Journal ArticleDOI
Exploring the viral world through metagenomics.
Karyna Rosario,Mya Breitbart +1 more
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TLDR
The intrinsic potential for virus discovery through viral metagenomics can help advance a wide array of disciplines including evolutionary biology, pathogen surveillance, and biotechnology.About:
This article is published in Current Opinion in Virology.The article was published on 2011-10-01. It has received 251 citations till now. The article focuses on the topics: Viral metagenomics & Metagenomics.read more
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Embracing the unknown: disentangling the complexities of the soil microbiome.
TL;DR: Although most soil microorganisms remain undescribed, the field is now poised to identify how to manipulate and manage the soil microbiome to increase soil fertility, improve crop production and improve the understanding of how terrestrial ecosystems will respond to environmental change.
Journal ArticleDOI
Revision of Begomovirus taxonomy based on pairwise sequence comparisons
Judith K. Brown,F. Murilo Zerbini,Jesús Navas-Castillo,Enrique Moriones,Roberto Ramos-Sobrinho,José Cleydson F. Silva,Elvira Fiallo-Olivé,Rob W. Briddon,Cecilia Hernández-Zepeda,Ali M. Idris,V. G. Malathi,Darren P. Martin,Rafael F. Rivera-Bustamante,Shigenori Ueda,Arvind Varsani +14 more
TL;DR: Revised guidelines for the classification and nomenclature of begomoviruses are proposed and genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomviruses belonging to different species and strains, respectively.
Journal ArticleDOI
Consensus statement: Virus taxonomy in the age of metagenomics
Peter Simmonds,Michael J. Adams,Mária Benkő,Mya Breitbart,J. Rodney Brister,Eric B. Carstens,Andrew J. Davison,Eric Delwart,Eric Delwart,Alexander E. Gorbalenya,Alexander E. Gorbalenya,Balázs Harrach,Roger Hull,Andrew M. Q. King,Eugene V. Koonin,Mart Krupovic,Jens H. Kuhn,Elliot J. Lefkowitz,Max L. Nibert,Richard J. Orton,Marilyn J. Roossinck,Sead Sabanadzovic,Matthew B. Sullivan,Curtis A. Suttle,Curtis A. Suttle,Robert B. Tesh,René van der Vlugt,Arvind Varsani,F. Murilo Zerbini +28 more
TL;DR: The rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy is considered, and present proposals that have been endorsed by the Executive Committee of the ITV.
Journal ArticleDOI
Global Organization and Proposed Megataxonomy of the Virus World
Eugene V. Koonin,Valerian V. Dolja,Mart Krupovic,Arvind Varsani,Arvind Varsani,Yuri I. Wolf,Natalya Yutin,F. Murilo Zerbini,Jens H. Kuhn +8 more
TL;DR: Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase, and propose a comprehensive hierarchical taxonomy of viruses.
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Gene transfer agents: phage-like elements of genetic exchange
TL;DR: The defining characteristics of the GTAs that have been identified to date are discussed, along with potential functions for these agents and the possible evolutionary forces that act on the genes involved in their production.
References
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Journal ArticleDOI
The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes
Folker Meyer,Folker Meyer,Daniel Paarmann,Mark D'Souza,Robert Olson,Elizabeth M. Glass,Michael Kubal,Tobias Paczian,Alexis A. Rodriguez,Rick Stevens,Rick Stevens,Andreas Wilke,Jared Wilkening,Robert Edwards,Robert Edwards +14 more
TL;DR: The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes that is stable, extensible, and freely available to all researchers.
Journal ArticleDOI
CRISPR/Cas, the Immune System of Bacteria and Archaea
TL;DR: Clustered regularly interspaced short palindromic repeats (CRISPR) form peculiar genetic loci, which provide acquired immunity against viruses and plasmids by targeting nucleic acid in a sequence-specific manner.
Journal ArticleDOI
A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder
Diana Cox-Foster,Sean Conlan,Edward C. Holmes,Edward C. Holmes,Gustavo Palacios,Jay D. Evans,Nancy A. Moran,Phenix Lan Quan,Thomas Briese,Mady Hornig,David M. Geiser,Vince Martinson,Dennis vanEngelsdorp,Dennis vanEngelsdorp,Abby L. Kalkstein,Andrew T. Drysdale,Jeffrey Hui,Junhui Zhai,Liwang Cui,Stephen K. Hutchison,Jan Fredrik Simons,Michael Egholm,Jeffery S. Pettis,W. Ian Lipkin +23 more
TL;DR: The observation that irradiated combs from affected colonies can be repopulated with naive bees suggests that infection may contribute to colony collapse disorder (CCD).
Journal ArticleDOI
Genomic analysis of uncultured marine viral communities
Mya Breitbart,Peter Salamon,Bjarne Andresen,Joseph M. Mahaffy,Anca M. Segall,David A. Mead,Farooq Azam,Forest Rohwer +7 more
TL;DR: 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.
Journal ArticleDOI
Functional metagenomic profiling of nine biomes
Elizabeth A. Dinsdale,Robert Edwards,Dana Hall,Florent E. Angly,Mya Breitbart,Jennifer M. Brulc,Mike Furlan,Christelle Desnues,Matthew Haynes,Linlin Li,Lauren D. McDaniel,Mary Ann Moran,Karen E. Nelson,Christina Nilsson,Robert Olson,John H. Paul,Beltran Rodriguez Brito,Yijun Ruan,Brandon K. Swan,Rick Stevens,David L. Valentine,Rebecca Vega Thurber,Linda Wegley,Bryan A. White,Forest Rohwer +24 more
TL;DR: The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.