Hall EK, Bernhardt ES, Bier RL, Bradford MA, Boot CM, Cotner JB, et al. Understanding how microbiomes influence the systems they inhabit. Nature Microbiol. 2018;3:977–82.
Google Scholar
Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nat. Med. 2018;24:392–400.
Suttle CA. Marine viruses-major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–12.
Google Scholar
Zimmerman AE, Howard-Varona C, Needham DM, John SG, Worden AZ, Sullivan MB, et al. Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems. Nat Rev Microbiol. 2020;18:21–34.
Howard-Varona C, Lindback MM, Bastien GE, Solonenko N, Zayed AA, Jang HB, et al. Phage-specific metabolic reprogramming of virocells. ISME J. 2020;14:881–95.
Google Scholar
Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol. 2006;4:1344–57.
Google Scholar
Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW. Photosynthesis genes in marine viruses yield proteins during host infection. Nature. 2005;438:86–9.
Google Scholar
Hurwitz BL, Hallam SJ, Sullivan MB. Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biol. 2013;14:R123.
Google Scholar
Thompson LR, Zeng Q, Kelly L, Huang KH, Singer AU, Stubbe J, et al. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proc Natl Acad Sci. 2011;108:E757–E764.
Google Scholar
Gazitúa MC, Vik DR, Roux S, Gregory AC, Bolduc B, Widner B, et al. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. ISME J. 2021;15:981–98.
Google Scholar
Vik D, Gazitúa MC, Sun CL, Zayed AA, Aldunate M, Mulholland MR, et al. Genome-resolved viral ecology in a marine oxygen minimum zone. Environ Microbiol. 2021;23:2858–74.
Google Scholar
Rosenwasser S, Ziv C, Creveld SG, van, Vardi A. Virocell metabolism: metabolic innovations during host–virus interactions in the ocean. Trends Microbiol. 2016;24:821–32.
Google Scholar
Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat Microbiol. 2018;3:870–80.
Google Scholar
Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems. 2018;3:1–21.
Zhong Z-P, Tian F, Roux S, Gazitúa MC, Solonenko NE, Li Y-F, et al. Glacier ice archives nearly 15,000-year-old microbes and phages. Microbiome. 2021;9:160.
Google Scholar
Zhong Z-P, Rapp JZ, Wainaina JM, Solonenko NE, Maughan H, Carpenter SD, et al. Viral ecogenomics of arctic cryopeg brine and sea ice. mSystems. 2020;5:e00246–20.
Anantharaman K, Duhaime MB, Breier JA, Wendt KA, Toner BM, Dick GJ. Sulfur oxidation genes in diverse deep-sea viruses. Science. 2014;344:757–60.
Google Scholar
Gao S-M, Schippers A, Chen N, Yuan Y, Zhang M-M, Li Q, et al. Depth-related variability in viral communities in highly stratified sulfidic mine tailings. Microbiome. 2020;8:89.
Google Scholar
Correa AMS, Howard-Varona C, Coy SR, Buchan A, Sullivan MB, Weitz JS. Revisiting the rules of life for viruses of microorganisms. Nat Rev Microbiol. 2021;19:501–13.
Google Scholar
Blazanin M, Turner PE. Community context matters for bacteria-phage ecology and evolution. ISME J. 2021;1–10.
Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, et al. Marine DNA viral macro- and microdiversity from pole to pole. Cell. 2019;177:1109–23. e14
Google Scholar
Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. The gut virome database reveals age-dependent patterns of virome diversity in the human gut. Cell Host and Microbe. 2020;28:724–40. e8
Google Scholar
Roux S, Páez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, et al. IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. Nucleic Acids Res. 2021;49:1–12.
Nayfach S, Páez-Espino D, Call L, Low SJ, Sberro H, Ivanova NN, et al. Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat Microbiol. 2021;6:960–70.
Google Scholar
Roux S, Matthijnssens J, Dutilh BE. Metagenomics in virology. Encycloped Virol. 2021;133–40. Published online 2021 Mar 1. https://doi.org/10.1016/B978-0-12-809633-8.20957-6.
Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory AC, Allen MJ, et al. Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands. PeerJ. 2019;7:e6800.
Google Scholar
Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, et al. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ. 2016;4:e2777.
Google Scholar
Simmonds P, Adams MJ, Benkő M, Breitbart M, Brister JR, Carstens EB, et al. Consensus statement: Virus taxonomy in the age of metagenomics. Nat Rev Microbiol. 2017;15:161–8.
Google Scholar
Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum Information about an Uncultivated Virus Genome (MIUViG): a community consensus on standards and best practices for describing genome sequences from uncultivated viruses. Nat Biotechnol. 2018;37:29–37.
Google Scholar
Jang HB, Bolduc B, Zablocki O, Kuhn JH, Roux S, Adriaenssens EM, et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat Biotechnol 2019;37:632–9.
Nishimura Y, Yoshida T, Kuronishi M, Uehara H, Ogata H, Goto S. ViPTree: the viral proteomic tree server. Bioinformatics. 2017;33:2379–80.
Moraru C, Varsani A, Kropinski AM. VIRIDIC-a novel tool to calculate the intergenomic similarities of prokaryote-infecting. Viruses. 2020;12:1268.
Google Scholar
Pons JC, Paez-Espino D, Riera G, Ivanova N, Kyrpides NC, Llabrés M. VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families. Bioinformatics. 2021;37:1805–13.
Bolduc B, Youens-Clark K, Roux S, Hurwitz BL, Sullivan MB. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. ISME J. 2017;11:7–14.
