Fig. 3

The steps in metagenomic study of the virome. Nucleic acid extraction: the virome can be studied by extraction of nucleic acids from both fractions of the total microbial community which includes bacteria and viruses (left) and purified viral-like particles (VLPs; right), and different types of VLP-enriching techniques might be applied to obtain the latter fraction (see main text for details). Genomic library preparation: the extracted viral genetic material is subjected to sequencing after genomic library preparation. Both the choice of genomic library preparation technique and the sequencing coverage can affect the representation of specific members of the viral community in the sample (see discussion in the main text). Quality control: the raw sequencing reads are further trimmed of sequencing adapters, and low-quality and overrepresented reads are discarded. Virome annotation: there are two main ways of studying viral communities—read-mapping to closed reference databases or de novo assembly of viral genomes with optional, but advised, validation of contigs via reference databases