cancer. Oncogenesis 12, 48 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Hajjar, R. et al. Basal levels of microbiota-driven subclinical inflammation are associated with anastomotic leak in patients with colorectal cancer. Gut 73, 1031–1033 (2024).

    Article  CAS  PubMed  Google Scholar 

  44. Hajjar, R. et al. Gut microbiota influence anastomotic healing in colorectal cancer surgery through modulation of mucosal proinflammatory cytokines. Gut 72, 1143–1154 (2023). This translational study shows how the gut microbiota modulates mucosal pro-inflammatory cytokines and, thereby, influences anastomotic healing after colorectal cancer surgery.

    Article  CAS  PubMed  Google Scholar 

  45. Hajjar, R. et al. Modulating gut microbiota prevents anastomotic leak to reduce local implantation and dissemination of colorectal cancer cells after surgery. Clin. Cancer Res. 30, 616–628 (2024).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Fu, K. et al. Streptococcus anginosus promotes gastric inflammation, atrophy, and tumorigenesis in mice. Cell 187, 882–896.e17 (2024).

    Article  CAS  PubMed  Google Scholar 

  48. Inaba, Y. et al. Expression of the antimicrobial peptide α-defensin/cryptdins in intestinal crypts decreases at the initial phase of intestinal inflammation in a model of inflammatory bowel disease, IL-10-deficient mice. Inflamm. Bowel Dis. 16, 1488–1495 (2010).

    Article  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Hajjar, R., Richard, C. & Santos, M. M. The gut barrier as a gatekeeper in colorectal cancer treatment. Oncotarget 15, 562–572 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  51. Li, D. K. et al. Inhibition of microbial deconjugation of micellar bile acids protects against intestinal permeability and liver injury. Sci. Adv. 8, eabo2794 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Rahal, Z. et al. Inflammation mediated by gut microbiome alterations promotes lung cancer development and an immunosuppressed tumor microenvironment. Cancer Immunol. Res. 12, 1736–1752 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Zhang, Q. et al. Gut microbiome directs hepatocytes to recruit MDSCs and promote cholangiocarcinoma. Cancer Discov. 11, 1248–1267 (2021).

    Article  CAS  PubMed  Google Scholar 

  54. Hajjar, R., Richard, C. S. & Santos, M. M. The role of butyrate in surgical and oncological outcomes in colorectal cancer. Am. J. Physiol. Gastrointest. Liver Physiol. 320, G601–G608 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Yang, L. et al. Dietary folate and cofactors accelerate age-dependent p16 epimutation to promote intestinal tumorigenesis. Cancer Res. Commun. 4, 164–169 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Qin, Y. et al. An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression. Genome Biol. 19, 7 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  57. 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, e0105522 (2022).

    Article  PubMed  Google Scholar 

  58. DeStefano Shields, C. E. et al. Bacterial-driven inflammation and mutant BRAF expression combine to promote murine colon tumorigenesis that is sensitive to immune checkpoint therapy. Cancer Discov. 11, 1792–1807 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  59. Yang, Y. et al. Fusobacterium nucleatum increases proliferation of colorectal cancer cells and tumor development in mice by activating Toll-like receptor 4 signaling to nuclear factor-κB, and up-regulating expression of microRNA-21. Gastroenterology 152, 851–866.e24 (2017).

    Article  CAS  PubMed  Google Scholar 

  60. Ansari, I. et al. The microbiota programs DNA methylation to control intestinal homeostasis and inflammation. Nat. Microbiol. 5, 610–619 (2020).

    Article  CAS  PubMed  Google Scholar 

  61. Korpela, K. et al. Selective maternal seeding and environment shape the human gut microbiome. Genome Res. 28, 561–568 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Nunez, H. et al. Early life gut microbiome and its impact on childhood health and chronic conditions. Gut Microbes 17, 2463567 (2025).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Reyman, M. et al. Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial. Nat. Commun. 13, 893 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Blaser, M. J. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat. Rev. Immunol. 17, 461–463 (2017).

