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Lim S, Park SY, Kim JS, Kwon H, Kim SG, Park SC, Han JE, Kim JH. Biological and genomic characterization of the novel bacteriophage vB_VpM-pA2SJ1, which infects Vibrio parahaemolyticus associated with acute hepatopancreatic necrosis disease. Arch Virol 2024; 169:196. [PMID: 39256248 DOI: 10.1007/s00705-024-06121-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/17/2024] [Indexed: 09/12/2024]
Abstract
Vibrio parahaemolyticus is a major seafood-borne zoonotic pathogen that causes gastroenteritis in humans and acute hepatopancreatic necrosis disease (AHPND) in shrimp. In this study, we isolated and characterized Vibrio phage vB_VpM-pA2SJ1, which infects clinical and AHPND-associated strains of V. parahaemolyticus. The phage genome is a linear dsDNA 51,054 bp in length with a G + C content of 43.7%, and it contains 89 open reading frames. Genome comparisons revealed basal similarity to other Vibrio phages, particularly Vibrio phage vB_VpP_1, with 84.2% identity and 46% coverage. Phylogenetic analysis based on the whole genome, the terminase large subunit, and the major capsid protein revealed that phage vB_VpM-pA2SJ1 did not cluster with other known phage families, thus indicating its uniqueness.
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Affiliation(s)
- Soojin Lim
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam, 13120, Republic of Korea
| | - Seon Young Park
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jun-Seob Kim
- Department of Nano-Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
- Institute for New Drug Development, College of Life Science and Bioengineering, Incheon National University, Incheon , 22012, Republic of Korea
| | - Hyemin Kwon
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sang Guen Kim
- Department of Biological Sciences, Kyonggi University, Suwon, 16227, Republic of Korea
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jee Eun Han
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine & Institute for Veterinary Biomedical Science, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Ji Hyung Kim
- Department of Food Science and Biotechnology, College of BioNano Technology, Gachon University, Seongnam, 13120, Republic of Korea.
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Schwarz C, Mathieu J, Laverde Gomez J, Miller MR, Tikhonova M, Hamor C, Alvarez PJJ. Isolation and Characterization of Six Novel Fusobacterium necrophorum Phages. PHAGE (NEW ROCHELLE, N.Y.) 2024; 5:63-75. [PMID: 39119211 PMCID: PMC11304844 DOI: 10.1089/phage.2023.0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Introduction Fusobacterium necrophorum, a human and animal pathogen, is the primary etiologic agent of bovine liver abscesses and a driving factor for prophylactic antibiotic use in the fed cattle industry. Considering calls to reduce agricultural antibiotic use, we isolated phages capable of killing F. necrophorum as an alternative or complementary biocontrol strategy. Methods Six novel phages (φFN37, φRTG5, φKSUM, φHugo, φPaco, and φBB) were isolated from rumen fluid or ruminal F. necrophorum isolates and subjected to host range testing on both F. necrophorum subspecies. Four F. necrophorum subspecies, necrophorum phages, were tested for cross-resistance and host growth inhibition individually and in pairs. Additionally, genomic sequencing, annotation, and analysis were performed.s. Results Four of six isolated phages were able to form lysogens, although all six contained lysogeny-related genes. φKSUM and φBB, did not form lysogens and were able to infect both subspecies. Four phages could infect F. necrophorum 8L1 (a liver abscess model challenge strain) in vitro. Genomic analysis showed that these phages belong to class Caudoviricetes with genome sizes ranging from 35 kbp to 111 kbp and GC values ranging from 26% to 36% and have extremely limited similarity to other deposited phage genomes infecting Fusobacterium or other genera. Conclusions Although all phages isolated contained sequences bearing similarities to genes implicated in lysogeny, the four selected for use in cocktails showed potential in inhibiting host growth, with several demonstrating promising attributes for biocontrol and therapeutic applications. Phage cocktails that may offer enhanced antibacterial activity were also identified, indicating the potential of some lysogenic phages to be adapted for biocontrol or therapeutic purposes when lytic phages are difficult to obtain.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
| | | | - Megan R. Miller
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
| | | | - Clark Hamor
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Pedro J. J. Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
- Sentinel Environmental, Houston, Texas, USA
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Bisen M, Kharga K, Mehta S, Jabi N, Kumar L. Bacteriophages in nature: recent advances in research tools and diverse environmental and biotechnological applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22199-22242. [PMID: 38411907 DOI: 10.1007/s11356-024-32535-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Bacteriophages infect and replicate within bacteria and play a key role in the environment, particularly in microbial ecosystems and bacterial population dynamics. The increasing recognition of their significance stems from their wide array of environmental and biotechnological uses, which encompass the mounting issue of antimicrobial resistance (AMR). Beyond their therapeutic potential in combating antibiotic-resistant infections, bacteriophages also find vast applications such as water quality monitoring, bioremediation, and nutrient cycling within environmental sciences. Researchers are actively involved in isolating and characterizing bacteriophages from different natural sources to explore their applications. Gaining insights into key aspects such as the life cycle of bacteriophages, their host range, immune interactions, and physical stability is vital to enhance their application potential. The establishment of diverse phage libraries has become indispensable to facilitate their wide-ranging uses. Consequently, numerous protocols, ranging from traditional to cutting-edge techniques, have been developed for the isolation, detection, purification, and characterization of bacteriophages from diverse environmental sources. This review offers an exploration of tools, delves into the methods of isolation, characterization, and the extensive environmental applications of bacteriophages, particularly in areas like water quality assessment, the food sector, therapeutic interventions, and the phage therapy in various infections and diseases.
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Affiliation(s)
- Monish Bisen
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Kusum Kharga
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Sakshi Mehta
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Nashra Jabi
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Lokender Kumar
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, 173229, India.
- Cancer Biology Laboratory, Raj Khosla Centre for Cancer Research, Shoolini University, Himachal Pradesh, Solan, 173229, India.
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Mahony J, Goulet A, van Sinderen D, Cambillau C. Partial Atomic Model of the Tailed Lactococcal Phage TP901-1 as Predicted by AlphaFold2: Revelations and Limitations. Viruses 2023; 15:2440. [PMID: 38140681 PMCID: PMC10747895 DOI: 10.3390/v15122440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Bacteria are engaged in a constant battle against preying viruses, called bacteriophages (or phages). These remarkable nano-machines pack and store their genomes in a capsid and inject it into the cytoplasm of their bacterial prey following specific adhesion to the host cell surface. Tailed phages possessing dsDNA genomes are the most abundant phages in the bacterial virosphere, particularly those with long, non-contractile tails. All tailed phages possess a nano-device at their tail tip that specifically recognizes and adheres to a suitable host cell surface receptor, being proteinaceous and/or saccharidic. Adhesion devices of tailed phages infecting Gram-positive bacteria are highly diverse and, for the majority, remain poorly understood. Their long, flexible, multi-domain-encompassing tail limits experimental approaches to determine their complete structure. We have previously shown that the recently developed protein structure prediction program AlphaFold2 can overcome this limitation by predicting the structures of phage adhesion devices with confidence. Here, we extend this approach and employ AlphaFold2 to determine the structure of a complete phage, the lactococcal P335 phage TP901-1. Herein we report the structures of its capsid and neck, its extended tail, and the complete adhesion device, the baseplate, which was previously partially determined using X-ray crystallography.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
| | - Adeline Goulet
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université—CNRS, UMR 7255, 13009 Marseille, France;
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
| | - Christian Cambillau
- School of Microbiology & APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université—CNRS, UMR 7255, 13009 Marseille, France;
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Barman RK, Chakrabarti AK, Dutta S. Screening of Potential Vibrio cholerae Bacteriophages for Cholera Therapy: A Comparative Genomic Approach. Front Microbiol 2022; 13:803933. [PMID: 35422793 PMCID: PMC9002330 DOI: 10.3389/fmicb.2022.803933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Cholera continues to be a major burden for developing nations, especially where sanitation, quality of water supply, and hospitalization have remained an issue. Recently, growing antimicrobial-resistant strains of Vibrio cholerae underscores alternative therapeutic strategies for cholera. Bacteriophage therapy is considered one of the best alternatives for antibiotic treatment. For the identification of potential therapeutic phages for cholera, we have introduced a comprehensive comparative analysis of whole-genome sequences of 86 Vibrio cholerae phages. We have witnessed extensive variation in genome size (ranging from 33 to 148 kbp), GC (G + C) content (varies from 34.5 to 50.8%), and the number of proteins (ranging from 15 to 232). We have identified nine clusters and three singletons using BLASTn, confirmed by nucleotide dot plot and sequence identity. A high degree of sequence and functional similarities in both the genomic and proteomic levels have been observed within the clusters. Evolutionary analysis confirms that phages are conserved within the clusters but diverse between the clusters. For each therapeutic phage, the top 2 closest phages have been identified using a system biology approach and proposed as potential therapeutic phages for cholera. This method can be applied for the classification of the newly isolated Vibrio cholerae phage. Furthermore, this systematic approach might be useful as a model for screening potential therapeutic phages for other bacterial diseases.
