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Shah SA, Deng L, Thorsen J, Pedersen AG, Dion MB, Castro-Mejía JL, Silins R, Romme FO, Sausset R, Jessen LE, Ndela EO, Hjelmsø M, Rasmussen MA, Redgwell TA, Leal Rodríguez C, Vestergaard G, Zhang Y, Chawes B, Bønnelykke K, Sørensen SJ, Bisgaard H, Enault F, Stokholm J, Moineau S, Petit MA, Nielsen DS. Expanding known viral diversity in the healthy infant gut. Nat Microbiol 2023; 8:986-998. [PMID: 37037943 PMCID: PMC10159846 DOI: 10.1038/s41564-023-01345-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/17/2023] [Indexed: 04/12/2023]
Abstract
The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother-child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.
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Affiliation(s)
- Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark.
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders G Pedersen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Moïra B Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
| | | | - Ronalds Silins
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Fie O Romme
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Romain Sausset
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Leon E Jessen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Eric Olo Ndela
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mathis Hjelmsø
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Morten A Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Tamsin A Redgwell
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Cristina Leal Rodríguez
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Gisle Vestergaard
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Yichang Zhang
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Francois Enault
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Quebec, Canada
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark.
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2
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Zucker F, Bischoff V, Olo Ndela E, Heyerhoff B, Poehlein A, Freese HM, Roux S, Simon M, Enault F, Moraru C. New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria. Virus Evol 2022; 8:veac070. [PMID: 36533142 PMCID: PMC9753089 DOI: 10.1093/ve/veac070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/24/2022] [Accepted: 07/28/2022] [Indexed: 10/01/2023] Open
Abstract
The Microviridae family represents one of the major clades of single-stranded DNA (ssDNA) phages. Their cultivated members are lytic and infect Proteobacteria, Bacteroidetes, and Chlamydiae. Prophages have been predicted in the genomes from Bacteroidales, Hyphomicrobiales, and Enterobacteriaceae and cluster within the 'Alpavirinae', 'Amoyvirinae', and Gokushovirinae. We have isolated 'Ascunsovirus oldenburgi' ICBM5, a novel phage distantly related to known Microviridae. It infects Sulfitobacter dubius SH24-1b and uses both a lytic and a carrier-state life strategy. Using ICBM5 proteins as a query, we uncovered in publicly available resources sixty-five new Microviridae prophages and episomes in bacterial genomes and retrieved forty-seven environmental viral genomes (EVGs) from various viromes. Genome clustering based on protein content and phylogenetic analysis showed that ICBM5, together with Rhizobium phages, new prophages, episomes, and EVGs cluster within two new phylogenetic clades, here tentatively assigned the rank of subfamily and named 'Tainavirinae' and 'Occultatumvirinae'. They both infect Rhodobacterales. Occultatumviruses also infect Hyphomicrobiales, including nitrogen-fixing endosymbionts from cosmopolitan legumes. A biogeographical assessment showed that tainaviruses and occultatumviruses are spread worldwide, in terrestrial and marine environments. The new phage isolated here sheds light onto new and diverse branches of the Microviridae tree, suggesting that much of the ssDNA phage diversity remains in the dark.
