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Title: iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

Abstract

Microbes affect nutrient and energy transformations throughout the world’s ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps’) for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromicsmore » as yet another tool to elucidate viral roles in nature.« less

Authors:
 [1];  [2]; ORCiD logo [1];  [2];  [3]
  1. The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
  2. Univ. of Arizona, Tucson, AZ (United States). Dept. of Agricultural and Biosystems Engineering
  3. The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology. Dept. of Civil, Environmental and Geodetic Engineering
Publication Date:
Research Org.:
Univ. of Arizona, Tucson, AZ (United States); The Ohio State Univ., Columbus, OH (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Gordon and Betty Moore Foundation (United States)
OSTI Identifier:
1473902
Grant/Contract Number:  
SC0010580; GBMF4491; GBMF4733; GBMF3305; GBMF3790
Resource Type:
Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 11; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; metagenomics; virology

Citation Formats

Bolduc, Benjamin, Youens-Clark, Ken, Roux, Simon, Hurwitz, Bonnie L., and Sullivan, Matthew B. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. United States: N. p., 2016. Web. doi:10.1038/ismej.2016.89.
Bolduc, Benjamin, Youens-Clark, Ken, Roux, Simon, Hurwitz, Bonnie L., & Sullivan, Matthew B. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. United States. doi:10.1038/ismej.2016.89.
Bolduc, Benjamin, Youens-Clark, Ken, Roux, Simon, Hurwitz, Bonnie L., and Sullivan, Matthew B. Fri . "iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure". United States. doi:10.1038/ismej.2016.89. https://www.osti.gov/servlets/purl/1473902.
@article{osti_1473902,
title = {iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure},
author = {Bolduc, Benjamin and Youens-Clark, Ken and Roux, Simon and Hurwitz, Bonnie L. and Sullivan, Matthew B.},
abstractNote = {Microbes affect nutrient and energy transformations throughout the world’s ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps’) for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.},
doi = {10.1038/ismej.2016.89},
journal = {The ISME Journal},
number = ,
volume = 11,
place = {United States},
year = {2016},
month = {7}
}

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Works referenced in this record:

High-Throughput Sequencing Technologies
journal, May 2015


Metagenomic Analysis of RNA Viruses in a Fresh Water Lake
journal, September 2009


The iPlant Collaborative: Cyberinfrastructure for Plant Biology
journal, January 2011

  • Goff, Stephen A.; Vaughn, Matthew; McKay, Sheldon
  • Frontiers in Plant Science, Vol. 2
  • DOI: 10.3389/fpls.2011.00034

Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses
journal, July 2014

  • Hurwitz, B. L.; Westveld, A. H.; Brum, J. R.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 29
  • DOI: 10.1073/pnas.1319778111

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome
journal, June 2012


Sequencing platform and library preparation choices impact viral metagenomes
journal, January 2013

  • Solonenko, Sergei A.; Ignacio-Espinoza, J.; Alberti, Adriana
  • BMC Genomics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2164-14-320

Determinants of community structure in the global plankton interactome
journal, May 2015


Viral metagenomics
journal, May 2005

  • Edwards, Robert A.; Rohwer, Forest
  • Nature Reviews Microbiology, Vol. 3, Issue 6
  • DOI: 10.1038/nrmicro1163

CAMERA: A Community Resource for Metagenomics
journal, March 2007


Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome
journal, August 2014

  • Hurwitz, Bonnie L.; Brum, Jennifer R.; Sullivan, Matthew B.
  • The ISME Journal, Vol. 9, Issue 2
  • DOI: 10.1038/ismej.2014.143

Bilinear Mixed-Effects Models for Dyadic Data
journal, March 2005


Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes
journal, February 2008

  • Lima-Mendez, G.; Van Helden, J.; Toussaint, A.
  • Molecular Biology and Evolution, Vol. 25, Issue 4
  • DOI: 10.1093/molbev/msn023

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
journal, March 2007


Metavir 2: new tools for viral metagenome comparison and assembled virome analysis
journal, January 2014


