Literature DB >> 25540374

Viromes, not gene markers, for studying double-stranded DNA virus communities.

Matthew B Sullivan1.   

Abstract

Microbes have recently been recognized as dominant forces in nature, with studies benefiting from gene markers that can be quickly, informatively, and universally surveyed. Viruses, where explored, have proven to be powerful modulators of locally and globally important microbes through mortality, horizontal gene transfer, and metabolic reprogramming. However, community-wide virus studies have been challenged by the lack of a universal marker. Here, I propose that viral metagenomics has advanced to largely take over study of double-stranded DNA viruses.
Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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Year:  2014        PMID: 25540374      PMCID: PMC4325738          DOI: 10.1128/JVI.03289-14

Source DB:  PubMed          Journal:  J Virol        ISSN: 0022-538X            Impact factor:   5.103


  20 in total

1.  Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans.

Authors:  Ilnam Kang; Hyun-Myung Oh; Dongmin Kang; Jang-Cheon Cho
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-24       Impact factor: 11.205

Review 2.  The global virome: not as big as we thought?

Authors:  J Cesar Ignacio-Espinoza; Sergei A Solonenko; Matthew B Sullivan
Journal:  Curr Opin Virol       Date:  2013-07-26       Impact factor: 7.090

3.  Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses.

Authors:  Eric G Sakowski; Erik V Munsell; Mara Hyatt; William Kress; Shannon J Williamson; Daniel J Nasko; Shawn W Polson; K Eric Wommack
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-13       Impact factor: 11.205

4.  Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.

Authors:  Li Deng; J Cesar Ignacio-Espinoza; Ann C Gregory; Bonnie T Poulos; Joshua S Weitz; Philip Hugenholtz; Matthew B Sullivan
Journal:  Nature       Date:  2014-07-13       Impact factor: 49.962

5.  Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses.

Authors:  Bonnie L Hurwitz; Anton H Westveld; Jennifer R Brum; Matthew B Sullivan
Journal:  Proc Natl Acad Sci U S A       Date:  2014-07-07       Impact factor: 11.205

6.  Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA.

Authors:  Nicholas J Parkinson; Siarhei Maslau; Ben Ferneyhough; Gang Zhang; Lorna Gregory; David Buck; Jiannis Ragoussis; Chris P Ponting; Michael D Fischer
Journal:  Genome Res       Date:  2011-11-16       Impact factor: 9.043

7.  Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.

Authors:  Andrew Adey; Hilary G Morrison; Xu Xun; Jacob O Kitzman; Emily H Turner; Bethany Stackhouse; Alexandra P MacKenzie; Nicholas C Caruccio; Xiuqing Zhang; Jay Shendure
Journal:  Genome Biol       Date:  2010-12-08       Impact factor: 13.583

8.  Metabolic reprogramming by viruses in the sunlit and dark ocean.

Authors:  Bonnie L Hurwitz; Steven J Hallam; Matthew B Sullivan
Journal:  Genome Biol       Date:  2013-11-07       Impact factor: 13.583

9.  The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology.

Authors:  Bonnie L Hurwitz; Matthew B Sullivan
Journal:  PLoS One       Date:  2013-02-28       Impact factor: 3.240

10.  VIROME: a standard operating procedure for analysis of viral metagenome sequences.

Authors:  K Eric Wommack; Jaysheel Bhavsar; Shawn W Polson; Jing Chen; Michael Dumas; Sharath Srinivasiah; Megan Furman; Sanchita Jamindar; Daniel J Nasko
Journal:  Stand Genomic Sci       Date:  2012-07-27
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  20 in total

Review 1.  Diversity and Ecology of Viruses in Hyperarid Desert Soils.

Authors:  Olivier Zablocki; Evelien M Adriaenssens; Don Cowan
Journal:  Appl Environ Microbiol       Date:  2015-11-20       Impact factor: 4.792

2.  IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses.

Authors:  Simon Roux; David Páez-Espino; I-Min A Chen; Krishna Palaniappan; Anna Ratner; Ken Chu; T B K Reddy; Stephen Nayfach; Frederik Schulz; Lee Call; Russell Y Neches; Tanja Woyke; Natalia N Ivanova; Emiley A Eloe-Fadrosh; Nikos C Kyrpides
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

3.  Marine DNA Viral Macro- and Microdiversity from Pole to Pole.

Authors:  Ann C Gregory; Ahmed A Zayed; Nádia Conceição-Neto; Ben Temperton; Ben Bolduc; Adriana Alberti; Mathieu Ardyna; Ksenia Arkhipova; Margaux Carmichael; Corinne Cruaud; Céline Dimier; Guillermo Domínguez-Huerta; Joannie Ferland; Stefanie Kandels; Yunxiao Liu; Claudie Marec; Stéphane Pesant; Marc Picheral; Sergey Pisarev; Julie Poulain; Jean-Éric Tremblay; Dean Vik; Marcel Babin; Chris Bowler; Alexander I Culley; Colomban de Vargas; Bas E Dutilh; Daniele Iudicone; Lee Karp-Boss; Simon Roux; Shinichi Sunagawa; Patrick Wincker; Matthew B Sullivan
Journal:  Cell       Date:  2019-04-25       Impact factor: 41.582

Review 4.  The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury.

Authors:  Kristina A Kigerl; Kylie Zane; Kia Adams; Matthew B Sullivan; Phillip G Popovich
Journal:  Exp Neurol       Date:  2019-10-22       Impact factor: 5.330

5.  Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages.

Authors:  Simon Roux; François Enault; Viviane Ravet; Olivier Pereira; Matthew B Sullivan
Journal:  Front Microbiol       Date:  2015-03-16       Impact factor: 5.640

6.  Pharmacometabolomics Informs Viromics toward Precision Medicine.

Authors:  Angeliki Balasopoulou; George P Patrinos; Theodora Katsila
Journal:  Front Pharmacol       Date:  2016-10-27       Impact factor: 5.810

7.  From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments.

Authors:  Cinzia Corinaldesi; Michael Tangherlini; Antonio Dell'Anno
Journal:  Sci Rep       Date:  2017-08-21       Impact factor: 4.379

Review 8.  Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches.

Authors:  Stephen Hayes; Jennifer Mahony; Arjen Nauta; Douwe van Sinderen
Journal:  Viruses       Date:  2017-05-24       Impact factor: 5.048

9.  Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics.

Authors:  Sigitas Šulčius; Gediminas Alzbutas; Viktorija Juknevičiūtė; Eugenijus Šimoliūnas; Petras Venckus; Monika Šimoliūnienė; Ričardas Paškauskas
Journal:  Genes (Basel)       Date:  2021-06-08       Impact factor: 4.096

10.  Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.

Authors:  Michelle Davison; Todd J Treangen; Sergey Koren; Mihai Pop; Devaki Bhaya
Journal:  PLoS One       Date:  2016-09-09       Impact factor: 3.240

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