Journal article
Strain displacement in microbiomes via ecological competition
- Abstract:
- Microorganisms commonly live in diverse communities where changes in composition can be critical for health, industry and the environment. Yet, what enables one strain to competitively replace another in these complex conditions remains poorly understood. Here we develop a mathematical model to determine general principles of strain displacement. Our modelling reveals that weak resource competition enables successful invasion while strong interference competition, for example, via antimicrobial production, enables successful displacement. We verify these predictions using in vitro assays with genetically engineered Escherichia coli . We then apply our principles to displace multidrug-resistant clinical isolates using strains that are equipped with a potent bacteriocin. Finally, we perform experiments with diverse human gut symbionts, which reveal that displacement relies on low resource competition not only between competing strains but also with the broader community, that is, limited nutrient blocking. These general rules for ecological success in microbial communities could be applied for targeted displacement of bacteria.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Files:
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(Preview, Version of record, pdf, 12.0MB, Terms of use)
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(Supplementary materials, zip, 479.6KB, Terms of use)
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- Publisher copy:
- 10.1038/s41564-025-02162-w
Authors
+ European Research Council
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- Funder identifier:
- https://ror.org/0472cxd90
- Grant:
- 787932
+ Swiss National Science Foundation
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- Funder identifier:
- https://ror.org/00yjd3n13
- Grant:
- P2EZP3_199916 and P500PB_210941
+ Wellcome Trust
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- Funder identifier:
- https://ror.org/029chgv08
- Grant:
- 209397/Z/17/Z
+ International Human Frontier Science Program Organization
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- Funder identifier:
- https://ror.org/02ebx7v45
- Grant:
- LT000798/2020
- Publisher:
- Springer Nature
- Journal:
- Nature Microbiology More from this journal
- Volume:
- 10
- Issue:
- 12
- Pages:
- 3122–3135
- Publication date:
- 2025-11-07
- Acceptance date:
- 2025-09-25
- DOI:
- EISSN:
-
2058-5276
- Language:
-
English
- Pubs id:
-
2324619
- UUID:
-
uuid_7c135336-42c0-49cf-8739-24fbb846bfbe
- Local pid:
-
pubs:2324619
- Source identifiers:
-
W4415988352
- Deposit date:
-
2025-11-12
- ARK identifier:
Terms of use
- Copyright holder:
- Bakkeren et al.
- Copyright date:
- 2025
- Rights statement:
- © The Author(s) 2025. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
- Licence:
- CC Attribution (CC BY)
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