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Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces

Author

Listed:
  • Piotr Rozwalak

    (Adam Mickiewicz University)

  • Jakub Barylski

    (Adam Mickiewicz University)

  • Yasas Wijesekara

    (University Medicine Greifswald)

  • Bas E. Dutilh

    (Friedrich Schiller University Jena
    Utrecht University)

  • Andrzej Zielezinski

    (Adam Mickiewicz University)

Abstract

Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from ancient palaeofaeces and human gut-content samples, and identify an ancient phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria. The DNA damage patterns of the genome are consistent with its ancient origin and, despite 1300 years of evolution, the ancient Mushuvirus genome shares 97.7% nucleotide identity with its modern counterpart, indicating a long-term relationship between the prophage and its host. In addition, we reconstruct and authenticate 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genome sequences, thus expanding the known virosphere and offering insights into phage-bacteria interactions spanning several millennia.

Suggested Citation

  • Piotr Rozwalak & Jakub Barylski & Yasas Wijesekara & Bas E. Dutilh & Andrzej Zielezinski, 2024. "Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-023-44370-0
    DOI: 10.1038/s41467-023-44370-0
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    References listed on IDEAS

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    1. Christopher M. Bellas & Declan C. Schroeder & Arwyn Edwards & Gary Barker & Alexandre M. Anesio, 2020. "Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    2. Marsha C. Wibowo & Zhen Yang & Maxime Borry & Alexander Hübner & Kun D. Huang & Braden T. Tierney & Samuel Zimmerman & Francisco Barajas-Olmos & Cecilia Contreras-Cubas & Humberto García-Ortiz & Angél, 2021. "Reconstruction of ancient microbial genomes from the human gut," Nature, Nature, vol. 594(7862), pages 234-239, June.
    3. Simon Roux & Blair G. Paul & Sarah C. Bagby & Stephen Nayfach & Michelle A. Allen & Graeme Attwood & Ricardo Cavicchioli & Ludmila Chistoserdova & Robert J. Gruninger & Steven J. Hallam & Maria E. Her, 2021. "Ecology and molecular targets of hypermutation in the global microbiome," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
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