Abstract
Prokaryotic viruses, or bacteriophages, are viruses that infect bacteria and archaea. These viruses have been known to associate with host systems for decades, yet only recently have their influence on the regulation of host-associated bacteria been appreciated. These studies have been conducted in many host systems, from the base of animal life in the Cnidarian phylum to mammals. These prokaryotic viruses are useful for regulating the number of bacteria in a host ecosystem and for regulating the strains of bacteria useful for the microbiome. These viruses are likely selected by the host to maintain bacterial populations. Viral metagenomics allows researchers to profile the communities of viruses associating with animal hosts, and importantly helps to determine the functional role these viruses play. Further, viral metagenomics show the sphere of viral involvement in gene flow and gene shuffling in an ever-changing host environment. The influence of prokaryotic viruses could, therefore, have a clear impact on host health.
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References
Grasis JA, Lachnit T, Anton-Erxleben F, Lim YM, Schmieder R, Fraune S et al (2014) Species-specific viromes in the ancestral holobiont hydra. PLoS One 9:e109952. https://doi.org/10.1371/journal.pone.0109952
Duerkop BA, Clements CV, Rollins D, Rodrigues JL, Hooper LV (2012) A composite bacteriophage alters colonization by an intestinal commensal bacterium. Proc Natl Acad Sci U S A 109:17621–17626. https://doi.org/10.1073/pnas.1206136109
Cadwell K (2015) The virome in host health and disease. Immunity 42:805–813. https://doi.org/10.1016/j.immuni.2015.05.003
Daly GM et al (2011) A viral discovery methodology for clinical biopsy samples utilizing massively parallel next generation sequencing. PLoS One 6:e28879. https://doi.org/10.1371/journal.pone.0028879
Hall RJ et al (2014) Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. J Virol Meth 195:194–204. https://doi.org/10.1016/j.jviromet.2013.08.035
Kleiner M et al (2015) Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes. BMC Genomics 16:7. https://doi.org/10.1186/s12864-014-1207-4
Ortmann AC, Suttle CA (2009) Determination of virus abundance by epifluorescence microscopy. In: Clokie MR, Kropinski AM (eds) Bacteriophages: methods and protocols, volume 1: isolation, characterization, and interactions, vol 501. Humana Press, New York, pp 87–95. https://doi.org/10.1007/978-1-60327-164-6_10
Ackermann H-W, Heldal M (2010) Basic electron microscopy of aquatic viruses. In: Wilhelm SW, Weinbauer MG, Suttle CA (eds) Manual of aquatic viral ecology, vol 18. American Society of Limnology and Oceanography, Waco, TX, pp 182–192. https://doi.org/10.4319/mave.2010.978-0-09845591-0-7.182
Ackermann H-W (2009) Basic phage electron microscopy. In: Clokie MR, Kropinski AM (eds) Bacteriophages: methods and protocols, volume 1: isolation, characterization, and interactions, vol 501. Humana Press, New York, pp 113–126. https://doi.org/10.1007/978-1-60327-164-6_12
Lim YW et al (2014) Purifying the impure: sequencing metagenomes and metagenomes from complex animal-associated samples. J Vis Exp 94:e52117. https://doi.org/10.3791/52117
Culley AI, Suttle CA, Steward GF (2010) Characterization of the diversity of marine RNA viruses. Manual of Aquatic Viral Ecol. 19:193–201. https://doi.org/10.4319/mave.2010.978-0-9845591-0-7.193
Weynberg KD et al (2014) Generating viral metagenomes from the coral holobiont. Front Microbiol 5:1–11. https://doi.org/10.3389/fmicb.2014.00206
Lawrence JE, Steward GF (2010) Purification of viruses by centrifugation. Manual of Aquatic Viral Ecol 17:166–181. https://doi.org/10.4319/mave.2010.978-0-9845591-0-7.166
Summers WC (1999) Felix d’Herelle and the origins of molecular biology. Yale University Press, USA, p 248
Williamson KE et al (2003) Sampling natural viral communities from soil for culture-independent analyses. Appl Environ Micro 69:6628–6633. https://doi.org/10.1128/AEM.69.11.6628-6633.2003
Hjelmso MH et al (2017) Evaluation of methods for the concentration and extraction of viruses from sewage in the context of metagenomic sequencing. PLoS One 12:e0170199. https://doi.org/10.1371/journal.pone.0170199
Forterre P, Soler N, Krupovic M, Marguet E, Ackermann H-W (2013) Fake virus particles generated by fluorescence microscopy. Trends Microbiol 21:1–5. https://doi.org/10.1016/j.tim.2012.10.005
Solonenko SA et al (2013) Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics 14:320. https://doi.org/10.1186/1471-2164-14-320
Duhaime MB, Deng L, Poulos BT, Sullivan MB (2012) Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environ Microbiol 14:2526–2537. https://doi.org/10.1111/j.1462-2920.2012.02791.x
Acknowledgements
This work was supported by NIH grant F32AI098418. Special thanks to Marisa Rojas for critical review of the protocol. The author declares no competing financial interests.
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Grasis, J.A. (2018). Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics. In: Pantaleo, V., Chiumenti, M. (eds) Viral Metagenomics. Methods in Molecular Biology, vol 1746. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7683-6_1
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