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. 2010 Jan;18(1):11-9.
doi: 10.1016/j.tim.2009.11.003. Epub 2009 Nov 26.

New dimensions of the virus world discovered through metagenomics

David M Kristensen  1 , Arcady R Mushegian, Valerian V Dolja, Eugene V Koonin
Affiliations

New dimensions of the virus world discovered through metagenomics

David M Kristensen et al. Trends Microbiol. 2010 Jan.

Abstract

Metagenomic analysis of viruses suggests novel patterns of evolution, changes the existing ideas of the composition of the virus world and reveals novel groups of viruses and virus-like agents. The gene composition of the marine DNA virome is dramatically different from that of known bacteriophages. The virome is dominated by rare genes, many of which might be contained within virus-like entities such as gene transfer agents. Analysis of marine metagenomes thought to consist mostly of bacterial genes revealed a variety of sequences homologous to conserved genes of eukaryotic nucleocytoplasmic large DNA viruses, resulting in the discovery of diverse members of previously undersampled groups and suggesting the existence of new classes of virus-like agents. Unexpectedly, metagenomics of marine RNA viruses showed that representatives of only one superfamily of eukaryotic viruses, the picorna-like viruses, dominate the RNA virome.

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Figures

Figure 1
Figure 1
Properties of marine DNA viromes compared with non-viral marine metagenomic samples. For each sample (definitions and color scheme given in Box 1), the proportions with matches to (a) known proteins in the GenBank non-redundant (NR) database, (b) conserved phage orthologous groups (POGs), (c) conserved cellular orthologous groups (COGs) and (d) taxonomic classification of best matches (among known proteins in NR) as prokaryotes (color) or phages (gray) are shown.
Figure 2
Figure 2
Correlation between functional compositions of viral and cellular metagenomes. The plotted data consist of mean percentages of the sequences from 45 microbial and 42 viral metagenomes that match characterized proteins in major functional categories. Data obtained from Ref. [11].
Figure 3
Figure 3
The diversity of positive-strand RNA viruses and their hosts. The schematic tree of the major groups of positive-strand RNA viruses is based on the analysis in Ref. [64], and the positions of Nidovirales [65] and Narnaviridae/Ourmiaviridae [66] are shown tentatively on the basis of subsequent studies. Host range is indicated for each branch. Data on viruses that infect unicellular eukaryotes (bold font) come primarily from metagenomic studies (see main text).
Figure I
Figure I
A schematic representation of the metagenomic datasets.
See this image and copyright information in PMC

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