iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Bolduc, Benjamin; Zablocki, Olivier; Guo, Jiarong; Zayed, Ahmed A.; Vik, Dean; Dehal, Paramvir; Wood-Charlson, Elisha M.; Arkin, Adam; Merchant, Nirav; Pett-Ridge, Jennifer; Roux, Simon; Vaughn, Matthew; Sullivan, Matthew B.

doi:10.1038/s43705-021-00083-3

Title: iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Journal Article · Tue Dec 14 00:00:00 EST 2021 · ISME Communications

DOI:https://doi.org/10.1038/s43705-021-00083-3· OSTI ID:1835644

;

; Guo, Jiarong; Zayed, Ahmed A.; Vik, Dean; Dehal, Paramvir;

; Arkin, Adam; Merchant, Nirav;

; Roux, Simon;

;

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into ‘iVirus’ on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus’s functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy’s Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as “live” protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems.

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

OSTI ID:: 1835644

Journal Information:: ISME Communications, Journal Name: ISME Communications Vol. 1 Journal Issue: 1; ISSN 2730-6151

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

References (54)

Rising to the challenge: accelerated pace of discovery transforms marine virology Brum, Jennifer R.; Sullivan, Matthew B. Nature Reviews Microbiology, Vol. 13, Issue 3 https://doi.org/10.1038/nrmicro3404	journal	February 2015
Glacier ice archives nearly 15,000-year-old microbes and phages Zhong, Zhi-Ping; Tian, Funing; Roux, Simon Microbiome, Vol. 9, Issue 1 https://doi.org/10.1186/s40168-021-01106-w	journal	July 2021
Anvi’o: an advanced analysis and visualization platform for ‘omics data Eren, A. Murat; Esen, Özcan C.; Quince, Christopher PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1319	journal	January 2015
DRAM for distilling microbial metabolism to automate the curation of microbiome function Shaffer, Michael; Borton, Mikayla A.; McGivern, Bridget B. Nucleic Acids Research, Vol. 48, Issue 16 https://doi.org/10.1093/nar/gkaa621	journal	August 2020
Sulfur Oxidation Genes in Diverse Deep-Sea Viruses Anantharaman, K.; Duhaime, M. B.; Breier, J. A. Science, Vol. 344, Issue 6185 https://doi.org/10.1126/science.1252229	journal	May 2014
VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families Pons, Joan Carles; Paez-Espino, David; Riera, Gabriel Bioinformatics https://doi.org/10.1093/bioinformatics/btab026	journal	January 2021
The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences Merchant, Nirav; Lyons, Eric; Goff, Stephen PLOS Biology, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pbio.1002342	journal	January 2016
Host-linked soil viral ecology along a permafrost thaw gradient Emerson, Joanne B.; Roux, Simon; Brum, Jennifer R. Nature Microbiology, Vol. 3, Issue 8 https://doi.org/10.1038/s41564-018-0190-y	journal	July 2018
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks Bin Jang, Ho; Bolduc, Benjamin; Zablocki, Olivier Nature Biotechnology, Vol. 37, Issue 6 https://doi.org/10.1038/s41587-019-0100-8	journal	May 2019
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing Trubl, Gareth; Jang, Ho Bin; Roux, Simon mSystems, Vol. 3, Issue 5 https://doi.org/10.1128/mSystems.00076-18	journal	October 2018
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome Nayfach, Stephen; Páez-Espino, David; Call, Lee Nature Microbiology, Vol. 6, Issue 7 https://doi.org/10.1038/s41564-021-00928-6	journal	June 2021
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer Gregory, Ann C.; Solonenko, Sergei A.; Ignacio-Espinoza, J. Cesar BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-3286-x	journal	November 2016
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters Gazitúa, M. Consuelo; Vik, Dean R.; Roux, Simon The ISME Journal, Vol. 15, Issue 4 https://doi.org/10.1038/s41396-020-00825-6	journal	November 2020
Virus taxonomy in the age of metagenomics Simmonds, Peter; Adams, Mike J.; Benkő, Mária Nature Reviews Microbiology, Vol. 15, Issue 3 https://doi.org/10.1038/nrmicro.2016.177	journal	January 2017
Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems Zimmerman, Amy E.; Howard-Varona, Cristina; Needham, David M. Nature Reviews Microbiology, Vol. 18, Issue 1 https://doi.org/10.1038/s41579-019-0270-x	journal	November 2019
