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Berryhill BA, Burke KB, Fontaine J, Brink CE, Harvill MG, Goldberg DA, Konstantinidis KT, Levin BR, Woodworth MH. Enteric Populations of Escherichia coli are Likely to be Resistant to Phages Due to O Antigen Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.08.566299. [PMID: 37986824 PMCID: PMC10659284 DOI: 10.1101/2023.11.08.566299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
There is a surfeit of bioinformatic data showing that bacteriophages abound in the enteric microbiomes of humans. What is the contribution of these viruses in shaping the bacterial strain and species composition of the gut microbiome and how are these phages maintained over time? To address these questions, we performed experiments with Escherichia coli and phages isolated from four fecal microbiota transplantation (FMT) doses as representative samples of non-dysbiotic enteric microbiota and develop and analyze the properties of a mathematical model of the population and evolutionary dynamics of bacteria and phage. Our models predict and experiments confirm that due to production of the O antigen, E. coli in the enteric microbiome are likely to be resistant to infection with co-occurring phages. Furthermore, our modeling suggests that the phages can be maintained in the population due to the high rates of host transition between resistant and sensitive states, which we call leaky resistance. Based on our observations and model predictions, we postulate that the phages found in the human gut are likely to play little role in shaping the composition of E. coli at the strain level in the enteric microbiome in healthy individuals. How general this is for other species of bacteria in the enteric flora is not yet clear, although O antigen expression is common across many taxa.
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Affiliation(s)
- Brandon A. Berryhill
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
- Program in Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Laney Graduate School, Emory University; Atlanta, Georgia, 30322, USA
| | - Kylie B. Burke
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Jake Fontaine
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Catherine E. Brink
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mason G. Harvill
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - David A. Goldberg
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Konstantinos T. Konstantinidis
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bruce R. Levin
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Michael H. Woodworth
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
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2
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Zhu Y, Shang J, Peng C, Sun Y. Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework. Front Microbiol 2022; 13:1032186. [PMID: 36590402 PMCID: PMC9800612 DOI: 10.3389/fmicb.2022.1032186] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to (viral) metagenomic sequencing, a large number of new bacteriophages have been discovered. However, lacking a standard and automatic virus classification pipeline, the taxonomic characterization of new viruses seriously lag behind the sequencing efforts. In particular, according to the latest version of ICTV, several large phage families in the previous classification system are removed. Therefore, a comprehensive review and comparison of taxonomic classification tools under the new standard are needed to establish the state-of-the-art. In this work, we retrained and tested four recently published tools on newly labeled databases. We demonstrated their utilities and tested them on multiple datasets, including the RefSeq, short contigs, simulated metagenomic datasets, and low-similarity datasets. This study provides a comprehensive review of phage family classification in different scenarios and a practical guidance for choosing appropriate taxonomic classification pipelines. To our best knowledge, this is the first review conducted under the new ICTV classification framework. The results show that the new family classification framework overall leads to better conserved groups and thus makes family-level classification more feasible.
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3
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Li Y, Li H, Jiang Y, Shao H, He H, Wang M. Isolation and Complete Sequence of One Novel Marine Bacteriophage PHS21 Infecting Pseudoalteromonas marina. Curr Microbiol 2022; 79:213. [PMID: 35672590 DOI: 10.1007/s00284-022-02886-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 04/21/2022] [Indexed: 11/28/2022]
Abstract
PHS21 against Pseudoalteromonas is isolated from Qingdao offshore seawater. The phage was characterized and identified by morphological examination, stability, whole genome sequencing, and bioinformatics analysis. Morphological analysis of PHS21 by transmission electron microscopy shows that belonged to the Siphoviridae family. PHS21 showed strong tolerance with a wide range of temperatures and pH. One-step growth assay indicates that the latent period is about 48 min and the burst size is approximately 218 PFU/cell (plaque forming unit/cell). Its complete genomic sequence is 35,802-bp long with 50 putative open reading frames. Phage PHS21 and PHS3 displayed a very close evolutionary relationship; however, having different DNA packaging proteins indicates that they may have already evolved distinct ways to package DNA in host cells. This study provides the detailed description and genomic characterization of a novel Pseudoalteromonas phage.
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Affiliation(s)
- Yan Li
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, People's Republic of China
| | - Huifang Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University (Xiang'an), Xiamen, People's Republic of China.,Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, People's Republic of China
| | - Yong Jiang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, People's Republic of China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, People's Republic of China
| | - Hui He
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, People's Republic of China.
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, People's Republic of China. .,The affiliated hospital of Qingdao University, Qingdao, People's Republic of China. .,UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, People's Republic of China.