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Affiliation(s)
- Falk Zucker
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Vera Bischoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Eric Olo Ndela
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, 1 Imp. Amélie Murat, Aubière 63170, Frankreich
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August-University Göttingen, Institute of Microbiology and Genetics, Grisebachstr. 8, Göttingen D-37077, Germany
| | - Heike M Freese
- Leibniz-Institut DSMZ, Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7 B, Braunschweig D-38124, Germany
| | - Simon Roux
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA 94720, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
| | - Francois Enault
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, 1 Imp. Amélie Murat, Aubière 63170, Frankreich
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9−11, Oldenburg D-26111, Germany
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3
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Aevarsson A, Kaczorowska AK, Adalsteinsson BT, Ahlqvist J, Al-Karadaghi S, Altenbuchner J, Arsin H, Átlasson ÚÁ, Brandt D, Cichowicz-Cieślak M, Cornish KAS, Courtin J, Dabrowski S, Dahle H, Djeffane S, Dorawa S, Dusaucy J, Enault F, Fedøy AE, Freitag-Pohl S, Fridjonsson OH, Galiez C, Glomsaker E, Guérin M, Gundesø SE, Gudmundsdóttir EE, Gudmundsson H, Håkansson M, Henke C, Helleux A, Henriksen JR, Hjörleifdóttir S, Hreggvidsson GO, Jasilionis A, Jochheim A, Jónsdóttir I, Jónsdóttir LB, Jurczak-Kurek A, Kaczorowski T, Kalinowski J, Kozlowski LP, Krupovic M, Kwiatkowska-Semrau K, Lanes O, Lange J, Lebrat J, Linares-Pastén J, Liu Y, Lorentsen SA, Lutterman T, Mas T, Merré W, Mirdita M, Morzywołek A, Ndela EO, Karlsson EN, Olgudóttir E, Pedersen C, Perler F, Pétursdóttir SK, Plotka M, Pohl E, Prangishvili D, Ray JL, Reynisson B, Róbertsdóttir T, Sandaa RA, Sczyrba A, Skírnisdóttir S, Söding J, Solstad T, Steen IH, Stefánsson SK, Steinegger M, Overå KS, Striberny B, Svensson A, Szadkowska M, Tarrant EJ, Terzian P, Tourigny M, Bergh TVD, Vanhalst J, Vincent J, Vroling B, Walse B, Wang L, Watzlawick H, Welin M, Werbowy O, Wons E, Zhang R. Going to extremes - a metagenomic journey into the dark matter of life. FEMS Microbiol Lett 2021; 368:6296640. [PMID: 34114607 DOI: 10.1093/femsle/fnab067] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.
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Affiliation(s)
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Josefin Ahlqvist
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Joseph Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hasan Arsin
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - David Brandt
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Magdalena Cichowicz-Cieślak
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Katy A S Cornish
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | | | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,Department of Informatics, University of Bergen, PO Box 7803, Thormøhlens gate 53 A/B, N-5020 Bergen, Norway
| | | | - Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Francois Enault
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Anita-Elin Fedøy
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Stefanie Freitag-Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | - Clovis Galiez
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eirin Glomsaker
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | - Sigurd E Gundesø
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | | | - Maria Håkansson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Christian Henke
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | | | | | - Gudmundur O Hreggvidsson
- Matis ohf, Vinlandsleid 12, Reykjavik 113, Iceland.,Faculty of Life and Environmental Sciences, University of Iceland, Askja-Sturlugata 7, Reykjavik, Iceland
| | - Andrius Jasilionis
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Annika Jochheim
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | - Agata Jurczak-Kurek
- Department of Molecular Evolution, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Lukasz P Kozlowski
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | - Mart Krupovic
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Karolina Kwiatkowska-Semrau
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Olav Lanes
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Joanna Lange
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | | | - Javier Linares-Pastén
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Ying Liu
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | | | - Tobias Lutterman
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Thibaud Mas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | - Milot Mirdita
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Agnieszka Morzywołek
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Eric Olo Ndela
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Eva Nordberg Karlsson
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Cathrine Pedersen
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Francine Perler
- Perls of Wisdom Biotech Consulting, 74 Fuller Street, Brookline, MA 02446, USA
| | | | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ehmke Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom.,Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - David Prangishvili
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jessica L Ray
