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 oral–gut microbiome axis in health and disease

Abstract

The human body hosts trillions of microorganisms throughout many diverse habitats with different physico-chemical characteristics. Among them, the oral cavity and the gut harbour some of the most dense and diverse microbial communities. Although these two sites are physiologically distinct, they are directly connected and can influence each other in several ways. For example, oral microorganisms can reach and colonize the gastrointestinal tract, particularly in the context of gut dysbiosis. However, the mechanisms of colonization and the role that the oral microbiome plays in causing or exacerbating diseases in other organs have not yet been fully elucidated. Here, we describe recent advances in our understanding of how the oral and intestinal microbiota interplay in relation to their impact on human health and disease.

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: The biogeography and physiology of the oral–gut axis.
Fig. 2: Associations between the oral microbiota and gut chronic diseases.

Similar content being viewed by others

References

  1. Gilbert, J. A. et al. Current understanding of the human microbiome. Nat. Med. 24, 392–400 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Honda, K. & Littman, D. R. The microbiota in adaptive immune homeostasis and disease. Nature 535, 75–84 (2016).

    Article  CAS  PubMed  Google Scholar 

  3. Gilbert, J. A. et al. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 535, 94–103 (2016).

    Article  CAS  PubMed  Google Scholar 

  4. Duvallet, C., Gibbons, S. M., Gurry, T., Irizarry, R. A. & Alm, E. J. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat. Commun. 8, 1784 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031 (2006).

    Article  PubMed  Google Scholar 

  6. Zhang, X. et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nat. Med. 21, 895–905 (2015).

    Article  CAS  PubMed  Google Scholar 

  7. Paun, A., Yau, C. & Danska, J. S. The influence of the microbiome on type 1 diabetes. J. Immunol. 198, 590–595 (2017).

    Article  CAS  PubMed  Google Scholar 

  8. Frank, D. N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl Acad. Sci. USA 104, 13780–13785 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kilian, M. The oral microbiome—friend or foe? Eur. J. Oral. Sci. 126, 5–12 (2018).

    Article  PubMed  Google Scholar 

  10. Baker, J. L. & Edlund, A. Exploiting the oral microbiome to prevent tooth decay: has evolution already provided the best tools? Front. Microbiol. 9, 3323 (2018).

    Article  PubMed  Google Scholar 

  11. Sedghi, L., DiMassa, V., Harrington, A., Lynch, S. V. & Kapila, Y. L. The oral microbiome: role of key organisms and complex networks in oral health and disease. Periodontol 2000 87, 107–131 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Pathak, J. L., Yan, Y., Zhang, Q., Wang, L. & Ge, L. The role of oral microbiome in respiratory health and diseases. Respir. Med. 185, 106475 (2021).

    Article  PubMed  Google Scholar 

  13. Irfan, M., Delgado, R. Z. R. & Frias-Lopez, J. The oral microbiome and cancer. Front. Immunol. 11, 591088 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Hajishengallis, G. Periodontitis: from microbial immune subversion to systemic inflammation. Nat. Rev. Immunol. 15, 30–44 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Hajishengallis, G. & Chavakis, T. Local and systemic mechanisms linking periodontal disease and inflammatory comorbidities. Nat. Rev. Immunol. 21, 426–440 (2021). This review highlights the potential causal links between periodontitis and other chronic inflammation-driven disorders, emphasising their multifaceted mechanistic causality.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Zheng, D., Liwinski, T. & Elinav, E. Interaction between microbiota and immunity in health and disease. Cell Res. 30, 492–506 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Fan, Y. & Pedersen, O. Gut microbiota in human metabolic health and disease. Nat. Rev. Microbiol. 19, 55–71 (2021).

    Article  CAS  PubMed  Google Scholar 

  18. Hou, K. et al. Microbiota in health and diseases. Signal. Transduct. Target. Ther. 7, 135 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  19. Fedoruk, M. J. & Hong, S. in Encyclopedia of Toxicology 3rd edn (ed. Wexler, P.) 702–705 (Academic, 2014).

  20. Takiishi, T., Fenero, C. I. M. & Câmara, N. O. S. Intestinal barrier and gut microbiota: shaping our immune responses throughout life. Tissue Barriers 5, e1373208 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  21. König, J. et al. Human intestinal barrier function in health and disease. Clin. Transl. Gastroenterol. 7, e196 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Willis, J. R. & Gabaldón, T. The human oral microbiome in health and disease: from sequences to ecosystems. Microorganisms 8, 308 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Baker, J. L., Mark Welch, J. L., Kauffman, K. M., McLean, J. S. & He, X. The oral microbiome: diversity, biogeography and human health. Nat. Rev. Microbiol. 22, 89–104 (2023). This review examines the biogeography of several oral niches at the species level, presenting not only bacteria but also microeukaryotes, archaea and viruses.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Diaz, P. I. & Dongari-Bagtzoglou, A. Critically appraising the significance of the oral mycobiome. J. Dent. Res. 100, 133–140 (2021).

    Article  CAS  PubMed  Google Scholar 

  25. Caselli, E. et al. Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture. BMC Microbiol. 20, 120 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Lloyd-Price, J., Abu-Ali, G. & Huttenhower, C. The healthy human microbiome. Genome Med. 8, 51 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  27. Donaldson, G. P., Lee, S. M. & Mazmanian, S. K. Gut biogeography of the bacterial microbiota. Nat. Rev. Microbiol. 14, 20–32 (2016).

