101
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Evseev P, Sykilinda N, Gorshkova A, Kurochkina L, Ziganshin R, Drucker V, Miroshnikov K. Pseudomonas Phage PaBG-A Jumbo Member of an Old Parasite Family. Viruses 2020; 12:E721. [PMID: 32635178 PMCID: PMC7412058 DOI: 10.3390/v12070721] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 11/17/2022] Open
Abstract
Bacteriophage PaBG is a jumbo Myoviridae phage isolated from water of Lake Baikal. This phage has limited diffusion ability and thermal stability and infects a narrow range of Pseudomonas aeruginosa strains. Therefore, it is hardly suitable for phage therapy applications. However, the analysis of the genome of PaBG presents a number of insights into the evolutionary history of this phage and jumbo phages in general. We suggest that PaBG represents an ancient group distantly related to all known classified families of phages.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
| | - Nina Sykilinda
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
| | - Anna Gorshkova
- Limnological Institute, Siberian Branch of Russian Academy of Sciences, 664033 Irkutsk, Russia; (A.G.); (V.D.)
| | - Lidia Kurochkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Rustam Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
| | - Valentin Drucker
- Limnological Institute, Siberian Branch of Russian Academy of Sciences, 664033 Irkutsk, Russia; (A.G.); (V.D.)
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
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102
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Lood C, Danis‐Wlodarczyk K, Blasdel BG, Jang HB, Vandenheuvel D, Briers Y, Noben J, van Noort V, Drulis‐Kawa Z, Lavigne R. Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages. Environ Microbiol 2020; 22:2165-2181. [PMID: 32154616 PMCID: PMC7318152 DOI: 10.1111/1462-2920.14979] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 03/06/2020] [Indexed: 11/28/2022]
Abstract
Pseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage-bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA-Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four non-coding RNAs (ncRNAs) and 93 virion-associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA-Seq revealed a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA-pncB1-nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position our isolate amongst other phages using a gene-sharing network. This integrative omics study illustrates the molecular diversity of jumbo viruses and raises new questions towards cellular regulation and phage-encoded hijacking mechanisms.
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Affiliation(s)
- Cédric Lood
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
- Department of Microbial and Molecular Systems, Laboratory of Computational Systems Biology, KU LeuvenLeuvenBelgium
| | - Katarzyna Danis‐Wlodarczyk
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
- Department of Pathogen Biology and ImmunologyInstitute of Genetics and Microbiology, University of WroclawWroclawPoland
| | - Bob G. Blasdel
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Ho Bin Jang
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Dieter Vandenheuvel
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Yves Briers
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
| | - Jean‐Paul Noben
- Biomedical Research Institute and Transnational University LimburgHasselt UniversityDiepenbeekBelgium
| | - Vera van Noort
- Department of Microbial and Molecular Systems, Laboratory of Computational Systems Biology, KU LeuvenLeuvenBelgium
- Institute of Biology, Leiden UniversityLeidenThe Netherlands
| | - Zuzanna Drulis‐Kawa
- Department of Pathogen Biology and ImmunologyInstitute of Genetics and Microbiology, University of WroclawWroclawPoland
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU LeuvenLeuvenBelgium
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103
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Ji X, Cui Z, Xiang Y, Zhang Q, Qin K, Tang B, Wei Y. Complete Genome Sequence Analysis of the Cold-active Siphoviridae Bacteriophage from Pseudomonas fluorescens. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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104
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Wagemans J, Tsonos J, Holtappels D, Fortuna K, Hernalsteens JP, De Greve H, Estrozi LF, Bacia-Verloop M, Moriscot C, Noben JP, Schoehn G, Lavigne R. Structural Analysis of Jumbo Coliphage phAPEC6. Int J Mol Sci 2020; 21:ijms21093119. [PMID: 32354127 PMCID: PMC7247149 DOI: 10.3390/ijms21093119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 01/24/2023] Open
Abstract
The phAPEC6 genome encodes 551 predicted gene products, with the vast majority (83%) of unknown function. Of these, 62 have been identified as virion-associated proteins by mass spectrometry (ESI-MS/MS), including the major capsid protein (Gp225; present in 1620 copies), which shows a HK97 capsid protein-based fold. Cryo-electron microscopy experiments showed that the 350-kbp DNA molecule of Escherichia coli virus phAPEC6 is packaged in at least 15 concentric layers in the phage capsid. A capsid inner body rod is also present, measuring about 91 nm by 18 nm and oriented along the portal axis. In the phAPEC6 contractile tail, 25 hexameric stacked rings can be distinguished, built of the identified tail sheath protein (Gp277). Cryo-EM reconstruction reveals the base of the unique hairy fibers observed during an initial transmission electron microscopy (TEM) analysis. These very unusual filaments are ordered at three annular positions along the contractile sheath, as well as around the capsid, and may be involved in host interaction.
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Affiliation(s)
- Jeroen Wagemans
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | - Jessica Tsonos
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
- Department of Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium;
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium;
| | - Dominique Holtappels
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | - Kiandro Fortuna
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | | | - Henri De Greve
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium;
- VIB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium
| | - Leandro F. Estrozi
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
| | - Maria Bacia-Verloop
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
| | - Christine Moriscot
- Univ. Grenoble Alpes, CNRS, CEA, EMBL, Integrated Structural Biology Grenoble (ISBG), F-38042 Grenoble, France;
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Agoralaan D, 3590 Hasselt, Belgium;
| | - Guy Schoehn
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
- Correspondence: (G.S.); (R.L.); Tel.: +33-4-5742-8568 (G.S.); +32-16-3795-24 (R.L.)
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
- Correspondence: (G.S.); (R.L.); Tel.: +33-4-5742-8568 (G.S.); +32-16-3795-24 (R.L.)
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105
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Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics. SOIL SYSTEMS 2020. [DOI: 10.3390/soilsystems4020023] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.
