Food, Global Health Reading time 7 min
Predicting the Emergence of New Communities in the Stable Environment of the Human Gut Microbiota
The human gut microbiota can display considerable variability in its microbial composition, even though it resides in a relatively stable environment.
Published on 13 February 2026
A single environment can sometimes harbour markedly different microbial communities.
A well-known example is the human gut microbiome. The same environment, such as the human gut, can give rise to distinct types of communities, often grouped into so-called enterotypes. It remains unclear why one individual develops one type rather than another, and this variation cannot be fully explained by genetics, country of origin, or diet.
Explaining the Phenomenon in the Human Gut Microbiota
To account for this phenomenon in the human microbiota, researchers from the INRAE PROSE unit hypothesised that the explanation might lie in multistability. Multistability is a phenomenon commonly observed in natural ecosystems, yet until now it had never been experimentally demonstrated in the human gut microbiota.
In a multistable system, several stable states can coexist under identical conditions, and it is the system’s history (its life history) that determines the state ultimately observed. A classic example is the Sahara — often described as a laboratory for climate change — which alternates between periods of intense greening and phases of extreme aridity, revealing a multistable state that shows that similar environmental conditions can lead to very different outcomes depending on past dynamics.
In order to verify this hypothesis regarding the differences observed in human gut microbiota, researchers from the INRAE PROSE unit constructed a small synthetic community composed of three well-characterised gut bacteria: Blautia hydrogenotrophica, Bacteroides thetaiotaomicron, and Roseburia intestinalis.
Experiments were conducted to investigate the behaviour (metabolic strategies) of these three bacterial types, which evolved in response to environmental changes — changes that were themselves induced by the bacteria’s own growth and activity.
The researchers demonstrated that this community could reach different stable compositions even when cultured in the same medium under identical conditions. This can be explained by the ability of microbes to modify the way they utilise available nutrients depending on what is present in their environment — a behaviour first described by Jacques Monod more than 70 years ago. While this concept is well established at the level of individual microorganisms, the researchers shows how such mechanisms can shape the dynamics of an entire community.
When microorganisms exploit different nutrients (for example glucose, mannose, trehalose, pyruvate, or glutamate), competition is limited and coexistence is possible. When they switch to using the same nutrient, competition intensifies and one species often becomes dominant. This leads to distinct yet stable community compositions within the same environment.
Modelling Based on Biological Data
To carry out these studies, the researchers performed in vitro experiments using a range of techniques (metabolic analyses, 16S rRNA analysis, flow cytometry, and RNA sequencing) in order to generate data for the integration and calibration of a mathematical model of the microbial community.
Using this model, the researchers were able to explore a wide variety of conditions and validate the multistability hypothesis as an explanation for the establishment of different communities within the same living environment — namely, the human gut.
The results of this study, conducted by researchers from the INRAE PROSE unit in collaboration with the Laboratory of Microbial Systems Ecology led by Karoline Faust at KU Leuven (Belgium), were published in Nature Communications under the title: “Emergence of alternative states in a synthetic human gut microbial community.”
Take the keystone concept further!
This work, published in Nature Reviews Microbiology in January 2026, was conducted by researchers from the INRAE PROSE unit in collaboration with the Laboratory of Microbial Systems Ecology at KU Leuven (Belgium). It focuses on the concept of keystone species and was carried out in parallel with the multistability study presented above.
Nature Reviews Microbiology: The Keystone Species Concept Revisited — Insights into Microbial Community Dynamics and Control
(Garza, D.R., Gonze, D. & Faust, K. Keystone concept revisited: insights into microbial community dynamics and control. Nat Rev Microbiol (2026). doi.org/10.1038/s41579-025-01266-8)
Interview with Daniel-Rios Garza, INRAE Researcher, PROSE Unit.
Why did you undertake this work? Is there a historical background to it?
This article is a perspective arising from the observation that the concept of a keystone species is not clearly defined in microbial ecology.
We sought to revisit this concept using the data, models, and computational approaches currently available, and to clarify how it should be applied to microbial communities.
What are the main findings?
We propose a clear definition of keystone taxa and functions that remains faithful to the original idea introduced by ecologist Robert Paine: elements within a community that exert a disproportionately large impact relative to their abundance.
More precisely, we define keystone elements as taxa or functions whose removal or alteration produces greater effects on the community as a whole than comparable changes affecting any other taxon or function.
This definition enables comparison across species, genes, and functions. Overall, we show that the keystone concept remains highly valuable in microbiology. However, many of the methods currently used to identify keystone species have significant limitations and require more robust experimental validation.
What methods did you use to achieve your objectives?
As a perspective article, this work focused on critically reviewing existing evidence and identifying gaps in current knowledge. We examined the principal approaches used to identify keystone species and discussed the insights that can be drawn from theoretical models.
In addition, we proposed new methods based on simulations of microbial community metabolism. By modelling how species transform nutrients and exchange metabolites, we can computationally remove species one by one and measure the impact of their removal on the remainder of the community.
This approach makes it possible to identify species or functions that exert a disproportionate influence on community structure and behaviour.
We also discussed, in the article, the implications of keystone species for the control and engineering of microbial communities.
References :
- Garza, D.R., Liu, B., van de Velde, C. et al. Emergence of alternative states in a synthetic human gut microbial community. Nat Commun 17, 326 (2026). doi.org/10.1038/s41467-025-67036-5
- Garza, D.R., Gonze, D. & Faust, K. Keystone concept revisited: insights into microbial community dynamics and control. Nat Rev Microbiol (2026). doi.org/10.1038/s41579-025-01266-8