    Article  CAS  PubMed  Google Scholar 

  28. Hillman, E. T., Lu, H., Yao, T. & Nakatsu, C. H. Microbial ecology along the gastrointestinal tract. Microbes Env. 32, 300–313 (2017).

    Article  Google Scholar 

  29. Assimakopoulos, S. F., Triantos, C., Maroulis, I. & Gogos, C. The role of the gut barrier function in health and disease. Gastroenterol. Res. Pract. 11, 261–263 (2018).

    Article  Google Scholar 

  30. Ding, T. & Schloss, P. D. Dynamics and associations of microbial community types across the human body. Nature 509, 357–360 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Schmidt, T. S. et al. Extensive transmission of microbes along the gastrointestinal tract. eLife 8, e42693 (2019). This study presents a metagenomic approach describing that the transmission to, and subsequent colonization of, the large intestine by oral microorganisms is common even among healthy individuals.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Kunath, B. J. et al. Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses. Microbiome 10, 243 (2022). This paper confirms the transmission of oral microorganisms to the gut and shows strain-level activities using metatranscriptomics and metaproteomics.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Kamada, N., Chen, G. Y., Inohara, N. & Núñez, G. Control of pathogens and pathobionts by the gut microbiota. Nat. Immunol. 14, 685–690 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Nakajima, M. et al. Oral administration of P. gingivalis induces dysbiosis of gut microbiota and impaired barrier function leading to dissemination of enterobacteria to the liver. PLoS ONE 10, e0134234 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  35. Vaishnava, S., Behrendt, C. L., Ismail, A. S., Eckmann, L. & Hooper, L. V. Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host–microbial interface. Proc. Natl Acad. Sci. USA 105, 20858–20863 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Atarashi, K. et al. Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. Science 358, 359–365 (2017). This study demonstrates that ectopic gut colonization by oral bacteria results in expansion of colitogenic T cells and the promotion of colitis in murine models.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Bao, J. et al. Periodontitis may induce gut microbiota dysbiosis via salivary microbiota. Int. J. Oral. Sci. 14, 32 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Tsukasaki, M. et al. Host defense against oral microbiota by bone-damaging T cells. Nat. Commun. 9, 701 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  39. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Imhann, F. et al. Proton pump inhibitors affect the gut microbiome. Gut 65, 740–748 (2016).

    Article  CAS  PubMed  Google Scholar 

  41. Guo, W. et al. Depletion of gut microbiota impairs gut barrier function and antiviral immune defense in the liver. Front. Immunol. 12, 636803 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Hunt, R. H. et al. The stomach in health and disease. Gut 64, 1650–1668 (2015).

    Article  CAS  PubMed  Google Scholar 

  43. Sato, K. et al. Aggravation of collagen-induced arthritis by orally administered Porphyromonas gingivalis through modulation of the gut microbiota and gut immune system. Sci. Rep. 7, 6955 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  44. Martínez-García, M. & Hernández-Lemus, E. Periodontal inflammation and systemic diseases: an overview. Front. Physiol. 12, 709438 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  45. Ramadan, D. E., Hariyani, N., Indrawati, R., Ridwan, R. D. & Diyatri, I. Cytokines and chemokines in periodontitis. Eur. J. Dent. 14, 483–495 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  46. Könönen, E. & Gursoy, U. K. Oral prevotella species and their connection to events of clinical relevance in gastrointestinal and respiratory tracts. Front. Microbiol. 12, 798763 (2021).

    Article  PubMed  Google Scholar 

  47. Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Heintz-Buschart, A. et al. Small RNA profiling of low biomass samples: identification and removal of contaminants. BMC Biol. 16, 52 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  49. Van Rossum, T., Ferretti, P., Maistrenko, O. M. & Bork, P. Diversity within species: interpreting strains in microbiomes. Nat. Rev. Microbiol. 18, 491–506 (2020). This paper discusses high-resolution strain and subspecies analyses in metagenomic data and how within-species variation can be studied and stratified directly within microbial communities.

    Article  PubMed  PubMed Central  Google Scholar 

  50. Sedghi, L. M., Bacino, M. & Kapila, Y. L. Periodontal disease: the good, the bad, and the unknown. Front. Cell. Infect. Microbiol. 11, 766944 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Curtis, M. A., Diaz, P. I. & Van Dyke, T. E. The role of the microbiota in periodontal disease. Periodontol 2000 83, 14–25 (2020).

    Article  PubMed  Google Scholar 

  52. Kinane, D. F., Stathopoulou, P. G. & Papapanou, P. N. Periodontal diseases. Nat. Rev. Dis. Prim. 3, 17038 (2017).

    Article  PubMed  Google Scholar 

  53. Tuominen, H. & Rautava, J. Oral Microbiota and cancer development. Pathobiology 88, 116–126 (2021).

    Article  CAS  PubMed  Google Scholar 

  54. Strauss, J. et al. Invasive potential of gut mucosa-derived Fusobacterium nucleatum positively correlates with IBD status of the host. Inflamm. Bowel Dis. 17, 1971–1978 (2011).

    Article  PubMed  Google Scholar 

  55. Carrillo-de-Albornoz, A., Figuero, E., Herrera, D. & Bascones-Martínez, A. Gingival changes during pregnancy: II. Influence of hormonal variations on the subgingival biofilm. J. Clin. Periodontol. 37, 230–240 (2010).