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Affiliation(s)
- Ranjan Kumar Barman
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Alok Kumar Chakrabarti
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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Nawel Z, Rima O, Amira B. An overview on Vibrio temperate phages: Integration mechanisms, pathogenicity, and lysogeny regulation. Microb Pathog 2022; 165:105490. [DOI: 10.1016/j.micpath.2022.105490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/21/2022]
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Skliros D, Karpouzis E, Kalloniati C, Katharios P, Flemetakis E. Comparative genomic analysis of dwarf Vibrio myoviruses defines a conserved gene cluster for successful phage infection. Arch Virol 2022; 167:501-516. [PMID: 35000006 DOI: 10.1007/s00705-021-05340-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 11/08/2021] [Indexed: 11/30/2022]
Abstract
Tailed bacteriophages have been at the center of attention, not only for their ability to infect and kill pathogenic bacteria but also due to their peculiar and intriguing complex contractile tail structure. Tailed bacteriophages with contractile tails are known to have a Myoviridae morphotype and are members of the order Caudovirales. Large bacteriophages with a genome larger than 150 kbp have been studied for their ability to use multiple infection and lysis strategies to replicate more efficiently. On the other hand, smaller bacteriophages with fewer genes are represented in the GenBank database in greater numbers, and have several genes with unknown function. Isolation and molecular characterization of a newly reported bacteriophage named Athena1 revealed that it is a strongly lytic bacteriophage with a genome size of 39,826 bp. This prompted us to perform a comparative genomic analysis of Vibrio myoviruses with a genome size of no more than 50 kbp. The results revealed a pattern of genomic organization that includes sets of genes responsible for virion morphogenesis, replication/recombination of DNA, and lysis/lysogeny switching. By studying phylogenetic gene markers, we were able to draw conclusions about evolutionary events that shaped the genomic mosaicism of these phages, pinpointing the importance of a conserved organization of the genomic region encoding the baseplate protein for successful infection of Gram-negative bacteria. In addition, we propose the creation of new genera for dwarf Vibrio myoviruses. Comparative genomics of phages infecting aquatic bacteria could provide information that is useful for combating fish pathogens in aquaculture, using novel strategies.
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Affiliation(s)
- Dimitrios Skliros
- Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Efthymios Karpouzis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Chrysanthi Kalloniati
- Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology, and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece. .,EU-CONEXUS European University, Athens, Greece.
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Miroshnikov KA, Evseev PV, Lukianova AA, Ignatov AN. Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae. Microorganisms 2021; 9:1819. [PMID: 34576713 PMCID: PMC8472413 DOI: 10.3390/microorganisms9091819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.
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Affiliation(s)
- Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bldg. 12, 119234 Moscow, Russia
| | - Alexander N Ignatov
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
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9
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Higgins KV, Woodie LN, Hallowell H, Greene MW, Schwartz EH. Integrative Longitudinal Analysis of Metabolic Phenotype and Microbiota Changes During the Development of Obesity. Front Cell Infect Microbiol 2021; 11:671926. [PMID: 34414128 PMCID: PMC8370388 DOI: 10.3389/fcimb.2021.671926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/15/2021] [Indexed: 01/04/2023] Open
Abstract
Obesity has increased at an alarming rate over the past two decades in the United States. In addition to increased body mass, obesity is often accompanied by comorbidities such as Type II Diabetes Mellitus and metabolic dysfunction-associated fatty liver disease, with serious impacts on public health. Our understanding of the role the intestinal microbiota in obesity has rapidly advanced in recent years, especially with respect to the bacterial constituents. However, we know little of when changes in these microbial populations occur as obesity develops. Further, we know little about how other domains of the microbiota, namely bacteriophage populations, are affected during the progression of obesity. Our goal in this study was to monitor changes in the intestinal microbiome and metabolic phenotype following western diet feeding. We accomplished this by collecting metabolic data and fecal samples for shotgun metagenomic sequencing in a mouse model of diet-induced obesity. We found that after two weeks of consuming a western diet (WD), the animals weighed significantly more and were less metabolically stable than their chow fed counterparts. The western diet induced rapid changes in the intestinal microbiome with the most pronounced dissimilarity at 12 weeks. Our study highlights the dynamic nature of microbiota composition following WD feeding and puts these events in the context of the metabolic status of the mammalian host.
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Affiliation(s)
- Keah V Higgins
- Department of Biological Sciences Auburn University, Auburn, AL, United States
| | - Lauren N Woodie
- Department of Nutrition, Dietetics and Hospitality Management, Auburn University, Auburn, AL, United States
| | - Haley Hallowell
- Department of Biological Sciences Auburn University, Auburn, AL, United States
| | - Michael W Greene
- Department of Nutrition, Dietetics and Hospitality Management, Auburn University, Auburn, AL, United States
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Skurnik M, Jaakkola S, Mattinen L, von Ossowski L, Nawaz A, Pajunen MI, Happonen LJ. Bacteriophages fEV-1 and fD1 Infect Yersinia pestis. Viruses 2021; 13:1384. [PMID: 34372590 PMCID: PMC8309999 DOI: 10.3390/v13071384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteriophages vB_YpeM_fEV-1 (fEV-1) and vB_YpeM_fD1 (fD1) were isolated from incoming sewage water samples in Turku, Finland, using Yersinia pestis strains EV76 and KIM D27 as enrichment hosts, respectively. Genomic analysis and transmission electron microscopy established that fEV-1 is a novel type of dwarf myovirus, while fD1 is a T4-like myovirus. The genome sizes are 38 and 167 kb, respectively. To date, the morphology and genome sequences of some dwarf myoviruses have been described; however, a proteome characterization such as the one presented here, has currently been lacking for this group of viruses. Notably, fEV-1 is the first dwarf myovirus described for Y. pestis. The host range of fEV-1 was restricted strictly to Y. pestis strains, while that of fD1 also included other members of Enterobacterales such as Escherichia coli and Yersinia pseudotuberculosis. In this study, we present the life cycles, genomes, and proteomes of two Yersinia myoviruses, fEV-1 and fD1.
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Affiliation(s)
- Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (S.J.); (L.M.); (A.N.); (M.I.P.)
- Division of Clinical Microbiology, HUSLAB, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Salla Jaakkola
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (S.J.); (L.M.); (A.N.); (M.I.P.)
| | - Laura Mattinen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (S.J.); (L.M.); (A.N.); (M.I.P.)
| | - Lotta von Ossowski
- Department of Medical Biochemistry, University of Turku, 20520 Turku, Finland;
| | - Ayesha Nawaz
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (S.J.); (L.M.); (A.N.); (M.I.P.)
| | - Maria I. Pajunen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (S.J.); (L.M.); (A.N.); (M.I.P.)
| | - Lotta J. Happonen
- Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University, 22184 Lund, Sweden;
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11
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Shebs-Maurine EL, Giotto FM, Laidler ST, de Mello AS. Effects of bacteriophages and peroxyacetic acid applications on beef contaminated with Salmonella during different grinding stages. Meat Sci 2020; 173:108407. [PMID: 33338779 DOI: 10.1016/j.meatsci.2020.108407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 11/25/2022]
Abstract
Research has suggested that the incidence of Salmonella in ground beef may be associated with contaminated lymph nodes that are not removed from trimmings destined for grinding. In this study, we tested the application of bacteriophages and peroxyacetic acid solutions on trimmings and on coarse and fine ground beef to simulate different scenarios of contamination. Overall, peroxyacetic acid applications did not reduce Salmonella loads on ground beef when applied on trimmings or at any stage of grinding. When applied on contaminated trim, bacteriophage solutions at 1 × 108 PFU/g and 1 × 109 PFU/g reduced more than 1 log cfu/g of Salmonella. When applied directly on contaminated coarse or fine ground beef, bacteriophage solutions at 1 × 109 PFU/g reduced approximately 1.6 log cfu/g. Results of this study suggest that bacteriophage applications on contaminated, comminuted beef may be used as an aid to decrease Salmonella loads.
