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Clinical translation of microbiome research

Nature Medicine volume 31, pages 1099–1113 (2025)Cite this article

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Abstract

The landscape of clinical microbiome research has dramatically evolved over the past decade. By leveraging in vivo and in vitro experimentation, multiomic approaches and computational biology, we have uncovered mechanisms of action and microbial metrics of association and identified effective ways to modify the microbiome in many diseases and treatment modalities. This Review explores recent advances in the clinical application of microbiome research over the past 5 years, while acknowledging existing barriers and highlighting opportunities. We focus on the translation of microbiome research into clinical practice, spearheaded by Food and Drug Administration (FDA)-approved microbiome therapies for recurrent Clostridioides difficile infections and the emerging fields of microbiome-based diagnostics and therapeutics. We highlight key examples of studies demonstrating how microbiome mechanisms, metrics and modifiers can advance clinical practice. We also discuss forward-looking perspectives on key challenges and opportunities toward integrating microbiome data into routine clinical practice, precision medicine and personalized healthcare and nutrition.

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Fig. 1: Illustrating mechanisms, metrics and modifiers through the example of IBD.
Fig. 2: Timeline of product discovery and development for the FDA-approved medication VOWST.

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Authors and Affiliations

  1. Department of Pediatrics, University of California San Diego, La Jolla, CA, USA

    Jack A. Gilbert & Rob Knight

  2. Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA

    Jack A. Gilbert

  3. Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA

    Jack A. Gilbert, Hiutung Chu, Katharine E. Gilbert & Rob Knight

  4. Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada

    Meghan B. Azad

  5. Manitoba Interdisciplinary Lactation Centre, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada

    Meghan B. Azad

  6. CIFAR Humans & the Microbiome Program, CIFAR, Toronto, Ontario, Canada

    Meghan B. Azad, Martin J. Blaser & Carolina Tropini

  7. Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden

    Fredrik Bäckhed

  8. Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden

    Fredrik Bäckhed

  9. Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA

    Martin J. Blaser

  10. Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA

    Mariana Byndloss

  11. Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN, USA

    Mariana Byndloss

  12. Department of Laboratory Medicine, University of California, San Fransisco, San Francisco, CA, USA

    Charles Y. Chiu

  13. Department of Medicine, Division of Infectious Diseases, University of California, San Fransisco, San Francisco, CA, USA

    Charles Y. Chiu

  14. Chan-Zuckerberg Biohub, San Francisco, CA, USA

    Charles Y. Chiu

  15. Department of Pathology, University of California San Diego, La Jolla, CA, USA

    Hiutung Chu

  16. Chiba University–UC San Diego Center for Mucosal Immunology, Allergy and Vaccines, La Jolla, CA, USA

    Hiutung Chu

  17. Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA

    Lara R. Dugas

  18. Division of Epidemiology and Biostatistics, School of Public Health, University of Cape Town, Cape Town, South Africa

    Lara R. Dugas

  19. Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel

    Eran Elinav

  20. Microbiome and Cancer Division, DKFZ, Heidelberg, Germany

    Eran Elinav

  21. Institute for Systems Biology, Seattle, WA, USA

    Sean M. Gibbons

  22. Department of Bioengineering, University of Washington, Seattle, WA, USA

    Sean M. Gibbons

  23. Department of Genome Sciences, University of Washington, Seattle, WA, USA

    Sean M. Gibbons

  24. eScience Institute, University of Washington, Seattle, WA, USA

    Sean M. Gibbons

  25. Seres Therapeutics, Inc., Cambridge, MA, USA

    Matthew R. Henn

  26. School of Food and Agriculture, University of Maine, Orono, ME, USA

    Suzanne L. Ishaq

  27. Microbes and Social Equity working group, Orono, ME, USA

    Suzanne L. Ishaq

  28. Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany

    Ruth E. Ley

  29. Benioff Center for Microbiome Medicine, Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA

    Susan V. Lynch

  30. Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel

    Eran Segal

  31. Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK

    Tim D. Spector

  32. ZOE Ltd, London, UK

    Tim D. Spector

  33. Holobiome, Boston, MA, USA

    Philip Strandwitz

  34. W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

    Jotham Suez

  35. Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada

    Carolina Tropini

  36. School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada

    Carolina Tropini

  37. Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA

    Katrine Whiteson

  38. Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA

    Rob Knight

  39. Shu Chien–Gene Lay Department of Bioengineering, University of California San Diego, San Diego, CA, USA

    Rob Knight

  40. Halıcıoğlu Data Science Institute, University of California San Diego, San Diego, CA, USA

    Rob Knight

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Correspondence to Jack A. Gilbert.

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Competing interests

J.A.G. is associated with Holobiome, BiomeSense, Bened Life and Sun Genomics. C.Y.C. is associated with Delve Bio and receives research support from Abbott Laboratories. P.S. is associated with Holobiome. E.E. and E.S. are associated with DayTwo. M.R.H. is associated with Seres Therapeutics. T.D.S. is associated with ZOE. S.V.L. is associated with Siolta Therapeutics. M.J.B. is associated with Seed Health, ProDermIQ and Elysium Health. M.B.A. is associated with Tiny Health. R.K. is associated with BiomeSense, GenCirq, DayTwo, Cybele and Biota.

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Gilbert, J.A., Azad, M.B., Bäckhed, F. et al. Clinical translation of microbiome research. Nat Med 31, 1099–1113 (2025). https://doi.org/10.1038/s41591-025-03615-9

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