Clinical translation of microbiome research

Jack A Gilbert^{1

2

3}, Meghan B Azad^{4

5

6}, Fredrik Bäckhed^{7

8}, Martin J Blaser^{6

9}, Mariana Byndloss^{10

11}, Charles Y Chiu^{12

13

14}, Hiutung Chu^{15

16

17}, Lara R Dugas^{18

19}, Eran Elinav^{20

21}, Sean M Gibbons^{22

23

24

25}, Katharine E Gilbert¹⁵, Matthew R Henn²⁶, Suzanne L Ishaq^{27

28}, Ruth E Ley²⁹, Susan V Lynch³⁰, Eran Segal³¹, Tim D Spector^{32

33}, Philip Strandwitz³⁴, Jotham Suez³⁵, Carolina Tropini^{6

36

37}, Katrine Whiteson³⁸, Rob Knight^{39

15

40

41

42}

Affiliations

¹ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. gilbertjack@gmail.com.
² Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. gilbertjack@gmail.com.
³ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. gilbertjack@gmail.com.
⁴ Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada.
⁵ Manitoba Interdisciplinary Lactation Centre, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
⁶ CIFAR Humans & the Microbiome Program, CIFAR, Toronto, Ontario, Canada.
⁷ Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
⁸ Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden.
⁹ Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA.
¹⁰ Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
¹¹ Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
¹² Department of Laboratory Medicine, University of California, San Fransisco, San Francisco, CA, USA.
¹³ Department of Medicine, Division of Infectious Diseases, University of California, San Fransisco, San Francisco, CA, USA.
¹⁴ Chan-Zuckerberg Biohub, San Francisco, CA, USA.
¹⁵ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
¹⁶ Department of Pathology, University of California San Diego, La Jolla, CA, USA.
¹⁷ Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines, La Jolla, CA, USA.
¹⁸ Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA.
¹⁹ Division of Epidemiology and Biostatistics, School of Public Health, University of Cape Town, Cape Town, South Africa.
²⁰ Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
²¹ Microbiome and Cancer Division, DKFZ, Heidelberg, Germany.
²² Institute for Systems Biology, Seattle, WA, USA.
²³ Department of Bioengineering, University of Washington, Seattle, WA, USA.
²⁴ Department of Genome Sciences, University of Washington, Seattle, WA, USA.
²⁵ eScience Institute, University of Washington, Seattle, WA, USA.
²⁶ Seres Therapeutics, Inc., Cambridge, MA, USA.
²⁷ School of Food and Agriculture, University of Maine, Orono, ME, USA.
²⁸ Microbes and Social Equity working group, Orono, ME, USA.
²⁹ Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany.
³⁰ Benioff Center for Microbiome Medicine, Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
³¹ Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
³² Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
³³ ZOE Ltd, London, UK.
³⁴ Holobiome, Boston, MA, USA.
³⁵ W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
³⁶ Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
³⁷ School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
³⁸ Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA.
³⁹ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
⁴⁰ Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
⁴¹ Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, San Diego, CA, USA.
⁴² Halıcıoğlu Data Science Institute, University of California San Diego, San Diego, CA, USA.

PMID: 40217076
DOI: 10.1038/s41591-025-03615-9

Review

Clinical translation of microbiome research

Jack A Gilbert et al. Nat Med. 2025 Apr.

. 2025 Apr;31(4):1099-1113.

doi: 10.1038/s41591-025-03615-9. Epub 2025 Apr 11.

Authors

Affiliations

¹ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. gilbertjack@gmail.com.
² Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. gilbertjack@gmail.com.
³ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. gilbertjack@gmail.com.
⁴ Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada.
⁵ Manitoba Interdisciplinary Lactation Centre, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada.
⁶ CIFAR Humans & the Microbiome Program, CIFAR, Toronto, Ontario, Canada.
⁷ Wallenberg Laboratory and Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
⁸ Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden.
⁹ Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA.
¹⁰ Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
¹¹ Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
¹² Department of Laboratory Medicine, University of California, San Fransisco, San Francisco, CA, USA.
¹³ Department of Medicine, Division of Infectious Diseases, University of California, San Fransisco, San Francisco, CA, USA.
¹⁴ Chan-Zuckerberg Biohub, San Francisco, CA, USA.
¹⁵ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
¹⁶ Department of Pathology, University of California San Diego, La Jolla, CA, USA.
¹⁷ Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines, La Jolla, CA, USA.
¹⁸ Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA.
¹⁹ Division of Epidemiology and Biostatistics, School of Public Health, University of Cape Town, Cape Town, South Africa.
²⁰ Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
²¹ Microbiome and Cancer Division, DKFZ, Heidelberg, Germany.
²² Institute for Systems Biology, Seattle, WA, USA.
²³ Department of Bioengineering, University of Washington, Seattle, WA, USA.
²⁴ Department of Genome Sciences, University of Washington, Seattle, WA, USA.
²⁵ eScience Institute, University of Washington, Seattle, WA, USA.
²⁶ Seres Therapeutics, Inc., Cambridge, MA, USA.
²⁷ School of Food and Agriculture, University of Maine, Orono, ME, USA.
²⁸ Microbes and Social Equity working group, Orono, ME, USA.
²⁹ Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany.
³⁰ Benioff Center for Microbiome Medicine, Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
³¹ Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
³² Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
³³ ZOE Ltd, London, UK.
³⁴ Holobiome, Boston, MA, USA.
³⁵ W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
³⁶ Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
³⁷ School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
³⁸ Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA.
³⁹ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
⁴⁰ Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
⁴¹ Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, San Diego, CA, USA.
⁴² Halıcıoğlu Data Science Institute, University of California San Diego, San Diego, CA, USA.

PMID: 40217076
DOI: 10.1038/s41591-025-03615-9

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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Conflict of interest statement

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.

References

1. Chang, D. et al. Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles. Nat. Commun. 15, 7447 (2024). - PubMed - PMC - DOI
1. Hickman, B. et al. Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants. Nat. Commun. 15, 8323 (2024). - PubMed - PMC - DOI
1. Schmartz, G. P. et al. Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics. Nat. Commun. 15, 8261 (2024). - PubMed - PMC - DOI
1. Weingarden, A. et al. Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection. Microbiome 3, 10 (2015). - PubMed - PMC - DOI
1. Ross, F. C. et al. The interplay between diet and the gut microbiome: implications for health and disease. Nat. Rev. Microbiol. 22, 671–686 (2024). - PubMed - DOI

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Clinical translation of microbiome research

Affiliations

Clinical translation of microbiome research

Authors

Affiliations

Abstract

Conflict of interest statement

References

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources

Miscellaneous