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Affiliation(s)
- E L Shebs-Maurine
- Department of Agriculture, Veterinary, and Rangeland Sciences, University of Nevada, 1664 N. Virginia St. mailstop 202, Reno, NV 89557, United States of America
| | - F M Giotto
- Department of Agriculture, Veterinary, and Rangeland Sciences, University of Nevada, 1664 N. Virginia St. mailstop 202, Reno, NV 89557, United States of America
| | - S T Laidler
- Department of Agriculture, Veterinary, and Rangeland Sciences, University of Nevada, 1664 N. Virginia St. mailstop 202, Reno, NV 89557, United States of America
| | - A S de Mello
- Department of Agriculture, Veterinary, and Rangeland Sciences, University of Nevada, 1664 N. Virginia St. mailstop 202, Reno, NV 89557, United States of America.
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12
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Park SY, Han JE, Kwon H, Park SC, Kim JH. Recent Insights into Aeromonas salmonicida and Its Bacteriophages in Aquaculture: A Comprehensive Review. J Microbiol Biotechnol 2020; 30:1443-1457. [PMID: 32807762 PMCID: PMC9728264 DOI: 10.4014/jmb.2005.05040] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022]
Abstract
The emergence and spread of antimicrobial resistance in pathogenic bacteria of fish and shellfish have caused serious concerns in the aquaculture industry, owing to the potential health risks to humans and animals. Among these bacteria, Aeromonas salmonicida, which is one of the most important primary pathogens in salmonids, is responsible for significant economic losses in the global aquaculture industry, especially in salmonid farming because of its severe infectivity and acquisition of antimicrobial resistance. Therefore, interest in the use of alternative approaches to prevent and control A. salmonicida infections has increased in recent years, and several applications of bacteriophages (phages) have provided promising results. For several decades, A. salmonicida and phages infecting this fish pathogen have been thoroughly investigated in various research areas including aquaculture. The general overview of phage usage to control bacterial diseases in aquaculture, including the general advantages of this strategy, has been clearly described in previous reviews. Therefore, this review specifically focuses on providing insights into the phages infecting A. salmonicida, from basic research to biotechnological application in aquaculture, as well as recent advances in the study of A. salmonicida.
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Affiliation(s)
- Seon Young Park
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea,Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jee Eun Han
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hyemin Kwon
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea,S.C.Park Phone: +82-2-880-1282 Fax: +82-2-880-1213 E-mail:
| | - Ji Hyung Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea,Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Republic of Korea,Corresponding authors J.H.Kim Phone: +82-42-879-8272 Fax: +82-42-879-8498 E-mail:
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13
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de Jonge PA, von Meijenfeldt FB, Costa AR, Nobrega FL, Brouns SJ, Dutilh BE. Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts. iScience 2020; 23:101439. [PMID: 32823052 PMCID: PMC7452251 DOI: 10.1016/j.isci.2020.101439] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/23/2020] [Accepted: 08/03/2020] [Indexed: 01/08/2023] Open
Abstract
An important viromics challenge is associating bacteriophages to hosts. To address this, we developed adsorption sequencing (AdsorpSeq), a readily implementable method to measure phages that are preferentially adsorbed to specific host cell envelopes. AdsorpSeq thus captures the key initial infection cycle step. Phages are added to cell envelopes, adsorbed phages are isolated through gel electrophoresis, after which adsorbed phage DNA is sequenced and compared with the full virome. Here, we show that AdsorpSeq allows for separation of phages based on receptor-adsorbing capabilities. Next, we applied AdsorpSeq to identify phages in a wastewater virome that adsorb to cell envelopes of nine bacteria, including important pathogens. We detected 26 adsorbed phages including common and rare members of the virome, a minority being related to previously characterized phages. We conclude that AdsorpSeq is an effective new tool for rapid characterization of environmental phage adsorption, with a proof-of-principle application to Gram-negative host cell envelopes.
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Affiliation(s)
- Patrick A. de Jonge
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, 3584 CH Utrecht, the Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | | | - Ana Rita Costa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Franklin L. Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Stan J.J. Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, 3584 CH Utrecht, the Netherlands
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14
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Birkholz N, Fagerlund RD, Smith LM, Jackson SA, Fineran PC. The autoregulator Aca2 mediates anti-CRISPR repression. Nucleic Acids Res 2019; 47:9658-9665. [PMID: 31428783 PMCID: PMC6765145 DOI: 10.1093/nar/gkz721] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas systems are widespread bacterial adaptive defence mechanisms that provide protection against bacteriophages. In response, phages have evolved anti-CRISPR proteins that inactivate CRISPR-Cas systems of their hosts, enabling successful infection. Anti-CRISPR genes are frequently found in operons with genes encoding putative transcriptional regulators. The role, if any, of these anti-CRISPR-associated (aca) genes in anti-CRISPR regulation is unclear. Here, we show that Aca2, encoded by the Pectobacterium carotovorum temperate phage ZF40, is an autoregulator that represses the anti-CRISPR–aca2 operon. Aca2 is a helix-turn-helix domain protein that forms a homodimer and interacts with two inverted repeats in the anti-CRISPR promoter. The inverted repeats are similar in sequence but differ in their Aca2 affinity, and we propose that they have evolved to fine-tune, and downregulate, anti-CRISPR production at different stages of the phage life cycle. Specific, high-affinity binding of Aca2 to the first inverted repeat blocks the promoter and induces DNA bending. The second inverted repeat only contributes to repression at high Aca2 concentrations in vivo, and no DNA binding was detectable in vitro. Our investigation reveals the mechanism by which an Aca protein regulates expression of its associated anti-CRISPR.
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Affiliation(s)
- Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Leah M Smith
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- To whom correspondence should be addressed. Tel: +64 3 479 7735;
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15
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Garin-Fernandez A, Wichels A. Looking for the hidden: Characterization of lysogenic phages in potential pathogenic Vibrio species from the North Sea. Mar Genomics 2019; 51:100725. [PMID: 31757758 DOI: 10.1016/j.margen.2019.100725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/30/2022]
Abstract
The incidence of potentially pathogenic Vibrio species in the marine environment around Europe, is correlated with the increase of surface seawater temperature. Despite their importance, little is known about the trigger factors of potential outbreak-causing strains in this region. As prophages may compose a major reservoir of virulence traits in marine ecosystems, this study aims to identify and characterize the genomes of lysogenic Vibrio phages exemplarily from the North Sea. Therefore, 31 isolates from potentially pathogenic Vibrio species from the North Sea were screened for inducible prophages with mitomycin C. From them, one V. cholerae isolate and 40% V. parahaemolyticus isolates carried inducible prophages. Three lysogenic phages were selected for genomic characterization. The phage vB_VpaM_VP-3212 (unclassified Myoviridae) has a genome with a length of 36.81 Kbp and 55 CDS were identified. This lysogenic phage of V. parahaemolyticus contains genes related to replicative transposition mechanism, such as transposase and mobile elements similar to Mu-like viruses. The phage vB_VpaP_VP-3220 (Podoviridae, unclassified Nona33virus) has a genome length of 58,14 Kbp and contains 63 CDS. This V. parahaemolyticus phage probably uses a headful (pac) packaging replication mechanism. The phage vB_VchM_VP-3213 (unclassified Myoviridae) has a genome with a length of 41 Kbp and 63 CDS were identified, including integrase and Xer system for lysogenic recombination. This lysogenic phage of V. cholerae has similar genomic features as lambdoid phages. Although no pathogenicity genes were identified, their similarity among other phage genomes indicates that these phages can affect the development of pathogenic Vibrio strains in marine environments.
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Affiliation(s)
- Alexa Garin-Fernandez
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research, Helgoland, Germany; Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Antje Wichels
- Department of Microbial Ecology, Biologische Anstalt Helgoland, Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research, Helgoland, Germany
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16
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Sváb D, Horváth B, Rohde M, Maróti G, Tóth I. R18C is a new viable P2-like bacteriophage of rabbit origin infecting Citrobacter rodentium and Shigella sonnei strains. Arch Virol 2019; 164:3157-3160. [PMID: 31641840 PMCID: PMC6823313 DOI: 10.1007/s00705-019-04424-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/06/2019] [Indexed: 12/18/2022]
Abstract
Here, we report a novel virulent P2-like bacteriophage, R18C, isolated from rabbit faeces, which, in addition to Escherichia coli K-12 strains, was able to be propagated on Citrobacter rodentium strain ICC169 and a range of Shigella sonnei strains with high efficiency of plating (EOP). It represents the first lytic bacteriophage originating from rabbit and the first infectious P2-like phage of animal origin. In the three characteristic moron-containing regions of P2-like phages, R18C contains genes with unknown function that have so far only been found in cryptic P2-like prophages.