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses Roux, Simon; Páez-Espino, David; Chen, I-Min A. Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa946	journal	November 2020
Revisiting the rules of life for viruses of microorganisms Correa, Adrienne M. S.; Howard-Varona, Cristina; Coy, Samantha R. Nature Reviews Microbiology, Vol. 19, Issue 8 https://doi.org/10.1038/s41579-021-00530-x	journal	March 2021
Marine DNA Viral Macro- and Microdiversity from Pole to Pole Gregory, Ann C.; Zayed, Ahmed A.; Conceição-Neto, Nádia Cell, Vol. 177, Issue 5 https://doi.org/10.1016/j.cell.2019.03.040	journal	May 2019
Marine viruses — major players in the global ecosystem Suttle, Curtis A. Nature Reviews Microbiology, Vol. 5, Issue 10 https://doi.org/10.1038/nrmicro1750	journal	October 2007
Putative archaeal viruses from the mesopelagic ocean Vik, Dean R.; Roux, Simon; Brum, Jennifer R. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3428	journal	January 2017
VIROME: a standard operating procedure for analysis of viral metagenome sequences Wommack, K. Eric; Bhavsar, Jaysheel; Polson, Shawn W. Standards in Genomic Sciences, Vol. 6, Issue 3 https://doi.org/10.4056/sigs.2945050	journal	July 2012
Towards quantitative viromics for both double-stranded and single-stranded DNA viruses Roux, Simon; Solonenko, Natalie E.; Dang, Vinh T. PeerJ, Vol. 4 https://doi.org/10.7717/peerj.2777	journal	January 2016
PHASTER: a better, faster version of the PHAST phage search tool Arndt, David; Grant, Jason R.; Marcu, Ana Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw387	journal	May 2016
Computational approaches to predict bacteriophage–host relationships Edwards, Robert A.; McNair, Katelyn; Faust, Karoline FEMS Microbiology Reviews, Vol. 40, Issue 2 https://doi.org/10.1093/femsre/fuv048	journal	December 2015
VirSorter: mining viral signal from microbial genomic data Roux, Simon; Enault, Francois; Hurwitz, Bonnie L. PeerJ, Vol. 3 https://doi.org/10.7717/peerj.985	journal	January 2015
Minimum Information about an Uncultivated Virus Genome (MIUViG) Roux, Simon; Adriaenssens, Evelien M.; Dutilh, Bas E. Nature Biotechnology, Vol. 37, Issue 1 https://doi.org/10.1038/nbt.4306	journal	December 2018
Protocols.io: Virtual Communities for Protocol Development and Discussion Teytelman, Leonid; Stoliartchouk, Alexei; Kindler, Lori PLOS Biology, Vol. 14, Issue 8 https://doi.org/10.1371/journal.pbio.1002538	journal	August 2016
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands Warwick-Dugdale, Joanna; Solonenko, Natalie; Moore, Karen PeerJ, Vol. 7 https://doi.org/10.7717/peerj.6800	journal	January 2019
Metabolic reprogramming by viruses in the sunlit and dark ocean Hurwitz, Bonnie L.; Hallam, Steven J.; Sullivan, Matthew B. Genome Biology, Vol. 14, Issue 11 https://doi.org/10.1186/gb-2013-14-11-r123	journal	January 2013
Genome‐resolved viral ecology in a marine oxygen minimum zone Vik, Dean; Gazitúa, Maria Consuelo; Sun, Christine L. Environmental Microbiology, Vol. 23, Issue 6 https://doi.org/10.1111/1462-2920.15313	journal	November 2020
Photosynthesis genes in marine viruses yield proteins during host infection Lindell, Debbie; Jaffe, Jacob D.; Johnson, Zackary I. Nature, Vol. 438, Issue 7064 https://doi.org/10.1038/nature04111	journal	October 2005
Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts Sullivan, Matthew B.; Lindell, Debbie; Lee, Jessica A. PLoS Biology, Vol. 4, Issue 8 https://doi.org/10.1371/journal.pbio.0040234	journal	July 2006
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses Guo, Jiarong; Bolduc, Ben; Zayed, Ahmed A. Microbiome, Vol. 9, Issue 1 https://doi.org/10.1186/s40168-020-00990-y	journal	February 2021
Phage-specific metabolic reprogramming of virocells Howard-Varona, Cristina; Lindback, Morgan M.; Bastien, G. Eric The ISME Journal, Vol. 14, Issue 4 https://doi.org/10.1038/s41396-019-0580-z	journal	January 2020
Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses Hurwitz, B. L.; Westveld, A. H.; Brum, J. R. Proceedings of the National Academy of Sciences, Vol. 111, Issue 29 https://doi.org/10.1073/pnas.1319778111	journal	July 2014
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
