Virome
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Virome refers to the collection of nucleic acids, both RNA and DNA, that make up the viral community associated with a particular ecosystem or holobiont. The word is derived from virus and genome and first used by Forest Rohwer and colleagues to describe viral shotgun metagenomes (McDaniel et al. 2008). All macro-organisms have viromes that include bacteriophage and viruses, including humans (link to the human virome).
Viromes are produced by separating virus-like particles form cellular components, usually using a combination of filtration, density centrifugation and enzymatic treatments to get rid of free nucleic acids (Thurber et al. 2009). Viromes are important in the nutrient and energy cycling (Wegley et al. 2007), development of immunity (Barr et al. 2013) and a major source of genes through lysogenic conversion (Sharon et al. 2007).
History
Viromes were the first examples of shotgun community sequence (Breitbart et al. 2002), which is now known as metagenomics. In the 2000s, the Rohwer lab sequenced viromes from seawater (Breitbart et al. 2002) (Angly et al 2006), marine sediments (Breitbart et al. 2004), adult human stool (Breitbart et al. 2003), infant human stool (Breitbart et al. 2008), soil (Breitbart et al. 2007) and blood (Breitbart et al. 2005). This group also performed the first RNA virome with collaborators from the Genomic Institute of Singapore (Zhang et al. 2005). From these early works, it was concluded that most of the genomic diversity is contained in the global virome and that most of this diversity remains uncharacterized (Edwards and Rohwer 2005). This view was supported by individual genomic sequencing project, particularly the mycobacterium phage (Rohwer 2003).
References
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Breitbart, M., Salamon, P., Andresen, B., Mahaffy, J.M., Segall, A.M., Mead, D., Azam, F. and Rohwer, F., 2002. Genomic analysis of uncultured marine viral communities. Proceedings of the National Academy of Sciences, 99(22), pp.14250-14255.
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McDaniel, L., Breitbart, M., Mobberley, J., Long, A., Haynes, M., Rohwer, F. and Paul, J.H., 2008. Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression. PLoS One, 3(9), p.e3263.
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Zhang, T., Breitbart, M., Lee, W.H., Run, J.Q., Wei, C.L., Soh, S.W.L., Hibberd, M.L., Liu, E.T., Rohwer, F. and Ruan, Y., 2005. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol, 4(1), p.e3.