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Affiliation(s)
- Domonkos Sváb
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Brunswick, Germany
| | - Gergely Maróti
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - István Tóth
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
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17
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Bai M, Cheng YH, Sun XQ, Wang ZY, Wang YX, Cui XL, Xiao W. Nine Novel Phages from a Plateau Lake in Southwest China: Insights into Aeromonas Phage Diversity. Viruses 2019; 11:v11070615. [PMID: 31284428 PMCID: PMC6669705 DOI: 10.3390/v11070615] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/18/2019] [Accepted: 07/02/2019] [Indexed: 11/16/2022] Open
Abstract
Aeromonas species are common pathogens of fish and some of them can opportunistically cause infectious diseases in humans. The overuse of antibiotics has led to the emergence of bacterial drug-resistance. To date, only 51 complete genome sequences of Aeromonas phages are available in GenBank. Here, we report the isolation of nine Aeromonas phages from a plateau lake in China. The protein cluster, dot plot and ANI analyses were performed on all 60 currently sequenced Aeromonas phage genomes and classified into nine clusters and thirteen singletons. Among the nine isolated phages, the DNA-packaging strategy of cluster 2L372D (including 2L372D, 2L372X, 4L372D, 4L372XY) is unknown, while the other five phages use the headful (P22/Sf6) DNA-packaging strategy. Notably, the isolated phages with larger genomes conservatively encode auxiliary metabolism genes, DNA replication and metabolism genes, while in smaller phage genomes, recombination-related genes were conserved. Finally, we propose a new classification scheme for Aeromonas phages.
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Affiliation(s)
- Meng Bai
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Ya-Hui Cheng
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming 650201, China
| | - Xue-Qin Sun
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Zi-Yi Wang
- Yunnan Engineering Laboratory of Soil Fertility and Pollution Remediation, Yunnan Agricultural University, Kunming 650201, China
| | - Yong-Xia Wang
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China
| | - Xiao-Long Cui
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China.
| | - Wei Xiao
- Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China.
- Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming 650500, China.
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18
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van Zyl LJ, Abrahams Y, Stander EA, Kirby-McCollough B, Jourdain R, Clavaud C, Breton L, Trindade M. Novel phages of healthy skin metaviromes from South Africa. Sci Rep 2018; 8:12265. [PMID: 30115980 PMCID: PMC6095929 DOI: 10.1038/s41598-018-30705-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 07/27/2018] [Indexed: 12/15/2022] Open
Abstract
Recent skin metagenomic studies have investigated the harbored viral diversity and its possible influence on healthy skin microbial populations, and tried to establish global patterns of skin-phage evolution. However, the detail associated with the phages that potentially play a role in skin health has not been investigated. While skin metagenome and -metavirome studies have indicated that the skin virome is highly site specific and shows marked interpersonal variation, they have not assessed the presence/absence of individual phages. Here, we took a semi-culture independent approach (metaviromic) to better understand the composition of phage communities on skin from South African study participants. Our data set adds over 130 new phage species of the skin to existing databases. We demonstrated that identical phages were present on different individuals and in different body sites, and we conducted a detailed analysis of the structural organization of these phages. We further found that a bacteriophage related to the Staphylococcus capitis phage Stb20 may be a common skin commensal virus potentially regulating its host and its activities on the skin.
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Affiliation(s)
- Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa.
| | - Yoonus Abrahams
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
| | - Emily Amor Stander
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
| | - Bronwyn Kirby-McCollough
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
| | - Roland Jourdain
- L'Oréal Research and Innovation, 1 Avenue Eugène Schueller, 93600, Aulnay sous Bois, France
| | - Cécile Clavaud
- L'Oréal Research and Innovation, 1 Avenue Eugène Schueller, 93600, Aulnay sous Bois, France
| | - Lionel Breton
- L'Oréal Research and Innovation, 1 Avenue Eugène Schueller, 93600, Aulnay sous Bois, France
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
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19
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Complete Genome Sequences of Vibrio cholerae-Specific Bacteriophages 24 and X29. GENOME ANNOUNCEMENTS 2017; 5:5/46/e01013-17. [PMID: 29146843 PMCID: PMC5690320 DOI: 10.1128/genomea.01013-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete genomes of two Vibrio cholerae bacteriophages of potential interest for cholera bacteriophage (phage) therapy were sequenced and annotated. The genome size of phage 24 is 44,395 bp encoding 71 putative proteins, and that of phage X29 is 41,569 bp encoding 68 putative proteins.
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20
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Vincent AT, Paquet VE, Bernatchez A, Tremblay DM, Moineau S, Charette SJ. Characterization and diversity of phages infecting Aeromonas salmonicida subsp. salmonicida. Sci Rep 2017; 7:7054. [PMID: 28765570 PMCID: PMC5539321 DOI: 10.1038/s41598-017-07401-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/27/2017] [Indexed: 01/21/2023] Open
Abstract
Phages infecting Aeromonas salmonicida subsp. salmonicida, the causative agent of the fish disease furunculosis, have been isolated for decades but very few of them have been characterized. Here, the host range of 12 virulent phages, including three isolated in the present study, was evaluated against a panel of 65 A. salmonicida isolates, including representatives of the psychrophilic subspecies salmonicida, smithia, masoucida, and the mesophilic subspecies pectinolytica. This bacterial set also included three isolates from India suspected of being members of a new subspecies. Our results allowed to elucidate a lytic dichotomy based on the lifestyle of A. salmonicida (mesophilic or psychrophilic) and more generally, on phage types (lysotypes) for the subspecies salmonicida. The genomic analyses of the 12 phages from this study with those available in GenBank led us to propose an A. salmonicida phage pan-virome. Our comparative genomic analyses also suggest that some phage genes were under positive selection and A. salmonicida phage genomes having a discrepancy in GC% compared to the host genome encode tRNA genes to likely overpass the bias in codon usage. Finally, we propose a new classification scheme for A. salmonicida phages.
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Affiliation(s)
- Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
| | - Valérie E Paquet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
| | - Alex Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
| | - Denise M Tremblay
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada.
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21
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Bacteriophage application on red meats and poultry: Effects on Salmonella population in final ground products. Meat Sci 2017; 127:30-34. [DOI: 10.1016/j.meatsci.2017.01.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/01/2017] [Accepted: 01/02/2017] [Indexed: 11/17/2022]
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22
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Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system. Nat Commun 2016; 7:12853. [PMID: 27694798 PMCID: PMC5059440 DOI: 10.1038/ncomms12853] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 08/08/2016] [Indexed: 12/20/2022] Open
Abstract
CRISPR–Cas systems provide bacteria with adaptive immunity against foreign nucleic acids by acquiring short, invader-derived sequences called spacers. Here, we use high-throughput sequencing to analyse millions of spacer acquisition events in wild-type populations of Pectobacterium atrosepticum. Plasmids not previously encountered, or plasmids that had escaped CRISPR–Cas targeting via point mutation, are used to provoke naive or primed spacer acquisition, respectively. The origin, location and order of spacer acquisition show that spacer selection through priming initiates near the site of CRISPR–Cas recognition (the protospacer), but on the displaced strand, and is consistent with 3′–5′ translocation of the Cas1:Cas2-3 acquisition machinery. Newly acquired spacers determine the location and strand specificity of subsequent spacers and demonstrate that interference-driven spacer acquisition (‘targeted acquisition') is a major contributor to adaptation in type I-F CRISPR–Cas systems. Finally, we show that acquisition of self-targeting spacers is occurring at a constant rate in wild-type cells and can be triggered by foreign DNA with similarity to the bacterial chromosome. Prokaryotic CRISPR-Cas systems provide adaptive immunity against foreign nucleic acids by acquiring short, invader-derived sequences called spacers. Here, Staals et al. analyse millions of such events in a native CRISPR-Cas system, showing that newly acquired spacers provoke additional rounds of spacer acquisition.