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106
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Serwer P, Wright ET. In-Gel Isolation and Characterization of Large (and Other) Phages. Viruses 2020; 12:v12040410. [PMID: 32272774 PMCID: PMC7232213 DOI: 10.3390/v12040410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/02/2020] [Accepted: 04/05/2020] [Indexed: 12/13/2022] Open
Abstract
We review some aspects of the rapid isolation of, screening for and characterization of jumbo phages, i.e., phages that have dsDNA genomes longer than 200 Kb. The first aspect is that, as plaque-supporting gels become more concentrated, jumbo phage plaques become smaller. Dilute agarose gels are better than conventional agar gels for supporting plaques of both jumbo phages and, prospectively, the even larger (>520 Kb genome), not-yet-isolated mega-phages. Second, dilute agarose gels stimulate propagation of at least some jumbo phages. Third, in-plaque techniques exist for screening for both phage aggregation and high-in-magnitude, negative average electrical surface charge density. The latter is possibly correlated with high phage persistence in blood. Fourth, electron microscopy of a thin section of a phage plaque reveals phage type, size and some phage life cycle information. Fifth, in-gel propagation is an effective preparative technique for at least some jumbo phages. Sixth, centrifugation through sucrose density gradients is a relatively non-destructive jumbo phage purification technique. These basics have ramifications in the development of procedures for (1) use of jumbo phages for phage therapy of infectious disease, (2) exploration of genomic diversity and evolution and (3) obtaining accurate metagenomic analyses.
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107
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Decewicz P, Golec P, Szymczak M, Radlinska M, Dziewit L. Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp. Int J Mol Sci 2020; 21:ijms21062096. [PMID: 32197547 PMCID: PMC7139368 DOI: 10.3390/ijms21062096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 12/26/2022] Open
Abstract
The Ochrobactrum genus consists of an extensive repertoire of biotechnologically valuable bacterial strains but also opportunistic pathogens. In our previous study, a novel strain, Ochrobactrum sp. POC9, which enhances biogas production in wastewater treatment plants (WWTPs) was identified and thoroughly characterized. Despite an insightful analysis of that bacterium, its susceptibility to bacteriophages present in WWTPs has not been evaluated. Using raw sewage sample from WWTP and applying the enrichment method, two virulent phages, vB_OspM_OC and vB_OspP_OH, which infect the POC9 strain, were isolated. These are the first virulent phages infecting Ochrobactrum spp. identified so far. Both phages were subjected to thorough functional and genomic analyses, which allowed classification of the vB_OspM_OC virus as a novel jumbo phage, with a genome size of over 227 kb. This phage encodes DNA methyltransferase, which mimics the specificity of cell cycle regulated CcrM methylase, a component of the epigenetic regulatory circuits in Alphaproteobacteria. In this study, an analysis of the overall diversity of Ochrobactrum-specific (pro)phages retrieved from databases and extracted in silico from bacterial genomes was also performed. Complex genome mining allowed us to build similarity networks to compare 281 Ochrobactrum-specific viruses. Analyses of the obtained networks revealed a high diversity of Ochrobactrum phages and their dissimilarity to the viruses infecting other bacteria.
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Affiliation(s)
- Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.D.); (M.R.)
| | - Piotr Golec
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.G.); (M.S.)
| | - Mateusz Szymczak
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.G.); (M.S.)
| | - Monika Radlinska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.D.); (M.R.)
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (P.D.); (M.R.)
- Correspondence: ; Tel.: +48-225-541-406
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108
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Lewis R, Clooney AG, Stockdale SR, Buttimer C, Draper LA, Ross RP, Hill C. Isolation of a Novel Jumbo Bacteriophage Effective Against Klebsiella aerogenes. Front Med (Lausanne) 2020; 7:67. [PMID: 32185177 PMCID: PMC7058600 DOI: 10.3389/fmed.2020.00067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/13/2020] [Indexed: 12/14/2022] Open
Abstract
Increasing levels of bacterial resistance to many common and last resort antibiotics has increased interest in finding new treatments. The low rate of approval of new antibiotics has led to the search for new and alternative antimicrobial compounds. Bacteriophages (phages) are bacterial viruses found in almost every environment. Phage therapy was historically investigated to control bacterial infections and is still in use in Georgia and as a treatment of last resort. Phage therapy is increasingly recognized as an alternative antimicrobial treatment for antibiotic resistant pathogens. A novel lytic Klebsiella aerogenes phage N1M2 was isolated from maize silage. Klebsiella aerogenes, a member of the ESKAPE bacterial pathogens, is an important target for new antimicrobial therapies. Klebsiella aerogenes can form biofilms on medical devices which aids its environmental persistence and for this reason we tested the effect of phage N1M2 against biofilms. Phage N1M2 successfully removed a pre-formed Klebsiella aerogenes biofilm. Biofilm assays were also carried out with Staphylococcus aureus and Phage K. Phage K successfully removed a preformed Staphylococcus aureus biofilm. Phage N1M2 and Phage K in combination were significantly better at removing a mixed community biofilm of Klebsiella aerogenes and Staphylococcus aureus than either phage alone.
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Affiliation(s)
- Rhea Lewis
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Adam G Clooney
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Stephen R Stockdale
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Buttimer
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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109
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Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, Castelle CJ, Olm MR, Bouma-Gregson K, Amano Y, He C, Méheust R, Brooks B, Thomas A, Lavy A, Matheus-Carnevali P, Sun C, Goltsman DSA, Borton MA, Sharrar A, Jaffe AL, Nelson TC, Kantor R, Keren R, Lane KR, Farag IF, Lei S, Finstad K, Amundson R, Anantharaman K, Zhou J, Probst AJ, Power ME, Tringe SG, Li WJ, Wrighton K, Harrison S, Morowitz M, Relman DA, Doudna JA, Lehours AC, Warren L, Cate JHD, Santini JM, Banfield JF. Clades of huge phages from across Earth's ecosystems. Nature 2020; 578:425-431. [PMID: 32051592 PMCID: PMC7162821 DOI: 10.1038/s41586-020-2007-4] [Citation(s) in RCA: 245] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 01/02/2020] [Indexed: 12/31/2022]
Abstract
Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.
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Affiliation(s)
- Basem Al-Shayeb
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Lin-Xing Chen
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Fred Ward
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Audra Devoto
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Cindy J Castelle
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Matthew R Olm
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Keith Bouma-Gregson
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai-mura, Japan
| | - Christine He
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Brandon Brooks
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alex Thomas
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Adi Lavy
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Christine Sun
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | | | - Mikayla A Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Allison Sharrar
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Alexander L Jaffe
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Tara C Nelson
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Rose Kantor
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ray Keren
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Katherine R Lane
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ibrahim F Farag
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Shufei Lei
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Kari Finstad
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Ronald Amundson
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Karthik Anantharaman
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | | | - Alexander J Probst
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Mary E Power
- Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kelly Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Sue Harrison
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Michael Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - David A Relman
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Anne-Catherine Lehours
- Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
| | - Lesley Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Jamie H D Cate
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
- School of Earth Sciences, University of Melbourne, Melbourne, Victoria, Australia.
