Examining the healthy human microbiome concept

Raphaela Joos; Katy Boucher; Aonghus Lavelle; Manimozhiyan Arumugam; Martin J. Blaser; Marcus J. Claesson; Gerard Clarke; Paul D. Cotter; Luisa De Sordi; Maria G. Dominguez-Bello; Bas E. Dutilh; Stanislav D. Ehrlich; Tarini Shankar Ghosh; Colin Hill; Christophe Junot; Leo Lahti; Trevor D. Lawley; Tine R. Licht; Emmanuelle Maguin; Thulani P. Makhalanyane; Julian R. Marchesi; Jelle Matthijnssens; Jeroen Raes; Jacques Ravel; Anne Salonen; Pauline D. Scanlan; Andrey Shkoporov; Catherine Stanton; Ines Thiele; Igor Tolstoy; Jens Walter; Bo Yang; Natalia Yutin; Alexandra Zhernakova; Hub Zwart; Human Microbiome Action Consortium; Joël Doré; R. Paul Ross

doi:10.1038/s41579-024-01107-0

Examining the healthy human microbiome concept

Raphaela Joos
, Katy Boucher
, Aonghus Lavelle
, Manimozhiyan Arumugam
, Martin J. Blaser
, Marcus J. Claesson
, Gerard Clarke
, Paul D. Cotter
, Luisa De Sordi
, Maria G. Dominguez-Bello
, Bas E. Dutilh
, Stanislav D. Ehrlich
, Tarini Shankar Ghosh
, Colin Hill
, Christophe Junot
, Leo Lahti
, Trevor D. Lawley
, Tine R. Licht
, Emmanuelle Maguin
, Thulani P. Makhalanyane

Julian R. Marchesi, Jelle Matthijnssens, Jeroen Raes, Jacques Ravel, Anne Salonen, Pauline D. Scanlan, Andrey Shkoporov, Catherine Stanton, Ines Thiele, Igor Tolstoy, Jens Walter, Bo Yang, Natalia Yutin, Alexandra Zhernakova, Hub Zwart, Human Microbiome Action Consortium, Joël Doré, R. Paul Ross^*

^*Corresponding author for this work

National Food Institute

University College Cork
University of Copenhagen
Rutgers - The State University of New Jersey, New Brunswick
Teagasc - Irish Agriculture and Food Development Authority
Sorbonne Université
Utrecht University
University College London
Indraprastha Institute of Information Technology Delhi
Université Paris-Saclay
University of Turku
Wellcome Sanger Institute
Stellenbosch University
Imperial College London
KU Leuven
University of Maryland, Baltimore
University of Helsinki
National Institutes of Health
Jiangnan University
University of Groningen
Erasmus University Rotterdam
University of Trento
European Molecular Biology Laboratory
Université Paris Cité
University of Naples Federico II
EU Microbiome Regulatory Science Center
European Biomedical Research Institute of Salerno
European Foundation for the Study of Chronic Liver Failure
Technical University of Munich
Agence de Medicale Education
University of Southern Denmark
European Food Information Council
Odense University Hospital
Columbia University
University of Münster
Harvard University
Institut Gustave Roussy

Research output: Contribution to journal › Journal article › Research › peer-review

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.

Original language	English
Journal	Nature Reviews Microbiology
Volume	23
Pages (from-to)	192-205
Number of pages	14
ISSN	1740-1526
DOIs	https://doi.org/10.1038/s41579-024-01107-0
Publication status	Published - 2025

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1038/s41579-024-01107-0

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Joos, R., Boucher, K., Lavelle, A., Arumugam, M., Blaser, M. J., Claesson, M. J., Clarke, G., Cotter, P. D., De Sordi, L., Dominguez-Bello, M. G., Dutilh, B. E., Ehrlich, S. D., Ghosh, T. S., Hill, C., Junot, C., Lahti, L., Lawley, T. D., Licht, T. R., Maguin, E., ... Ross, R. P. (2025). Examining the healthy human microbiome concept. Nature Reviews Microbiology, 23, 192-205. https://doi.org/10.1038/s41579-024-01107-0

