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Resolving the structure of phage–bacteria interactions in the context of natural diversity

Author

Listed:
  • Kathryn M. Kauffman

    (Massachusetts Institute of Technology
    The University at Buffalo)

  • William K. Chang

    (Albert Einstein College of Medicine)

  • Julia M. Brown

    (Albert Einstein College of Medicine
    Bigelow Laboratory for Ocean Sciences)

  • Fatima A. Hussain

    (Massachusetts Institute of Technology
    Ragon Institute of MGH, MIT, and Harvard)

  • Joy Yang

    (Massachusetts Institute of Technology)

  • Martin F. Polz

    (Massachusetts Institute of Technology
    University of Vienna)

  • Libusha Kelly

    (Albert Einstein College of Medicine
    Albert Einstein College of Medicine)

Abstract

Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse—with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.

Suggested Citation

  • Kathryn M. Kauffman & William K. Chang & Julia M. Brown & Fatima A. Hussain & Joy Yang & Martin F. Polz & Libusha Kelly, 2022. "Resolving the structure of phage–bacteria interactions in the context of natural diversity," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-021-27583-z
    DOI: 10.1038/s41467-021-27583-z
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    Cited by:

    1. Rubén Barcia-Cruz & David Goudenège & Jorge A. Moura de Sousa & Damien Piel & Martial Marbouty & Eduardo P. C. Rocha & Frédérique Roux, 2024. "Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Florian Tesson & Alexandre Hervé & Ernest Mordret & Marie Touchon & Camille d’Humières & Jean Cury & Aude Bernheim, 2022. "Systematic and quantitative view of the antiviral arsenal of prokaryotes," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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