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  • Perspective
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Examining the healthy human microbiome concept

Nature Reviews Microbiology volume 23, pages 192–205 (2025)Cite this article

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An Author Correction to this article was published on 16 December 2024

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Abstract

Human microbiomes are essential to health throughout the lifespan and are increasingly recognized and studied for their roles in metabolic, immunological and neurological processes. Although the full complexity of these microbial communities is not fully understood, their clinical and industrial exploitation is well advanced and expanding, needing greater oversight guided by a consensus from the research community. One of the most controversial issues in microbiome research is the definition of a ‘healthy’ human microbiome. This concept is complicated by the microbial variability over different spatial and temporal scales along with the challenge of applying a unified definition to the spectrum of healthy microbiome configurations. In this Perspective, we examine the progress made and the key gaps that remain to be addressed to fully harness the benefits of the human microbiome. We propose a road map to expand our knowledge of the microbiome–health relationship, incorporating epidemiological approaches informed by the unique ecological characteristics of these communities.

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Fig. 1: Using the microbiome as a reporter and predictor of health.
Fig. 2: Satellite model for microbiome research.

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Acknowledgements

The authors thank all those who helped facilitate the Human Microbiome Action (HMA) workshop on 6 October 2022, including workshop attendees, postdoctoral scribes, audiovisual experts and staff of the River Lee Hotel in Cork. This publication has been supported by the project entitled International Human Microbiome Coordination and Support Action (IHMCSA), which receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 964590.

Author information

Authors and Affiliations

  1. APC Microbiome Ireland, University College Cork, Cork, Ireland

    Raphaela Joos, Katy Boucher, Aonghus Lavelle, Marcus J. Claesson, Gerard Clarke, Paul D. Cotter, Colin Hill, Pauline D. Scanlan, Andrey Shkoporov, Catherine Stanton, Ines Thiele, Jens Walter, Marcus Claesson, Aonghus Lavelle & R. Paul Ross

  2. School of Microbiology, University College Cork, Cork, Ireland

    Raphaela Joos, Marcus J. Claesson, Colin Hill, Pauline D. Scanlan, Andrey Shkoporov, Jens Walter, Marcus Claesson & R. Paul Ross

  3. Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland

    Aonghus Lavelle & Aonghus Lavelle

  4. Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Manimozhiyan Arumugam, Vitalina Morozova & Arjun Sarati

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

    Martin J. Blaser

  6. Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland

    Gerard Clarke

  7. Teagasc Food Research Centre and VistaMilk SFI Research Centre, Moorepark, Fermoy, Moorepark, Ireland

    Paul D. Cotter & Catherine Stanton

  8. Centre de Recherche Saint Antoine, Sorbonne Université, INSERM, Paris, France

    Luisa De Sordi

  9. Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA

    Maria G. Dominguez-Bello

  10. Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany

    Bas E. Dutilh

  11. Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands

    Bas E. Dutilh

  12. Université Paris-Saclay, INRAE, MetaGenoPolis (MGP), Jouy-en-Josas, France

    Stanislav D. Ehrlich, Hervé Blottière, Nicolas Pons, Patrick Veiga & Joël Doré

  13. Department of Clinical and Movement Neurosciences, University College London, London, UK

    Stanislav D. Ehrlich

  14. Department of Computational Biology, Indraprastha Institute of Information Technology Delhi (IIIT-Delhi), New Delhi, India

    Tarini Shankar Ghosh

  15. Département Médicaments et Technologies pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, MetaboHUB, Gif-sur-Yvette, France

    Christophe Junot

  16. Department of Computing, University of Turku, Turku, Finland

    Leo Lahti

  17. Host–Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK

    Trevor D. Lawley

  18. National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark

    Tine R. Licht

  19. Université Paris-Saclay, INRAE, AgroParisTech, MICALIS, Jouy-en-Josas, France

    Emmanuelle Maguin, Hervé Blottière, Aicha Kriaa, Moez Rhimi & Joël Doré

  20. Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa

    Thulani P. Makhalanyane

  21. Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK

    Julian R. Marchesi

  22. KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium

    Jelle Matthijnssens & Jeroen Raes

  23. Vlaams Instituut voor Biotechnologie (VIB) Center for Microbiology, Leuven, Belgium

    Jeroen Raes

  24. Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA

    Jacques Ravel

  25. Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA

    Jacques Ravel

  26. Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland

    Anne Salonen

  27. School of Medicine, University of Ireland, Galway, Ireland

    Ines Thiele

  28. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

    Igor Tolstoy & Natalia Yutin

  29. Department of Medicine, University College Cork, Cork, Ireland

    Jens Walter

  30. State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China

    Bo Yang

  31. School of Food Science and Technology, Jiangnan University, Wuxi, China

    Bo Yang

  32. Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands

    Alexandra Zhernakova

  33. Erasmus School of Philosophy, Erasmus University Rotterdam, Rotterdam, The Netherlands

    Hub Zwart

  34. Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy

    Francesco Asnicar, Federica Pinto & Nicola Segata

  35. Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

    Athanasios Typas & Diënty H. M. J. Hazenbrink

  36. Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

    Athanasios Typas, Peer Bork, Diënty H. M. J. Hazenbrink & Anandhi Iyappan

  37. CRBIP, Institut Pasteur, Université Paris-Cité, Paris, France

    Fay Betsou

  38. Nantes Université/INRAE, UMR 1280, PhAN, Nantes, France

    Hervé Blottière

  39. Max Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany

    Peer Bork & Diënty H. M. J. Hazenbrink

  40. Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany

    Peer Bork

  41. Université Paris Cité and Université Sorbonne Paris Nord, INSERM, INRAe, Centre for Research in Epidemiology and Statistics (CRESS), Hopital Hotel Dieu, Paris, France

