Evidence map›Paper›PMID 39453741›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2024

Bacterial defense and phage counterdefense lead to coexistence in a modeled ecosystem.

Ofer Kimchi, Yigal Meir, Ned S Wingreen

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Ofer KimchiLewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.ORCID 0000-0002-0801-0727
Yigal MeirDepartment of Physics, Ben-Gurion University, Be'er Sheva 84105, Israel.ORCID 0000-0003-1606-8969
Ned S WingreenLewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.ORCID 0000-0001-7384-2821

Funding

Chan Zuckerberg Initiative (CZI) DAF2024-342781ETH Zürich Foundation (ETH Zurich Foundation) Branco Weiss FellowshipNational Science Foundation (NSF) PHY-1607611National Science Foundation (NSF) PHY-1734030Princeton University (PU) Peter B. Lewis '55 Lewis-Sigler Institute/Genomics Fund
6 · The paper itself

Abstract

Bacteria have evolved many defenses against invading viruses (phage). Despite the many bacterial defenses and phage counterdefenses, in most environments, bacteria and phage coexist, with neither driving the other to extinction. How is coexistence realized in the context of the bacteria/phage arms race, and how are immune repertoire sizes determined in conditions of coexistence? Here we develop a simple mathematical model to consider the evolutionary and ecological dynamics of competing bacteria and phage with different immune/counterimmune repertoires. We find an ecologically stable fixed point exhibiting coexistence, in agreement with the experimental observation that each individual bacterium typically carries multiple defense systems, though fewer than the maximum number possible. However, in simulations, the populations typically remain dynamic, exhibiting chaotic fluctuations around this fixed point. These dynamics enable coexistence even when phage (predator) strains outnumber bacteria (prey) strains. We obtain quantitative predictions for the mean, amplitude, and timescale of these dynamics. Our results provide a framework for understanding the evolutionary and ecological dynamics of the bacteria/phage arms race and demonstrate how bacteria/phage coexistence can stably arise from the coevolution of bacterial defense systems and phage counterdefense systems.

Indexed as

BacteriaBacteriophagesEcosystemBiological EvolutionModels, Biologicalbacteriacoexistenceecologymodelphage

Identifiers

PMID39453741
PMCPMC11536147

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.