    Article  PubMed  Google Scholar 

  56. Abusleme, L. et al. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J. 7, 1016–1025 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Kitamoto, S., Nagao-Kitamoto, H., Hein, R., Schmidt, T. M. & Kamada, N. The bacterial connection between the oral cavity and the gut diseases. J. Dent. Res. 99, 1021–1029 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Franzosa, E. A. et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat. Microbiol. 4, 293–305 (2019). This study integrates metagenomic analyses with in-depth metabolomic measurements and highlights possible mechanistic relationships that are perturbed in IBD.

    Article  CAS  PubMed  Google Scholar 

  59. Schirmer, M. et al. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat. Microbiol. 3, 337–346 (2018). This study integrates metagenomic analysis with metatranscriptomic measurements, identifying keystone species in terms of activities and providing finer insight into the role of the microbiome in IBD.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Vandeputte, D. et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature 551, 507–511 (2017). This paper presents a method that can provide information about the extent or directionality of changes in taxa abundance or metabolic potential by bypassing compositionality effects in the reconstruction of gut microbiota interaction networks.

    Article  CAS  PubMed  Google Scholar 

  61. Ohkusa, T. et al. Fusobacterium varium localized in the colonic mucosa of patients with ulcerative colitis stimulates species-specific antibody. J. Gastroenterol. Hepatol. 17, 849–853 (2002).

    Article  PubMed  Google Scholar 

  62. Gevers, D. et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe 15, 382–392 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Kirk, K. F., Nielsen, H. L., Thorlacius-Ussing, O. & Nielsen, H. Optimized cultivation of Campylobacter concisus from gut mucosal biopsies in inflammatory bowel disease. Gut Pathog. 8, 27 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  64. Huh, J.-W. & Roh, T.-Y. Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis. BMC Microbiol. 20, 208 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Lee, Y.-C. et al. The periodontopathic pathogen, Porphyromonas gingivalis, involves a gut inflammatory response and exacerbates inflammatory bowel disease. Pathogens 11, 84 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Said, H. S. et al. Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers. DNA Res. 21, 15–25 (2014).

    Article  CAS  PubMed  Google Scholar 

  67. Xun, Z., Zhang, Q., Xu, T., Chen, N. & Chen, F. Dysbiosis and ecotypes of the salivary microbiome associated with inflammatory bowel diseases and the assistance in diagnosis of diseases using oral bacterial profiles. Front. Microbiol. 9, 1136 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  68. Kelsen, J. et al. Alterations of the subgingival microbiota in pediatric Crohn’s disease studied longitudinally in discovery and validation cohorts. Inflamm. Bowel Dis. 21, 2797–2805 (2015).

    Article  PubMed  Google Scholar 

  69. Elzayat, H. et al. Deciphering salivary microbiome signature in Crohn’s disease patients with different factors contributing to dysbiosis. Sci. Rep. 13, 19198 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Abdelbary, M. M. H. et al. The oral–gut axis: salivary and fecal microbiome dysbiosis in patients with inflammatory bowel disease. Front. Cell. Infect. Microbiol. 12, 1010853 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Zhang, T. et al. Dynamics of the salivary microbiome during different phases of Crohn’s disease. Front. Cell. Infect. Microbiol. 10, 544704 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Madsen, G. R. et al. The impact of periodontitis on inflammatory bowel disease activity. Inflamm. Bowel Dis. 29, 396–404 (2023).

    Article  PubMed  Google Scholar 

  73. Koutsochristou, V. et al. Dental caries and periodontal disease in children and adolescents with inflammatory bowel disease: a case–control study. Inflamm. Bowel Dis. 21, 1839–1846 (2015).

    Article  PubMed  Google Scholar 

  74. She, Y.-Y. et al. Periodontitis and inflammatory bowel disease: a meta-analysis. BMC Oral. Health 20, 67 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  75. Baima, G. et al. Periodontitis prevalence and severity in inflammatory bowel disease: a case–control study. J. Periodontol. 94, 313–322 (2023).

    Article  CAS  PubMed  Google Scholar 

  76. Papageorgiou, S. N. et al. Inflammatory bowel disease and oral health: systematic review and a meta-analysis. J. Clin. Periodontol. 44, 382–393 (2017).

    Article  PubMed  Google Scholar 

  77. Zhou, P., Li, X., Huang, I.-H. & Qi, F. Veillonella catalase protects the growth of Fusobacterium nucleatum in microaerophilic and Streptococcus gordonii-resident environments. Appl. Environ. Microbiol. 83, e01079–e01117 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Lenartova, M. et al. The oral microbiome in periodontal health. Front. Cell. Infect. Microbiol. 11, 629723 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Carrion, J. et al. Microbial carriage state of peripheral blood dendritic cells (DCs) in chronic periodontitis influences DC differentiation, atherogenic potential. J. Immunol. 189, 3178–3187 (2012).

    Article  CAS  PubMed  Google Scholar 

  80. Xue, Y. et al. Indoleamine 2,3-dioxygenase expression regulates the survival and proliferation of Fusobacterium nucleatum in THP-1-derived macrophages. Cell Death Dis. 9, 355 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  81. Chen, Y. et al. Fusobacterium nucleatum facilitates ulcerative colitis through activating IL-17F signaling to NF-κB via the upregulation of CARD3 expression. J. Pathol. 250, 170–182 (2020).