    Article  CAS  PubMed  Google Scholar 

  65. Lam, K. C. et al. Microbiota triggers STING-type I IFN-dependent monocyte reprogramming of the tumor microenvironment. Cell 184, 5338–5356.e21 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Vatanen, T. et al. The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature 562, 589–594 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Agrawal, M. et al. Early life exposures and the risk of inflammatory bowel disease: systematic review and meta-analyses. eClinicalMedicine 36, 100884 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  68. Peppas, I., Ford, A. M., Furness, C. L. & Greaves, M. F. Gut microbiome immaturity and childhood acute lymphoblastic leukaemia. Nat. Rev. Cancer 23, 565–576 (2023).

    Article  CAS  PubMed  Google Scholar 

  69. 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, 1971–1978 (2019).

    Article  CAS  PubMed  Google Scholar 

  70. 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, 38–46 (2022).

    Article  PubMed  Google Scholar 

  71. Zimmermann, M., Zimmermann-Kogadeeva, M., Wegmann, R. & Goodman, A. L. Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature 570, 462–467 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Klunemann, M. et al. Bioaccumulation of therapeutic drugs by human gut bacteria. Nature 597, 533–538 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  73. Spanogiannopoulos, P. et al. Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism. Nat. Microbiol. 7, 1605–1620 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Liu, D. et al. Anaerostipes hadrus, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil. mSphere 9, e0081623 (2024).

    Article  PubMed  Google Scholar 

  75. Javdan, B. et al. Personalized mapping of drug metabolism by the human gut microbiome. Cell 181, 1661–1679.e22 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Geller, L. T. et al. Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Science 357, 1156–1160 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Trepka, K. R. et al. Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity. Sci. Transl. Med. 17, eadq8870 (2025).

    Article  CAS  PubMed  Google Scholar 

  78. Wallace, B. D. et al. Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. Science 330, 831–835 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. LaCourse, K. D. et al. The cancer chemotherapeutic 5-fluorouracil is a potent Fusobacterium nucleatum inhibitor and its activity is modified by intratumoral microbiota. Cell Rep. 41, 111625 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. McQuade, R. M., Al Thaalibi, M. & Nurgali, K. Impact of chemotherapy-induced enteric nervous system toxicity on gastrointestinal mucositis. Curr. Opin. Support. Palliat. Care 14, 293–300 (2020).

    Article  PubMed  Google Scholar 

  81. Xie, M., Li, X., Lau, H. C. & Yu, J. The gut microbiota in cancer immunity and immunotherapy. Cell Mol. Immunol. 22, 1012–1031 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Sharma, P. et al. Immune checkpoint therapy — current perspectives and future directions. Cell 186, 1652–1669 (2023).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  84. Sharma, P. & Allison, J. P. The future of immune checkpoint therapy. Science 348, 56–61 (2015).

    Article  CAS  PubMed  Google Scholar 

  85. Matson, V. et al. The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science 359, 104–108 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Gopalakrishnan, V. et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science 359, 97–103 (2018).

    Article  CAS  PubMed  Google Scholar 

  87. Derosa, L. et al. Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer. Nat. Med. 28, 315–324 (2022). This study combines human and mouse evidence, demonstrating that intermediate (but not low or high) levels of A. muciniphila enhance PD1 blockade efficacy via promotion of T cell-mediated antitumour immunity.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Gunjur, A. et al. A gut microbial signature for combination immune checkpoint blockade across cancer types. Nat. Med. 30, 797–809 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Sivan, A. et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 350, 1084–1089 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Derosa, L. et al. Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome. Cell 187, 3373–3389.e16 (2024).

    Article  CAS  PubMed  Google Scholar 

  91. Mager, L. F. et al. Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy. Science 369, 1481–1489 (2020).

    Article  CAS  PubMed  Google Scholar 

  92. Griffin, M. E. et al. Enterococcus peptidoglycan remodeling promotes checkpoint inhibitor cancer immunotherapy. Science 373, 1040–1046 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. He, Y. et al. Gut microbial metabolites facilitate anticancer therapy efficacy by modulating cytotoxic CD8+ T cell immunity. Cell Metab. 33, 988–1000.e7 (2021).