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110
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A jumbo phage that forms a nucleus-like structure evades CRISPR-Cas DNA targeting but is vulnerable to type III RNA-based immunity. Nat Microbiol 2019; 5:48-55. [PMID: 31819217 DOI: 10.1038/s41564-019-0612-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages1. However, DNA modification2,3, the production of anti-CRISPR proteins4,5 and potentially other strategies enable phages to evade CRISPR-Cas. Here, we discovered a Serratia jumbo phage that evades type I CRISPR-Cas systems, but is sensitive to type III immunity. Jumbo phage infection resulted in a nucleus-like structure enclosed by a proteinaceous phage shell-a phenomenon only reported recently for distantly related Pseudomonas phages6,7. All three native CRISPR-Cas complexes in Serratia-type I-E, I-F and III-A-were spatially excluded from the phage nucleus and phage DNA was not targeted. However, the type III-A system still arrested jumbo phage infection by targeting phage RNA in the cytoplasm in a process requiring Cas7, Cas10 and an accessory nuclease. Type III, but not type I, systems frequently targeted nucleus-forming jumbo phages that were identified in global viral sequence datasets. The ability to recognize jumbo phage RNA and elicit immunity probably contributes to the presence of both RNA- and DNA-targeting CRISPR-Cas systems in many bacteria1,8. Together, our results support the model that jumbo phage nucleus-like compartments serve as a barrier to DNA-targeting, but not RNA-targeting, defences, and that this phenomenon is widespread among jumbo phages.
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111
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Kawato Y, Istiqomah I, Gaafar AY, Hanaoka M, Ishimaru K, Yasuike M, Nishiki I, Nakamura Y, Fujiwara A, Nakai T. A novel jumbo Tenacibaculum maritimum lytic phage with head-fiber-like appendages. Arch Virol 2019; 165:303-311. [PMID: 31786689 DOI: 10.1007/s00705-019-04485-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/26/2019] [Indexed: 01/21/2023]
Abstract
A novel jumbo bacteriophage (myovirus) is described. The lytic phage of Tenacibaculum maritimum, which is the etiological agent of tenacibaculosis in a variety of farmed marine fish worldwide, was plaque-isolated from seawater around a fish aquaculture field in Japan. The phage had an isometric head 110-120 nm in diameter, from which several 50- to 100-nm-long flexible fiber-like appendages emanate, and a 150-nm-long rigid contractile tail. The full genomes of the two representative phages (PTm1 and PTm5) were 224,680 and 226,876 bp long, respectively, both with 29.7% GC content, and the number of predicted open reading frames (ORFs) was 308 and 306, respectively. The average nucleotide sequence identity between PTm1 and PTm5 was 99.95%, indicating they are quite similar to each other. A genetic relationship was found in 15.0-16.6% of the predicted ORFs among the T. maritimum phages PTm1 and PTm5, the Tenacibaculum spp. phage pT24, and the Sphingomonas paucimobilis phage PAU. Phylogenetic analysis based on the terminase large subunit genes revealed that these four phages (PTm1, PTm5, pT24 and PAU) are more closely related than the other 10 jumbo myoviruses that have similar genome sizes. Transmission electron microscopy observations suggest that the head fibers of the T. maritimum phage function as tentacles to search and recognize the host cell surface to facilitate infection.
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Affiliation(s)
- Yasuhiko Kawato
- Nansei Main Station, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Watarai, Mie, Japan
| | - Indah Istiqomah
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Fisheries, Faculty of Agriculture, Gadjah Mada University, Yogyakarta, Indonesia
| | - Alkhateib Y Gaafar
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.,Veterinary Research Division, National Research Centre, Cairo, Egypt
| | - Makoto Hanaoka
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Katsuya Ishimaru
- Aquaculture Research Institute, Kindai University, Wakayama, Japan
| | - Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Toshihiro Nakai
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan.
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112
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Imam M, Alrashid B, Patel F, Dowah ASA, Brown N, Millard A, Clokie MRJ, Galyov EE. vB_PaeM_MIJ3, a Novel Jumbo Phage Infecting Pseudomonas aeruginosa, Possesses Unusual Genomic Features. Front Microbiol 2019; 10:2772. [PMID: 31849908 PMCID: PMC6892783 DOI: 10.3389/fmicb.2019.02772] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/13/2019] [Indexed: 01/06/2023] Open
Abstract
Phages are the most abundant biological entity on Earth. There are many variants in phage virion sizes, morphology, and genome sizes. Large virion sized phages, with genome sizes greater than 200 kbp have been identified and termed as Jumbo phages. These phages exhibit certain characteristics that have not been reported in phages with smaller genomes. In this work, a jumbo phage named MIJ3 (vB_PaeM_MIJ3) that infects Pseudomonas aeruginosa PAO1 was isolated from an equine livery yard in Leicestershire, United Kingdom. The genome and biological characteristics of this phage have been investigated. MIJ3 is a Myovirus with multiple long tail fibers. Assessment of the host range of MIJ3 revealed that it has the ability to infect many clinical isolates of P. aeruginosa. Bioinformatics analysis of the phage genome indicated that MIJ3 is closely related to the Pseudomonas phage, PA5oct. MIJ3 possesses several unusual features that are either rarely present in other phages or have not yet been reported. In particular, MIJ3 encodes a FtsH-like protein, and a putative lysidine synthase, TilS. These two proteins have not been reported in phages. MIJ3 also possesses a split DNA polymerase B with a novel intein. Of particular interest, unlike other jumbo phages infecting Pseudomonas spp., MIJ3 lacks the genetic elements required for the formation of the phage nucleus, which was believed to be conserved across jumbo Pseudomonas phages.
