Microbiome definition re-visited: old concepts and new challenges
Open accessAbstract
The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role.
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Complex microbial communities exist everywhere in nature and microorganisms have been mutating and evolving to adapt to ever-changing ecosystems.
“Complex microbial communities exist everywhere in nature and, over the years, microorganisms have been mutating and evolving to adapt to ever-changing ecosystems [1,2].”
From Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking (2025) · cites this paper as [1]
The historical overview says microorganisms are widespread in natural environments and occur in complex assemblages. The Host-microbe coevolution section describes evolutionary adaptation, but the cited passages do not establish the claim that microorganisms have been mutating to adapt to ever-changing ecosystems. No page numbers are available in our copy. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThese interactions are critical for adaptation to stress, survival, evolution, and the expression of diverse phenotypes.
“These interactions are critical for adaptation to stress, survival, evolution, and the expression of diverse phenotypes [1,10,22,36,37].”
From Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking (2025) · cites this paper as [1]
The ‘Microbial networks and interactions’ section says interactions affect microbial fitness, support survival in competitive environments, and can shape phenotypes. That section and the Conclusions also link interactions to evolutionary dynamics. The passages found do not establish that interactions are critical for adaptation to stress; the paper instead says stress-tolerance strategies can influence the outcomes of interactions. Page numbers were unavailable in our copy. (LLM, conf=0.85)
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Microbial-derived metabolites as a risk factor of age-related cognitive decline and dementia
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- Authors
- Berg, G., Rybakova, D., Fischer, D., Cernava, T., Vergès, M.-C. C., Charles, T., Chen, X., Cocolin, L., Eversole, K., Corral, G. H., Kazou, M., Kinkel, L., Lange, L., Lima, N., Loy, A., Macklin, J. A., Maguin, E., Mauchline, T., McClure, R., Mitter, B., Ryan, M., Sarand, I., Smidt, H., Schelkle, B., Roume, H., Kiran, G. S., Selvin, J., Souza, R. S. C. D., van Overbeek, L., Singh, B. K., Wagner, M., Walsh, A., Sessitsch, A., & Schloter, M.
- Affiliations
- Graz University of Technology (AT)
- Helmholtz Munich (DE)
- University of Waterloo (CA)
- Guizhou University (CN)
- European Food Information Council (BE)
- Département Microbiologie et Chaîne Alimentaire (FR)
- University of Minnesota (US)
- University of Vienna (AT)
- Agriculture and Agri-Food Canada (CA)
- AgroParisTech (FR)
- Rothamsted Research (GB)
- Pacific Northwest National Laboratory (US)
- AIT Austrian Institute of Technology GmbH (AT)
- CAB International (GB)
- Tallinn University of Technology (EE)
- Wageningen University & Research (NL)
- MetaGenoPolis (FR)
- Pondicherry University (IN)
- Universidade Estadual de Campinas (UNICAMP) (BR)
- Western Sydney University (AU)
- Teagasc - The Irish Agriculture and Food Development Authority (IE)
- Corresponding author
- Berg, Gabriele
- Schloter, Michael
- ORCID
- Berg, Gabriele
- Rybakova, Daria
- Fischer, Doreen
- Cernava, Tomislav
- Charles, Trevor
- Chen, Xiaoyulong
- Cocolin, Luca
- Eversole, Kellye
- Kinkel, Linda
- Lange, Lene
- Loy, Alexander
- Macklin, James A.
- Maguin, Emmanuelle
- Mauchline, Tim
- McClure, Ryan
- Mitter, Birgit
- Ryan, Matthew
- Sarand, Inga
- Smidt, Hauke
- Roume, Hugo
- Kiran, G. Seghal
- Selvin, Joseph
- Souza, Rafael Soares Correa de
- Singh, Brajesh K.
- Wagner, Michael
- Walsh, Aaron
- Sessitsch, Angela
- Schloter, Michael
- Venue
- Microbiome
- Published
- 2020-06-30
- Volume
- 8
- Issue
- 1
- Pages
- 103-103
- ISSN
- 2049-2618 (ISSN-L)
- PMC
- PMC7329523
- OpenAlex
- W3040245690
- Cited by
- 2,275
- References
- 201
- Citations by year
- 2026: 329 · 2025: 443 · 2024: 444 · 2023: 425 · 2022: 367 · 2021: 230 · 2020: 34 · 2019: 1 · 2017: 2
- FWCI
- 140.07
- Type
- journal article
- Language
- en
- Update notices
- correction (2020-08-20)
- Open access
- gold
- doi.org
- Locations
- Microbiome (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion, cc-by)
- Arrow@dit (Dublin Institute of Technology) (acceptedVersion)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion, other-oa)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion, cc-by)
- HAL (submittedVersion, cc-by)
- HAL (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Site cant be reached (submittedVersion, cc-by)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, other-oa)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, cc-by-nc-nd)
- T-Stór (Teagasc) (submittedVersion, cc-by-nc-sa)
- Lenus, The Irish Health Repository (Dr Steevens Hospital Library) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
- Funders
- Horizon 2020 (European Union's Horizon 2020)
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
- Keywords
- microbiota, core microbiome, keystone species, microbial community dynamics, microbial network stability, host-microbe interactions, interspecies interactions, planetary health, anthropogenic change
- MeSH terms
- Terminology as Topic, Surveys and Questionnaires, Microbiota
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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