    Article  CAS  PubMed  Google Scholar 

  94. Zhu, X. et al. Microbial metabolite butyrate promotes anti-PD-1 antitumor efficacy by modulating T cell receptor signaling of cytotoxic CD8 T cell. Gut Microbes 15, 2249143 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  95. Luu, M. et al. Microbial short-chain fatty acids modulate CD8+ T cell responses and improve adoptive immunotherapy for cancer. Nat. Commun. 12, 4077 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. He, L. et al. Gut microbiota-derived butyrate restores impaired regulatory T cells in patients with AChR myasthenia gravis via mTOR-mediated autophagy. Cell Commun. Signal. 22, 215 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Coutzac, C. et al. Systemic short chain fatty acids limit antitumor effect of CTLA-4 blockade in hosts with cancer. Nat. Commun. 11, 2168 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Xiong, Z. et al. Targeting PPAR-gamma counteracts tumour adaptation to immune-checkpoint blockade in hepatocellular carcinoma. Gut 72, 1758–1773 (2023).

    Article  CAS  PubMed  Google Scholar 

  99. Damotte, D. et al. The tumor inflammation signature (TIS) is associated with anti-PD-1 treatment benefit in the CERTIM pan-cancer cohort. J. Transl. Med. 17, 357 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  100. Sui, Q. et al. Inflammation promotes resistance to immune checkpoint inhibitors in high microsatellite instability colorectal cancer. Nat. Commun. 13, 7316 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Huang, J. et al. Ginseng polysaccharides alter the gut microbiota and kynurenine/tryptophan ratio, potentiating the antitumour effect of antiprogrammed cell death 1/programmed cell death ligand 1 (anti-PD-1/PD-L1) immunotherapy. Gut 71, 734–745 (2022).

    Article  CAS  PubMed  Google Scholar 

  102. Qin, R. et al. Tryptophan potentiates CD8+ T cells against cancer cells by TRIP12 tryptophanylation and surface PD-1 downregulation. J. Immunother. Cancer 9, e002840 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  103. Jia, D. et al. Microbial metabolite enhances immunotherapy efficacy by modulating T cell stemness in pan-cancer. Cell 187, 1651–1665.e21 (2024). This preclinical study demonstrates that the gut microbial metabolite indole-3-propionic acid broadly enhanced the effectiveness of immune checkpoint blockade across diverse cancer types by epigenetically programming CD8+ T cells into a stem-like, therapeutically responsive state.

    Article  CAS  PubMed  Google Scholar 

  104. Alves Costa Silva, C. et al. Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial. Nat. Commun. 15, 1633 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Uribe-Herranz, M. et al. Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12. JCI Insight 3, e94952 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  106. Smith, M. et al. Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy. Nat. Med. 28, 713–723 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Marcos-Kovandzic, L. et al. Gut microbiota modulation through Akkermansia spp. supplementation increases CAR T-cell potency. Cancer Discov. 15, 1905–1926 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Khuat, L. T., Dave, M. & Murphy, W. J. The emerging roles of the gut microbiome in allogeneic hematopoietic stem cell transplantation. Gut Microbes 13, 1966262 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  109. Chen, J., Deutsch, E., Kroemer, G., Galluzzi, L. & Zitvogel, L. The microbiota in radiotherapy-induced cancer immunosurveillance. Nat. Rev. Clin. Oncol. 22, 667–679 (2025).

    Article  PubMed  Google Scholar 

  110. Ji, M. et al. Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota. Nat. Metab. 5, 1526–1543 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Oh, M. H. et al. Targeting glutamine metabolism enhances tumor-specific immunity by modulating suppressive myeloid cells. J. Clin. Invest. 130, 3865–3884 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Cuisiniere, T. et al. Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model. Microbiome 13, 100 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Westdorp, H. et al. Mechanisms of immune checkpoint inhibitor-mediated colitis. Front. Immunol. 12, 768957 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Gao, Y. Q., Tan, Y. J. & Fang, J. Y. Roles of the gut microbiota in immune-related adverse events: mechanisms and therapeutic intervention. Nat. Rev. Clin. Oncol. 22, 499–516 (2025).

