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Volume 169, Issue 8

Genomic characterization of the antiviral arsenal of Actinobacteria Open Access

This article is part of the Microbial Evolution collection.

Abstract

Phages are ubiquitous in nature, and bacteria with very different genomics, metabolisms, and lifestyles are subjected to their predation. Yet, the defence systems that allow bacteria to resist their phages have rarely been explored experimentally outside a very limited number of model organisms. Actinobacteria (Actinomycetota) are a phylum of GC-rich Gram-positive bacteria, which often produce an important diversity of secondary metabolites. Despite being ubiquitous in a wide range of environments, from soil to fresh and sea water but also the gut microbiome, relatively little is known about the anti-phage arsenal of Actinobacteria. In this work, we used DefenseFinder to systematically detect 131 anti-phage defence systems in 22803 fully sequenced prokaryotic genomes, among which are 2253 Actinobacteria of more than 700 species. We show that, like other bacteria, Actinobacteria encode many diverse anti-phage systems that are often encoded on mobile genetic elements. We further demonstrate that most detected defence systems are absent or rarer in Actinobacteria than in other bacteria, while a few rare systems are enriched (notably gp29-gp30 and Wadjet). We characterize the spatial distribution of anti-phage systems on chromosomes and show that some defence systems (e.g. RM systems) tend to be encoded in the core region, while others (e.g. Lamassu and Wadjet) are enriched towards the extremities. Overall, our results suggest that Actinobacteria might be a source of novel anti-phage systems and provide clues to characterize mechanistic aspects of known anti-phage systems.

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  • Accepted:
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Keyword(s): Actinobacteria , bacteriophages , defense systems , evolutionary genomics and Streptomyces
Funding
This study was supported by the:
  • HORIZON EUROPE Framework Programme (Award 945298)
    • Principle Award Recipient: HelenaShomar
  • HORIZON EUROPE European Research Council (Award 101040529)
    • Principle Award Recipient: AudeBernheim
  • Inserm (Award R21042KS)
    • Principle Award Recipient: AudeBernheim
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. The Microbiology Society waived the open access fees for this article.
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2023-08-02
2024-04-29
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Genomic characterization of the antiviral arsenal of Actinobacteria
Microbiology 169, 001374 (2023); https://doi.org/10.1099/mic.0.001374
/content/journal/micro/10.1099/mic.0.001374
/content/journal/micro/10.1099/mic.0.001374
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