Sequencing platform and library preparation choices impact viral metagenomes Solonenko, Sergei A.; Ignacio-Espinoza, J.; Alberti, Adriana BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-320	journal	January 2013
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences Kieft, Kristopher; Zhou, Zhichao; Anantharaman, Karthik Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00867-0	journal	June 2020
Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism Thompson, L. R.; Zeng, Q.; Kelly, L. Proceedings of the National Academy of Sciences, Vol. 108, Issue 39 https://doi.org/10.1073/pnas.1102164108	journal	August 2011
Metavir: a web server dedicated to virome analysis Roux, Simon; Faubladier, Michaël; Mahul, Antoine Bioinformatics, Vol. 27, Issue 21 https://doi.org/10.1093/bioinformatics/btr519	journal	September 2011
Identifying viruses from metagenomic data using deep learning Ren, Jie; Song, Kai; Deng, Chao Quantitative Biology, Vol. 8, Issue 1 https://doi.org/10.1007/s40484-019-0187-4	journal	January 2020
MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins Amgarten, Deyvid; Braga, Lucas P. P.; da Silva, Aline M. Frontiers in Genetics, Vol. 9 https://doi.org/10.3389/fgene.2018.00304	journal	August 2018
Virocell Metabolism: Metabolic Innovations During Host–Virus Interactions in the Ocean Rosenwasser, Shilo; Ziv, Carmit; Creveld, Shiri Graff van Trends in Microbiology, Vol. 24, Issue 10 https://doi.org/10.1016/j.tim.2016.06.006	journal	October 2016
Depth-related variability in viral communities in highly stratified sulfidic mine tailings Gao, Shao-Ming; Schippers, Axel; Chen, Nan Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00848-3	journal	June 2020
VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses Moraru, Cristina; Varsani, Arvind; Kropinski, Andrew M. Viruses, Vol. 12, Issue 11 https://doi.org/10.3390/v12111268	journal	November 2020
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs Galiez, Clovis; Siebert, Matthias; Enault, François Bioinformatics, Vol. 33, Issue 19 https://doi.org/10.1093/bioinformatics/btx383	journal	July 2017
iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure Bolduc, Benjamin; Youens-Clark, Ken; Roux, Simon The ISME Journal, Vol. 11, Issue 1 https://doi.org/10.1038/ismej.2016.89	journal	July 2016
ViPTree: the viral proteomic tree server Nishimura, Yosuke; Yoshida, Takashi; Kuronishi, Megumi Bioinformatics, Vol. 33, Issue 15 https://doi.org/10.1093/bioinformatics/btx157	journal	March 2017
CheckV assesses the quality and completeness of metagenome-assembled viral genomes Nayfach, Stephen; Camargo, Antonio Pedro; Schulz, Frederik Nature Biotechnology, Vol. 39, Issue 5 https://doi.org/10.1038/s41587-020-00774-7	journal	December 2020
Archaeal dominance in the mesopelagic zone of the Pacific Ocean Karner, Markus B.; DeLong, Edward F.; Karl, David M. Nature, Vol. 409, Issue 6819 https://doi.org/10.1038/35054051	journal	January 2001
Understanding how microbiomes influence the systems they inhabit Hall, Ed K.; Bernhardt, Emily S.; Bier, Raven L. Nature Microbiology, Vol. 3, Issue 9 https://doi.org/10.1038/s41564-018-0201-z	journal	August 2018
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut Gregory, Ann C.; Zablocki, Olivier; Zayed, Ahmed A. Cell Host & Microbe, Vol. 28, Issue 5 https://doi.org/10.1016/j.chom.2020.08.003	journal	November 2020
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3243	journal	January 2017
Current understanding of the human microbiome Gilbert, Jack A.; Blaser, Martin J.; Caporaso, J. Gregory Nature Medicine, Vol. 24, Issue 4 https://doi.org/10.1038/nm.4517	journal	April 2018

Similar Records

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

Journal Article · Fri Jul 15 00:00:00 EDT 2016 · The ISME Journal · OSTI ID:1835644

Bolduc, Benjamin; Youens-Clark, Ken; Roux, Simon; +2 more

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

Journal Article · Wed May 03 00:00:00 EDT 2017 · PeerJ · OSTI ID:1835644

Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem; +3 more

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Journal Article · Mon Feb 01 00:00:00 EST 2021 · Microbiome · OSTI ID:1835644

Guo, Jiarong; Bolduc, Ben; Zayed, Ahmed A.; +8 more

Title: iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Citation Formats

References (54)

Similar Records

Related Subjects