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The pan-immune system of bacteria: antiviral defence as a community resource

Nature Reviews Microbiology volume 18, pages 113–119 (2020)Cite this article

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Abstract

Viruses and their hosts are engaged in a constant arms race leading to the evolution of antiviral defence mechanisms. Recent studies have revealed that the immune arsenal of bacteria against bacteriophages is much more diverse than previously envisioned. These discoveries have led to seemingly contradictory observations: on one hand, individual microorganisms often encode multiple distinct defence systems, some of which are acquired by horizontal gene transfer, alluding to their fitness benefit. On the other hand, defence systems are frequently lost from prokaryotic genomes on short evolutionary time scales, suggesting that they impose a fitness cost. In this Perspective article, we present the ‘pan-immune system’ model in which we suggest that, although a single strain cannot carry all possible defence systems owing to their burden on fitness, it can employ horizontal gene transfer to access immune defence mechanisms encoded by closely related strains. Thus, the ‘effective’ immune system is not the one encoded by the genome of a single microorganism but rather by its pan-genome, comprising the sum of all immune systems available for a microorganism to horizontally acquire and use.

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Fig. 1: Antiviral defence systems in bacteria.
Fig. 2: Closely related bacterial strains encode diverse defence systems.
Fig. 3: The pan-immune system model.

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Acknowledgements

The authors thank S. Doron and A. Millman for their help in the analysis presented in Box 1 and Figure 2, M. Voichek and N. Tal for their helpful comments on the figures in this study, and J. Cury and the Sorek laboratory members for comments on earlier versions of this manuscript. A.B. is the recipient of a European Molecular Biology Organization (EMBO) Long Term Fellowship (EMBO ALTF 186-2018). R.S. was supported, in part, by the Israel Science Foundation (personal grant 1360/16), the European Research Council (grant ERC-CoG 681203), the German Research Council (DFG) priority programme SPP 2002 (grant SO 1611/1-1), the Ernest and Bonnie Beutler Research Program of Excellence in Genomic Medicine and the Knell Family Center for Microbiology.

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  1. Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel

    Aude Bernheim & Rotem Sorek

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  1. Aude Bernheim
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Correspondence to Rotem Sorek.

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R.S. is a scientific cofounder and consultant of BiomX Ltd, Pantheon Ltd and EcoPhage Ltd. All other authors declare no competing interests.

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Bernheim, A., Sorek, R. The pan-immune system of bacteria: antiviral defence as a community resource. Nat Rev Microbiol 18, 113–119 (2020). https://doi.org/10.1038/s41579-019-0278-2

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