    Article  PubMed  Google Scholar 

  115. Andrews, M. C. et al. Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade. Nat. Med. 27, 1432–1441 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Hu, M. et al. Gut microbiome for predicting immune checkpoint blockade-associated adverse events. Genome Med. 16, 16 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Liu, W. et al. Intestinal microbiome associated with immune-related adverse events for patients treated with anti-PD-1 inhibitors, a real-world study. Front. Immunol. 12, 756872 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Dubin, K. et al. Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nat. Commun. 7, 10391 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Cascone, T. et al. Neoadjuvant nivolumab or nivolumab plus ipilimumab in operable non-small cell lung cancer: the phase 2 randomized NEOSTAR trial. Nat. Med. 27, 504–514 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. McCulloch, J. A. et al. Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1. Nat. Med. 28, 545–556 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Bjork, J. R. et al. Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma. Nat. Med. 30, 785–796 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Lo, J. W. et al. Immune checkpoint inhibitor-induced colitis is mediated by polyfunctional lymphocytes and is dependent on an IL23/IFNγ axis. Nat. Commun. 14, 6719 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Lo, B. C. et al. Microbiota-dependent activation of CD4+ T cells induces CTLA-4 blockade-associated colitis via Fcγ receptors. Science 383, 62–70 (2024). This study introduces a preclinical model for ICI-colitis by colonizing mice with wild rodent gut microbiota, which enabled robust development of CTLA4 blockade-associated colitis.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Gao, Y. et al. Faecalibacterium prausnitzii abrogates intestinal toxicity and promotes tumor immunity to increase the efficacy of dual CTLA4 and PD-1 checkpoint blockade. Cancer Res. 83, 3710–3725 (2023).

    Article  CAS  PubMed  Google Scholar 

  125. Wang, T. et al. Probiotics Lactobacillus reuteri abrogates immune checkpoint blockade-associated colitis by inhibiting group 3 innate lymphoid cells. Front. Immunol. 10, 1235 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Yi, Y. et al. Gut microbiome components predict response to neoadjuvant chemoradiotherapy in patients with locally advanced rectal cancer: a prospective, longitudinal study. Clin. Cancer Res. 27, 1329–1340 (2021).

    Article  CAS  PubMed  Google Scholar 

  127. Shaikh, F. Y. et al. Fecal microbiome composition correlates with pathologic complete response in patients with operable esophageal cancer treated with combined chemoradiotherapy and immunotherapy. Cancers 16, 3644 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Viaud, S. et al. The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science 342, 971–976 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Vatanen, T. et al. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165, 842–853 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Sulit, A. K. et al. Bacterial lipopolysaccharide modulates immune response in the colorectal tumor microenvironment. NPJ Biofilms Microbiomes 9, 59 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Hu, Y. et al. CAR-T cell therapy-related cytokine release syndrome and therapeutic response is modulated by the gut microbiome in hematologic malignancies. Nat. Commun. 13, 5313 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Fertitta, V. et al. Akkermansia muciniphila- and pathogenic bacteria-derived endotoxins differently regulate human dendritic cell generation and γδ T lymphocyte activation. Biomolecules 14, 1571 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Roberti, M. P. et al. Chemotherapy-induced ileal crypt apoptosis and the ileal microbiome shape immunosurveillance and prognosis of proximal colon cancer. Nat. Med. 26, 919–931 (2020).

    Article  CAS  PubMed  Google Scholar 

  134. Louie, T. et al. VE303, a defined bacterial consortium, for prevention of recurrent Clostridioides difficile infection: a randomized clinical trial. JAMA 329, 1356–1366 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  136. Kurt, F. et al. Co-cultivation is a powerful approach to produce a robust functionally designed synthetic consortium as a live biotherapeutic product (LBP). Gut Microbes 15, 2177486 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  137. Menon, R. et al. Multi-omic profiling a defined bacterial consortium for treatment of recurrent Clostridioides difficile infection. Nat. Med. 31, 223–234 (2025).

    Article  CAS  PubMed  Google Scholar 

  138. Kang, Z. et al. A polyvalent vaccine for selectively killing tumor-associated bacteria to prevent cancer metastasis. Sci. Adv. 11, eadt0341 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Diamantis, S. et al. The production of antibiotics must be reoriented: repositioning old narrow-spectrum antibiotics, developing new microbiome-sparing antibiotics. Antibiotics 11, 924 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Ritz, N. L. et al. The gut virome is associated with stress-induced changes in behaviour and immune responses in mice. Nat. Microbiol. 9, 359–376 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  141. Zechner, E. L. & Kienesberger, S. Microbiota-derived small molecule genotoxins: host interactions and ecological impact in the gut ecosystem. Gut Microbes 16, 2430423 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  142. Bossuet-Greif, N. et al. Escherichia coli ClbS is a colibactin resistance protein. Mol. Microbiol. 99, 897–908 (2016).

