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NetoVIR: Modular Approach to Customize Sample Preparation Procedures for Viral Metagenomics

  • Nádia Conceição-Neto
  • Kwe Claude Yinda
  • Marc Van Ranst
  • Jelle MatthijnssensEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1838)

Abstract

The democratization of next-generation sequencing (NGS) technologies has enabled scientists to explore the diversity of microbial life in various ecological niches in an unpreceded depth. The role of viruses as a key player in health and disease is becoming increasingly clear. To address the need for an up scalable, reproducible protocol to purify RNA and DNA viruses from a sample, we describe our optimized method. The Novel Enrichment Technique Of Viromes (NetoVIR) allows researchers to attain a fast, reproducible, and high-throughput sample preparation protocol for NGS gut viromics studies. With appropriate prior homogenization steps, this protocol can be extended to any biological samples.

Key words

Viromics Sample preparation Next-generation sequencing Virome 

Notes

Acknowledgment

We would like to thank Lila Close for insightful tips and tricks.

References

  1. 1.
    Pride DT, Salzman J, Haynes M et al (2012) Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J 6:915–926CrossRefPubMedGoogle Scholar
  2. 2.
    Kapoor A, Kumar A, Simmonds P et al (2015) Virome analysis of transfusion recipients reveals a novel human virus that shares genomic features with hepaciviruses and pegiviruses. MBio 6(5):e01466-15CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Lim ES, Zhou Y, Zhao G et al (2015) Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med 21:1228–1234CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Hannigan GD, Meisel JS, Tyldsley AS et al (2015) The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. MBio 6(5):e01578-15CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Conceição-Neto N, Zeller M, Lefrère H et al (2015) Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Sci Rep 5:16532CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Norman JM, Handley SA, Baldridge MT et al (2015) Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160:447–460CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Picelli S, Faridani OR, Björklund AK et al (2014) Full-length RNAseq from single cells using Smart-seq2. Nat Protoc 9(1):171–181.Google Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Nádia Conceição-Neto
    • 1
    • 2
  • Kwe Claude Yinda
    • 1
    • 2
  • Marc Van Ranst
    • 2
  • Jelle Matthijnssens
    • 1
    Email author
  1. 1.Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega InstituteKU Leuven – University of LeuvenLeuvenBelgium
  2. 2.Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega InstituteKU Leuven – University of LeuvenLeuvenBelgium

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