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Affiliation(s)
- Mohammed Imam
- Department of Respiratory Sciences, College of Life Sciences, University of Leicester, Leicester, United Kingdom.,Laboratory Department, University Medical Center, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Bandar Alrashid
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom.,King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Faizal Patel
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Ahmed S A Dowah
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Nathan Brown
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Edouard E Galyov
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
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113
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Yamaki S, Kuronuma S, Kawai Y, Yamazaki K. Inhibitory effect of a combination with novel jumbo bacteriophages ΦMV-1 and ΦMV-4 on Morganella morganii subsp. morganii growth and histamine accumulation. Int J Food Microbiol 2019; 317:108457. [PMID: 31816558 DOI: 10.1016/j.ijfoodmicro.2019.108457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 12/11/2022]
Abstract
Histamine (scombroid) poisoning is a foodborne illness caused by ingestion of histamine-contaminated seafood; therefore, inhibition of the growth of histamine-producing bacteria is key for it prevention. Infection of pathogenic bacteria by bacteriophages (phages) is being developed to prevent multiple foodborne illnesses. Here, we describe the inhibitory effect of a phage mixture on growth and histamine accumulation of Morganella morganii subsp. morganii, the primary causative agent of histamine poisoning in fish meat. We isolated novel two phages, ΦMV-1 and ΦMV-4, which infected M. morganii subsp. morganii strains tested in this study. ΦMV-1 and ΦMV-4 belong to family Myoviridae. Pulsed-field gel electrophoresis revealed that these phages are jumbo bacteriophages with large genomes. The latent period, rise period and burst size of ΦMV-1 were 30 min, 60 min, and 224 PFU per infected cell, respectively, and those of ΦMV-4 were 60 min, 50 min, and 62 PFU per infected cell, respectively. A mixture of ΦMV-1 and ΦMV-4 effectively prevented regrowth of M. morganii subsp. morganii after phage treatment, suggesting that the phage mixture treatment is more effective for inhibition of growth and histamine accumulation by M. morganii subsp. morganii than single phage treatment. Treatment with phage mixture inhibited growth and histamine accumulation by M. morganii subsp. morganii in canned and fresh tuna. The phage mixture might be an effective way to prevent growth of the histamine producer and accumulation of histamine in seafood.
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Affiliation(s)
- Shogo Yamaki
- Laboratory of Marine Food Science and Technology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
| | - Soya Kuronuma
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Yuji Kawai
- Laboratory of Marine Food Science and Technology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Koji Yamazaki
- Laboratory of Marine Food Science and Technology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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114
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Olszak T, Danis-Wlodarczyk K, Arabski M, Gula G, Maciejewska B, Wasik S, Lood C, Higgins G, Harvey BJ, Lavigne R, Drulis-Kawa Z. Pseudomonas aeruginosa PA5oct Jumbo Phage Impacts Planktonic and Biofilm Population and Reduces Its Host Virulence. Viruses 2019; 11:E1089. [PMID: 31771160 PMCID: PMC6950013 DOI: 10.3390/v11121089] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
The emergence of phage-resistant mutants is a key aspect of lytic phages-bacteria interaction and the main driver for the co-evolution between both organisms. Here, we analyze the impact of PA5oct jumbo phage treatment on planktonic/cell line associated and sessile P. aeruginosa population. Besides its broad-spectrum activity and efficient bacteria reduction in both airway surface liquid (ASL) model, and biofilm matrix degradation, PA5oct appears to persist in most of phage-resistant clones. Indeed, a high percentage of resistance (20/30 clones) to PA5oct is accompanied by the presence of phage DNA within bacterial culture. Moreover, the maintenance of this phage in the bacterial population correlates with reduced P. aeruginosa virulence, coupled with a sensitization to innate immune mechanisms, and a significantly reduced growth rate. We observed rather unusual consequences of PA5oct infection causing an increased inflammatory response of monocytes to P. aeruginosa. This phenomenon, combined with the loss or modification of the phage receptor, makes most of the phage-resistant clones significantly less pathogenic in in vivo model. These findings provide new insights into the general knowledge of giant phages biology and the impact of their application in phage therapy.
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Affiliation(s)
- Tomasz Olszak
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Katarzyna Danis-Wlodarczyk
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Michal Arabski
- Department of Biochemistry and Genetics, Institute of Biology, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Grzegorz Gula
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Slawomir Wasik
- Department of Molecular Physics, Institute of Physics, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Cédric Lood
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
- Laboratory of Computational Systems Biology, KU Leuven, 3000 Leuven, Belgium
| | - Gerard Higgins
- National Children Research Centre, Our Lady’s Children’s Hospital, Crumlin, 12 Dublin, Ireland;
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Brian J. Harvey
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
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115
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Sharma R, Pielstick BA, Bell KA, Nieman TB, Stubbs OA, Yeates EL, Baltrus DA, Grose JH. A Novel, Highly Related Jumbo Family of Bacteriophages That Were Isolated Against Erwinia. Front Microbiol 2019; 10:1533. [PMID: 31428059 PMCID: PMC6690015 DOI: 10.3389/fmicb.2019.01533] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 01/17/2023] Open
Abstract
Erwinia amylovora is a plant pathogen from the Erwiniaceae family and a causative agent of the devastating agricultural disease fire blight. Here we characterize eight lytic bacteriophages of E. amylovora that we isolated from the Wasatch front (Utah, United States) that are highly similar to vB_EamM_Ea35-70 which was isolated in Ontario, Canada. With the genome size ranging from 271 to 275 kb, this is a novel jumbo family of bacteriophages. These jumbo bacteriophages were further characterized through genomic and proteomic comparison, mass spectrometry, host range and burst size. Their proteomes are highly unstudied, with over 200 putative proteins with no known homologs. The production of 27 of these putative proteins was confirmed by mass spectrometry analysis. These bacteriophages appear to be most similar to bacteriophages that infect Pseudomonas and Ralstonia rather than Enterobacteriales bacteria by protein similarity, however, we were only able to detect infection of Erwinia and the closely related strains of Pantoea.
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Affiliation(s)
- Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Brittany A. Pielstick
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Kimberly A. Bell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Tanner B. Nieman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Olivia A. Stubbs
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Edward L. Yeates
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - David A. Baltrus
- School of Plant Sciences, The University of Arizona, Tucson, AZ, United States
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
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116
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Thanki AM, Brown N, Millard AD, Clokie MRJ. Genomic Characterization of Jumbo Salmonella Phages That Effectively Target United Kingdom Pig-Associated Salmonella Serotypes. Front Microbiol 2019; 10:1491. [PMID: 31312191 PMCID: PMC6614189 DOI: 10.3389/fmicb.2019.01491] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022] Open
Abstract
A common cause of human food poisoning is through ingestion of pork products contaminated with Salmonella spp. Worryingly multi-drug resistant (MDR) Salmonella strains have been isolated from pigs, which motivates the need for alternative antimicrobials. In this study isolation and characterization of 21 lytic Salmonella phages is described. All 21 phages, labeled as SPFM phages were shown to efficiently infect MDR Salmonella strains isolated from United Kingdom pigs and phages SPFM1, SPFM3, SPFM10, SPFM14, SPFM15, SPFM17, and SPFM19 could lyse 100% of strains tested. The phage genome sizes range from 233 to 242 Kb, which qualifies them as jumbo phages. All SPFM phage genomes are approximately 95% similar to each other by average nucleotide identity, they encode between 258-307 coding sequences and share 188 core genes. Phylogenetic analysis shows these phages are most similar to phages of the genus Seoulvirus and to further characterize phages within the genus, genes under positive selection were identified. Several of the genes under evolutionary selection pressure were predicted to encode for proteins that interact with bacteria. We describe the phenotypic and genetic characterization of this novel Salmonella phage set. As the phages efficiently kill MDR Salmonella strains, they may offer a promising alternative to antibiotics.
