Phage–host coevolution in natural populations

Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage–host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host–phage pairs delineated a modular network where phages are best at infecting co-occurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.

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Supplementary Figs. 1–13.
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Reporting Summary
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Peer Review File
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Tables 1–11.
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Source Data Fig. 3 Cross-infection matrix of 299 vibrio and 274 phages.
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Source Data Fig. 4 All data of defence finder with number of infecting phages and genome size for each V. crassostreae strain (all strains and clade-by-clade).
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Source Data Fig. 4 Results of statistical analysis in c).
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Source Data Fig. 5 Results of two distinct experiments used for statistical analysis.
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Source Data Fig. 6 Results of two distinct experiments used for statistical analysis.
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Source Data Extended Data Fig. 1 Dynamics of Vibrio crassostreae.
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Source Data Extended Data Fig. 7 Results of two distinct experiments used for statistical analysis.
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Piel Damien, Bruto Maxime, Labreuche Yannick, Blanquart François, Goudenège David, Barcia-Cruz Rubén, Chenivesse Sabine, Le Panse Sophie, James Adele, Dubert Javier, Petton Bruno, Lieberman Erica, Wegner K. Mathias, Hussain Fatima A., Kauffman Kathryn M., Polz Martin F., Bikard David, Gandon Sylvain, Rocha Eduardo P. C., Le Roux Frederique (2022). Phage–host coevolution in natural populations. Nature Microbiology. 7 (7). 1075-1086. https://doi.org/10.1038/s41564-022-01157-1, https://archimer.ifremer.fr/doc/00780/89208/

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