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,NORCE Environment, NORCE Norwegian Research Centre AS, Nygårdsgaten 112, 5008 Bergen, Norway
| | | | | | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | - Johannes Söding
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Terese Solstad
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - Martin Steinegger
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | - Bernd Striberny
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Anders Svensson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Emma J Tarrant
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Paul Terzian
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | | | | | - Jonathan Vincent
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Bas Vroling
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | - Björn Walse
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Lei Wang
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hildegard Watzlawick
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Martin Welin
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Olesia Werbowy
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ruoshi Zhang
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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4
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Adriaenssens EM, Wittmann J, Kuhn JH, Turner D, Sullivan MB, Dutilh BE, Jang HB, van Zyl LJ, Klumpp J, Lobocka M, Moreno Switt AI, Rumnieks J, Edwards RA, Uchiyama J, Alfenas-Zerbini P, Petty NK, Kropinski AM, Barylski J, Gillis A, Clokie MRC, Prangishvili D, Lavigne R, Aziz RK, Duffy S, Krupovic M, Poranen MM, Knezevic P, Enault F, Tong Y, Oksanen HM, Rodney Brister J. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Arch Virol 2018; 163:1125-1129. [PMID: 29356990 DOI: 10.1007/s00705-018-3723-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/15/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Evelien M Adriaenssens
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Johannes Wittmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124, Braunschweig, Germany
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA
| | - Dann Turner
- Faculty of Health and Applied Sciences, UWE Bristol, Frenchay Campus, Bristol, BS16 1QY, United Kingdom
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Leonardo J van Zyl
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville, Cape Town, 7535, South Africa
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
| | - Malgorzata Lobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Andrea I Moreno Switt
- Faculty of Ecology and Natural Resources School, Universidad Andres Bello, 8370146, Santiago, Chile
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Center, Riga, LV-1067, Latvia
| | - Robert A Edwards
- Departments of Computer Science and Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Jumpei Uchiyama
- School of Veterinary Medicine, Azabu University, Fuchinobe 1-7-71, Chuo-ku Sagamihara-shi, Kanagawa, 252-0206, Japan
| | - Poliane Alfenas-Zerbini
- Laboratory of Industrial Microbiology,Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Nicola K Petty
- The ithree institute, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Andrew M Kropinski
- Departments of Food Science, and Pathobiology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.
| | - Jakub Barylski
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznan, Poland
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Martha R C Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, LE1 9HN, United Kingdom
| | - David Prangishvili
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015, Paris, France
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001, Leuven, Belgium
| | - Ramy Karam Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Qasr El-Ainy St, 11562, Cairo, Egypt
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Mart Krupovic
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015, Paris, France
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Francois Enault
- Université Clermont Auvergne, CNRS, LMGE, 63000, Clermont-Ferrand, France
| | - Yigang Tong
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing, People's Republic of China
| | - Hanna M Oksanen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
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5
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Adriaenssens EM, Krupovic M, Knezevic P, Ackermann HW, Barylski J, Brister JR, Clokie MRC, Duffy S, Dutilh BE, Edwards RA, Enault F, Jang HB, Klumpp J, Kropinski AM, Lavigne R, Poranen MM, Prangishvili D, Rumnieks J, Sullivan MB, Wittmann J, Oksanen HM, Gillis A, Kuhn JH. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee. Arch Virol 2016; 162:1153-1157. [PMID: 28040838 DOI: 10.1007/s00705-016-3173-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/27/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Evelien M Adriaenssens
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom.,Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Mart Krupovic
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015, Paris, France
| | - Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Hans-Wolfgang Ackermann
- L'Institut de biologie intégrative et des systems, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec, QC, G1V 0A6, Canada
| | - Jakub Barylski
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznan, Poland
