Uncovering Earth’s virome

  title={Uncovering Earth’s virome},
  author={David P{\'a}ez-Espino and Emiley A. Eloe-Fadrosh and Georgios A. Pavlopoulos and Alex D. Thomas and Marcel Huntemann and Natalia A. Mikhailova and Edward M. Rubin and Natalia N. Ivanova and Nikos C. Kyrpides},
Viruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome. Here we analysed over 5 Tb of metagenomic sequence data from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses. We discovered over 125,000 partial DNA viral genomes, including the largest phage yet identified, and increased the… 

Diversity, evolution, and classification of virophages uncovered through global metagenomics

The approach has increased the number of known virophage genomes by 10-fold and revealed patterns of genome evolution and global viroPHage distribution.

Charting the diversity of uncultured viruses of Archaea and Bacteria

P phylogenomic analysis of nearly 200,000 viral nucleotide sequences were performed to establish GL-UVAB: Genomic Lineages of Uncultured Viruses of Archaea and Bacteria, providing insights about the genomic diversity and ecology of viruses of prokaryotes.

Assessing the viral content of uncultured picoeukaryotes in the global‐ocean by single cell genomics

The results point to single‐cell genomics as a powerful tool to investigate viral associations in uncultured protists, suggesting a wide distribution of these relationships, and providing new insights into the global viral diversity.

Investigation of recombination-intense viral groups and their genes in the Earth’s virome

This study systematically examined signatures of recombination in every gene from 211 species-level viral groups in a recently obtained dataset of the Earth’s virome that contain corresponding information on the host bacterial species to identify recombination-intense genes that are significantly enriched for encoding phage morphogenesis proteins.

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates, which indicates that vSAGs likely best represent the dsDNA viral populations dominating the oceans.

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean

The analysis indicates that marine cyanophages are already well represented in genome databases and that one of the EVGs likely represents a new cyanophage lineage, and suggests that there is a selection pressure on these marine viruses to accumulate genes for specific viral propagation strategies.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

IMG/VR is presented, the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples, serving as an essential resource in the viral genomics community.

Manual resolution of virome dark matter uncovers hundreds of viral families in the infant gut

Together, the viral families found in this study represent a major expansion of current bacteriophage taxonomy, and the sequences have been put online for use and validation by the community.

Untapped viral diversity in global soil metagenomes

The global distribution of more than 24,000 soil viral sequences and their potential hosts, including >1,600 sequences associated with giant viruses are determined, generating a new paradigm of how viruses can serve as exchange vectors of carbon metabolism across domains of life.

Metaviromics coupled with phage-host identification to open the viral ‘black box’

It is concluded that although metaviromics is a key tool for the study of viral ecology, this approach must be supplemented withphage-host identification, which in turn requires the cultivation of phage-bacteria systems.



Computational approaches to predict bacteriophage–host relationships

Analysis of 820 phages with annotated hosts shows how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications.

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes, illustrating the value of mining viral signal from microbial genomes.

VirSorter: mining viral signal from microbial genomic data

VirSorter is a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses.

Computational prospecting the great viral unknown.

The aim of this paper is to offer an overview of current computational methodologies for virome analysis and to provide an example of reference-independent approaches using human skin viromes, and to present methods to carefully validate AMGs from host contamination.

Global distribution of nearly identical phage-encoded DNA sequences.

It is reported that T7-like Podophage DNA polymerase sequences occur in every major biome investigated, including marine, freshwater, sediment, terrestrial, extreme, and metazoan-associated, suggesting that these phages are moving between biomes in recent evolutionary time and that the global genomic pool for T6-like phages may be smaller than previously hypothesized.

Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation

Although evasion and defense were evident, both hosts and viruses also may benefit from viruses carrying and expressing host genes, thereby potentially enhancing genetic variation and phenotypic differences within populations.

Methods for virus classification and the challenge of incorporating metagenomic sequence data.

A separate system is clearly needed by which virus variants that lack biological information might be incorporated into the ICTV classification even if based solely on sequence relationships to existing taxa.

Viral metagenomics

Metagenomic analyses of uncultured viral communities circumvent limitations and can provide insights into the composition and structure of environmental viral communities.