Competition and coevolution drive the evolution and the diversification of CRISPR immunity

Martin Guillemet, Hélène Chabas, Antoine Nicot, François Gatchich, Enrique Ortega-Abboud, Cornelia Buus, Lotte Hindhede, Geneviève M. Rousseau, Thomas Bataillon, Sylvain Moineau, Sylvain Gandon*

*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

1 Citation (Scopus)


The diversity of resistance challenges the ability of pathogens to spread and to exploit host populations. Yet, how this host diversity evolves over time remains unclear because it depends on the interplay between intraspecific competition among host genotypes and coevolution with pathogens. Here we study experimentally the effect of coevolving phage populations on the diversification of bacterial CRISPR immunity across space and time. We demonstrate that the negative-frequency-dependent selection generated by coevolution is a powerful force that maintains host resistance diversity and selects for new resistance mutations in the host. We also find that host evolution is driven by asymmetries in competitive abilities among different host genotypes. Even if the fittest host genotypes are targeted preferentially by the evolving phages, they often escape extinctions through the acquisition of new CRISPR immunity. Together, these fluctuating selective pressures maintain diversity, but not by preserving the pre-existing host composition. Instead, we repeatedly observe the introduction of new resistance genotypes stemming from the fittest hosts in each population. These results highlight the importance of competition on the transient dynamics of host–pathogen coevolution.

Original languageEnglish
JournalNature Ecology and Evolution
Pages (from-to)1480-1488
Number of pages9
Publication statusPublished - Oct 2022


  • Bacteria/genetics
  • Bacteriophages/genetics
  • Clustered Regularly Interspaced Short Palindromic Repeats


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