Google Scholar
Merchant N, Lyons E, Goff S, Vaughn M, Ware D, Micklos D, et al. The iPlant Collaborative: cyberinfrastructure for enabling data to discovery for the life sciences. PLOS Biol. 2016;14:e1002342.
Google Scholar
Teytelman L, Stoliartchouk A, Kindler L, Hurwitz BL. Protocols.io: virtual communities for protocol development and discussion. PLOS Biol. 2016;14:e1002538.
Google Scholar
Kindler L, Stoliartchouk A, Gomez C, Thornton J, Teytelman L, Hurwitz BL. VERVENet: the viral ecology research and virtual exchange network. PeerJ. 2021; in press.
Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44:W16–21.
Google Scholar
Sousa AL de, Maués D, Lobato A, Franco EF, Pinheiro K, Araújo F, et al. PhageWeb—web interface for rapid identification and characterization of prophages in bacterial genomes. Front Genet. 2018; 9.
Tynecki P, Guziński A, Kazimierczak J, Jadczuk M, Dastych J, Onisko A. PhageAI—bacteriophage life cycle recognition with machine learning and natural language processing. bioRxiv 2020; 2020.07.11.198606.
Wommack KE, Bhavsar J, Polson SW, Chen J, Dumas M, Srinivasiah S, et al. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Standards Genom Sci. 2012;6:427–39.
Roux S, Faubladier M, Mahul A, Paulhe N, Bernard A, Debroas D, et al. Metavir: a web server dedicated to virome analysis. Bioinformatics. 2011;27:3074–5.
Google Scholar
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States department of energy systems biology knowledgebase. Nat Biotechnol. 2018;36:566–9.
Google Scholar
Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ. 2015;3:e985.
Google Scholar
Bolduc B, Jang HB, Doulcier G, You Z-QZ, Roux S, Sullivan MB. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ. 2017;5:e3243.
Google Scholar
Hurwitz BL, Westveld AH, Brum JR, Sullivan MB. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. Proc Natl Acad Sci. 2014;111:10714–9.
Google Scholar
Guo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, Delmont TO, et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 2021;9:37.
Google Scholar
Ren J, Kai S, Chao D, Nathan A, Ahlgren, JA, Fuhrman, YL, et al. Identifying viruses from metagenomic data using deep learning. Quant Biol. 2020;8:64–77. https://doi.org/10.1007/s40484-019-0187-4.
Amgarten D, Braga LPP, da Silva AM, Setubal JC. MARVEL, a tool for prediction of bacteriophage sequences in metagenomic bins. Front Genet. 2018;9:1–8.
Pratama A, Bolduc B, Zayed AA, Zhong Z-P, Guo J, Vik DR, et al. Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation. PeerJ. 2021; In Press.
Kieft, K., Zhou, Z. & Anantharaman, K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome. 2020;8:90. https://doi.org/10.1186/s40168-020-00867-0.
Karner MB, DeLong EF, Karl DM. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature. 2001;409:507–10.
Google Scholar
Vik DR, Roux S, Brum JR, Bolduc B, Emerson JB, Padilla CCC, et al. Putative archaeal viruses from the mesopelagic ocean. PeerJ. 2017;5:e3428.
Google Scholar
Vik D, Bolduc B, Roux S, Krupovic M, Sullivan MB. MArVDv2: a machine learning approach to metagenomic archaeal virus detection. bioRxiv 2021; In Press..
Tisza MJ, Pastrana DV, Welch NL, Stewart B, Peretti A, Starrett GJ, et al. Discovery of several thousand highly diverse circular DNA viruses. eLife. 2020;9:1–26.
Tisza MJ, Belford AK, Domínguez-Huerta G, Bolduc B, Buck CB. Cenote-Taker 2 democratizes virus discovery and sequence annotation. Virus Evolut. 2021;7:1–12.
Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, Solden LM, et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 2020;48:8883–8900.
Google Scholar
Edwards RA, McNair K, Faust K, Raes J, Dutilh BE. Computational approaches to predict bacteriophage–host relationships. FEMS Microbiol Rev. 2016;40:258–72.
Google Scholar
Galiez C, Siebert M, Enault F, Vincent J, Söding J. WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs. Bioinformatics. 2017;33:3113–14.
Nayfach S, Camargo AP, Schulz F, Eloe-Fadrosh E, Roux S & Kyrpides NC. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol 2021;39:578–85. https://doi.org/10.1038/s41587-020-00774-7.
Gregory AC, Solonenko SA, Ignacio-Espinoza JC, LaButti K, Copeland A, Sudek S, et al. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC Genom. 2016;17:930.
Brum JR, Sullivan MB. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol. 2015;13:147–59.
Google Scholar
Gregory AC, Gerhardt K, Zhong Z-P, Bolduc B, Temperton B, Konstantinidis KT, et al. MetaPop: a pipeline for macro- and micro-diversity analyses and visualization of microbial and viral metagenome-derived populations. bioRxiv 2020; 2020.11.01.363960.
Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319.
Google Scholar
Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G, et al. MGnify: the microbiome analysis resource in 2020. Nucleic Acids Res. 2019;48:D570–D578.
Google Scholar
Solonenko SA, Ignacio-Espinoza JC, Alberti A, Cruaud C, Hallam S, Konstantinidis K, et al. Sequencing platform and library preparation choices impact viral metagenomes. BMC Genom. 2013;14:320.
Google Scholar
Wood-Charlson EM, Anubhav, Auberry D, Blanco H, Borkum MI, Corilo YE, et al. The National Microbiome Data Collaborative: enabling microbiome science. Nat Rev Microbiol. 2020;18:313–4.
Google Scholar
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