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Affiliation(s)
| | | | | | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
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117
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Hesse S, Adhya S. Phage Therapy in the Twenty-First Century: Facing the Decline of the Antibiotic Era; Is It Finally Time for the Age of the Phage? Annu Rev Microbiol 2019; 73:155-174. [PMID: 31185183 DOI: 10.1146/annurev-micro-090817-062535] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Burgeoning problems of antimicrobial resistance dictate that new solutions be developed to combat old foes. Use of lytic bacteriophages (phages) for the treatment of drug-resistant bacterial infections is one approach that has gained significant traction in recent years. Fueled by reports of experimental phage therapy cases with very positive patient outcomes, several early-stage clinical trials of therapeutic phage products have been launched in the United States. Eventual licensure enabling widespread access to phages is the goal; however, new paths to regulatory approval and mass-market distribution, distinct from those of small-molecule antibiotics, must be forged first. This review highlights unique aspects related to the clinical use of phages, including advantages to be reaped as well as challenges to be overcome.
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Affiliation(s)
- Shayla Hesse
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA; ,
| | - Sankar Adhya
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA; ,
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118
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Wojtus JK, Frampton RA, Warring S, Hendrickson H, Fineran PC. Genome Sequence of a Jumbo Bacteriophage That Infects the Kiwifruit Phytopathogen Pseudomonas syringae pv. actinidiae. Microbiol Resour Announc 2019; 8:e00224-19. [PMID: 31147429 PMCID: PMC6544186 DOI: 10.1128/mra.00224-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/06/2019] [Indexed: 12/24/2022] Open
Abstract
Bacteriophage ϕPsa21 is a potential biocontrol agent that infects the kiwifruit phytopathogen Pseudomonas syringae pv. actinidiae. ϕPsa21 is a "jumbo" phage with a genome of ∼305 kb. Here, we present the genome sequence of ϕPsa21 and discuss potential genes indicative of the formation of nucleoid structures during viral replication.
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Affiliation(s)
- Joanna K Wojtus
- Massey Phage Whānau, School of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rebekah A Frampton
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Suzanne Warring
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Heather Hendrickson
- Massey Phage Whānau, School of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand
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119
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Korf IHE, Meier-Kolthoff JP, Adriaenssens EM, Kropinski AM, Nimtz M, Rohde M, van Raaij MJ, Wittmann J. Still Something to Discover: Novel Insights into Escherichia coli Phage Diversity and Taxonomy. Viruses 2019; 11:E454. [PMID: 31109012 PMCID: PMC6563267 DOI: 10.3390/v11050454] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/29/2019] [Accepted: 05/15/2019] [Indexed: 12/18/2022] Open
Abstract
The aim of this study was to gain further insight into the diversity of Escherichia coli phagesfollowed by enhanced work on taxonomic issues in that field. Therefore, we present the genomiccharacterization and taxonomic classification of 50 bacteriophages against E. coli isolated fromvarious sources, such as manure or sewage. All phages were examined for their host range on a setof different E. coli strains, originating, e.g., from human diagnostic laboratories or poultry farms.Transmission electron microscopy revealed a diversity of morphotypes (70% Myo-, 22% Sipho-, and8% Podoviruses), and genome sequencing resulted in genomes sizes from ~44 to ~370 kb.Annotation and comparison with databases showed similarities in particular to T4- and T5-likephages, but also to less-known groups. Though various phages against E. coli are already describedin literature and databases, we still isolated phages that showed no or only few similarities to otherphages, namely phages Goslar, PTXU04, and KWBSE43-6. Genome-based phylogeny andclassification of the newly isolated phages using VICTOR resulted in the proposal of new generaand led to an enhanced taxonomic classification of E. coli phages.
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Affiliation(s)
- Imke H E Korf
- Leibniz Institute DSMZ⁻German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig,Germany.
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ⁻German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig,Germany.
| | | | - Andrew M Kropinski
- Departments of Food Science and Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Manfred Nimtz
- Protein Analytics Platform, Helmholtz-Centre for Infection Research (HZI), 38124 Braunschweig,Germany.
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), 38124 Braunschweig,Germany.
| | - Mark J van Raaij
- Department of Macromolecular Structure, Centro Nacional de Biotecnologia CNB-CSIC, 28049 Madrid,Spain.
| | - Johannes Wittmann
- Leibniz Institute DSMZ⁻German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig,Germany.
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120
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Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nat Microbiol 2019; 4:693-700. [PMID: 30692672 PMCID: PMC6784885 DOI: 10.1038/s41564-018-0338-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/05/2018] [Indexed: 02/06/2023]
Abstract
Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.
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121
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Abstract
It is widely assumed that there is a clear distinction between eukaryotes, with cell nuclei, and prokaryotes, which lack nuclei. This suggests the evolution of nuclear compartmentation is a singular event. However, emerging knowledge of the diversity of bacterial internal cell structures suggests the picture may not be as black-and-white as previously thought. For instance, some members of the bacterial PVC superphylum appear to have nucleus-like compartmentation, where transcription and translation are physically separated, and some jumbophages have recently been shown to create nucleus-like structures within their Pseudomonad hosts. Moreover, there is also tantalizing metagenomic identification of new Archaea that carry homologs of genes associated with internal cell membrane structure in eukaryotes. All these cases invite comparison with eukaryote cell biology. While the bacterial cases of genetic compartmentation are likely convergent, and thus viewed by many as not germane to the question of eukaryote origins, we argue here that, in addressing the broader question of the evolution of compartmentation, other instances are at least as important: they provide us with a point of comparison which is critical for a more general understanding of both the conditions favoring the emergence of intracellular compartmentation of DNA and the evolutionary consequences of such cellular architecture. Finally, we consider three classes of explanation for the emergence of compartmentation: physical protection, crosstalk avoidance and nonadaptive origins.
