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Community structure follows simple assembly rules in microbial microcosms
Open accessPublished version of a preprint
Abstract
Microorganisms typically form diverse communities of interacting species, whose activities have tremendous impact on the plants, animals and humans they associate with. The ability to predict the structure of these complex communities is crucial to understanding and managing them. Here, we propose a simple, qualitative assembly rule that predicts community structure from the outcomes of competitions between small sets of species, and experimentally assess its predictive power using synthetic microbial communities composed of up to eight soil bacterial species. Nearly all competitions resulted in a unique, stable community, whose composition was independent of the initial species fractions. Survival in three-species competitions was predicted by the pairwise outcomes with an accuracy of ~90%. Obtaining a similar level of accuracy in competitions between sets of seven or all eight species required incorporating additional information regarding the outcomes of the three-species competitions. Our results demonstrate experimentally the ability of a simple bottom-up approach to predict community structure. Such an approach is key for anticipating the response of communities to changing environments, designing interventions to steer existing communities to more desirable states and, ultimately, rationally designing communities de novo.
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“In procaryotes, intercellular communication and multicellular coordination are widespread and influence the expression and intensity of multiple phenotypes [6,8,9,10,11,12].”
From Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking (2025) · cites this paper as [12]
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Metadata
- Authors
- Friedman, J., Higgins, L. M., & Gore, J.
- Affiliations
- Massachusetts Institute of Technology (US)
- Corresponding author
- Friedman, Jonathan
- Gore, Jeff
- Venue
- Nature Ecology & Evolution
- Published
- 2017-03-27
- Volume
- 1
- Issue
- 5
- Pages
- 109-109
- ISSN
- 2397-334X (ISSN-L)
- OpenAlex
- W2952570005
- Cited by
- 557
- References
- 34
- Citations by year
- 2026: 56 · 2025: 51 · 2024: 63 · 2023: 62 · 2022: 76 · 2021: 81 · 2020: 62 · 2019: 54 · 2018: 38 · 2017: 14
- FWCI
- 34.63
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- Funders
- National Science Foundation (CAREER)
- National Institutes of Health (NIH DP2)
- Defense Advanced Research Projects Agency
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Physical Sciences › Environmental Science › Nature and Landscape Conservation › Ecology and Vegetation Dynamics Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- microbial community assembly, synthetic microbial communities, soil bacteria, pairwise competition, species interactions, community stability, community design, microbial ecology
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