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23
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Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B. mBio 2016; 7:mBio.00667-16. [PMID: 27302758 PMCID: PMC4916379 DOI: 10.1128/mbio.00667-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
UNLABELLED Here we present the first genomic characterization of viruses infecting Nostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infect Nostoc sp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids of Cyanothece sp. strain PCC 7424, Nostoc sp. strain PCC 7120, and Anabaena variabilis ATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome of Nostoc sp. strain PCC 7524. The Nostoc cyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages. IMPORTANCE Filamentous cyanobacteria belonging to the genus Nostoc are widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of cyanophages infecting filamentous freshwater cyanobacteria, revealing that their gene content is unlike that of other cyanophages. In addition to sharing many gene homologues with freshwater cyanobacteria, cyanophage N-1 encodes a CRISPR array and expresses it upon infection. Also, both viruses contain a DNA polymerase B-encoding gene with high similarity to genes found in proteobacterial plasmids of filamentous cyanobacteria. The observation that phages can acquire CRISPRs from their hosts suggests that phages can also move them among hosts, thereby conferring resistance to competing phages. The presence in these cyanophages of CRISPR and DNA polymerase B sequences, as well as a suite of other host-related genes, illustrates the long and complex evolutionary history of these viruses and their hosts.
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24
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Korol N, Van den Bossche A, Romaniuk L, Noben JP, Lavigne R, Tovkach F. Experimental evidence for proteins constituting virion components and particle morphogenesis of bacteriophage ZF40. FEMS Microbiol Lett 2016; 363:fnw042. [PMID: 26887841 DOI: 10.1093/femsle/fnw042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2016] [Indexed: 11/13/2022] Open
Abstract
Bacteriophage ZF40 is the only currently available, temperate Myoviridae phage infecting the potato pathogen Pectobacterium carotovorum subsp. carotovorum. Despite its unusual tail morphology, its major tail sheath and tube proteins remained uncharacterized after the initial genome annotation. Using ESI tandem mass-spectrometry, 24 structural proteins of the ZF40 virion were identified, with a sequence coverage ranging between 15.8% and 87.8%. The putative function of 16 proteins could be elucidated based on secondary structure analysis and conservative domain searches. The experimental annotation of 35% of the encoded gene products within the structural region of the genome represents a complete view of the virion structure, which can serve as the basis for future structural analysis as a model phage.
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Affiliation(s)
- Natalia Korol
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, NAS of Ukraine, D03680 Kyiv, Ukraine
| | - An Van den Bossche
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium Division of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Liudmyla Romaniuk
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, NAS of Ukraine, D03680 Kyiv, Ukraine
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Fedor Tovkach
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, NAS of Ukraine, D03680 Kyiv, Ukraine
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Functional Analysis of Bacteriophage Immunity through a Type I-E CRISPR-Cas System in Vibrio cholerae and Its Application in Bacteriophage Genome Engineering. J Bacteriol 2015; 198:578-90. [PMID: 26598368 DOI: 10.1128/jb.00747-15] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/16/2015] [Indexed: 01/05/2023] Open
Abstract
UNLABELLED The classical and El Tor biotypes of Vibrio cholerae serogroup O1, the etiological agent of cholera, are responsible for the sixth and seventh (current) pandemics, respectively. A genomic island (GI), GI-24, previously identified in a classical biotype strain of V. cholerae, is predicted to encode clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins); however, experimental evidence in support of CRISPR activity in V. cholerae has not been documented. Here, we show that CRISPR-Cas is ubiquitous in strains of the classical biotype but excluded from strains of the El Tor biotype. We also provide in silico evidence to suggest that CRISPR-Cas actively contributes to phage resistance in classical strains. We demonstrate that transfer of GI-24 to V. cholerae El Tor via natural transformation enables CRISPR-Cas-mediated resistance to bacteriophage CP-T1 under laboratory conditions. To elucidate the sequence requirements of this type I-E CRISPR-Cas system, we engineered a plasmid-based system allowing the directed targeting of a region of interest. Through screening for phage mutants that escape CRISPR-Cas-mediated resistance, we show that CRISPR targets must be accompanied by a 3' TT protospacer-adjacent motif (PAM) for efficient interference. Finally, we demonstrate that efficient editing of V. cholerae lytic phage genomes can be performed by simultaneously introducing an editing template that allows homologous recombination and escape from CRISPR-Cas targeting. IMPORTANCE Cholera, caused by the facultative pathogen Vibrio cholerae, remains a serious public health threat. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) provide prokaryotes with sequence-specific protection from invading nucleic acids, including bacteriophages. In this work, we show that one genomic feature differentiating sixth pandemic (classical biotype) strains from seventh pandemic (El Tor biotype) strains is the presence of a CRISPR-Cas system in the classical biotype. We demonstrate that the CRISPR-Cas system from a classical biotype strain can be transferred to a V. cholerae El Tor biotype strain and that it is functional in providing resistance to phage infection. Finally, we show that this CRISPR-Cas system can be used as an efficient tool for the editing of V. cholerae lytic phage genomes.
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Ariff A, Wise MJ, Kahler CM, Tay CY, Peters F, Perkins TT, Chang BJ. Novel Moraxella catarrhalis prophages display hyperconserved non-structural genes despite their genomic diversity. BMC Genomics 2015; 16:860. [PMID: 26497500 PMCID: PMC4619438 DOI: 10.1186/s12864-015-2104-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/16/2015] [Indexed: 11/25/2022] Open
Abstract
Background Moraxella catarrhalis is an important pathogen that often causes otitis media in children, a disease that is not currently vaccine preventable. Asymptomatic colonisation of the human upper respiratory tract is common and lack of clearance by the immune system is likely due to the emergence of seroresistant genetic lineages. No active bacteriophages or prophages have been described in this species. This study was undertaken to identify and categorise prophages in M. catarrhalis, their genetic diversity and the relationship of such diversity with the host-species phylogeny. Results This study presents a comparative analysis of 32 putative prophages identified in 95 phylogenetically variable, newly sequenced M. catarrhalis genomes. The prophages were genotypically classified into four diverse clades. The genetic synteny of each clade is similar to the group 1 phage family Siphoviridae, however, they form genotypic clusters that are distinct from other members of this family. No core genetic sequences exist across the 32 prophages despite clades 2, 3, and 4 sharing the most sequence identity. The analysis of non-structural prophage genes (coding the integrase, and terminase), and portal gene showed that the respective genes were identical for clades 2, 3, and 4, but unique for clade 1. Empirical analysis calculated that these genes are unexpectedly hyperconserved, under purifying selection, suggesting a tightly regulated functional role. As such, it is improbable that the prophages are decaying remnants but stable components of a fluctuating, flexible and unpredictable system ultimately maintained by functional constraints on non-structural and packaging genes. Additionally, the plate encoding genes were well conserved across all four prophage clades, and the tail fibre genes, commonly responsible for receptor recognition, were clustered into three major groups distributed across the prophage clades. A pan-genome of 283,622 bp was identified, and the prophages were mapped onto the diverse M. catarrhalis multi-locus sequence type (MLST) backbone. Conclusion This study has provided the first evidence of putatively mobile prophages in M. catarrhalis, identifying a diverse and fluctuating system dependent on the hyperconservation of a few key, non-structural genes. Some prophages harbour virulence-related genes, and potentially influence the physiology and virulence of M. catarrhalis. Importantly our data will provide supporting information on the identification of novel prophages in other species by adding greater weight to the identification of non-structural genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2104-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amir Ariff
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Michael J Wise
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA, Australia.
| | - Charlene M Kahler
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Chin Yen Tay
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Fanny Peters
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Timothy T Perkins
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Barbara J Chang
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
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Puxty RJ, Millard AD, Evans DJ, Scanlan DJ. Shedding new light on viral photosynthesis. PHOTOSYNTHESIS RESEARCH 2015; 126:71-97. [PMID: 25381655 DOI: 10.1007/s11120-014-0057-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 10/29/2014] [Indexed: 06/04/2023]
Abstract
Viruses infecting the environmentally important marine cyanobacteria Prochlorococcus and Synechococcus encode 'auxiliary metabolic genes' (AMGs) involved in the light and dark reactions of photosynthesis. Here, we discuss progress on the inventory of such AMGs in the ever-increasing number of viral genome sequences as well as in metagenomic datasets. We contextualise these gene acquisitions with reference to a hypothesised fitness gain to the phage. We also report new evidence with regard to the sequence and predicted structural properties of viral petE genes encoding the soluble electron carrier plastocyanin. Viral copies of PetE exhibit extensive modifications to the N-terminal signal peptide and possess several novel residues in a region responsible for interaction with redox partners. We also highlight potential knowledge gaps in this field and discuss future opportunities to discover novel phage-host interactions involved in the photosynthetic process.