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Affiliation(s)
- Heather L. Hendrickson
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Anthony M. Poole
- Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
- Te Ao Mârama/Centre for Fundamental Inquiry, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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122
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Jacquemot L, Bettarel Y, Monjol J, Corre E, Halary S, Desnues C, Bouvier T, Ferrier-Pagès C, Baudoux AC. Therapeutic Potential of a New Jumbo Phage That Infects Vibrio coralliilyticus, a Widespread Coral Pathogen. Front Microbiol 2018; 9:2501. [PMID: 30405564 PMCID: PMC6207643 DOI: 10.3389/fmicb.2018.02501] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/01/2018] [Indexed: 11/13/2022] Open
Abstract
Biological control using bacteriophages is a promising approach for mitigating the devastating effects of coral diseases. Several phages that infect Vibrio coralliilyticus, a widespread coral pathogen, have been isolated, suggesting that this bacterium is permissive to viral infection and is, therefore, a suitable candidate for treatment by phage therapy. In this study, we combined functional and genomic approaches to evaluate the therapeutic potential of BONAISHI, a novel V. coralliilyticus phage, which was isolated from the coral reef in Van Phong Bay (Vietnam). BONAISHI appears to be strictly lytic for several pathogenic strains of V. coralliilyticus and remains infectious over a broad range of environmental conditions. This candidate has an unusually large dsDNA genome (303 kb), with no genes that encode known toxins or implicated in lysogeny control. We identified several proteins involved in host lysis, which may offer an interesting alternative to the use of whole bacteriophages for controlling V. coralliilyticus. A preliminary therapy test showed that adding BONAISHI to an infected culture of Symbiodinium sp. cells reduced the impact of V. coralliilyticus on Symbiodinium sp. photosynthetic activity. This study showed that BONAISHI is able to mitigate V. coralliilyticus infections, making it a good candidate for phage therapy for coral disease.
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Affiliation(s)
- Loïc Jacquemot
- Sorbonne Universités UPMC Paris 06, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Yvan Bettarel
- MARBEC, Université Montpellier, IRD, CNRS, Ifremer, Montpellier, France
| | - Joanne Monjol
- Sorbonne Universités UPMC Paris 06, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Erwan Corre
- Sorbonne Universités UPMC Paris 06, CNRS, FR2424 Fédération de Recherche, Station Biologique de Roscoff, Roscoff, France
| | - Sébastien Halary
- Aix Marseille Université, Microbes, Evolution Phylogeny and infection (MEPHI), CNRS FRE2013, IRD 198, AP-HM, IHU - Méditerranée Infection, Marseille, France
| | - Christelle Desnues
- Aix Marseille Université, Microbes, Evolution Phylogeny and infection (MEPHI), CNRS FRE2013, IRD 198, AP-HM, IHU - Méditerranée Infection, Marseille, France
| | - Thierry Bouvier
- MARBEC, Université Montpellier, IRD, CNRS, Ifremer, Montpellier, France
| | | | - Anne-Claire Baudoux
- Sorbonne Universités UPMC Paris 06, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
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Day A, Ahn J, Salmond GPC. Jumbo Bacteriophages Are Represented Within an Increasing Diversity of Environmental Viruses Infecting the Emerging Phytopathogen, Dickeya solani. Front Microbiol 2018; 9:2169. [PMID: 30258425 PMCID: PMC6143709 DOI: 10.3389/fmicb.2018.02169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/23/2018] [Indexed: 11/13/2022] Open
Abstract
Dickeya species are economically important phytopathogens widespread in mainland Europe that can reduce crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of these pathogens in the field, and limited field trials have been conducted. To date the majority of bacteriophages capable of infecting Dickeya solani, one of the more aggressive species, are from the same family, the Ackermannviridae, many representatives of which have been shown to be unsuitable for use in the field due to their capacity for generalized transduction. Members of this family are also only capable of forming individual plaques on D. solani. Here we describe novel bacteriophages from environmental sources isolated on D. solani, including members of two other viral families; Myoviridae and Podoviridae, most of which are capable of forming plaques on multiple Dickeya species. Full genomic sequencing revealed that the Myoviridae family members form two novel clusters of jumbo bacteriophages with genomes over 250 kbp, with one cluster containing phages of another phytopathogen Erwinia amylovora. Transduction experiments showed that the majority of the new environmental bacteriophages are also capable of facilitating efficient horizontal gene transfer, however the single Podoviridae family member is not. This particular phage therefore has potential for use as a biocontrol agent against multiple species of Dickeya.
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Affiliation(s)
- Andrew Day
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jiyoon Ahn
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Attai H, Boon M, Phillips K, Noben JP, Lavigne R, Brown PJB. Larger Than Life: Isolation and Genomic Characterization of a Jumbo Phage That Infects the Bacterial Plant Pathogen, Agrobacterium tumefaciens. Front Microbiol 2018; 9:1861. [PMID: 30154772 PMCID: PMC6102473 DOI: 10.3389/fmicb.2018.01861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/24/2018] [Indexed: 01/21/2023] Open
Abstract
Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease, leading to the damage of agriculturally-important crops. As part of an effort to discover new phages that can potentially be used as biocontrol agents to prevent crown gall disease, we isolated and characterized phage Atu_ph07 from Sawyer Creek in Springfield, MO, using the virulent Agrobacterium tumefaciens strain C58 as a host. After surveying its host range, we found that Atu_ph07 exclusively infects Agrobacterium tumefaciens. Time-lapse microscopy of A. tumefaciens cells subjected to infection at a multiplicity of infection (MOI) of 10 with Atu_ph07 reveals that lysis occurs within 3 h. Transmission electron microscopy (TEM) of virions shows that Atu_ph07 has a typical Myoviridae morphology with an icosahedral head, long tail, and tail fibers. The sequenced genome of Atu_ph07 is 490 kbp, defining it as a jumbo phage. The Atu_ph07 genome contains 714 open reading frames (ORFs), including 390 ORFs with no discernable homologs in other lineages (ORFans), 214 predicted conserved hypothetical proteins with no assigned function, and 110 predicted proteins with a functional annotation based on similarity to conserved proteins. The proteins with predicted functional annotations share sequence similarity with proteins from bacteriophages and bacteria. The functionally annotated genes are predicted to encode DNA replication proteins, structural proteins, lysis proteins, proteins involved in nucleotide metabolism, and tRNAs. Characterization of the gene products reveals that Atu_ph07 encodes homologs of 16 T4 core proteins and is closely related to Rak2-like phages. Using ESI-MS/MS, the majority of predicted structural proteins could be experimentally confirmed and 112 additional virion-associated proteins were identified. The genomic characterization of Atu_ph07 suggests that this phage is lytic and the dynamics of Atu_ph07 interaction with its host indicate that this phage may be suitable for inclusion in a phage cocktail to be used as a biocontrol agent.
