Minimum Information about an Uncultivated Virus Genome (MIUViG)

Roux, Simon; Adriaenssens, Evelien M.; Dutilh, Bas E.; Koonin, Eugene V.; Kropinski, Andrew M.; Krupovìč, Mart; Kuhn, Jens H.; Lavigne, Rob; Brister, J. Rodney; Varsani, Arvind; Amid, Clara; Aziz, Ramy K.; Bordenstein, Seth R.; Bork, Peer; Breitbart, Mya; Cochrane, Guy; Daly, Rebecca A.; Desnues, Christelle; Duhaime, Melissa B.; Emerson, Joanne B.; Enault, François; Fuhrman, Jed A.; Hingamp, Pascal; Hugenholtz, Philip; Hurwitz, Bonnie; Ivanova, Natalia; Labonté, Jessica M.; Lee, Kyung Bum; Malmstrom, Rex R.; Martínez‐García, Manuel; Karsch-Mizrachi, Ilene; Ogata, Hiroyuki; Páez-Espino, David; Petit, Marie-Agnès; Putonti, Catherine; Rattei, Thomas; Reyes, Alejandro; Rodrı́guez-Valera, Francisco; Rosario, Karyna; Schriml, Lynn M.; Schulz, Frederik; Steward, Grieg F.; Sullivan, Matthew B.; Sunagawa, Shinichi; Suttle, Curtis A.; Temperton, Ben; Tringe, Susannah G.; Thurber, Rebecca Vega; Webster, Nicole S.; Whiteson, Katrine; Wilhelm, Steven W.; Wommack, K. Eric; Woyke, Tanja; Wrighton, Kelly; Yilmaz, Pelin; Yoshida, Takashi; Young, Mark; Yutin, Natalya; Allen, Lisa Zeigler; Kyrpides, Nikos C.; Eloe‐Fadrosh, Emiley A.

doi:10.1038/nbt.4306

Cited by 429 publications

(442 citation statements)

References 93 publications

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“…S2). Although sequence-based virus taxonomy is under debate (Simmonds et al, 2017;Roux et al, 2019), our molecular data (both nucleotide and amino acid level), marker capsid gene of virus 37-F6 (gene 9), and gene synteny data taken together suggest that these viral contigs in Osaka Bay belonged to same genus. However, it cannot be ruled out that some of these viruses might even belong to the same sub-family, as previously discussed Martinez-Hernandez et al, 2017).…”

Section: Discussionmentioning

confidence: 82%

“…B) at an average amino acid identities (AAI) between 50% and 81% with very high gene synteny (Fig. S2), and in all cases, at <95% average genome nucleotide identities (gANI), approximating genus‐level relatedness or even probably in some cases to subfamily level (Mizuno et al ., ; Roux et al ., , ; Martinez‐Hernandez et al ., ). In addition, most of these viral contigs from Osaka Bay related to vSAG 37‐F6 had the specific capsid marker gene, representing viral group 37‐F6 (gene 9), which was the most abundant marine viral protein (Brum et al ., ; Martinez‐Hernandez et al ., ).…”

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confidence: 99%

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Diel cycling of the cosmopolitan abundant Pelagibacter virus 37‐F6: one of the most abundant viruses on earth

Martínez-Hernández

Luo

Tominaga

et al. 2020

Environ Microbiol Rep

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Summary The spatiotemporal dynamics for marine viral populations has only recently been explored. However, nothing is known about temporal activities of the uncultured Pelagibacter virus vSAG 37‐F6, which was discovered by single‐virus genomics as potentially the most abundant marine virus. Here, we investigate the diel cycling of 37‐F6 virus and the putative SAR11 host using coastal and oceanic transcriptomic and viromic time‐series data from Osaka Bay and North Pacific Subtropical Gyre. Virus 37‐F6 and relatives displayed diel cycling of transcriptional activities synchronized with its putative host. In both virus and host, the lowest transcription rates were observed at 14:00–15:00, coinciding roughly with maximum solar irradiance, while higher transcriptional rates were detected during the night/early morning and afternoon. Diel abundance of free viruses of 37‐F6 in seawater roughly mirrored the transcriptional activities of both virus and host. In Osaka Bay, among viral relatives (genus level), virus 37‐F6 specifically showed the highest ratio of transcriptional activity to virome abundance, a proxy for viral transcriptional activity relative to free viral particle abundance. This high ratio suggests high infection rate efficiencies in vSAG 37‐F6 virus compared to viral relatives. Thus, time‐series data revealed temporal transcript activities in one of the most abundant viruses in Earth.