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Affiliation(s)
- Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Andrew D Millard
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - David J Evans
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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Full-genome sequence of a novel myovirus, GF-2, infecting Edwardsiella tarda: comparison with other Edwardsiella myoviral genomes. Arch Virol 2015; 160:2129-33. [PMID: 26049743 DOI: 10.1007/s00705-015-2472-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/27/2015] [Indexed: 01/23/2023]
Abstract
Edwardsiellosis, which is caused by Edwardsiella tarda, a Gram-negative bacterium, is one of the most serious infectious diseases in both marine and freshwater fish farms worldwide. Previously, we reported the complete genome sequences of three E. tarda-lytic bacteriophages (two podoviruses and a myovirus), which were isolated from fish tissues and fish-rearing seawater. Further genomic information regarding E. tarda phages is important for understanding phage-host interactions as well as for applications of the phages for the control of disease. Here, we report the complete genome sequence of a novel E. tarda phage (GF-2) of myovirus morphology (family Myoviridae), isolated from tissue homogenates of a cultured Japanese flounder (Paralichthys olivaceus) that succumbed to edwardsiellosis in Japan. The size of the entire genome was 43,129 bp, with a GC content of 51.3 % and containing 82 open reading frames (ORFs). The GF-2 genome possesses lysogeny-related genes that have not been found in the reported Edwardsiella phage genomes. Comparative genomics of Edwardsiella myophages suggest that the C-terminal domains of the tail fiber proteins have relevance to their host specificity. Thus, GF-2 genome information provides a novel resource for our understanding of the molecular mechanisms involved in their host specificity and for detection of E. tarda in aquaculture environments.
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Mattenberger Y, Silva F, Belin D. 55.2, a phage T4 ORFan gene, encodes an inhibitor of Escherichia coli topoisomerase I and increases phage fitness. PLoS One 2015; 10:e0124309. [PMID: 25875362 PMCID: PMC4396842 DOI: 10.1371/journal.pone.0124309] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 03/11/2015] [Indexed: 12/03/2022] Open
Abstract
Topoisomerases are enzymes that alter the topological properties of DNA. Phage T4 encodes its own topoisomerase but it can also utilize host-encoded topoisomerases. Here we characterized 55.2, a phage T4 predicted ORF of unknown function. High levels of expression of the cloned 55.2 gene are toxic in E. coli. This toxicity is suppressed either by increased topoisomerase I expression or by partial inactivation of the ATPase subunit of the DNA gyrase. Interestingly, very low-level expression of 55.2, which is non-lethal to wild type E. coli, prevents the growth of a deletion mutant of the topoisomerase I (topA) gene. In vitro, gp55.2 binds DNA and blocks specifically the relaxation of negatively supercoiled DNA by topoisomerase I. In vivo, expression of gp55.2 at low non-toxic levels alters the steady state DNA supercoiling of a reporter plasmid. Although 55.2 is not an essential gene, competition experiments indicate that it is required for optimal phage growth. We propose that the role of gp55.2 is to subtly modulate host topoisomerase I activity during infection to insure optimal T4 phage yield.
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Affiliation(s)
- Yves Mattenberger
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Filo Silva
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Dominique Belin
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
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Henry M, Bobay LM, Chevallereau A, Saussereau E, Ceyssens PJ, Debarbieux L. The search for therapeutic bacteriophages uncovers one new subfamily and two new genera of Pseudomonas-infecting Myoviridae. PLoS One 2015; 10:e0117163. [PMID: 25629728 PMCID: PMC4309531 DOI: 10.1371/journal.pone.0117163] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 12/19/2014] [Indexed: 11/18/2022] Open
Abstract
In a previous study, six virulent bacteriophages PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5 and CHA_P1 were evaluated for their in vivo efficacy in treating Pseudomonas aeruginosa infections using a mouse model of lung infection. Here, we show that their genomes are closely related to five other Pseudomonas phages and allow a subdivision into two clades, PAK_P1-like and KPP10-like viruses, based on differences in genome size, %GC and genomic contents, as well as number of tRNAs. These two clades are well delineated, with a mean of 86% and 92% of proteins considered homologous within individual clades, and 25% proteins considered homologous between the two clades. By ESI-MS/MS analysis we determined that their virions are composed of at least 25 different proteins and electron microscopy revealed a morphology identical to the hallmark Salmonella phage Felix O1. A search for additional bacteriophage homologs, using profiles of protein families defined from the analysis of the 11 genomes, identified 10 additional candidates infecting hosts from different species. By carrying out a phylogenetic analysis using these 21 genomes we were able to define a new subfamily of viruses, the Felixounavirinae within the Myoviridae family. The new Felixounavirinae subfamily includes three genera: Felixounalikevirus, PAK_P1likevirus and KPP10likevirus. Sequencing genomes of bacteriophages with therapeutic potential increases the quantity of genomic data on closely related bacteriophages, leading to establishment of new taxonomic clades and the development of strategies for analyzing viral genomes as presented in this article.
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Affiliation(s)
- Marine Henry
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
| | - Louis-Marie Bobay
- Institut Pasteur, Microbial Evolutionary Genomics Unit, Department of Genomes and Genetics, Paris, France
- CNRS, UMR3525, Paris, France
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
| | - Anne Chevallereau
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Emilie Saussereau
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Division of Gene Technology, Katholieke Universiteit Leuven, Heverlee, B-3001, Belgium
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Laurent Debarbieux
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
- * E-mail:
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Lara E, Holmfeldt K, Solonenko N, Sà EL, Ignacio-Espinoza JC, Cornejo-Castillo FM, Verberkmoes NC, Vaqué D, Sullivan MB, Acinas SG. Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the northwestern Mediterranean Sea. PLoS One 2015; 10:e0114829. [PMID: 25587991 PMCID: PMC4294664 DOI: 10.1371/journal.pone.0114829] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 11/14/2014] [Indexed: 11/18/2022] Open
Abstract
Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new ‘rare virosphere’ phage–host model system.
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Affiliation(s)
- Elena Lara
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Karin Holmfeldt
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Natalie Solonenko
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Elisabet Laia Sà
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - J. Cesar Ignacio-Espinoza
- University of Arizona, Department of Molecular and Cellular Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Francisco M. Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Nathan C. Verberkmoes
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Matthew B. Sullivan
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
- University of Arizona, Department of Molecular and Cellular Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Silvia G. Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
- * E-mail:
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He Y, Yang H. The gastrointestinal phage communities of the cultivated freshwater fishes. FEMS Microbiol Lett 2014; 362:fnu027. [DOI: 10.1093/femsle/fnu027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Lopes A, Tavares P, Petit MA, Guérois R, Zinn-Justin S. Automated classification of tailed bacteriophages according to their neck organization. BMC Genomics 2014; 15:1027. [PMID: 25428721 PMCID: PMC4362835 DOI: 10.1186/1471-2164-15-1027] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/29/2014] [Indexed: 11/12/2022] Open
Abstract
Background The genetic diversity observed among bacteriophages remains a major obstacle for the identification of homologs and the comparison of their functional modules. In the structural module, although several classes of homologous proteins contributing to the head and tail structure can be detected, proteins of the head-to-tail connection (or neck) are generally more divergent. Yet, molecular analyses of a few tailed phages belonging to different morphological classes suggested that only a limited number of structural solutions are used in order to produce a functional virion. To challenge this hypothesis and analyze proteins diversity at the virion neck, we developed a specific computational strategy to cope with sequence divergence in phage proteins. We searched for homologs of a set of proteins encoded in the structural module using a phage learning database. Results We show that using a combination of iterative profile-profile comparison and gene context analyses, we can identify a set of head, neck and tail proteins in most tailed bacteriophages of our database. Classification of phages based on neck protein sequences delineates 4 Types corresponding to known morphological subfamilies. Further analysis of the most abundant Type 1 yields 10 Clusters characterized by consistent sets of head, neck and tail proteins. We developed Virfam, a webserver that automatically identifies proteins of the phage head-neck-tail module and assign phages to the most closely related cluster of phages. This server was tested against 624 new phages from the NCBI database. 93% of the tailed and unclassified phages could be assigned to our head-neck-tail based categories, thus highlighting the large representativeness of the identified virion architectures. Types and Clusters delineate consistent subgroups of Caudovirales, which correlate with several virion properties. Conclusions Our method and webserver have the capacity to automatically classify most tailed phages, detect their structural module, assign a function to a set of their head, neck and tail genes, provide their morphologic subtype and localize these phages within a “head-neck-tail” based classification. It should enable analysis of large sets of phage genomes. In particular, it should contribute to the classification of the abundant unknown viruses found on assembled contigs of metagenomic samples. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1027) contains supplementary material, which is available to authorized users.
