Viral metagenomics

  title={Viral metagenomics},
  author={Robert A. Edwards and Forest L. Rohwer},
  journal={Nature Reviews Microbiology},
Viruses, most of which infect microorganisms, are the most abundant biological entities on the planet. Identifying and measuring the community dynamics of viruses in the environment is complicated because less than one percent of microbial hosts have been cultivated. Also, there is no single gene that is common to all viral genomes, so total uncultured viral diversity cannot be monitored using approaches analogous to ribosomal DNA profiling. Metagenomic analyses of uncultured viral communities… 
A Molecular Battiscope for Freshwater Viral Ecology
A snapshot of the diversity of the DNA viruses harvested from a standing pond on a cattle farm has been obtained and a high abundance of viral genotypes were present within the virome.
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The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e., phages) in aquatic ecosystems, which form the bulk of the authors' knowledge in modern environmental viral ecology.
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This study highlights recent advances in the field of metagenomics for analyzing microbial communities in different ecosystems ranging from oceans to the human microbiome and provides a snapshot for the recent advances.
Metagenomic Analysis of the Viral Communities in Fermented Foods
It is indicated that fermented foods contain less complex viral communities than many other environmental habitats, such as seawater, human feces, marine sediment, and soil.
Single-virus genomics and beyond.
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Genomic analysis of uncultured marine viral communities
Diversity of the viral communities was extremely high, and the results showed that it would be possible to sequence the entire genome of an uncultured marine viral community.
Virioplankton: Viruses in Aquatic Ecosystems
Novel applications of molecular genetic techniques have provided good evidence that viral infection can significantly influence the composition and diversity of aquatic microbial communities, supporting the hypothesis that viruses play a significant role in microbial food webs.
Biotechnological prospects from metagenomics.
Metagenomic Analyses of an Uncultured Viral Community from Human Feces
The first metagenomic analyses of an uncultured viral community from human feces, using partial shotgun sequencing, show that the recognizable viruses were mostly siphophages, and the community contained an estimated 1,200 viral genotypes.
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.
Metagenomics: Application of Genomics to Uncultured Microorganisms
  • J. Handelsman
  • Biology
    Microbiology and Molecular Biology Reviews
  • 2004
Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community.
Community structure and metabolism through reconstruction of microbial genomes from the environment
Reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II and analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.
The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage
The Phage Proteomic Tree is presented, which is based on the overall similarity of 105 completely sequenced phage genomes, and proposed as the basis of a genome-based taxonomical system for phage.
Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms
Phylogenetic analysis of 16S rRNA gene sequences recovered from one of the libraries indicates that the BAC libraries contain DNA from a wide diversity of microbial phyla, including sequences from diverse taxa such as the low-G+C, gram-positive Acidobacterium,Cytophagales, and Proteobacteria.