    Article  CAS  PubMed  Google Scholar 

  143. Tripathi, P. et al. ClbS is a cyclopropane hydrolase that confers colibactin resistance. J. Am. Chem. Soc. 139, 17719–17722 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Oliero, M. et al. Putrescine supplementation limits the expansion of pks+ Escherichia coli and tumor development in the colon. Cancer Res. Commun. 4, 1777–1792 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Ledala, N. et al. Bacterial indole as a multifunctional regulator of Klebsiella oxytoca complex enterotoxicity. mBio 13, e0375221 (2022).

    Article  PubMed  Google Scholar 

  146. Volpe, M. R. et al. A small molecule inhibitor prevents gut bacterial genotoxin production. Nat. Chem. Biol. 19, 159–167 (2023).

    Article  CAS  PubMed  Google Scholar 

  147. Lopez-Romero, D. et al. Evidence of some natural products with antigenotoxic effects. Part 2: plants, vegetables, and natural resin. Nutrients 10, 1954 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  148. Chou, P. J. et al. Epigenetics of dietary phytochemicals in cancer prevention: fact or fiction. Cancer J. 30, 320–328 (2024).

    Article  PubMed  Google Scholar 

  149. Yin, Q. et al. Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations. Nat. Microbiol. 10, 541–553 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Hecht, A. L. et al. Dietary carbohydrates regulate intestinal colonization and dissemination of Klebsiella pneumoniae. J. Clin. Invest. 134, e174726 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Thakur, B. K. et al. Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer. Nat. Microbiol. 10, 855–870 (2025).

    Article  CAS  PubMed  Google Scholar 

  152. Furuichi, M. et al. Commensal consortia decolonize Enterobacteriaceae via ecological control. Nature 633, 878–886 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Jacobs, J. P. et al. Human milk oligosaccharides modulate the intestinal microbiome of healthy adults. Sci. Rep. 13, 14308 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Ervin, S. M. et al. Targeting regorafenib-induced toxicity through inhibition of gut microbial β-glucuronidases. ACS Chem. Biol. 14, 2737–2744 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Chamseddine, A. N. et al. Intestinal bacterial β-glucuronidase as a possible predictive biomarker of irinotecan-induced diarrhea severity. Pharmacol. Ther. 199, 1–15 (2019).

    Article  CAS  PubMed  Google Scholar 

  156. Ianiro, G. et al. Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma. Nat. Commun. 11, 4333 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  157. Mego, M. et al. Prevention of irinotecan induced diarrhea by probiotics: a randomized double blind, placebo controlled pilot study. Complement. Ther. Med. 23, 356–362 (2015).

    Article  PubMed  Google Scholar 

  158. Davar, D. et al. Fecal microbiota transplant overcomes resistance to anti-PD-1 therapy in melanoma patients. Science 371, 595–602 (2021). This phase I clinical trial demonstrates that FMT from anti-PD1 responders might overcome resistance to anti-PD1 therapy in patients with melanoma who had not responded to ICIs previously.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  160. Routy, B. et al. Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial. Nat. Med. 29, 2121–2132 (2023).

    Article  CAS  PubMed  Google Scholar 

  161. Ciccarese, C. et al. LBA77 fecal microbiota transplantation (FMT) versus placebo in patients receiving pembrolizumab plus axitinib for metastatic renal cell carcinoma: preliminary results of the randomized phase II TACITO trial. Ann. Oncol. 35, 51264 (2024).

    Article  Google Scholar 

  162. Wang, Y. et al. Fecal microbiota transplantation for refractory immune checkpoint inhibitor-associated colitis. Nat. Med. 24, 1804–1808 (2018). This pilot study shows that FMT can be efficient in alleviating ICI-associated colitis.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Duttagupta, S. et al. Microbiome profiling reveals that fecal microbiota transplantation (FMT) modulates response and toxicity when combined with immunotherapy in patients with lung cancer and melanoma (FMT-LUMINate NCT04951583). Cancer Res. 85, abstr. 2210 (2025).

