IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-41075-2.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-41075-2
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-41075-2?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Hannah G. Hampton & Bridget N. J. Watson & Peter C. Fineran, 2020. "The arms race between bacteria and their phage foes," Nature, Nature, vol. 577(7790), pages 327-336, January.
    2. Natalya Yutin & Sean Benler & Sergei A. Shmakov & Yuri I. Wolf & Igor Tolstoy & Mike Rayko & Dmitry Antipov & Pavel A. Pevzner & Eugene V. Koonin, 2021. "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    3. Simon Roux & Jennifer R. Brum & Bas E. Dutilh & Shinichi Sunagawa & Melissa B. Duhaime & Alexander Loy & Bonnie T. Poulos & Natalie Solonenko & Elena Lara & Julie Poulain & Stéphane Pesant & Stefanie , 2016. "Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses," Nature, Nature, vol. 537(7622), pages 689-693, September.
    4. Cormac M. Kinsella & Aldert Bart & Martin Deijs & Patricia Broekhuizen & Joanna Kaczorowska & Maarten F. Jebbink & Tom Gool & Matthew Cotten & Lia Hoek, 2020. "Entamoeba and Giardia parasites implicated as hosts of CRESS viruses," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    5. Robert D. Stewart & Marc D. Auffret & Amanda Warr & Andrew H. Wiser & Maximilian O. Press & Kyle W. Langford & Ivan Liachko & Timothy J. Snelling & Richard J. Dewhurst & Alan W. Walker & Rainer Roehe , 2018. "Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    6. Kristopher Kieft & Zhichao Zhou & Rika E. Anderson & Alison Buchan & Barbara J. Campbell & Steven J. Hallam & Matthias Hess & Matthew B. Sullivan & David A. Walsh & Simon Roux & Karthik Anantharaman, 2021. "Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Meishun Yu & Menghui Zhang & Runying Zeng & Ruolin Cheng & Rui Zhang & Yanping Hou & Fangfang Kuang & Xuejin Feng & Xiyang Dong & Yinfang Li & Zongze Shao & Min Jin, 2024. "Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Samantha L. Peters & Adair L. Borges & Richard J. Giannone & Michael J. Morowitz & Jillian F. Banfield & Robert L. Hettich, 2022. "Experimental validation that human microbiome phages use alternative genetic coding," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    3. Tzu-Ping Ko & Yu-Chuan Wang & Chia-Shin Yang & Mei-Hui Hou & Chao-Jung Chen & Yi-Fang Chiu & Yeh Chen, 2022. "Crystal structure and functional implication of bacterial STING," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    4. Ruonan Wu & Michelle R. Davison & William C. Nelson & Montana L. Smith & Mary S. Lipton & Janet K. Jansson & Ryan S. McClure & Jason E. McDermott & Kirsten S. Hofmockel, 2023. "Hi-C metagenome sequencing reveals soil phage–host interactions," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    5. Jack P. K. Bravo & Cristian Aparicio-Maldonado & Franklin L. Nobrega & Stan J. J. Brouns & David W. Taylor, 2022. "Structural basis for broad anti-phage immunity by DISARM," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    6. Lerato Molieleng & Pieter Fourie & Ifeoma Nwafor, 2021. "Adoption of Climate Smart Agriculture by Communal Livestock Farmers in South Africa," Sustainability, MDPI, vol. 13(18), pages 1-18, September.
    7. Clemente F. Arias & Francisco J. Acosta & Federica Bertocchini & Miguel A. Herrero & Cristina Fernández-Arias, 2022. "The coordination of anti-phage immunity mechanisms in bacterial cells," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    8. Gabriel Magno Freitas Almeida & Ville Hoikkala & Janne Ravantti & Noora Rantanen & Lotta-Riina Sundberg, 2022. "Mucin induces CRISPR-Cas defense in an opportunistic pathogen," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    9. M. C. Ramaboli & S. Ocvirk & M. Khan Mirzaei & B. L. Eberhart & M. Valdivia-Garcia & A. Metwaly & K. Neuhaus & G. Barker & J. Ru & L. T. Nesengani & D. Mahdi-Joest & A. S. Wilson & S. K. Joni & D. C. , 2024. "Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    10. Yuxuan Du & Jed A. Fuhrman & Fengzhu Sun, 2023. "ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    11. Rebecca Conners & Mathew McLaren & Urszula Łapińska & Kelly Sanders & M. Rhia L. Stone & Mark A. T. Blaskovich & Stefano Pagliara & Bertram Daum & Jasna Rakonjac & Vicki A. M. Gold, 2021. "CryoEM structure of the outer membrane secretin channel pIV from the f1 filamentous bacteriophage," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    12. Rafael Gonzalez-Serrano & Riccardo Rosselli & Juan J. Roda-Garcia & Ana-Belen Martin-Cuadrado & Francisco Rodriguez-Valera & Matthew Dunne, 2023. "Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    13. Ning Duan & Emily Hand & Mannuku Pheko & Shikha Sharma & Akintunde Emiola, 2024. "Structure-guided discovery of anti-CRISPR and anti-phage defense proteins," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    14. Yoann G. Santin & Adrià Sogues & Yvann Bourigault & Han K. Remaut & Géraldine Laloux, 2024. "Lifecycle of a predatory bacterium vampirizing its prey through the cell envelope and S-layer," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    15. Mingfang Bi & Wenjing Su & Jiafu Li & Xiaobing Mo, 2024. "Insights into the inhibition of protospacer integration via direct interaction between Cas2 and AcrVA5," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    16. Zhi-Ping Zhong & Jingjie Du & Stephan Köstlbacher & Petra Pjevac & Sandi Orlić & Matthew B. Sullivan, 2024. "Viral potential to modulate microbial methane metabolism varies by habitat," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    17. Sanzhima Garmaeva & Trishla Sinha & Anastasia Gulyaeva & Nataliia Kuzub & Johanne E. Spreckels & Sergio Andreu-Sánchez & Ranko Gacesa & Arnau Vich Vila & Siobhan Brushett & Marloes Kruk & Jackie Deken, 2024. "Transmission and dynamics of mother-infant gut viruses during pregnancy and early life," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    18. Pauline C. Göller & Tabea Elsener & Dominic Lorgé & Natasa Radulovic & Viona Bernardi & Annika Naumann & Nesrine Amri & Ekaterina Khatchatourova & Felipe Hernandes Coutinho & Martin J. Loessner & Elen, 2021. "Multi-species host range of staphylococcal phages isolated from wastewater," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    19. Javier Lopez-Simon & Marina Vila-Nistal & Aleksandra Rosenova & Daniele Corte & Federico Baltar & Manuel Martinez-Garcia, 2023. "Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    20. Yuxuan Du & Fengzhu Sun, 2023. "MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41075-2. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.