The global virome: not as big as we thought?
journal, October 2013

  • Cesar Ignacio-Espinoza, J.; Solonenko, Sergei A.; Sullivan, Matthew B.
  • Current Opinion in Virology, Vol. 3, Issue 5
  • DOI: 10.1016/j.coviro.2013.07.004

QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

  • Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
  • Nature Methods, Vol. 7, Issue 5
  • DOI: 10.1038/nmeth.f.303

Patterns and ecological drivers of ocean viral communities
journal, May 2015


SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters
journal, November 2009

  • Rattei, Thomas; Tischler, Patrick; Götz, Stefan
  • Nucleic Acids Research, Vol. 38, Issue suppl_1
  • DOI: 10.1093/nar/gkp949

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
journal, January 2011


VIROME: a standard operating procedure for analysis of viral metagenome sequences
journal, July 2012

  • Wommack, K. Eric; Bhavsar, Jaysheel; Polson, Shawn W.
  • Standards in Genomic Sciences, Vol. 6, Issue 3
  • DOI: 10.4056/sigs.2945050

Rapid evolution of the human gut virome
journal, July 2013

  • Minot, S.; Bryson, A.; Chehoud, C.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 30
  • DOI: 10.1073/pnas.1300833110

The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome
journal, October 2015

  • Hannigan, Geoffrey D.; Meisel, Jacquelyn S.; Tyldsley, Amanda S.
  • mBio, Vol. 6, Issue 5
  • DOI: 10.1128/mBio.01578-15

Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline
journal, December 2012


Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs
journal, September 2015

  • Munson-McGee, Jacob H.; Field, Erin K.; Bateson, Mary
  • Applied and Environmental Microbiology, Vol. 81, Issue 22
  • DOI: 10.1128/AEM.01539-15

An efficient algorithm for large-scale detection of protein families
journal, April 2002


VirSorter: mining viral signal from microbial genomic data
journal, January 2015

  • Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.
  • PeerJ, Vol. 3
  • DOI: 10.7717/peerj.985

The EMBL Nucleotide Sequence Database
journal, December 2004


Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
journal, July 2015


Database resources of the National Center for Biotechnology
journal, January 2003


Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics
journal, March 2012


GenBank
journal, January 1998


Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012

  • Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
  • The ISME Journal, Vol. 6, Issue 8
  • DOI: 10.1038/ismej.2012.8

Metabolic reprogramming by viruses in the sunlit and dark ocean
journal, January 2013


Comparative metagenomics of microbial traits within oceanic viral communities
journal, February 2011

  • Sharon, Itai; Battchikova, Natalia; Aro, Eva-Mari
  • The ISME Journal, Vol. 5, Issue 7
  • DOI: 10.1038/ismej.2011.2

Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community: Halite metagenome
journal, March 2016

  • Crits-Christoph, Alexander; Gelsinger, Diego R.; Ma, Bing
  • Environmental Microbiology, Vol. 18, Issue 6
  • DOI: 10.1111/1462-2920.13259

Genomic analysis of uncultured marine viral communities
journal, October 2002

  • Breitbart, M.; Salamon, P.; Andresen, B.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 22
  • DOI: 10.1073/pnas.202488399

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics
journal, August 2015

  • Brum, Jennifer R.; Hurwitz, Bonnie L.; Schofield, Oscar
  • The ISME Journal, Vol. 10, Issue 2
  • DOI: 10.1038/ismej.2015.125

    Works referencing / citing this record:

    Multiple mechanisms drive phage infection efficiency in nearly identical hosts
    journal, March 2018

    • Howard-Varona, Cristina; Hargreaves, Katherine R.; Solonenko, Natalie E.
    • The ISME Journal, Vol. 12, Issue 6
    • DOI: 10.1038/s41396-018-0099-8

    Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages
    journal, May 2019


    Mining, analyzing, and integrating viral signals from metagenomic data
    journal, March 2019


    Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
    journal, January 2019