    Article  Google Scholar 

  164. Spencer, C. N. et al. Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response. Science 374, 1632–1640 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  165. Zhang, X. et al. Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial. eBioMedicine 98, 104873 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Farias, R. M. et al. Diet and Immune Effects Trial (DIET) — a randomized, double-blinded dietary intervention study in patients with melanoma receiving immunotherapy. BMC Cancer 24, 1493 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  167. Jiang, Y. et al. The DIET study: a randomized controlled trial of a high fiber diet intervention (HFDI) in patients (pts) with melanoma receiving immune checkpoint blockade (ICB). J. Clin. Oncol. https://doi.org/10.1200/JCO.2024.42.16_suppl.9558 (2024).

  168. Ferrere, G. et al. Ketogenic diet and ketone bodies enhance the anticancer effects of PD-1 blockade. JCI Insight 6, e145207 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  169. Plamada, D. & Vodnar, D. C. Polyphenols–gut microbiota interrelationship: a transition to a new generation of prebiotics. Nutrients 14, 137 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  170. Messaoudene, M. et al. A natural polyphenol exerts antitumor activity and circumvents anti-PD-1 resistance through effects on the gut microbiota. Cancer Discov. 12, 1070–1087 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Giampazolias, E. et al. Vitamin D regulates microbiome-dependent cancer immunity. Science 384, 428–437 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Qureshi, Z., Jamil, A., Altaf, F. & Siddique, R. Efficacy and safety of probiotics as adjunctive therapy in cancer treatment: a comprehensive systematic review and meta-analysis. Am. J. Clin. Oncol. 48, 148–161 (2025).

    Article  CAS  PubMed  Google Scholar 

  173. Liu, Y. C., Wu, C. R. & Huang, T. W. Preventive effect of probiotics on oral mucositis induced by cancer treatment: a systematic review and meta-analysis. Int. J. Mol. Sci. 23, 13268 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  174. Han, Y., Wang, Y. & Guan, M. Preventive effect of probiotics on infections following colorectal cancer surgery: an umbrella meta-analysis. World J. Gastrointest. Surg. 16, 3546–3558 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  175. Zhao, S. et al. Assessing the impact of probiotics on immunotherapy effectiveness and antibiotic-mediated resistance in cancer: a systematic review and meta-analysis. Front. Immunol. 16, 1538969 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  176. Fong, W. et al. Lactobacillus gallinarum-derived metabolites boost anti-PD1 efficacy in colorectal cancer by inhibiting regulatory T cells through modulating IDO1/Kyn/AHR axis. Gut 72, 2272–2285 (2023).

    Article  CAS  PubMed  Google Scholar 

  177. Redenti, A. et al. Probiotic neoantigen delivery vectors for precision cancer immunotherapy. Nature 635, 453–461 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  178. Kwon, S. Y., Thi-Thu Ngo, H., Son, J., Hong, Y. & Min, J. J. Exploiting bacteria for cancer immunotherapy. Nat. Rev. Clin. Oncol. 21, 569–589 (2024).

    Article  PubMed  Google Scholar 

  179. Canale, F. P. et al. Metabolic modulation of tumours with engineered bacteria for immunotherapy. Nature 598, 662–666 (2021). This preclinical study reports that engineered probiotic bacteria that convert intratumoural ammonia into l-arginine can locally boost cytotoxic T cell immunity and amplify checkpoint therapy effects.

    Article  CAS  PubMed  Google Scholar 

  180. Geiger, R. et al. L-Arginine modulates T cell metabolism and enhances survival and anti-tumor activity. Cell 167, 829–842.e13 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  181. Zhao, H. et al. Inosine enhances the efficacy of immune-checkpoint inhibitors in advanced solid tumors: a randomized, controlled, phase 2 study. Cancer Med. 13, e70143 (2024). Building on an earlier preclinical work on gut-derived inosine, this rare phase II randomized clinical trial has found that oral supplementation of inosine significantly enhanced ICI efficacy in patients with solid tumours.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Talpin, A. et al. Mimicry-based strategy between human and commensal antigens for the development of a new family of immune therapies for cancer. J. Immunother. Cancer 13, e010192 (2025).