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Martha R C Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, LE1 9HN, UK
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Robert A Edwards
- Departments of Computer Science and Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Francois Enault
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France.,CNRS UMR 6023, LMGE, Aubière, France
| | - Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
| | - Andrew M Kropinski
- Departments of Food Science, Molecular and Cellular Biologyand PathobiologyUniversity of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001, Leuven, Belgium
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - David Prangishvili
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015, Paris, France
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Center, Riga, LV-1067, Latvia
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Johannes Wittmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124, Braunschweig, Germany
| | - Hanna M Oksanen
- Department of Biosciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA
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6
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Krupovic M, Dutilh BE, Adriaenssens EM, Wittmann J, Vogensen FK, Sullivan MB, Rumnieks J, Prangishvili D, Lavigne R, Kropinski AM, Klumpp J, Gillis A, Enault F, Edwards RA, Duffy S, Clokie MRC, Barylski J, Ackermann HW, Kuhn JH. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Arch Virol 2016; 161:1095-9. [PMID: 26733293 DOI: 10.1007/s00705-015-2728-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 12/12/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Mart Krupovic
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University, Medical Centre, Nijmegen, The Netherlands
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Evelien M Adriaenssens
- Department of Genetics, Centre for Microbial Ecology and Genomics, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Johannes Wittmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Finn K Vogensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Mathew B Sullivan
- Department of Microbiology, Ohio State University, 496 W 12th Ave, Columbus, OH, 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, 470 Hitchcock Hall, 2070 Neil Avenue, Columbus, OH, 43210, USA
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV, 1067, Latvia
| | - David Prangishvili
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21-box 2462, 3001, Leuven, Belgium
| | - Andrew M Kropinski
- Departments of Food Science, Molecular and Cellular Biology, and Pathobiology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, Croix du Sud 2, L7.05.12, 1348, Louvain-la-Neuve, Belgium
| | - Francois Enault
- Clermont Université, Université Blaise Pascal, Laboratoire "Microorganismes: Génome et Environnement", Clermont-Ferrand, France
- CNRS UMR 6023, LMGE, Aubière, France
| | - Rob A Edwards
- Bioinformatics Lab, Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-7720, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Rd, New Brunswick, NJ, 08901, USA
| | - Martha R C Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester, LE1 9HN, UK
| | - Jakub Barylski
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
| | - Hans-Wolfgang Ackermann
- L'Institut de biologie intégrative et des systems, Université Laval, Pavillon Charles-Eugène-Marchand, 1030, avenue de la Médecine, Quebec, QC, G1V 0A6, Canada
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA
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7
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Roux S, Enault F, Ravet V, Colombet J, Bettarel Y, Auguet JC, Bouvier T, Lucas-Staat S, Vellet A, Prangishvili D, Forterre P, Debroas D, Sime-Ngando T. Analysis of metagenomic data reveals common features of halophilic viral communities across continents. Environ Microbiol 2015; 18:889-903. [PMID: 26472517 DOI: 10.1111/1462-2920.13084] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 09/28/2015] [Accepted: 10/08/2015] [Indexed: 12/31/2022]
Abstract
Microbial communities from hypersaline ponds, dominated by halophilic archaea, are considered specific of such extreme conditions. The associated viral communities have accordingly been shown to display specific features, such as similar morphologies among different sites. However, little is known about the genetic diversity of these halophilic viral communities across the Earth. Here, we studied viral communities in hypersaline ponds sampled on the coast of Senegal (8-36% of salinity) using metagenomics approach, and compared them with hypersaline viromes from Australia and Spain. The specificity of hyperhalophilic viruses could first be demonstrated at a community scale, salinity being a strong discriminating factor between communities. For the major viral group detected in all samples (Caudovirales), only a limited number of halophilic Caudovirales clades were highlighted. These clades gather viruses from different continents and display consistent genetic composition, indicating that they represent related lineages with a worldwide distribution. Non-tailed hyperhalophilic viruses display a greater rate of gene transfer and recombination, with uncharacterized genes conserved across different kind of viruses and plasmids. Thus, hypersaline viral communities around the world appear to form a genetically consistent community that are likely to harbour new genes coding for enzymes specifically adapted to these environments.