@article{9815bb5f1a924e09989d9aede4d4b604,

title = "Examining the healthy human microbiome concept",

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 {\textquoteleft}healthy{\textquoteright} 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.",

author = "Raphaela Joos and Katy Boucher and Aonghus Lavelle and Manimozhiyan Arumugam and Blaser, \{Martin J.\} and Claesson, \{Marcus J.\} and Gerard Clarke and Cotter, \{Paul D.\} and \{De Sordi\}, Luisa and Dominguez-Bello, \{Maria G.\} and Dutilh, \{Bas E.\} and Ehrlich, \{Stanislav D.\} and Ghosh, \{Tarini Shankar\} and Colin Hill and Christophe Junot and Leo Lahti and Lawley, \{Trevor D.\} and Licht, \{Tine R.\} and Emmanuelle Maguin and Makhalanyane, \{Thulani P.\} and Marchesi, \{Julian R.\} and Jelle Matthijnssens and Jeroen Raes and Jacques Ravel and Anne Salonen and Scanlan, \{Pauline D.\} and Andrey Shkoporov and Catherine Stanton and Ines Thiele and Igor Tolstoy and Jens Walter and Bo Yang and Natalia Yutin and Alexandra Zhernakova and Hub Zwart and \{Human Microbiome Action Consortium\} and Manimozhiyan Arumugam and Francesco Asnicar and Athanasios Typas and Fay Betsou and Herv{\'e} Blotti{\`e}re and Peer Bork and Katy Boucher and Isabelle Boutron and Federica Carraturo and Marcus Claesson and Magali Cordaillat-Simmons and Jo{\"e}l Dor{\'e} and Celine Druart and Alessio Fasano and Yolanda Godoy and Dirk Haller and Zahra Hassani and Hazenbrink, \{Di{\"e}nty H. M. J.\} and Colin Hill and Mads Israelsen and Anandhi Iyappan and Alexander Jarde and Raphaela Joos and Stephan Kampshoff and Aleksander Krag and Aicha Kriaa and Aonghus Lavelle and Emmanuelle Maguin and Amira Metwaly and Vitalina Morozova and Federica Pinto and Nicolas Pons and Prost, \{Pierre Louis\} and Philippe Ravaud and Moez Rhimi and Julie Rodriguez and Ross, \{R. Paul\} and Arjun Sarati and Robert Schierwagen and Nicola Segata and Debora Serra and Jonel Trebicka and Corrado Vecchi and Patrick Veiga and Laurence Zitvogel and Hub Zwart and Lisa Derosa and Jo{\"e}l Dor{\'e} and Ross, \{R. Paul\}",

note = "Publisher Copyright: {\textcopyright} Springer Nature Limited 2024.",

year = "2025",

doi = "10.1038/s41579-024-01107-0",

language = "English",

volume = "23",

pages = "192--205",

journal = "Nature Reviews Microbiology",

issn = "1740-1526",

publisher = "Nature Research",

}

Joos, R, Boucher, K, Lavelle, A, Arumugam, M, Blaser, MJ, Claesson, MJ, Clarke, G, Cotter, PD, De Sordi, L, Dominguez-Bello, MG, Dutilh, BE, Ehrlich, SD, Ghosh, TS, Hill, C, Junot, C, Lahti, L, Lawley, TD, Licht, TR, Maguin, E, Makhalanyane, TP, Marchesi, JR, Matthijnssens, J, Raes, J, Ravel, J, Salonen, A, Scanlan, PD, Shkoporov, A, Stanton, C, Thiele, I, Tolstoy, I, Walter, J, Yang, B, Yutin, N, Zhernakova, A, Zwart, H, Human Microbiome Action Consortium, Doré, J & Ross, RP 2025, 'Examining the healthy human microbiome concept', Nature Reviews Microbiology, vol. 23, pp. 192-205. https://doi.org/10.1038/s41579-024-01107-0

TY - JOUR

T1 - Examining the healthy human microbiome concept

AU - Joos, Raphaela

AU - Boucher, Katy

AU - Lavelle, Aonghus

AU - Arumugam, Manimozhiyan

AU - Blaser, Martin J.