    Article  CAS  PubMed  Google Scholar 

  82. Tang, W. et al. Impairment of intestinal barrier function induced by early weaning via autophagy and apoptosis associated with gut microbiome and metabolites. Front. Immunol. 12, 804870 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Feng, Y.-K. et al. Oral P. gingivalis impairs gut permeability and mediates immune responses associated with neurodegeneration in LRRK2 R1441G mice. J. Neuroinflammation 17, 347 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. van der Post, S. et al. Site-specific O-glycosylation on the MUC2 mucin protein inhibits cleavage by the Porphyromonas gingivalis secreted cysteine protease (RgpB). J. Biol. Chem. 288, 14636–14646 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  85. Kitamoto, S. et al. The intermucosal connection between the mouth and gut in commensal pathobiont-driven colitis. Cell 182, 447–462.e14 (2020). This study shows that oral bacteria-specific TH17 cells, which expand during experimental periodontitis, migrate to the gut where they are activated by translocated oral bacteria and contribute to the development of colitis.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. 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 

  87. Ternes, D. et al. Microbiome in colorectal cancer: how to get from meta-omics to mechanism? Trends Microbiol. 28, 401–423 (2020). This review presents new experimental approaches for gaining ecosystem-level mechanistic understanding of the gut microbiome’s role in cancer pathogenesis.

    Article  CAS  PubMed  Google Scholar 

  88. Simpson, R. C., Shanahan, E. R., Scolyer, R. A. & Long, G. V. Towards modulating the gut microbiota to enhance the efficacy of immune-checkpoint inhibitors. Nat. Rev. Clin. Oncol. 20, 697–715 (2023). This review discusses the mechanisms by which the microbiota modulates antitumour immunity.

    Article  PubMed  Google Scholar 

  89. 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 

  90. 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 

  91. Routy, B. et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 359, 91–97 (2018).

    Article  CAS  PubMed  Google Scholar 

  92. Flemer, B. et al. The oral microbiota in colorectal cancer is distinctive and predictive. Gut 67, 1454–1463 (2018).

    Article  CAS  PubMed  Google Scholar 

  93. Li, S. et al. Prognostic impact of oral microbiome on survival of malignancies: a systematic review and meta-analysis. Syst. Rev. 13, 41 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Lee, W.-H. et al. Bacterial alterations in salivary microbiota and their association in oral cancer. Sci. Rep. 7, 16540 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  95. Pushalkar, S. et al. Microbial diversity in saliva of oral squamous cell carcinoma. FEMS Immunol. Med. Microbiol. 61, 269–277 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Schmidt, B. L. et al. Changes in abundance of oral microbiota associated with oral cancer. PLoS ONE 9, e98741 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  97. Torres, P. J. et al. Characterization of the salivary microbiome in patients with pancreatic cancer. PeerJ 3, e1373 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  98. Peters, B. A. et al. Oral microbiome composition reflects prospective risk for esophageal cancers. Cancer Res. 77, 6777–6787 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Fan, X. et al. Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case–control study. Gut 67, 120–127 (2018).

    Article  CAS  PubMed  Google Scholar 

  100. Conde-Pérez, K. et al. Parvimonas micra can translocate from the subgingival sulcus of the human oral cavity to colorectal adenocarcinoma. Mol. Oncol. 18, 1143–1173 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Chen, M.-F., Lu, M.-S., Hsieh, C.-C. & Chen, W.-C. Porphyromonas gingivalis promotes tumor progression in esophageal squamous cell carcinoma. Cell. Oncol. 44, 373–384 (2021).

    Article  CAS  Google Scholar 

  103. Wen, L. et al. Porphyromonas gingivalis promotes oral squamous cell carcinoma progression in an immune microenvironment. J. Dent. Res. 99, 666–675 (2020).

    Article  CAS  PubMed  Google Scholar 

  104. Michaud, D. S. et al. Plasma antibodies to oral bacteria and risk of pancreatic cancer in a large European prospective cohort study. Gut 62, 1764–1770 (2013).

    Article  PubMed  Google Scholar 

  105. Saba, E. et al. Oral bacteria accelerate pancreatic cancer development in mice. Gut 73, 770–786 (2024).

    Article  PubMed  Google Scholar 

  106. Sztukowska, M. N. et al. Porphyromonas gingivalis initiates a mesenchymal-like transition through ZEB1 in gingival epithelial cells. Cell. Microbiol. 18, 844–858 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Haerinck, J., Goossens, S. & Berx, G. The epithelial–mesenchymal plasticity landscape: principles of design and mechanisms of regulation. Nat. Rev. Genet. 24, 590–609 (2023).

    Article  CAS  PubMed  Google Scholar 

  108. Ternes, D. et al. The gut microbial metabolite formate exacerbates colorectal cancer progression. Nat. Metab. 4, 458–475 (2022). This study describes molecular signatures linking CRC phenotypes with Fusobacterium spp. abundance and identifies formate as a gut-derived oncometabolite relevant for CRC progression.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Komiya, Y. et al. Patients with colorectal cancer have identical strains of Fusobacterium nucleatum in their colorectal cancer and oral cavity. Gut 68, 1335–1337 (2019).

    Article  PubMed  Google Scholar 

  110. Nosho, K. et al. Association of Fusobacterium nucleatum with immunity and molecular alterations in colorectal cancer. World J. Gastroenterol. 22, 557–566 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Tahara, T. et al. Fusobacterium in colonic flora and molecular features of colorectal carcinoma. Cancer Res. 74, 1311–1318 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Kim, H. S. et al. Fusobacterium nucleatum induces a tumor microenvironment with diminished adaptive immunity against colorectal cancers. Front. Cell. Infect. Microbiol. 13, 1101291 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Kosuke, M. et al. Fusobacterium nucleatum and T cells in colorectal carcinoma. JAMA Oncol. 1, 653–661 (2015).