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Affiliation(s)
- Hedieh Attai
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Maarten Boon
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Kenya Phillips
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Hasselt, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Pamela J B Brown
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
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125
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Azam AH, Hoshiga F, Takeuchi I, Miyanaga K, Tanji Y. Analysis of phage resistance in Staphylococcus aureus SA003 reveals different binding mechanisms for the closely related Twort-like phages ɸSA012 and ɸSA039. Appl Microbiol Biotechnol 2018; 102:8963-8977. [DOI: 10.1007/s00253-018-9269-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/15/2018] [Accepted: 07/22/2018] [Indexed: 02/01/2023]
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126
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Parras-Moltó M, Rodríguez-Galet A, Suárez-Rodríguez P, López-Bueno A. Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses. MICROBIOME 2018; 6:119. [PMID: 29954453 PMCID: PMC6022446 DOI: 10.1186/s40168-018-0507-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/19/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology and discovering new viruses. Unfortunately, several sources of bias lead to the misrepresentation of certain viruses within metagenomics workflows, hindering the shift from merely descriptive studies towards quantitative comparisons of communities. Therefore, benchmark studies on virus enrichment and random amplification protocols are required to better understand the sources of bias. RESULTS We assessed the bias introduced by viral enrichment on mock assemblages composed of seven DNA viruses, and the bias from random amplification methods on human saliva DNA viromes, using qPCR and deep sequencing, respectively. While iodixanol cushions and 0.45 μm filtration preserved the original composition of nuclease-protected viral genomes, low-force centrifugation and 0.22 μm filtration removed large viruses. Comparison of unamplified and randomly amplified saliva viromes revealed that multiple displacement amplification (MDA) induced stochastic bias from picograms of DNA template. However, the type of bias shifted to systematic using 1 ng, with only a marginal influence by amplification time. Systematic bias consisted of over-amplification of small circular genomes, and under-amplification of those with extreme GC content, a negative bias that was shared with the PCR-based sequence-independent, single-primer amplification (SISPA) method. MDA based on random priming provided by a DNA primase activity slightly outperformed those based on random hexamers and SISPA, which may reflect differences in ability to handle sequences with extreme GC content. SISPA viromes showed uneven coverage profiles, with high coverage peaks in regions with low linguistic sequence complexity. Despite misrepresentation of certain viruses after random amplification, ordination plots based on dissimilarities among contig profiles showed perfect overlapping of related amplified and unamplified saliva viromes and strong separation from unrelated saliva viromes. This result suggests that random amplification bias has a minor impact on beta diversity studies. CONCLUSIONS Benchmark analyses of mock and natural communities of viruses improve understanding and mitigate bias in metagenomics surveys. Bias induced by random amplification methods has only a minor impact on beta diversity studies of human saliva viromes.
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Affiliation(s)
- Marcos Parras-Moltó
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Ana Rodríguez-Galet
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Patricia Suárez-Rodríguez
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Alberto López-Bueno
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain.
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127
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Buttimer C, Born Y, Lucid A, Loessner MJ, Fieseler L, Coffey A. Erwinia amylovora phage vB_EamM_Y3 represents another lineage of hairy Myoviridae. Res Microbiol 2018; 169:505-514. [PMID: 29777834 DOI: 10.1016/j.resmic.2018.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/23/2018] [Indexed: 10/16/2022]
Abstract
To date, a small number of jumbo myoviruses have been reported to possess atypical whisker-like structures along the surface of their contractile tails. Erwinia amylovora phage vB_EamM_Y3 is another example. It possesses a genome of 261,365 kbp with 333 predicted ORFs. Using a combination of BLASTP, Interproscan and HHpred, about 21% of its putative proteins could be assigned functions involved in nucleotide metabolism, DNA replication, virion structure and cell wall degradation. The phage was found to have a signal-arrest-release (SAR) endolysin (Y3_301) possessing a soluble lytic transglycosylase domain. Like other SAR endolysins, inducible expression of Y3_301 caused Escherichia coli lysis, which is dependent on the presence of an N-terminal signal sequence. Phylogenetic analysis showed that its closest relatives are other jumbo phages including Pseudomonas aeruginosa phage PaBG and P. putida phage Lu11, sharing 105 and 87 homologous proteins respectively. Like these phages, Y3 also shares a distant relationship to Ralstonia solanacearum phage ΦRSL1 (sharing 55 homologous proteins). As these phages are unrelated to the Rak2-like group of hairy phages, Y3 along with Lu11 represent a second lineage of hairy myoviruses.
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Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland.
| | - Yannick Born
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland; Agroscope, Research Division Plant Protection, Wädenswil, Switzerland.
| | - Alan Lucid
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - Martin J Loessner
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland.
| | - Lars Fieseler
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland.
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland; APC Microbiome Institute, University College, Cork, Ireland.
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128
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Abstract
Xanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins and presents the longest (66 kbp) direct terminal repeats (DTRs) among sequenced viral genomes. The DTRs harbor 56 tRNA genes, which correspond to all 20 amino acids and represent the largest number of tRNA genes reported in a viral genome. Codon usage analysis revealed a propensity for the phage encoded tRNAs to target codons that are highly used by the phage but less frequently by its host. The existence of these tRNA genes and seven additional translation-related genes as well as a chaperonin gene found in the XacN1 genome suggests a relative independence of phage replication on host molecular machinery, leading to a prediction of a wide host range for this jumbo phage. We confirmed the prediction by showing a wider host range of XacN1 than other X. citri phages in an infection test against a panel of host strains. Phylogenetic analyses revealed a clade of phages composed of XacN1 and ten other jumbo phages, indicating an evolutionary stable large genome size for this group of phages.
