Abstract
The human enteric virome consists of endogenous retro elements and viruses that infect the host and members of the gut microbiome (GM). Mounting evidence suggests that the gut virome plays a central role in maintaining homeostasis and via the GM influences immunology of the host. To thoroughly characterize the gut virome, it is often very useful to first separate and concentrate extracellular viral-like particles (eVLPs) enabling an integrative characterization of them. Here, we describe a detailed protocol for extraction and concentration of the viral fraction from fecal samples based on a polyethylene glycol precipitation (PEG) approach. These procedures maximize the yields of eVLPs (and their DNA) with high purity well suited for down-stream analysis such as quantification and morphological assessment, determination of phage-host pairs as well as virome sequencing.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Wu H, Tremaroli V, Bäckhed F (2015) Linking microbiota to human diseases : a systems biology perspective. Trends Endocrinol Metab 26:758–770
Reyes A, Blanton LV, Cao S et al (2015) Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proc Natl Acad Sci U S A 112:1941–11946
Zhao G, Vatanen T, drit L et al (2017) Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children. Proc Natl Acad Sci U S A 114:E6166–E6175
Barr JJ, Auro R, Furlan M et al (2013) Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A 110:10771–10776
Norman JM, Handley SA, Baldridge MT et al (2015) Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160:447–460
Lim ES, Zhou Y, Zhao G et al (2015) Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med 21:1228–1234
Sullivan MB (2015) Virome, not gene markers, for studying double-stranded DNA virus communities. J Virol 89:2459–2461
Hurwitz BL, Ren JMU, Youens-clark K (2016) Computational prospecting the great viral unknown. FEMS Microbiol Lett 363:fnw077
Thurber RV, Haynes M, Breitbart M et al (2009) Laboratory procedures to generate viral metagenomes. Nat Protoc 4:470–483
Wommack KE, Williamson, KE, Helton, RR et al (2009). Mehtods for the isolation of viruses from environmental samples. Methods Mol Biol 501:3–14
Conceição-Neto N, Zeller M, Lefrêre H et al (2015) Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Nat Publ Gr 5:16532
Hall RJ, Wang J, Todd AK et al (2014) Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. J Virol Methods 195:194–204
Kleiner M, Hooper LV, Duerkop BA (2015) Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes. BMC Genomics 16:7
Hoyles L, McCartney AL, Neve H et al (2014) Characterization of virus-like particles associated with the human faecal and caecal microbiota. Res Microbiol 165:803–812
Castro-Mejía J, Muhammed MK, Kot W et al (2015) Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut. Microbiome 3:64
Hayes S, Mahony J, Nauta A et al (2017) Metagenomic approaches to assess bacteriophages in various environmental niches. Viruses 9:127
Acknowledgments
This work was supported by “CALM” – Counteracting Age-related Loss of Skeletal Muscle Mass (J.L.C.) and “EarlyVir—Influence of diet on early life gut virome—a key player in shaping the gut microbiota”. Joint Programming Initiative, Healthy Diet for a Healthy Living program (L.D.)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Castro-Mejía, J.L., Deng, L., Vogensen, F.K., Reyes, A., Nielsen, D.S. (2018). Extraction and Purification of Viruses from Fecal Samples for Metagenome and Morphology Analyses. In: Moya, A., Pérez Brocal, V. (eds) The Human Virome. Methods in Molecular Biology, vol 1838. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8682-8_5
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8682-8_5
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8681-1
Online ISBN: 978-1-4939-8682-8
eBook Packages: Springer Protocols