Evidence map›Paper›PMID 31127947›Full record

ArticleSystematic biology2020

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages.

Jakub Barylski, François Enault, Bas E Dutilh, Margo Bp Schuller, Robert A Edwards, Annika Gillis, Jochen Klumpp, Petar Knezevic, Mart Krupovic, Jens H Kuhn and 11 more

Open access · hybridAbstract read
In one paragraph

Article in Systematic biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.

0numbers the graph read from it
0cells of the map it votes in
83citing papers in PubMed
14.5field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

83 citing papers in PubMed, 137 citations in OpenAlex.

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  14. In Vitro Susceptibility of Clinical and Carrier Strains ofInternational journal of molecular sciences · 2024
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23 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors at 18 institutions in 12 countries.

Jakub BarylskiDepartment of Molecular Virology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Collegium Biologicum - Umultowska 89, 61-614 Poznań, Poland.
François EnaultUniversité Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France.
Bas E DutilhTheoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
Margo Bp SchullerTheoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
Robert A EdwardsDepartment of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA.
Annika GillisLaboratory of Food and Environmental Microbiology, Université Catholique de Louvain, Croix du Sud 2-L7.05.12, 1348 Louvain-la-Neuve, Belgium.
Jochen KlumppInstitute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
Petar KnezevicDepartment of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia.
Mart KrupovicUnité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, 25 rue du Dr. Roux, 75015 Paris, France.
Jens H KuhnIntegrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA.
Rob LavigneLaboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 - box 2462, 3001 Leuven, Belgium.
Hanna M OksanenMolecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56 (Viikinkaari 9B), 00014 Helsinki, Finland.
Matthew B SullivanDepartment of Microbiology, The Ohio State University, 496 W 12thAvenue, Columbus, OH 43210, USA.
Ho Bin JangDepartment of Microbiology, The Ohio State University, 496 W 12thAvenue, Columbus, OH 43210, USA.
Peter SimmondsNuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford OX1 3SY, UK.
Pakorn AiewsakunNuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford OX1 3SY, UK.
Johannes WittmannLeibniz-Institut DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124 Braunschweig, Germany.
Igor TolstoyNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda MD 20894, USA.
J Rodney BristerNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda MD 20894, USA.
Andrew M KropinskiDepartment of Food Science, University of Guelph, Guelph, Ontario, Canada.
Evelien M AdriaenssensDepartment of Functional & Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK.
National Institutes of Health · USThe Ohio State University · USAdam Mickiewicz University in Poznań · PLCentre National de la Recherche Scientifique · FRETH Zurich · CHInstitut Pasteur · FRKU Leuven · BELeibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures · DEMahidol University · THRadboud University Nijmegen · NLSan Diego State University · USUCLouvain · BEUniversity of Guelph · CAUniversity of Helsinki · FIUniversity of Liverpool · GBUniversity of Novi Sad · RSUniversity of Oxford · GBUtrecht University · NL

Funding

National Biomedical Information ServicesZIHLM200888 · NLM · NATIONAL LIBRARY OF MEDICINE · PI PALTOO, DINA · 2009 to 2025
$5200.7M
Biotechnology and Biological Sciences Research Council BB/R012490/1Biotechnology and Biological Sciences Research Council BBS/E/F/000PR10353NIAID NIH HHS HHSN272200700016I
6 · The paper itself

Abstract

Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order-Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods-including comparative genomics, core genome analysis, and marker gene phylogenetics-to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae-a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.

Indexed as

PhylogenyCaudoviralesClassificationGenome, ViralCaudoviralesHerelleviridaephylogeneticsphylogenomicsspounavirusvirus classificationvirus taxonomy

Identifiers

PMID31127947
PMCPMC7409376
OpenAlexW2945040646

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.