    Isabelle Boutron, Alexander Jarde & Philippe Ravaud

  42. Centre d’Epidemiologie Clinique, Hopital Hotel Dieu, Assistance Publique des Hopitaux de Paris, Paris, France

    Isabelle Boutron, Alexander Jarde & Philippe Ravaud

  43. Department of Biology, Complesso Universitario Monte Sant’Angelo, University of Naples Federico II, Naples, Italy

    Federica Carraturo

  44. Pharmabiotic Research Institute, EU Microbiome Regulatory Science Center, Narbonne, France

    Magali Cordaillat-Simmons, Celine Druart & Julie Rodriguez

  45. European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy

    Alessio Fasano

  46. Division of Pediatric Gastroenterology and Nutrition, Department of Pediatrics, MassGeneral Hospital for Children, Harvard Medical School, Boston, MA, USA

    Alessio Fasano & Corrado Vecchi

  47. Mucosal Immunology and Biology Research Center, MassGeneral Hospital, Boston, MA, USA

    Alessio Fasano

  48. European Foundation for the Study of Chronic Liver Failure (EF-CLIF), Barcelona, Spain

    Yolanda Godoy, Robert Schierwagen & Jonel Trebicka

  49. Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany

    Dirk Haller & Amira Metwaly

  50. ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany

    Dirk Haller

  51. KPL-Paris, Agence de Medicale Education, Paris, France

    Zahra Hassani & Pierre-Louis Prost

  52. Centre for Liver Research, Department of Gastroenterology and Hepatology, Odense University Hospital, Odense, Denmark

    Mads Israelsen & Aleksander Krag

  53. Department for Clinical Research, University of Southern Denmark, Odense, Denmark

    Mads Israelsen & Aleksander Krag

  54. European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

    Anandhi Iyappan

  55. Department of Health Sciences, University of York, York, UK

    Alexander Jarde

  56. European Food Information Council, Brussels, Belgium

    Stephan Kampshoff & Debora Serra

  57. Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA

    Philippe Ravaud

  58. Department of Internal Medicine B, University of Münster, Münster, Germany

    Robert Schierwagen & Jonel Trebicka

  59. Danone Nutricia Research, Gif-sur-Yvette, France

    Patrick Veiga

  60. Institute Gustave Roussy, Villejuif, France

    Laurence Zitvogel & Lisa Derosa

  61. Institut National de la Santé Et de la Recherche Médicale (INSERM), UMR 1015, ClinicObiome, Équipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France

    Laurence Zitvogel & Lisa Derosa

  62. Université Paris-Saclay, Ile-de-France, France

    Laurence Zitvogel & Lisa Derosa

  63. Center of Clinical Investigations in Biotherapies of Cancer (BIOTHERIS), Villejuif, France

    Laurence Zitvogel & Lisa Derosa

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  37. R. Paul Ross
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Consortia

Human Microbiome Action Consortium

  • Manimozhiyan Arumugam
  • , Francesco Asnicar
  • , Athanasios Typas
  • , Fay Betsou
  • , Hervé Blottière
  • , Peer Bork
  • , Katy Boucher
  • , Isabelle Boutron
  • , Federica Carraturo
  • , Marcus Claesson
  • , Magali Cordaillat-Simmons
  • , Joël Doré
  • , Celine Druart
  • , Alessio Fasano
  • , Yolanda Godoy
  • , Dirk Haller
  • , Zahra Hassani
  • , Diënty H. M. J. Hazenbrink
  • , Colin Hill
  • , Mads Israelsen
  • , Anandhi Iyappan
  • , Alexander Jarde
  • , Raphaela Joos
  • , Stephan Kampshoff
  • , Aleksander Krag
  • , Aicha Kriaa
  • , Aonghus Lavelle
  • , Emmanuelle Maguin
  • , Amira Metwaly
  • , Vitalina Morozova
  • , Federica Pinto
  • , Nicolas Pons
  • , Pierre-Louis Prost
  • , Philippe Ravaud
  • , Moez Rhimi
  • , Julie Rodriguez
  • , R. Paul Ross
  • , Arjun Sarati
  • , Robert Schierwagen
  • , Nicola Segata
  • , Debora Serra
  • , Jonel Trebicka
  • , Corrado Vecchi
  • , Patrick Veiga
  • , Laurence Zitvogel
  • , Hub Zwart
  •  & Lisa Derosa

Contributions

R.J., K.B., A.L. and R.P.R. wrote the article. All authors contributed substantially to discussion of the content, and reviewed and edited the manuscript before submission.

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Correspondence to R. Paul Ross.

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M.J.C. and P.D.C. are co-founders of SeqBiome Ltd. The remaining authors declare no competing interests.

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Nature Reviews Microbiology thanks Eugene B. Chang, who co-reviewed with Orlando DeLeon, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Joos, R., Boucher, K., Lavelle, A. et al. Examining the healthy human microbiome concept. Nat Rev Microbiol 23, 192–205 (2025). https://doi.org/10.1038/s41579-024-01107-0

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