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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Published on: June 11, 2015
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VIRE: a metagenome-derived, planetary-scale virome resource with environmental context
Suguru Nishijima1,2, Anthony Fullam1, Thomas S B Schmidt3
1Molecular Systems Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Nucleic Acids Research
|November 29, 2025
Summary
Scientists created VIRE, a database of over 1.7 million viral genomes from diverse environments. This resource aids in exploring global viral diversity, evolution, and ecology.
Area of Science:
- Virology
- Bioinformatics
- Ecology
Background:
- Viruses are Earth's most abundant biological entities, but their global diversity is largely unknown.
- Understanding viral diversity is crucial for ecological and evolutionary studies.
Purpose of the Study:
- To present VIRE, a comprehensive resource for exploring global viral diversity.
- To provide a scalable platform for investigating viral genomes, evolution, and ecology.
Main Methods:
- Systematic assembly of viral genomes from >100,000 public metagenomes using a unified pipeline.
- Detailed annotation including genome completeness, taxonomy, lifestyle, and host assignment (CRISPR spacers).
- Integration with microbiome resources SPIRE and Metalog for joint data exploration.
Main Results:
- VIRE comprises >1.7 million high- and medium-quality viral genomes from diverse ecosystems.
- Contains >89 million predicted viral open reading frames with functional annotations.
- Provides host assignment based on CRISPR spacer matches.
Conclusions:
- VIRE offers an open-access, scalable platform for planetary-scale viral research.
- Facilitates the exploration of viral diversity, evolution, and ecological roles.
- Enables joint analysis of viral genomes with microbiome and metadata.
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