    Article  PubMed  PubMed Central  Google Scholar 

  183. Courneya, K. S. et al. Structured exercise after adjuvant chemotherapy for colon cancer. N. Engl. J. Med. 393, 13–25 (2025).

    Article  CAS  PubMed  Google Scholar 

  184. Phelps, C. M. et al. Exercise-induced microbiota metabolite enhances CD8 T cell antitumor immunity promoting immunotherapy efficacy. Cell https://doi.org/10.1016/j.cell.2025.06.018 (2025).

    Article  PubMed  Google Scholar 

  185. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Tito, R. Y. et al. Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development. Nat. Med. 30, 1339–1348 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  188. Fierer, N. et al. Guidelines for preventing and reporting contamination in low-biomass microbiome studies. Nat. Microbiol. 10, 1570–1580 (2025).

    Article  CAS  PubMed  Google Scholar 

  189. Gihawi, A. et al. Major data analysis errors invalidate cancer microbiome findings. mBio 14, e0160723 (2023).

    Article  PubMed  Google Scholar 

  190. Austin, G. I. & Korem, T. Compositional transformations can reasonably introduce phenotype-associated values into sparse features. mSystems 10, e0002125 (2025).

    Article  PubMed  Google Scholar 

  191. Sepich-Poore, G. D. et al. Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 43, 1127–1148 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Ge, Y., Lu, J., Puiu, D., Revsine, M. & Salzberg, S. L. Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project. Sci. Transl. Med. 17, eads6335 (2025).

    Article  CAS  PubMed  Google Scholar 

  193. Chang, D. et al. Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles. Nat. Commun. 15, 7447 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  194. Wu, G. et al. A core microbiome signature as an indicator of health. Cell 187, 6550–6565.e11 (2024).

    Article  CAS  PubMed  Google Scholar 

  195. Yonekura, S. et al. Cancer induces a stress ileopathy depending on β-adrenergic receptors and promoting dysbiosis that contributes to carcinogenesis. Cancer Discov. 12, 1128–1151 (2022). This translational study proposes that many cancers could have a shared effect on the gut microbiome, which might then act as a modulator of subsequent disease course.

    Article  CAS  PubMed  Google Scholar 

  196. Kartal, E. et al. A faecal microbiota signature with high specificity for pancreatic cancer. Gut 71, 1359–1372 (2022). This research shows an example of a high-quality faecal microbiota classifier that has been developed to detect pancreatic cancer and has been validated across multiple independent cohorts and external datasets.

    Article  CAS  PubMed  Google Scholar 

  197. Simpson, R. C. et al. Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome. Nat. Med. 28, 2344–2352 (2022).

    Article  CAS  PubMed  Google Scholar 

  198. Glitza, I. C. et al. Randomized placebo-controlled, biomarker-stratified phase Ib microbiome modulation in melanoma: impact of antibiotic preconditioning on microbiome and immunity. Cancer Discov. 14, 1161–1175 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. Yin, Q. et al. Immune-related adverse events of immune checkpoint inhibitors: a review. Front. Immunol. 14, 1167975 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Wu, G., Zhao, N., Zhang, C., Lam, Y. Y. & Zhao, L. Guild-based analysis for understanding gut microbiome in human health and diseases. Genome Med. 13, 22 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  201. Muller, E., Shiryan, I. & Borenstein, E. Multi-omic integration of microbiome data for identifying disease-associated modules. Nat. Commun. 15, 2621 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  202. Wang, N. et al. MSFT-transformer: a multistage fusion tabular transformer for disease prediction using metagenomic data. Brief. Bioinform. 26, bbaf217 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Hall, A. B. et al. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med. 9, 103 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  204. Hernandez Medina, R. et al. Machine learning and deep learning applications in microbiome research. ISME Commun. 2, 98 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  205. Dang, T., Lysenko, A., Boroevich, K. A. & Tsunoda, T. VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data. Brief. Bioinform. 26, bbaf300 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Ding, Y. et al. Identification of gut microbial bile acid metabolic enzymes via an AI-assisted pipeline. Cell https://doi.org/10.1016/j.cell.2025.07.017 (2025).