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Complete genome sequence analysis of two Pseudomonas plecoglossicida phages, potential therapeutic agents. Appl Environ Microbiol 2014; 81:874-81. [PMID: 25416766 DOI: 10.1128/aem.03038-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas plecoglossicida is a lethal pathogen of ayu (Plecoglossus altivelis) in Japan and is responsible for substantial economic costs to ayu culture. Previously, we demonstrated the efficacy of phage therapy against P. plecoglossicida infection using two lytic phages (PPpW-3 and PPpW-4) (S. C. Park, I. Shimamura, M. Fukunaga, K. Mori, and T. Nakai, Appl Environ Microbiol 66:1416-1422, 2000, http://dx.doi.org/10.1128/AEM.66.4.1416-1422.2000; S. C. Park and T. Nakai, Dis Aquat Org 53:33-39, 2003, http://dx.doi.org/10.3354/dao053033). In the present study, the complete genome sequences of these therapeutic P. plecoglossicida phages were determined and analyzed for deleterious factors as therapeutic agents. The genome of PPpW-3 (myovirus) consisted of 43,564 bp with a GC content of 61.1% and 66 predicted open reading frames (ORFs). Approximately half of the genes were similar to the genes of the Escherichia coli phage vB_EcoM_ECO1230-10 (myovirus). The genome of PPpW-4 (podovirus) consisted of 41,386 bp with a GC content of 56.8% and 50 predicted ORFs. More than 70% of the genes were similar to the genes of Pseudomonas fluorescens phage ϕIBB-PF7A and Pseudomonas putida phage ϕ15 (podoviruses). The whole-genome analysis revealed that no known virulence genes were present in PPpW-3 and PPpW-4. An integrase gene was found in PPpW-3, but other factors used for lysogeny were not confirmed. The PCR detection of phage genes in phage-resistant variants provided no evidence of lysogenic activity in PPpW-3 and PPpW-4. We conclude that these two lytic phages qualify as therapeutic agents.
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Merrill BD, Grose JH, Breakwell DP, Burnett SH. Characterization of Paenibacillus larvae bacteriophages and their genomic relationships to firmicute bacteriophages. BMC Genomics 2014; 15:745. [PMID: 25174730 PMCID: PMC4168068 DOI: 10.1186/1471-2164-15-745] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 08/26/2014] [Indexed: 01/10/2023] Open
Abstract
Background Paenibacillus larvae is a Firmicute bacterium that causes American Foulbrood, a lethal disease in honeybees and is a major source of global agricultural losses. Although P. larvae phages were isolated prior to 2013, no full genome sequences of P. larvae bacteriophages were published or analyzed. This report includes an in-depth analysis of the structure, genomes, and relatedness of P. larvae myoviruses Abouo, Davis, Emery, Jimmer1, Jimmer2, and siphovirus phiIBB_Pl23 to each other and to other known phages. Results P. larvae phages Abouo, Davies, Emery, Jimmer1, and Jimmer2 are myoviruses with ~50 kbp genomes. The six P. larvae phages form three distinct groups by dotplot analysis. An annotated linear genome map of these six phages displays important identifiable genes and demonstrates the relationship between phages. Sixty phage assembly or structural protein genes and 133 regulatory or other non-structural protein genes were identifiable among the six P. larvae phages. Jimmer1, Jimmer2, and Davies formed stable lysogens resistant to superinfection by genetically similar phages. The correlation between tape measure protein gene length and phage tail length allowed identification of co-isolated phages Emery and Abouo in electron micrographs. A Phamerator database was assembled with the P. larvae phage genomes and 107 genomes of Firmicute-infecting phages, including 71 Bacillus phages. Phamerator identified conserved domains in 1,501 of 6,181 phamilies (only 24.3%) encoded by genes in the database and revealed that P. larvae phage genomes shared at least one phamily with 72 of the 107 other phages. The phamily relationship of large terminase proteins was used to indicate putative DNA packaging strategies. Analyses from CoreGenes, Phamerator, and electron micrograph measurements indicated Jimmer1, Jimmer2, Abouo and Davies were related to phages phiC2, EJ-1, KC5a, and AQ113, which are small-genome myoviruses that infect Streptococcus, Lactobacillus, and Clostridium, respectively. Conclusions This paper represents the first comparison of phage genomes in the Paenibacillus genus and the first organization of P. larvae phages based on sequence and structure. This analysis provides an important contribution to the field of bacteriophage genomics by serving as a foundation on which to build an understanding of the natural predators of P. larvae. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-745) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Sandra H Burnett
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT, USA.
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Niu YD, McAllister TA, Nash JHE, Kropinski AM, Stanford K. Four Escherichia coli O157:H7 phages: a new bacteriophage genus and taxonomic classification of T1-like phages. PLoS One 2014; 9:e100426. [PMID: 24963920 PMCID: PMC4070988 DOI: 10.1371/journal.pone.0100426] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 05/23/2014] [Indexed: 11/24/2022] Open
Abstract
The T1-like bacteriophages vB_EcoS_AHP24, AHS24, AHP42 and AKS96 of the family Siphoviridae were shown to lyse common phage types of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157:H7), but not non-O157 E. coli. All contained circularly permuted genomes of 45.7–46.8 kb (43.8–44 mol% G+C) encoding 74–81 open reading frames and 1 arginyl-tRNA. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the structural proteins were identical among the four phages. Further proteomic analysis identified seven structural proteins responsible for tail fiber, tail tape measure protein, major capsid, portal protein as well as major and minor tail proteins. Bioinformatic analyses on the proteins revealed that genomes of AHP24, AHS24, AHP42 and AKS96 did not encode for bacterial virulence factors, integration-related proteins or antibiotic resistance determinants. All four phages were highly lytic to STEC O157:H7 with considerable potential as biocontrol agents. Comparative genomic, proteomic and phylogenetic analysis suggested that the four phages along with 17 T1-like phage genomes from database of National Center for Biotechnology Information (NCBI) can be assigned into a proposed subfamily “Tunavirinae” with further classification into five genera, namely “Tlslikevirus” (TLS, FSL SP-126), “Kp36likevirus” (KP36, F20), Tunalikevirus (T1, ADB-2 and Shf1), “Rtplikevirus” (RTP, vB_EcoS_ACG-M12) and “Jk06likevirus” (JK06, vB_EcoS_Rogue1, AHP24, AHS24, AHP42, AKS96, phiJLA23, phiKP26, phiEB49). The fact that the viruses related to JK06 have been isolated independently in Israel (JK06) (GenBank Assession #, NC_007291), Canada (vB_EcoS_Rogue1, AHP24, AHS24, AHP42, AKS96) and Mexico (phiKP26, phiJLA23) (between 2005 and 2011) indicates that these similar phages are widely distributed, and that horizontal gene transfer does not always prevent the characterization of bacteriophage evolution. With this new scheme, any new discovered phages with same type can be more properly identified. Genomic- and proteomic- based taxonomic classification of phages would facilitate better understanding phages diversity and genetic traits involved in phage evolution.
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Affiliation(s)
- Yan D. Niu
- Alberta Agriculture and Rural Development, Agriculture Centre, Lethbridge, Alberta, Canada
- * E-mail: (YDN); (KS)
| | - Tim A. McAllister
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - John H. E. Nash
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario, Canada
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Andrew M. Kropinski
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario, Canada
- Department of Cellular and Molecular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Kim Stanford
- Alberta Agriculture and Rural Development, Agriculture Centre, Lethbridge, Alberta, Canada
- * E-mail: (YDN); (KS)
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Complete Genome Sequence of the Edwardsiella ictaluri-Specific Bacteriophage PEi21, Isolated from River Water in Japan. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00228-14. [PMID: 24699953 PMCID: PMC3974935 DOI: 10.1128/genomea.00228-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We present the complete genome sequence for a novel Edwardsiella ictaluri-specific bacteriophage, PEi21, isolated from river water in Japan. An initial comparative genome analysis revealed that the phage was closely related to the previously reported Edwardsiella tarda phage MSW-3 isolated from a red sea bream farm in Japan.