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Affiliation(s)
- Simon Roux
- Université Blaise Pascal, Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Clermont-Ferrand, France.,CNRS UMR 6023, LMGE, Aubière, France
| | - Francois Enault
- Université Blaise Pascal, Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Clermont-Ferrand, France.,CNRS UMR 6023, LMGE, Aubière, France
| | - Viviane Ravet
- Université Blaise Pascal, Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Clermont-Ferrand, France.,CNRS UMR 6023, LMGE, Aubière, France
| | - Jonathan Colombet
- Université Blaise Pascal, Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Clermont-Ferrand, France.,CNRS UMR 6023, LMGE, Aubière, France
| | - Yvan Bettarel
- IRD UMR 5119 ECOSYM, Université Montpellier 2, Montpellier, 34095, France
| | - Jean-Christophe Auguet
- Marine Biodiversity, Exploitation and Conservation (MARBEC), UMR CNRS 9190, Montpellier University, Place Eugéne Bataillon, Montpellier, France
| | - Thierry Bouvier
- IRD UMR 5119 ECOSYM, Université Montpellier 2, Montpellier, 34095, France
| | - Soizick Lucas-Staat
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Agnès Vellet
- Université Blaise Pascal, Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Clermont-Ferrand, France.,CNRS UMR 6023, LMGE, Aubière, France
| | - David Prangishvili
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Patrick Forterre
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France.,Laboratoire de Biologie Moléculaire du Gène chez les Extrêmophiles, CNRS UMR 8621, Université Paris Sud, Institut de Génétique et Microbiologie, Orsay, France
| | - Didier Debroas
- Université Blaise Pascal, Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Clermont-Ferrand, France.,CNRS UMR 6023, LMGE, Aubière, France
| | - Telesphore Sime-Ngando
- Université Blaise Pascal, Laboratoire 'Microorganismes: Génome et Environnement', Clermont Université, Clermont-Ferrand, France.,CNRS UMR 6023, LMGE, Aubière, France
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8
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Abstract
Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant Cyberinfrastructure that provides a web-based user interface interconnected with the required computing resources. VirSorter thus complements existing prophage prediction softwares to better leverage fragmented, SAG and metagenomic datasets in a way that will scale to modern sequencing. Given these features, VirSorter should enable the discovery of new viruses in microbial datasets, and further our understanding of uncultivated viral communities across diverse ecosystems.
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Affiliation(s)
- Simon Roux
- Ecology and Evolutionary Biology, University of Arizona , USA
| | - Francois Enault
- Clermont Université, Université Blaise Pascal, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand , France ; CNRS UMR 6023, LMGE , Aubière , France
| | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona , USA
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9
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Roux S, Enault F, Robin A, Ravet V, Personnic S, Theil S, Colombet J, Sime-Ngando T, Debroas D. Assessing the diversity and specificity of two freshwater viral communities through metagenomics. PLoS One 2012; 7:e33641. [PMID: 22432038 PMCID: PMC3303852 DOI: 10.1371/journal.pone.0033641] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 02/14/2012] [Indexed: 01/21/2023] Open
Abstract
Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale. To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.
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Affiliation(s)
- Simon Roux
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Francois Enault
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
- * E-mail:
| | - Agnès Robin
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Viviane Ravet
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Sébastien Personnic
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Sébastien Theil
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Jonathan Colombet
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Télesphore Sime-Ngando
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
| | - Didier Debroas
- Laboratoire “Microorganismes: Génome et Environnement”, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubière, France
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10
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Abstract
MOTIVATION Phylogenomic profiling is a large-scale comparative genomic method used to infer protein function from evolutionary information first described in a binary form by Pellegrini et al. (1999). Here, we propose improvements of this approach including the use of normalized Blastp bit scores, a normalization of the matrix of profiles to take into account the evolutionary distances between bacteria, the definition of a phylogenomic neighborhood based on continuous pairwise distances between genes and an original annotation procedure including the computation of a p-value for each functional assignment. RESULTS The method presented here increases the number of Ecocyc enzymes identified as being evolutionarily related by about 25% with respect to the original binary form (absent/present) method. The fraction of 'false' positives is shown to be smaller than 20%. Based on their phylogenomic relationships, genes of unknown function can then be automatically related to annotated genes. Each gene annotation predicted is associated with a p-value, i.e. its probability to be obtained by chance. The validity of this method was extensively tested on a large set of genes of known function using the MultiFun database. We find that 50% of 3122 function attributions that can be made at a p-value level of 10(-11) correspond to the actual gene annotation. The method can be readily applied to any newly sequenced microbial genome. In contrast to earlier work on the same topic, our approach avoids the use of arbitrary cut-off values, and provides a reliability estimate of the functional predictions in form of p-values.
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Affiliation(s)
- F Enault
- Structural and Genomic Information, CNRS-UPR 2589, 31 chemin Joseph Aiguier, 13009 Marseille, France.
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