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. 2013 Dec 11;3(12):130160.
doi: 10.1098/rsob.130160.

Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences

Simon Roux  1 , Mart Krupovic, Didier Debroas, Patrick Forterre, François Enault
Affiliations

Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences

Simon Roux et al. Open Biol. .

Abstract

Although the importance of viruses in natural ecosystems is widely acknowledged, the functional potential of viral communities is yet to be determined. Viral genomes are traditionally believed to carry only those genes that are directly pertinent to the viral life cycle, though this view was challenged by the discovery of metabolism genes in several phage genomes. Metagenomic approaches extended these analyses to a community scale, and several studies concluded that microbial and viral communities encompass similar functional potentials. However, these conclusions could originate from the presence of cellular DNA within viral metagenomes. We developed a computational method to estimate the proportion and origin of cellular sequences in a set of 67 published viromes. A quarter of the datasets were found to contain a substantial amount of sequences originating from cellular genomes. When considering only viromes with no cellular DNA detected, the functional potential of viral and microbial communities was found to be fundamentally different-a conclusion more consistent with the actual picture drawn from known viruses. Yet a significant number of cellular metabolism genes was still retrieved in these viromes, suggesting that the presence of auxiliary genes involved in various metabolic pathways within viral genomes is a general trend in the virosphere.

Keywords: functional potential; metagenomics; phages; viruses.

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Figures

Figure 1.
Figure 1.
(a) Distribution of relative number of rDNA genes detected in viromes. The three defined categories are coloured green for virome free from cellular DNA, orange for a low level of cellular DNA and red for a high level of cellular DNA. (b) PHR/MHR plot for each metagenome, either viral (filled dots) or microbial (black circles). For each dataset, the MHR represents the proportion of reads having a significant similarity in a prokaryote genome. For reads having a hit in a bacterial genome, the PHR represents the proportion of these microbial reads that are found in a prophage-like region. Viromes are coloured according to their number of rDNA genes detected.
Figure 2.
Figure 2.
Recruitment plots for three virome–microbial genome associations. Virome reads were affiliated to the KEGG genome with the best tBlastx score. Reads were then plotted at the position of the hit on the corresponding genome (x-axis), the sequence conservation being displayed as the identity percentage between read and genome on the y-axis. (a) 17 444 reads of the Lake Bourget virome are recruited by Candidatus Vesicomyosocius okutanii. (b) ‘36 Coral Atol’ reads recruited by Pelagibacter ubique (1973 reads). (c) Recruitment of 91 315 reads from the ‘34 Arctic Vir’ virome by the genome of the Alphaproteobacteria Sphingopyxis alaskensis.
Figure 3.
Figure 3.
Comparison of the functional profiles of viromes and microbiomes, considering (a) all viromes, (b) viromes with clearly identified microbial-originating sequences (‘red’ viromes) and (c) viromes considered as mostly composed of viral sequences (‘green’ and ‘orange’ viromes). The percentage of reads affiliated to each SEED category (level 1) is indicated for microbiomes (x-axis) and viromes (y-axis).
Figure 4.
Figure 4.
Mapping of virome-retrieved functions on the different types of photosystem. On this general representation of the photosystems, KO retrieved in uncontaminated viromes are highlighted in red on the list of KO at the bottom, and when possible on the chart at the top.
Figure 5.
Figure 5.
Mapping of virome-retrieved functions on oxydative phosphorylation pathway. On this general representation of the oxydative phosphorylation pathway, KO retrieved in uncontaminated viromes are highlighted in red on the list of KO at the bottom, and when possible on the chart at the top.
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