Explaining Microbial Population Genomics through Phage Predation
Open accessAbstract
The remarkable differences that have been detected by metagenomics in the genomes of strains of the same bacterial species are difficult to reconcile with the widely accepted paradigm that periodic selection within bacterial populations will regularly purge genomic diversity by clonal replacement. We have found that many of the genes that differ between strains affect regions that are potential phage recognition targets. We therefore propose the constant-diversity dynamics model, in which the diversity of prokaryotic populations is preserved by phage predation. We provide supporting evidence for this model from metagenomics, mathematical analysis and computer simulations. Periodic selection and phage predation dynamics are not mutually exclusive; we compare their predictions to shed light on the ecological circumstances under which each type of dynamics could predominate.
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Bacteriophages have a regulatory role in population dynamics through density-dependent predation.
“Analogously, bacteriophages have a regulatory role in population dynamics through density-dependent predation [29].”
From Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking (2025) · cites this paper as [29]
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- Authors
- Rodriguez-Valera, F., Martin-Cuadrado, A.-B., Rodriguez-Brito, B., Pašić, L., Thingstad, T. F., Rohwer, F., & Mira, A.
- Affiliations
- University of Ljubljana (SI)
- University of Bergen (NO)
- San Diego State University (US)
- Venue
- Nature Reviews Microbiology
- Published
- 2009-11
- Volume
- 7
- Issue
- 11
- Pages
- 828-836
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- OpenAlex
- W1991604124
- Cited by
- 663
- References
- 69
- Citations by year
- 2026: 17 · 2025: 38 · 2024: 36 · 2023: 34 · 2022: 43 · 2021: 45 · 2020: 39 · 2019: 46 · 2018: 45 · 2017: 47 · 2016: 36 · 2015: 52 · 2014: 47 · 2013: 41 · 2012: 44
- FWCI
- 3.71
- Type
- journal article
- Language
- en
- Open access
- Licence
- other-oa
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Repository of the University of Ljubljana (University of Ljubljana) (publishedVersion, other-oa)
- Topics
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- phage predation, bacterial diversity, metagenomics, clonal replacement
- MeSH terms
- Bacteria, Bacteriophages, Models, Biological, Population Dynamics, Selection, Genetic, Species Specificity, Genome, Bacterial, Computational Biology, Genomics
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