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Vibriophages and their interactions with the fish pathogen Vibrio anguillarum. Appl Environ Microbiol 2014; 80:3128-40. [PMID: 24610858 DOI: 10.1128/aem.03544-13] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Vibrio anguillarum is an important pathogen in aquaculture, responsible for the disease vibriosis in many fish and invertebrate species. Disease control by antibiotics is a concern due to potential development and spread of antibiotic resistance. The use of bacteriophages to control the pathogen may offer a non-antibiotic-based approach to reduce vibriosis. A detailed understanding of the phage-host interaction is needed to evaluate the potential of phages to control the pathogen. In this study, we examined the diversity and interactions of 11 vibriophages, 24 V. anguillarum strains, and 13 Vibrio species strains. Together, the host ranges of the 11 phages covered all of the tested 37 Vibrio sp. host strains, which represented considerable temporal (20 years) and geographical (9 countries) differences in their origins of isolation. Thus, despite the occurrence of unique susceptibility patterns of the individual host isolates, key phenotypic properties related to phage susceptibility are distributed worldwide and maintained in the global Vibrio community for decades. The phage susceptibility pattern of the isolates did not show any relation to the physiological relationships obtained from Biolog GN2 profiles, demonstrating that similar phage susceptibility patterns occur across broad phylogenetic and physiological differences in Vibrio strains. Subsequent culture experiments with two phages and two V. anguillarum hosts demonstrated an initial strong lytic potential of the phages. However, rapid regrowth of both phage-resistant and phage-sensitive cells following the initial lysis suggested that several mechanisms of protection against phage infection had developed in the host populations.
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39
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Barylski J, Nowicki G, Goździcka-Józefiak A. The discovery of phiAGATE, a novel phage infecting Bacillus pumilus, leads to new insights into the phylogeny of the subfamily Spounavirinae. PLoS One 2014; 9:e86632. [PMID: 24466180 PMCID: PMC3900605 DOI: 10.1371/journal.pone.0086632] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 12/16/2013] [Indexed: 01/05/2023] Open
Abstract
The Bacillus phage phiAGATE is a novel myovirus isolated from the waters of Lake Góreckie (a eutrophic lake in western Poland). The bacteriophage infects Bacillus pumilus, a bacterium commonly observed in the mentioned reservoir. Analysis of the phiAGATE genome (149844 base pairs) resulted in 204 predicted protein-coding sequences (CDSs), of which 53 could be functionally annotated. Further investigation revealed that the bacteriophage is a member of a previously undescribed cluster of phages (for the purposes of this study we refer to it as "Bastille group") within the Spounavirinae subfamily. Here we demonstrate that these viruses constitute a distinct branch of the Spounavirinae phylogenetic tree, with limited similarity to phages from the Twortlikevirus and Spounalikevirus genera. The classification of phages from the Bastille group into any currently accepted genus proved extremely difficult, prompting concerns about the validity of the present taxonomic arrangement of the subfamily.
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Affiliation(s)
- Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Grzegorz Nowicki
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Anna Goździcka-Józefiak
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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40
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Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses. ISME JOURNAL 2013; 7:1738-51. [PMID: 23635867 DOI: 10.1038/ismej.2013.67] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/16/2013] [Accepted: 03/19/2013] [Indexed: 11/08/2022]
Abstract
Viruses influence oceanic ecosystems by causing mortality of microorganisms, altering nutrient and organic matter flux via lysis and auxiliary metabolic gene expression and changing the trajectory of microbial evolution through horizontal gene transfer. Limited host range and differing genetic potential of individual virus types mean that investigations into the types of viruses that exist in the ocean and their spatial distribution throughout the world's oceans are critical to understanding the global impacts of marine viruses. Here we evaluate viral morphological characteristics (morphotype, capsid diameter and tail length) using a quantitative transmission electron microscopy (qTEM) method across six of the world's oceans and seas sampled through the Tara Oceans Expedition. Extensive experimental validation of the qTEM method shows that neither sample preservation nor preparation significantly alters natural viral morphological characteristics. The global sampling analysis demonstrated that morphological characteristics did not vary consistently with depth (surface versus deep chlorophyll maximum waters) or oceanic region. Instead, temperature, salinity and oxygen concentration, but not chlorophyll a concentration, were more explanatory in evaluating differences in viral assemblage morphological characteristics. Surprisingly, given that the majority of cultivated bacterial viruses are tailed, non-tailed viruses appear to numerically dominate the upper oceans as they comprised 51-92% of the viral particles observed. Together, these results document global marine viral morphological characteristics, show that their minimal variability is more explained by environmental conditions than geography and suggest that non-tailed viruses might represent the most ecologically important targets for future research.
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41
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Biswas A, Gagnon JN, Brouns SJ, Fineran PC, Brown CM. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol 2013; 10:817-27. [PMID: 23492433 PMCID: PMC3737339 DOI: 10.4161/rna.24046] [Citation(s) in RCA: 226] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 12/19/2022] Open
Abstract
The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs (http://bioanalysis.otago.ac.nz/CRISPRTarget). This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems.
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Affiliation(s)
- Ambarish Biswas
- Department of Biochemistry; University of Otago; Dunedin, New Zealand
| | - Joshua N. Gagnon
- Department of Biochemistry; University of Otago; Dunedin, New Zealand
| | - Stan J.J. Brouns
- Laboratory of Microbiology; Wageningen University; Wageningen, Netherlands
| | - Peter C. Fineran
- Laboratory of Microbiology; Wageningen University; Wageningen, Netherlands
- Department of Microbiology and Immunology; University of Otago; Dunedin, New Zealand
- Genetics Otago; University of Otago; New Zealand
| | - Chris M. Brown
- Department of Biochemistry; University of Otago; Dunedin, New Zealand
- Genetics Otago; University of Otago; New Zealand
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Šimoliūnas E, Kaliniene L, Truncaitė L, Zajančkauskaitė A, Staniulis J, Kaupinis A, Ger M, Valius M, Meškys R. Klebsiella phage vB_KleM-RaK2 - a giant singleton virus of the family Myoviridae. PLoS One 2013; 8:e60717. [PMID: 23593293 PMCID: PMC3622015 DOI: 10.1371/journal.pone.0060717] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 03/01/2013] [Indexed: 11/19/2022] Open
Abstract
At 346 kbp in size, the genome of a jumbo bacteriophage vB_KleM-RaK2 (RaK2) is the largest Klebsiella infecting myovirus genome sequenced to date. In total, 272 out of 534 RaK2 ORFs lack detectable database homologues. Based on the similarity to biologically defined proteins and/or MS/MS analysis, 117 of RaK2 ORFs were given a functional annotation, including 28 RaK2 ORFs coding for structural proteins that have no reliable homologues to annotated structural proteins in other organisms. The electron micrographs revealed elaborate spike-like structures on the tail fibers of Rak2, suggesting that this phage is an atypical myovirus. While head and tail proteins of RaK2 are mostly myoviridae-related, the bioinformatics analysis indicate that tail fibers/spikes of this phage are formed from podovirus-like peptides predominantly. Overall, these results provide evidence that bacteriophage RaK2 differs profoundly from previously studied viruses of the Myoviridae family.
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Affiliation(s)
- Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
- * E-mail:
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Aurelija Zajančkauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Juozas Staniulis
- Laboratory of Plant Viruses, Institute of Botany, Nature Research Centre, Vilnius, Lithuania
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Marija Ger
- Proteomics Centre, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Vilnius, Lithuania
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43
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Complete Genome Sequence of a Novel Myovirus Which Infects Atypical Strains of Edwardsiella tarda. GENOME ANNOUNCEMENTS 2013; 1:genomeA00248-12. [PMID: 23469359 PMCID: PMC3587953 DOI: 10.1128/genomea.00248-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 01/17/2013] [Indexed: 11/25/2022]
Abstract
We present the genome sequence of a novel Edwardsiella tarda-lytic bacteriophage, MSW-3, which specifically infects atypical E. tarda strains. The morphological and genomic features of MSW-3 suggest that this phage is a new member of the dwarf myoviruses, which have been much less studied than other groups of myoviruses.
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