    Article  Google Scholar 

  115. Serna, G. et al. Fusobacterium nucleatum persistence and risk of recurrence after preoperative treatment in locally advanced rectal cancer. Ann. Oncol. 31, 1366–1375 (2020).

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  PubMed Central  Google Scholar 

  117. Li, X. et al. Fusobacterium nucleatum promotes the progression of colorectal cancer through Cdk5-activated Wnt/β-catenin signaling. Front. Microbiol. 11, 545251 (2020).

    Article  PubMed  Google Scholar 

  118. Coppenhagen-Glazer, S. et al. Fap2 of Fusobacterium nucleatum is a galactose-inhibitable adhesin involved in coaggregation, cell adhesion, and preterm birth. Infect. Immun. 83, 1104–1113 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. 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 

  120. Liu, Y. et al. Fusobacterium nucleatum confers chemoresistance by modulating autophagy in oesophageal squamous cell carcinoma. Br. J. Cancer 124, 963–974 (2021).

    Article  CAS  PubMed  Google Scholar 

  121. Jiang, S.-S. et al. Fusobacterium nucleatum-derived succinic acid induces tumor resistance to immunotherapy in colorectal cancer. Cell Host Microbe 31, 781–797.e9 (2023).

    Article  CAS  PubMed  Google Scholar 

  122. 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 

  123. Higashi, D. L. et al. Who is in the driver’s seat? Parvimonas micra: an understudied pathobiont at the crossroads of dysbiotic disease and cancer. Environ. Microbiol. Rep. 15, 254–264 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  124. Bergsten, E. et al. Parvimonas micra, an oral pathobiont associated with colorectal cancer, epigenetically reprograms human colonocytes. Gut Microbes 15, 2265138 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Xu, J. et al. Alteration of the abundance of Parvimonas micra in the gut along the adenoma–carcinoma sequence. Oncol. Lett. 20, 106 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  127. Genco, R. J. et al. The subgingival microbiome relationship to periodontal disease in older women. J. Dent. Res. 98, 975–984 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Marchesan, J. et al. TLR4, NOD1 and NOD2 mediate immune recognition of putative newly identified periodontal pathogens. Mol. Oral. Microbiol. 31, 243–258 (2016).

    Article  CAS  PubMed  Google Scholar 

  129. Sakanaka, A. et al. Fusobacterium nucleatum metabolically integrates commensals and pathogens in oral biofilms. mSystems 7, e0017022 (2022).

    Article  PubMed  Google Scholar 

  130. 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).

    Article  CAS  PubMed  Google Scholar 

  131. Zhang, Y. Epidemiology of esophageal cancer. World J. Gastroenterol. 19, 5598–5606 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  132. Yano, Y., Etemadi, A. & Abnet, C. C. Microbiome and cancers of the esophagus: a review. Microorganisms 9, 1764 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  133. Chen, X. et al. Oral microbiota and risk for esophageal squamous cell carcinoma in a high-risk area of China. PLoS ONE 10, e0143603 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  134. Zhao, Q. et al. Alterations of oral microbiota in chinese patients with esophageal cancer. Front. Cell. Infect. Microbiol. 10, 541144 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Snider, E. J. et al. Barrett’s esophagus is associated with a distinct oral microbiome. Clin. Transl. Gastroenterol. 9, 135 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  136. Shao, D. et al. Microbial characterization of esophageal squamous cell carcinoma and gastric cardia adenocarcinoma from a high-risk region of China. Cancer 125, 3993–4002 (2019).

    Article  CAS  PubMed  Google Scholar 

  137. Li, D. et al. Characterization of the esophageal microbiota and prediction of the metabolic pathways involved in esophageal cancer. Front. Cell. Infect. Microbiol. 10, 268 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Yamamura, K. et al. Human microbiome Fusobacterium nucleatum in esophageal cancer tissue is associated with prognosis. Clin. Cancer Res. 22, 5574–5581 (2016).

    Article  CAS  PubMed  Google Scholar 

  139. Gao, S. et al. Presence of Porphyromonas gingivalis in esophagus and its association with the clinicopathological characteristics and survival in patients with esophageal cancer. Infect. Agent. Cancer 11, 3 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  140. Farrell, J. J. et al. Variations of oral microbiota are associated with pancreatic diseases including pancreatic cancer. Gut 61, 582–588 (2012).

    Article  CAS  PubMed  Google Scholar 

  141. Stingu, C.-S., Eschrich, K., Rodloff, A. C., Schaumann, R. & Jentsch, H. Periodontitis is associated with a loss of colonization by Streptococcus sanguinis. J. Med. Microbiol. 57, 495–499 (2008).

    Article  PubMed  Google Scholar 

  142. Teughels, W. et al. Bacteria interfere with A. actinomycetemcomitans colonization. J. Dent. Res. 86, 611–617 (2007).

    Article  CAS  PubMed  Google Scholar 

  143. Andrukhov, O. et al. Serum cytokine levels in periodontitis patients in relation to the bacterial load. J. Periodontol. 82, 885–892 (2011).

    Article  CAS  PubMed  Google Scholar 

  144. Gemmell, E., Marshall, R. I. & Seymour, G. J. Cytokines and prostaglandins in immune homeostasis and tissue destruction in periodontal disease. Periodontol 2000 14, 112–143 (1997).

    Article  CAS  PubMed  Google Scholar 

  145. Nauseef, W. M. & Borregaard, N. Neutrophils at work. Nat. Immunol. 15, 602–611 (2014).

    Article  CAS  PubMed  Google Scholar 

  146. Fine, N. et al. Primed PMNs in healthy mouse and human circulation are first responders during acute inflammation. Blood Adv. 3, 1622–1637 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Fine, N. et al. Periodontal inflammation primes the systemic innate immune response. J. Dent. Res. 100, 318–325 (2021).

