DOI:10.1038/nrmicro1163 - Corpus ID: 8059643
Viral metagenomics
@article{Edwards2005ViralM, title={Viral metagenomics}, author={Robert A. Edwards and Forest L. Rohwer}, journal={Nature Reviews Microbiology}, year={2005}, volume={3}, pages={504-510}, url={https://api.semanticscholar.org/CorpusID:8059643} }
- R. Edwards, F. Rohwer
- Published in Nature Reviews Microbiology 2005
- Environmental Science, Biology
Metagenomic analyses of uncultured viral communities circumvent limitations and can provide insights into the composition and structure of environmental viral communities.
848 Citations
848 Citations
Viromics approaches for the study of viral diversity and ecology in microbiomes.
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Large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.
A Molecular Battiscope for Freshwater Viral Ecology
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- 2016
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.
Comparative Viral Metagenomics of Environmental Samples from Korea
- Min-Soo KimT. WhonJ. Bae
- Biology, Environmental Science
- 2013
This review considers the current state of viral metagenomics, based on examples from Korean viral meetagenomic studies-i.e., rice paddy soil, fermented foods, human gut, seawater, and the near-surface atmosphere.
Uncovering Earth’s virome
- David Páez-EspinoE. Eloe-Fadrosh N. Kyrpides
- Environmental Science, Biology
- 2016
Analysis of viral distribution across diverse ecosystems revealed strong habitat-type specificity for the vast majority of viruses, but also identified some cosmopolitan groups, and detailed insight into viral habitat distribution and host–virus interactions is provided.
Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
- S. HayesJ. MahonyA. NautaD. van Sinderen
- Environmental Science, Biology
- 2017
The evolution of viral metagenomic methodologies is reviewed, as well as providing an overview of some of the most significant applications and findings in this field of research.
Finding and identifying the viral needle in the metagenomic haystack: trends and challenges
- Hayssam SoueidanLou SchmittT. CandresseM. Nikolski
- Biology, Computer Science
- 2015
The trends in current research for the identification of viral sequences in a metagenomic sample are examined, the intrinsic computational difficulties for the Identification of novel viral sequences within metagenomics samples are pinpointed, and possible avenues to overcome them are suggested.
454-Pyrosequencing: A Molecular Battiscope for Freshwater Viral Ecology
- D. J. RooksDarren L. SmithJ. McDonaldM. WoodwardA. MccarthyH. Allison
- Biology, Environmental Science
- 2010
The techniques and analysis described here provide a fresh approach to the monitoring of viral populations in the aquatic environment, with the potential to become integral to the development of risk analysis tools for monitoring the dissemination of viral agents of animal, plant and human diseases.
Environmental bacteriophages: viruses of microbes in aquatic ecosystems
- T. Sime-Ngando
- Environmental Science
- 2014
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.
The Use of Metagenomic Approaches to Analyze Changes in Microbial Communities
- Girish NeelakantaHameeda Sultana
- Environmental Science, Biology
- 2013
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.
Virophages to viromes: a report from the frontier of viral oceanography.
- Alexander I. Culley
- Biology, Environmental Science
- 2011
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66 References
Genomic analysis of uncultured marine viral communities
- M. BreitbartP. Salamon F. Rohwer
- Environmental Science, Biology
- 2002
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
- K. WommackR. Colwell
- Environmental Science, Biology
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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.
Origins of Highly Mosaic Mycobacteriophage Genomes
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- Biology, Environmental Science
- 2003
Biotechnological prospects from metagenomics.
- P. SchlossJ. Handelsman
- Biology, Environmental Science
- 2003
Metagenomic Analyses of an Uncultured Viral Community from Human Feces
- M. BreitbartI. Hewson F. Rohwer
- Biology, Environmental Science
- 2003
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.
- M. BreitbartJ. MiyakeF. Rohwer
- Biology, Environmental Science
- 2004
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
- Environmental Science, Biology
- 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
- G. TysonJarrod Chapman J. Banfield
- Environmental Science, Biology
- 2004
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
- F. RohwerR. Edwards
- Biology, Environmental Science
- 2002
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
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- Environmental Science, Biology
- 2000
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.
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