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Section: Discussionmentioning

confidence: 82%

mentioning

confidence: 99%

Diel cycling of the cosmopolitan abundant Pelagibacter virus 37‐F6: one of the most abundant viruses on earth

Martínez-Hernández

Luo

Tominaga

et al. 2020

Environ Microbiol Rep

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“…Efforts to define the minimal standards to support the evaluation and interpretation of experiments have been made in various areas of biomedical research, such as microbiology (47)(48)(49), molecular studies (50), extracellular vesicle studies (51)(52)(53), immunopeptidomics (54), HIV research (55,56), and biobanking (57). Standard definitions have also been shown to significantly improve the reproducibility of clinical flow cytometry experiments.…”

Section: Discussionmentioning

confidence: 99%

MiSet RFC Standards: Defining a Universal Minimum Set of Standards Required for Reproducibility and Rigor in Research Flow Cytometry Experiments

et al. 2019

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Poor adherence to best practices, insufficient training, and pressure to produce data quickly may lead to publications of suboptimal biomedical research flow cytometry data, which contributes to the body of irreproducible research findings. In addition, documentation of compliance with best flow cytometry practices for submission, visualization, and publication of flow cytometry data is currently endorsed by very few scientific journals, which is particularly concerning as numerous peer-reviewed flow cytometry publications emphasize instrumentation, experimental design, and data analysis as important sources of variability. Guidelines and resources for adequate reporting, annotation and deposition of flow cytometry experiments are provided by MIFlowCyt and the FlowRepository database, and comprehensive expert recommendations covering principles and techniques of field-specific flow cytometry applications have been published. To facilitate the integration of quality-defining parameters into manuscript and grant submission and publication requirements across biomedical fields that rely on the use of flow-cytometry-based techniques, a single comprehensive yet easily and universally applicable document is needed. To produce such a list of gold-standard parameters that assess whether a research flow cytometry experiment has been planned, conducted, interpreted, and reported at the highest standard, a new initiative defining the minimum set of standards a robust and rigorous research flow experiment must fulfill (MiSet RFC Standards) was proposed at CYTO 2019. MiSet RFC Standards will integrate and simplify existing resources to provide a universal benchmark a flow cytometry experiment can easily be measured against. The goal of MiSET RFC Standards is its integration into peerreview and publication procedures through partnership with stakeholders, journals and publishers in biomedical and translational research. This article introduces the aims and anticipated timeline and discusses strategies for interdisciplinary consensus and implementation. A single-resource broadly applicable guideline will harmonize standards across different fields of biomedical research and lead to publication of more robust research findings.

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“…First, given the growing number of published articles reporting new viruses sequenced from environmental sample or isolates (Pope et al ., ; Páez‐Espino et al ., ; Roux et al ., ; Emerson et al ., ), a global contextualized database for viruses of microbes is certainly on its way. As highlighted in the recently published “Minimum Information on an Uncultivated Virus Genome” framework (Roux et al ., ), viral genomes will most likely form the backbone of this database. Current efforts include >700,000 complete and partial genomes (Páez‐Espino et al ., ), and should reach 10s of millions of genomes in the coming years, especially once complete genomes can be sequenced from single templates using long read sequencing (Houldcroft et al ., ).…”

Section: Story 1 a Real‐time Investigation Of Virus‐host Interactionmentioning

confidence: 99%

A viral reckoning: viruses emerge as essential manipulators of global ecosystems

Roux

Brum

2018

Environ Microbiol Rep

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Minimum Information about an Uncultivated Virus Genome (MIUViG)

Abstract: This paper presents standards and best practices for reporting genome sequences of uncultivated viruses.Supplementary informationThe online version of this article (doi:10.1038/nbt.4306) contains supplementary material, which is available to authorized users.

Cited by 429 publications

References 93 publications

Diel cycling of the cosmopolitan abundant Pelagibacter virus 37‐F6: one of the most abundant viruses on earth

Diel cycling of the cosmopolitan abundant Pelagibacter virus 37‐F6: one of the most abundant viruses on earth

MiSet RFC Standards: Defining a Universal Minimum Set of Standards Required for Reproducibility and Rigor in Research Flow Cytometry Experiments

A viral reckoning: viruses emerge as essential manipulators of global ecosystems

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