    Article  CAS  PubMed  Google Scholar 

  148. Fine, N. et al. Distinct oral neutrophil subsets define health and periodontal disease states. J. Dent. Res. 95, 931–938 (2016).

    Article  CAS  PubMed  Google Scholar 

  149. Hajishengallis, G., Chavakis, T., Hajishengallis, E. & Lambris, J. D. Neutrophil homeostasis and inflammation: novel paradigms from studying periodontitis. J. Leukoc. Biol. 98, 539–548 (2015).

    Article  CAS  PubMed  Google Scholar 

  150. Rossol, M. et al. LPS-induced cytokine production in human monocytes and macrophages. Crit. Rev. Immunol. 31, 379–446 (2011).

    Article  CAS  PubMed  Google Scholar 

  151. Zijnge, V., Kieselbach, T. & Oscarsson, J. Proteomics of protein secretion by Aggregatibacter actinomycetemcomitans. PLoS ONE 7, e41662 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Konig, M. F. et al. Aggregatibacter actinomycetemcomitans-induced hypercitrullination links periodontal infection to autoimmunity in rheumatoid arthritis. Sci. Transl. Med. 8, 369ra176 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  153. Stobernack, T. et al. Extracellular proteome and citrullinome of the oral pathogen Porphyromonas gingivalis. J. Proteome Res. 15, 4532–4543 (2016).

    Article  CAS  PubMed  Google Scholar 

  154. Farrugia, C. et al. Mechanisms of vascular damage by systemic dissemination of the oral pathogen Porphyromonas gingivalis. FEBS J. 288, 1479–1495 (2021).

    Article  CAS  PubMed  Google Scholar 

  155. Gimbrone, M. A. Jr & García-Cardeña, G. Endothelial cell dysfunction and the pathobiology of atherosclerosis. Circ. Res. 118, 620–636 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Bajaj, J. S. et al. Periodontal therapy favorably modulates the oral–gut–hepatic axis in cirrhosis. Am. J. Physiol. Gastrointest. Liver Physiol. 315, G824–G837 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  157. Schenkein, H. A., Papapanou, P. N., Genco, R. & Sanz, M. Mechanisms underlying the association between periodontitis and atherosclerotic disease. Periodontol 2000 83, 90–106 (2020).

    Article  PubMed  Google Scholar 

  158. D’Aiuto, F., Orlandi, M. & Gunsolley, J. C. Evidence that periodontal treatment improves biomarkers and CVD outcomes. J. Clin. Periodontol. 40, S85–S105 (2013).

    PubMed  Google Scholar 

  159. Sanz, M. et al. Periodontitis and cardiovascular diseases: consensus report. J. Clin. Periodontol. 47, 268–288 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  160. Teeuw, W. J., Gerdes, V. E. A. & Loos, B. G. Effect of periodontal treatment on glycemic control of diabetic patients: a systematic review and meta-analysis. Diabetes Care 33, 421–427 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  161. Teshome, A. & Yitayeh, A. The effect of periodontal therapy on glycemic control and fasting plasma glucose level in type 2 diabetic patients: systematic review and meta-analysis. BMC Oral. Health 17, 31 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  162. Tanwar, H. et al. Unraveling the link between periodontitis and inflammatory bowel disease: challenges and outlook. Preprint at arXiv https://doi.org/10.48550/arXiv.2308.10907 (2023).

  163. Zhang, Y. et al. The association between periodontitis and inflammatory bowel disease: a systematic review and meta-analysis. Biomed. Res. Int. 2021, 6692420 (2021).

    PubMed  PubMed Central  Google Scholar 

  164. Pietropaoli, D. et al. Occurrence of spontaneous periodontal disease in the SAMP1/YitFc murine model of Crohn disease. J. Periodontol. 85, 1799–1805 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  165. Teles, F., Wang, Y., Hajishengallis, G., Hasturk, H. & Marchesan, J. T. Impact of systemic factors in shaping the periodontal microbiome. Periodontol 2000 85, 126–160 (2021).

    Article  PubMed  Google Scholar 

  166. Genco, R. J. & Sanz, M. Clinical and public health implications of periodontal and systemic diseases: an overview. Periodontol 2000 83, 7–13 (2020).

    Article  PubMed  Google Scholar 

  167. Xiao, E. et al. Diabetes enhances IL-17 expression and alters the oral microbiome to increase its pathogenicity. Cell Host Microbe 22, 120–128.e4 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. D’Aiuto, F. et al. Systemic effects of periodontitis treatment in patients with type 2 diabetes: a 12 month, single-centre, investigator-masked, randomised trial. Lancet Diabetes Endocrinol. 6, 954–965 (2018). This study shows favourable effects of local periodontal treatment on systemic inflammatory markers and glycaemic control in patients with type 2 diabetes mellitus.

    Article  PubMed  Google Scholar 

  169. Duarte, P. M. et al. Local levels of inflammatory mediators in uncontrolled type 2 diabetic subjects with chronic periodontitis. J. Clin. Periodontol. 41, 11–18 (2014).

    Article  CAS  PubMed  Google Scholar 

  170. Lalla, E., Lamster, I. B., Stern, D. M. & Schmidt, A. M. Receptor for advanced glycation end products, inflammation, and accelerated periodontal disease in diabetes: mechanisms and insights into therapeutic modalities. Ann. Periodontol. 6, 113–118 (2001).

