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Interrogating the viral dark matter of the rumen ecosystem with a global virome database

Author

Listed:
  • Ming Yan

    (The Ohio State University
    The Ohio State University)

  • Akbar Adjie Pratama

    (The Ohio State University
    The Ohio State University)

  • Sripoorna Somasundaram

    (The Ohio State University
    The Ohio State University)

  • Zongjun Li

    (Northwest A&F University)

  • Yu Jiang

    (Northwest A&F University)

  • Matthew B. Sullivan

    (The Ohio State University
    The Ohio State University
    The Ohio State University)

  • Zhongtang Yu

    (The Ohio State University
    The Ohio State University)

Abstract

The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-level viral operational taxonomic units (vOTUs), RVD substantially increases the detection rate of rumen viruses from metagenomes compared with IMG/VR V3. Most of the classified vOTUs belong to Caudovirales, differing from those found in the human gut. The rumen virome is predicted to infect the core rumen microbiome, including fiber degraders and methanogens, carries diverse auxiliary metabolic genes, and thus likely impacts the rumen ecosystem in both a top-down and a bottom-up manner. RVD and the findings provide useful resources and a baseline framework for future research to investigate how viruses may impact the rumen ecosystem and digestive physiology.

Suggested Citation

  • Ming Yan & Akbar Adjie Pratama & Sripoorna Somasundaram & Zongjun Li & Yu Jiang & Matthew B. Sullivan & Zhongtang Yu, 2023. "Interrogating the viral dark matter of the rumen ecosystem with a global virome database," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41075-2
    DOI: 10.1038/s41467-023-41075-2
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    1. Jiandui Mi & Xiaoping Jing & Chouxian Ma & Fuyu Shi & Ze Cao & Xin Yang & Yiwen Yang & Apurva Kakade & Weiwei Wang & Ruijun Long, 2024. "A metagenomic catalogue of the ruminant gut archaeome," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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