    Article  PubMed  Google Scholar 

  207. Tang, X. et al. OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks. Nucleic Acids Res. 52, e99 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  208. Mock, F., Kretschmer, F., Kriese, A., Bocker, S. & Marz, M. Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks. Proc. Natl Acad. Sci. USA 119, e2122636119 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  209. Consens, M. E. et al. Transformers and genome language models. Nat. Mach. Intell. 7, 346–362 (2025).

    Article  Google Scholar 

  210. De Domenico, M. et al. Challenges and opportunities for digital twins in precision medicine from a complex systems perspective. NPJ Digit. Med. 8, 37 (2025).

    Article  PubMed  PubMed Central  Google Scholar 

  211. Sizemore, N. et al. A digital twin of the infant microbiome to predict neurodevelopmental deficits. Sci. Adv. 10, eadj0400 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Tripathi, P. & Bruner, S. D. Structural basis for the interactions of the colibactin resistance gene product ClbS with DNA. Biochemistry 60, 1619–1625 (2021).

    Article  CAS  PubMed  Google Scholar 

  213. Chagneau, C. V. et al. The polyamine spermidine modulates the production of the bacterial genotoxin colibactin. mSphere 4, e00414–e00419 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  214. Minot, S. S. et al. Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change. Sci. Rep. 14, 23646 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  215. Roje, B. et al. Gut microbiota carcinogen metabolism causes distal tissue tumours. Nature 632, 1137–1144 (2024). This preclinical study reveals that gut bacteria metabolize nitrosamine carcinogens into oxidized metabolites that accumulate in distal organs beyond the gastrointestinal tract, thereby increasing tumour susceptibility in these tissues.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  216. Ervin, S. M. et al. Gut microbial β-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens. J. Biol. Chem. 294, 18586–18599 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  217. Hebels, D. G. et al. N-Nitroso compound exposure-associated transcriptomic profiles are indicative of an increased risk for colorectal cancer. Cancer Lett. 309, 1–10 (2011).

    Article  CAS  PubMed  Google Scholar 

  218. Meyer, C. et al. Chronic inflammation promotes myeloid-derived suppressor cell activation blocking antitumor immunity in transgenic mouse melanoma model. Proc. Natl Acad. Sci. USA 108, 17111–17116 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  219. Ternes, D. et al. The gut microbial metabolite formate exacerbates colorectal cancer progression. Nat. Metab. 4, 458–475 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  220. Yu, T. et al. Fusobacterium nucleatum promotes chemoresistance to colorectal cancer by modulating autophagy. Cell 170, 548–563.e16 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  221. Gao, Y. et al. Fusobacterium nucleatum enhances the efficacy of PD-L1 blockade in colorectal cancer. Signal Transduct. Target. Ther. 6, 398 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  222. Abdeen, S. K., Mastandrea, I., Stinchcombe, N., Puschhof, J. & Elinav, E. Diet-microbiome interactions in cancer. Cancer Cell 43, 680–707 (2025).

    Article  CAS  PubMed  Google Scholar 

  223. Bagheri, A., Asoudeh, F., Rezaei, S., Babaei, M. & Esmaillzadeh, A. The effect of Mediterranean diet on body composition, inflammatory factors, and nutritional status in patients with cachexia induced by colorectal cancer: a randomized clinical trial. Integr. Cancer Ther. 22, 15347354231195322 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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The authors thank L. Busby (Mayo Clinic, Rochester, MN, USA) for the administrative assistance.

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All authors researched data for the article, contributed substantially to the discussion of the content, wrote the article, and reviewed and/or edited the manuscript before submission.

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P.C.K. is a member of the scientific advisory board of the International Observatory of Biocodex Microbiota Institute, chair of the scientific advisory board of the American Gastroenterology Association Center for Gut Microbiome Education and Research, ad hoc advisory board member for Pendulum and Intrinsic Medicine, and advisory board member for 32 Biosciences for which he receives equity option as compensation. R.A.T.M. serves as a founding adviser of Tiny Health. R.H. declares no competing interests.

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Hajjar, R., Mars, R.A.T. & Kashyap, P.C. Harnessing the microbiome for cancer therapy. Nat Rev Microbiol (2026). https://doi.org/10.1038/s41579-025-01268-6

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