    Article  CAS  PubMed  Google Scholar 

  171. Sato, K. et al. Obesity-related gut microbiota aggravates alveolar bone destruction in experimental periodontitis through elevation of uric acid. MBio 12, e0077121 (2021).

    Article  PubMed  Google Scholar 

  172. Kato, T. et al. Oral administration of Porphyromonas gingivalis alters the gut microbiome and serum metabolome. mSphere 3, https://doi.org/10.1128/msphere.00460-18 (2018).

  173. Blasco-Baque, V. et al. Periodontitis induced by Porphyromonas gingivalis drives periodontal microbiota dysbiosis and insulin resistance via an impaired adaptive immune response. Gut 66, 872–885 (2017).

    Article  CAS  PubMed  Google Scholar 

  174. Goettel, J. A. et al. Fatal autoimmunity in mice reconstituted with human hematopoietic stem cells encoding defective FOXP3. Blood 125, 3886–3895 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Wahl, A. et al. A germ-free humanized mouse model shows the contribution of resident microbiota to human-specific pathogen infection. Nat. Biotechnol. 42, 905–915 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  176. Bai, L., Chen, B.-Y., Liu, Y., Zhang, W.-C. & Duan, S.-Z. A mouse periodontitis model with humanized oral bacterial community. Front. Cell. Infect. Microbiol. 12, 842845 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Li, B. et al. Oral bacteria colonize and compete with gut microbiota in gnotobiotic mice. Int. J. Oral. Sci. 11, 10 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  178. de Nies, L. et al. Altered infective competence of the human gut microbiome in COVID-19. Microbiome 11, 46 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  179. Segata, N. et al. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 13, R42 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. van ’t Hof, W., Veerman, E. C. I., Nieuw Amerongen, A. V. & Ligtenberg, A. J. M. Antimicrobial defense systems in saliva. Monogr. Oral. Sci. 24, 40–51 (2014).

    Article  PubMed  Google Scholar 

  181. Amerongen, A. V. N. & Veerman, E. C. I. Saliva—the defender of the oral cavity. Oral. Dis. 8, 12–22 (2002).

    Article  PubMed  Google Scholar 

  182. Lynge Pedersen, A. M. & Belstrøm, D. The role of natural salivary defences in maintaining a healthy oral microbiota. J. Dent. 80, S3–S12 (2019).

    Article  CAS  PubMed  Google Scholar 

  183. Ahuja, M. et al. Orai1-mediated antimicrobial secretion from pancreatic acini shapes the gut microbiome and regulates gut innate immunity. Cell Metab. 25, 635–646 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Martinsen, T. C., Bergh, K. & Waldum, H. L. Gastric juice: a barrier against infectious diseases. Basic. Clin. Pharmacol. Toxicol. 96, 94–102 (2005).

    Article  CAS  PubMed  Google Scholar 

  185. Tennant, S. M. et al. Influence of gastric acid on susceptibility to infection with ingested bacterial pathogens. Infect. Immun. 76, 639–645 (2008).

    Article  CAS  PubMed  Google Scholar 

  186. Bischoff, S. C. et al. Intestinal permeability—a new target for disease prevention and therapy. BMC Gastroenterol. 14, 189 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  187. Odenwald, M. A. & Turner, J. R. The intestinal epithelial barrier: a therapeutic target? Nat. Rev. Gastroenterol. Hepatol. 14, 9–21 (2017).

    Article  CAS  PubMed  Google Scholar 

  188. Pott, J. & Hornef, M. Innate immune signalling at the intestinal epithelium in homeostasis and disease. EMBO Rep. 13, 684–698 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Dillon, A. & Lo, D. D. M cells: intelligent engineering of mucosal immune surveillance. Front. Immunol. 10, 1499 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  190. Huus, K. E., Petersen, C. & Finlay, B. B. Diversity and dynamism of IgA–microbiota interactions. Nat. Rev. Immunol. 21, 514–525 (2021).

    Article  CAS  PubMed  Google Scholar 

  191. Buffie, C. G. & Pamer, E. G. Microbiota-mediated colonization resistance against intestinal pathogens. Nat. Rev. Immunol. 13, 790–801 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Pickard, J. M., Zeng, M. Y., Caruso, R. & Núñez, G. Gut microbiota: role in pathogen colonization, immune responses, and inflammatory disease. Immunol. Rev. 279, 70–89 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  193. Parker, C. T., Tindall, B. J. & Garrity, G. M. (eds) International code of nomenclature of prokaryotes. Int. J. Syst. Evol. Microbiol. 69, S1–S111 (2019).

    Article  Google Scholar 

  194. Tikhonov, M., Leach, R. W. & Wingreen, N. S. Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J. 9, 68–80 (2015).

    Article  PubMed  Google Scholar 

  195. Amir, A. et al. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2, e00191–e00216 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  196. Johnson, J. S. et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat. Commun. 10, 5029 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  197. Alneberg, J. et al. Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. Microbiome 6, 173 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  198. Zolfo, M., Tett, A., Jousson, O., Donati, C. & Segata, N. MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples. Nucleic Acids Res. 45, e7 (2017).