AU - Claesson, Marcus J.

AU - Clarke, Gerard

AU - Cotter, Paul D.

AU - De Sordi, Luisa

AU - Dominguez-Bello, Maria G.

AU - Dutilh, Bas E.

AU - Ehrlich, Stanislav D.

AU - Ghosh, Tarini Shankar

AU - Hill, Colin

AU - Junot, Christophe

AU - Lahti, Leo

AU - Lawley, Trevor D.

AU - Licht, Tine R.

AU - Maguin, Emmanuelle

AU - Makhalanyane, Thulani P.

AU - Marchesi, Julian R.

AU - Matthijnssens, Jelle

AU - Raes, Jeroen

AU - Ravel, Jacques

AU - Salonen, Anne

AU - Scanlan, Pauline D.

AU - Shkoporov, Andrey

AU - Stanton, Catherine

AU - Thiele, Ines

AU - Tolstoy, Igor

AU - Walter, Jens

AU - Yang, Bo

AU - Yutin, Natalia

AU - Zhernakova, Alexandra

AU - Zwart, Hub

AU - Human Microbiome Action Consortium

AU - Doré, Joël

AU - Ross, R. Paul

A2 - Arumugam, Manimozhiyan

A2 - Asnicar, Francesco

A2 - Typas, Athanasios

A2 - Betsou, Fay

A2 - Blottière, Hervé

A2 - Bork, Peer

A2 - Boucher, Katy

A2 - Boutron, Isabelle

A2 - Carraturo, Federica

A2 - Claesson, Marcus

A2 - Cordaillat-Simmons, Magali

A2 - Doré, Joël

A2 - Druart, Celine

A2 - Fasano, Alessio

A2 - Godoy, Yolanda

A2 - Haller, Dirk

A2 - Hassani, Zahra

A2 - Hazenbrink, Diënty H. M. J.

A2 - Hill, Colin

A2 - Israelsen, Mads

A2 - Iyappan, Anandhi

A2 - Jarde, Alexander

A2 - Joos, Raphaela

A2 - Kampshoff, Stephan

A2 - Krag, Aleksander

A2 - Kriaa, Aicha

A2 - Lavelle, Aonghus

A2 - Maguin, Emmanuelle

A2 - Metwaly, Amira

A2 - Morozova, Vitalina

A2 - Pinto, Federica

A2 - Pons, Nicolas

A2 - Prost, Pierre Louis

A2 - Ravaud, Philippe

A2 - Rhimi, Moez

A2 - Rodriguez, Julie

A2 - Ross, R. Paul

A2 - Sarati, Arjun

A2 - Schierwagen, Robert

A2 - Segata, Nicola

A2 - Serra, Debora

A2 - Trebicka, Jonel

A2 - Vecchi, Corrado

A2 - Veiga, Patrick

A2 - Zitvogel, Laurence

A2 - Zwart, Hub

A2 - Derosa, Lisa

PY - 2025

Y1 - 2025

N2 - 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.

AB - 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.

UR - https://www.nature.com/articles/s41579-024-01145-8

U2 - 10.1038/s41579-024-01107-0

DO - 10.1038/s41579-024-01107-0

M3 - Journal article

C2 - 39443812

AN - SCOPUS:85207670282

SN - 1740-1526

VL - 23

SP - 192

EP - 205

JO - Nature Reviews Microbiology

JF - Nature Reviews Microbiology

ER -

Examining the healthy human microbiome concept

Abstract

UN SDGs

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