Viral Metagenomics: Exploring the Hidden Layer of the Microbiome

When we analyse shotgun metagenomic data, we often focus on the bacterial and archaeal genomes present in a sample. But this represents only part of the biological community.

Hidden within the same sequencing data is another largely unexplored component: the virome.

Viral metagenomics uses shotgun sequencing data to identify and characterise viruses, bacteriophages and other viral genetic material within a sample. This can provide an additional layer of biological information that is often overlooked in conventional metagenomic analysis.

Using the nf-core viral metagenomics workflow, viral sequences can be investigated using both database-dependent and de novo approaches. Database-based methods identify sequences with similarity to known viral genomes, while de novo analysis can reconstruct viral genomes or contigs that may have little or no close match in existing databases.

This is particularly important because the viral world remains far less characterised than the bacterial world. Many viral sequences recovered from environmental, animal or clinical samples may represent previously undescribed viruses.

The biological relevance can extend well beyond the viruses themselves.

Bacteriophages, for example, can influence bacterial populations through infection, selection and horizontal gene transfer. Changes in the phage community may therefore help explain changes in bacterial abundance and community structure that cannot be understood from bacterial profiling alone.

In host-associated samples, viruses may also contribute to host health through interactions with both bacteria and host cells. The result is a more complete view of the microbial ecosystem: not just which bacteria are present, but also the viral populations that may be shaping them.

For this reason, viral metagenomics can be viewed as an additional layer of information already present within shotgun sequencing data.

The data may already be there. The question is whether we are looking for it.

This is where outsourcing bioinformatics can provide a practical advantage. Rather than investing time in building and maintaining analysis pipelines, troubleshooting software dependencies and learning unfamiliar tools, researchers can outsource the computational analysis and focus on interpreting the biological results.

Stephen Stockdale of BioFigR provides independent bioinformatics and data visualisation support for biological research projects. Analysis can begin with raw FASTQ files, using established workflows such as nf-core pipelines to process and investigate sequencing data. Alternatively, existing count tables, taxonomic profiles or other processed datasets can be used as the starting point.

The support does not have to end with the analysis.

BioFigR can help transform complex results into publication-ready figures, support the generation and refinement of figures for manuscripts, and help researchers explore the data when the most appropriate visualisation or statistical approach is not immediately obvious.

Whether the requirement is a complete shotgun metagenomic analysis, exploration of the viral component of an existing dataset, creation of custom figures, or support during manuscript preparation, outsourcing can provide access to specialist bioinformatics expertise without the need to build that expertise internally.

The aim is simple: take biological data and turn it into clear, defensible and useful scientific insight.

Sometimes the most interesting part of a dataset is the part that has not yet been analysed.