    Article  PubMed  Google Scholar 

  199. Smillie, C. S. et al. Strain tracking reveals the determinants of bacterial engraftment in the human gut following fecal microbiota transplantation. Cell Host Microbe 23, 229–240.e5 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C. & Segata, N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 27, 626–638 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  201. Nayfach, S., Rodriguez-Mueller, B., Garud, N. & Pollard, K. S. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res. 26, 1612–1625 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  202. Albanese, D. & Donati, C. Strain profiling and epidemiology of bacterial species from metagenomic sequencing. Nat. Commun. 8, 2260 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  203. Shaiber, A. & Eren, A. M. Composite metagenome-assembled genomes reduce the quality of public genome repositories. mBio 10, e00725–e00819 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Lo Curto, A. et al. Survival of probiotic lactobacilli in the upper gastrointestinal tract using an in vitro gastric model of digestion. Food Microbiol. 28, 1359–1366 (2011).

    Article  PubMed  Google Scholar 

  205. Minekus, M. et al. A standardised static in vitro digestion method suitable for food—an international consensus. Food Funct. 5, 1113–1124 (2014).

    Article  CAS  PubMed  Google Scholar 

  206. Zmora, N. et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell 174, 1388–1405.e21 (2018).

    Article  CAS  PubMed  Google Scholar 

  207. Van den Abbeele, P. et al. Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX. Appl. Environ. Microbiol. 76, 5237–5246 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  208. Van den Abbeele, P. et al. Incorporating a mucosal environment in a dynamic gut model results in a more representative colonization by lactobacilli. Microb. Biotechnol. 5, 106–115 (2012).

    Article  PubMed  Google Scholar 

  209. Minekus, M., Marteau, P., Havenaar, R. & Veld, J. H. J. H. I. A multicompartmental dynamic computer-controlled model simulating the stomach and small intestine. Altern. Lab. Anim. 23, 197–209 (1995).

    Article  Google Scholar 

  210. Thévenot, J. et al. Enterohemorrhagic Escherichia coli O157:H7 survival in an in vitro model of the human large intestine and interactions with probiotic yeasts and resident microbiota. Appl. Environ. Microbiol. 79, 1058–1064 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  211. Etienne-Mesmin, L. et al. In vitro modelling of oral microbial invasion in the human colon. Microbiol. Spectr. 11, e0434422 (2023).

    Article  PubMed  Google Scholar 

  212. Calatayud, M. et al. Salivary and gut microbiomes play a significant role in in vitro oral bioaccessibility, biotransformation, and intestinal absorption of arsenic from food. Environ. Sci. Technol. 52, 14422–14435 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  213. Marzorati, M. et al. The HMI™ module: a new tool to study the host–microbiota interaction in the human gastrointestinal tract in vitro. BMC Microbiol. 14, 133 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  214. Shah, P. et al. A microfluidics-based in vitro model of the gastrointestinal human–microbe interface. Nat. Commun. 7, 11535 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  215. Jalili-Firoozinezhad, S. et al. A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip. Nat. Biomed. Eng. 3, 520–531 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  216. Xavier, M. et al. From mouth to gut: microfluidic in vitro simulation of human gastro-intestinal digestion and intestinal permeability. Analyst 148, 3193–3203 (2023).

    Article  CAS  PubMed  Google Scholar 

  217. Molero-Abraham, M. et al. Human oral epithelial cells impair bacteria-mediated maturation of dendritic cells and render T cells unresponsive to stimulation. Front. Immunol. 10, 1434 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  218. Zhang, Y. et al. Stable reconstructed human gingiva–microbe interaction model: differential response to commensals and pathogens. Front. Cell. Infect. Microbiol. 12, 991128 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  219. Shang, L. et al. Multi-species oral biofilm promotes reconstructed human gingiva epithelial barrier function. Sci. Rep. 8, 16061 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  220. Shang, L. et al. Commensal and pathogenic biofilms alter Toll-like receptor signaling in reconstructed human gingiva. Front. Cell. Infect. Microbiol. 9, 282 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  221. Adelfio, M. et al. Three-dimensional humanized model of the periodontal gingival pocket to study oral microbiome. Adv. Sci. 10, e2205473 (2023).

    Article  Google Scholar 

  222. Rahimi, C. et al. Oral mucosa-on-a-chip to assess layer-specific responses to bacteria and dental materials. Biomicrofluidics 12, 054106 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  223. Makkar, H., Zhou, Y., Tan, K. S., Lim, C. T. & Sriram, G. Modeling crevicular fluid flow and host–oral microbiome interactions in a gingival crevice-on-chip. Adv. Healthc. Mater. 12, e2202376 (2023).

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 863664). This work was further supported by the Luxembourg National Research Fund (FNR) under grants CORE/15/BM/10404093 and CORE/19/BM/13684739 to P.W. This work was also supported by a Fulbright Research Scholarship from the Commission for Educational Exchange between the United States, Belgium and Luxembourg to P.W. Additional funding was provided by the FNR under INTERMOBILITY/23/17856242. E.L. was supported by the FNR and the Fondation Cancer Luxembourg under grant CORE/C20/BM/14591557, as well as by FNRS-Télévie grants 7.4565.21, 7.6603.02, 7.4560.22.

Author information

Authors and Affiliations

Authors

Contributions

The authors contributed equally to all aspects of the manuscript.

Corresponding authors

Correspondence to Benoit J. Kunath or Paul Wilmes.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Reviews Microbiology thanks Xuesong He and the other, anonymous, reviewers 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

Kunath, B.J., De Rudder, C., Laczny, C.C. et al. The oral–gut microbiome axis in health and disease. Nat Rev Microbiol (2024). https://doi.org/10.1038/s41579-024-01075-5

Download citation

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1038/s41579-024-01075-5

Search

Quick links

Nature Briefing Microbiology

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

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology