ArticleScientific reports2016
Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 33 citations in OpenAlex.
- Thousands-years-old deep-sea DNA viruses reveal the evolution of human pathogenic viruses.Journal of advanced research · 2026Article
- Diversity and cross-species transmission of viruses in a remote island ecosystem: implications for wildlife conservation.Virus evolution · 2025Article
- Revolutionized virome research using systems microbiology approaches.Experimental biology and medicine (Maywood, N.J.) · 2022Review
- Diversity and distribution of viruses inhabiting the deepest ocean on Earth.The ISME journal · 2021Article
- A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses.Microorganisms · 2021Review
- The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.Communications biology · 2021Article
- Potential Applications of Human Viral Metagenomics and Reference Materials: Considerations for Current and Future Viruses.Applied and environmental microbiology · 2020Review
- Review
- Overview of Virus Metagenomic Classification Methods and Their Biological Applications.Frontiers in microbiology · 2018Review
- Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan.Frontiers in microbiology · 2018Article
- From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments.Scientific reports · 2017Article
- Review
- VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.Virology · 2017Article
- Metavirome Sequencing of the Termite Gut Reveals the Presence of an Unexplored Bacteriophage Community.Frontiers in microbiology · 2017Article
- Virome Assembly and Annotation: A Surprise in the Namib Desert.Frontiers in microbiology · 2017Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In benthic deep-sea ecosystems, which represent the largest biome on Earth, viruses have a recognised key ecological role, but their diversity is still largely unknown. Identifying the taxonomic composition of viruses is crucial for understanding virus-host interactions, their role in food web functioning and evolutionary processes. Here, we compared the performance of various bioinformatic tools (BLAST, MG-RAST, NBC, VMGAP, MetaVir, VIROME) for analysing the viral taxonomic composition in simulated viromes and viral metagenomes from different benthic deep-sea ecosystems. The analyses of simulated viromes indicate that all the BLAST tools, followed by MetaVir and VMGAP, are more reliable in the affiliation of viral sequences and strains. When analysing the environmental viromes, tBLASTx, MetaVir, VMGAP and VIROME showed a similar efficiency of sequence annotation; however, MetaVir and tBLASTx identified a higher number of viral strains. These latter tools also identified a wider range of viral families than the others, providing a wider view of viral taxonomic diversity in benthic deep-sea ecosystems. Our findings highlight strengths and weaknesses of available bioinformatic tools for investigating the taxonomic diversity of viruses in benthic ecosystems in order to improve our comprehension of viral diversity in the oceans and its relationships with host diversity and ecosystem functioning.
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