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129
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Xiang Y, Wang S, Li J, Wei Y, Zhang Q, Lin L, Ji X. Isolation and characterization of two lytic cold-active bacteriophages infecting Pseudomonas fluorescens from the Napahai plateau wetland. Can J Microbiol 2017; 64:183-190. [PMID: 29253355 DOI: 10.1139/cjm-2017-0572] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As the "kidneys of the Earth", wetlands play important roles as biodiversity reservoirs, in water purification, and in flood control. In this study, 2 lytic cold-active bacteriophages, named VW-6S and VW-6B, infecting Pseudomonas fluorescens W-6 cells from the Napahai plateau wetland in China were isolated and characterized. Electron microscopy showed that both VW-6S and VW-6B had an icosahedral head (66.7 and 61.1 nm, respectively) and a long tail (8.3 nm width × 233.3 nm length and 11.1 nm width × 166.7 nm length, respectively). The bacteriophages VW-6S and VW-6B were classified as Siphoviridae and had an approximate genome size of 30-40 kb. The latent and burst periods of VW-6S were 60 and 30 min, whereas those of VW-6B were 30 and 30 min, respectively. The optimal pH values for the bacteriophages VW-6S and VW-6B were 8.0 and 10.0, respectively, and their activity decreased rapidly at temperatures higher than 60 °C. These cold-active bacteriophages provide good materials for further study of cold-adaptation mechanisms and interaction with the host P. fluorescens.
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Affiliation(s)
- Yingying Xiang
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.,b Department of Stomatology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming 650031, China
| | - Shuang Wang
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jiankai Li
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Yunlin Wei
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Qi Zhang
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Lianbing Lin
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Xiuling Ji
- a Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
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130
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Zablocki O, van Zyl LJ, Kirby B, Trindade M. Diversity of dsDNA Viruses in a South African Hot Spring Assessed by Metagenomics and Microscopy. Viruses 2017; 9:E348. [PMID: 29156552 PMCID: PMC5707555 DOI: 10.3390/v9110348] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/31/2017] [Accepted: 11/15/2017] [Indexed: 01/15/2023] Open
Abstract
The current view of virus diversity in terrestrial hot springs is limited to a few sampling sites. To expand our current understanding of hot spring viral community diversity, this study aimed to investigate the first African hot spring (Brandvlei hot spring; 60 °C, pH 5.7) by means of electron microscopy and sequencing of the virus fraction. Microscopy analysis revealed a mixture of regular- and 'jumbo'-sized tailed morphotypes (Caudovirales), lemon-shaped virions (Fuselloviridae-like; salterprovirus-like) and pleiomorphic virus-like particles. Metavirome analysis corroborated the presence of His1-like viruses and has expanded the current clade of salterproviruses using a polymerase B gene phylogeny. The most represented viral contig was to a cyanophage genome fragment, which may underline basic ecosystem functioning provided by these viruses. Furthermore, a putative Gemmata-related phage was assembled with high coverage, a previously undocumented phage-host association. This study demonstrated that a moderately thermophilic spring environment contained a highly novel pool of viruses and should encourage future characterization of a wider temperature range of hot springs throughout the world.
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Affiliation(s)
- Olivier Zablocki
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
| | - Bronwyn Kirby
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, 7535 Bellville, South Africa.
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131
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Serwer P. Restoring logic and data to phage-cures for infectious disease. AIMS Microbiol 2017; 3:706-712. [PMID: 31294183 PMCID: PMC6604969 DOI: 10.3934/microbiol.2017.4.706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/10/2017] [Indexed: 02/02/2023] Open
Abstract
Antibiotic therapy for infectious disease is being compromised by emergence of multi-drug-resistant bacterial strains, often called superbugs. A response is to use a cocktail of several bacteria-infecting viruses (bacteriophages or phages) to supplement antibiotic therapy. Use of such cocktails is called phage therapy, which has the advantage of response to bacterial resistance that is rapid and not exhaustible. A procedure of well-established success is to make cocktails from stockpiles of stored environmental phages. New phages are added to stockpiles when phage therapy becomes thwarted. The scientific subtext includes optimizing the following aspects: (1) procedure for rapidly detecting, purifying, storing and characterizing phages for optimization of phage cocktails, (2) use of directed evolution in the presence of bacteriostatic compounds to obtain phages that can be most efficiently used for therapy in the presence of these compounds, (3) phage genome sequencing technology and informatics to improve the characterization of phages, and (4) database technology to make optimal use of all relevant information and to rapidly retrieve phages for cocktails that will vary with the infection(s) involved. The use of phage stockpiles has an established record, including a recent major human-therapy success by the US Navy. However, I conclude that most research is not along this track and, therefore, is not likely to lead to real world success. I find that a strong case exists for action to rectify this situation.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Center, 7703 Floyd Curl Drive, San Antonio, Texas 28229-3900, USA
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Matsui T, Yoshikawa G, Mihara T, Chatchawankanphanich O, Kawasaki T, Nakano M, Fujie M, Ogata H, Yamada T. Replications of Two Closely Related Groups of Jumbo Phages Show Different Level of Dependence on Host-encoded RNA Polymerase. Front Microbiol 2017; 8:1010. [PMID: 28659872 PMCID: PMC5468394 DOI: 10.3389/fmicb.2017.01010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 05/22/2017] [Indexed: 11/13/2022] Open
Abstract
Ralstonia solanacearum phages ΦRP12 and ΦRP31 are jumbo phages isolated in Thailand. Here we show that they exhibit similar virion morphology, genome organization and host range. Genome comparisons as well as phylogenetic and proteomic tree analyses support that they belong to the group of ΦKZ-related phages, with their closest relatives being R. solanacearum phages ΦRSL2 and ΦRSF1. Compared with ΦRSL2 and ΦRSF1, ΦRP12 and ΦRP31 possess larger genomes (ca. 280 kbp, 25% larger). The replication of ΦRP12 and ΦRP31 was not affected by rifampicin treatment (20 μg/ml), suggesting that phage-encoded RNAPs function to start and complete the infection cycle of these phages without the need of host-encoded RNAPs. In contrast, ΦRSL2 and ΦRSF1, encoding the same set of RNAPs, did not produce progeny phages in the presence of rifampicin (5 μg/ml). This observation opens the possibility that some ΦRP12/ΦRP31 factors that are absent in ΦRSL2 and ΦRSF1 are involved in their host-independent transcription.
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Affiliation(s)
- Takeru Matsui
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| | - Genki Yoshikawa
- Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyoto, Japan
| | - Tomoko Mihara
- Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyoto, Japan
| | - Orawan Chatchawankanphanich
- Plant Research Laboratory, National Center for Genetic Engineering and Biotechnology, NSTDAPathum Thani, Thailand.,Center for Agricultural Biotechnology, Kasetsart UniversityNakhon Pathom, Thailand
| | - Takeru Kawasaki
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| | - Miyako Nakano
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| | - Makoto Fujie
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyoto, Japan
| | - Takashi Yamada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
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