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4
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Rogovski P, Cadamuro RD, da Silva R, de Souza EB, Bonatto C, Viancelli A, Michelon W, Elmahdy EM, Treichel H, Rodríguez-Lázaro D, Fongaro G. Uses of Bacteriophages as Bacterial Control Tools and Environmental Safety Indicators. Front Microbiol 2021; 12:793135. [PMID: 34917066 PMCID: PMC8670004 DOI: 10.3389/fmicb.2021.793135] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/11/2021] [Indexed: 11/19/2022] Open
Abstract
Bacteriophages are bacterial-specific viruses and the most abundant biological form on Earth. Each bacterial species possesses one or multiple bacteriophages and the specificity of infection makes them a promising alternative for bacterial control and environmental safety, as a biotechnological tool against pathogenic bacteria, including those resistant to antibiotics. This application can be either directly into foods and food-related environments as biocontrol agents of biofilm formation. In addition, bacteriophages are used for microbial source-tracking and as fecal indicators. The present review will focus on the uses of bacteriophages like bacterial control tools, environmental safety indicators as well as on their contribution to bacterial control in human, animal, and environmental health.
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Affiliation(s)
- Paula Rogovski
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Rafael Dorighello Cadamuro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Raphael da Silva
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Estêvão Brasiliense de Souza
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Charline Bonatto
- Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, Brazil
- Laboratory of Microbiology and Bioprocesses, Federal University of Fronteira Sul (UFFS), Erechim, Brazil
| | | | | | - Elmahdy M. Elmahdy
- Laboratory of Environmental Virology, Environmental Research Division, Department of Water Pollution Research, National Research Centre, Giza, Egypt
| | - Helen Treichel
- Laboratory of Microbiology and Bioprocesses, Federal University of Fronteira Sul (UFFS), Erechim, Brazil
| | - David Rodríguez-Lázaro
- Division of Microbiology, Department of Biotechnology and Food Science, Universidad de Burgos, Burgos, Spain
- Centre for Emerging Pathogens and Global Health, Universidad de Burgos, Burgos, Spain
| | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
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Dąbrowska K, Abedon ST. Pharmacologically Aware Phage Therapy: Pharmacodynamic and Pharmacokinetic Obstacles to Phage Antibacterial Action in Animal and Human Bodies. Microbiol Mol Biol Rev 2019; 83:e00012-19. [PMID: 31666296 PMCID: PMC6822990 DOI: 10.1128/mmbr.00012-19] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The use of viruses infecting bacteria (bacteriophages or phages) to treat bacterial infections has been ongoing clinically for approximately 100 years. Despite that long history, the growing international crisis of resistance to standard antibiotics, abundant anecdotal evidence of efficacy, and one successful modern clinical trial of efficacy, this phage therapy is not yet a mainstream approach in medicine. One explanation for why phage therapy has not been subject to more widespread implementation is that phage therapy research, both preclinical and clinical, can be insufficiently pharmacologically aware. Consequently, here we consider the pharmacological obstacles to phage therapy effectiveness, with phages in phage therapy explicitly being considered to serve as drug equivalents. The study of pharmacology has traditionally been differentiated into pharmacokinetic and pharmacodynamic aspects. We therefore separately consider the difficulties that phages as virions can have in traveling through body compartments toward reaching their target bacteria (pharmacokinetics) and the difficulties that phages can have in exerting antibacterial activity once they have reached those bacteria (pharmacodynamics). The latter difficulties, at least in part, are functions of phage host range and bacterial resistance to phages. Given the apparently low toxicity of phages and the minimal side effects of phage therapy as practiced, phage therapy should be successful so long as phages can reach the targeted bacteria in sufficiently high numbers, adsorb, and then kill those bacteria. Greater awareness of what obstacles to this success generally or specifically can exist, as documented in this review, should aid in the further development of phage therapy toward wider use.
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Affiliation(s)
- Krystyna Dąbrowska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, USA
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Liu X, Tang K, Zhang D, Li Y, Liu Z, Yao J, Wood TK, Wang X. Symbiosis of a P2‐family phage and deep‐sea
Shewanella putrefaciens. Environ Microbiol 2019; 21:4212-4232. [DOI: 10.1111/1462-2920.14781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/12/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaoxiao Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Dali Zhang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Yangmei Li
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhe Liu
- Guangdong Provincial Center for Disease Control and Prevention Guangdong Provincial Institute of Public Health Guangzhou 511430 China
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Thomas K. Wood
- Department of Chemical Engineering Pennsylvania State University University Park PA 16802‐4400 USA
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences Beijing 100049 China
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7
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García-López R, Pérez-Brocal V, Moya A. Beyond cells - The virome in the human holobiont. MICROBIAL CELL (GRAZ, AUSTRIA) 2019; 6:373-396. [PMID: 31528630 PMCID: PMC6717880 DOI: 10.15698/mic2019.09.689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/14/2019] [Accepted: 04/03/2019] [Indexed: 01/01/2023]
Abstract
Viromics, or viral metagenomics, is a relatively new and burgeoning field of research that studies the complete collection of viruses forming part of the microbiota in any given niche. It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. Historically, most studies have deconstructed the concept of viruses into a simplified perception of viral agents as mere pathogens, which demerits the scope of large-scale viromic analyses. Viruses are, in fact, much more than regular parasites. They are by far the most dynamic and abundant entity and the greatest killers on the planet, as well as the most effective geo-transforming genetic engineers and resource recyclers, acting on all life strata in any habitat. Yet, most of this uncanny viral world remains vastly unexplored to date, greatly hindered by the bewildering complexity inherent to such studies and the methodological and conceptual limitations. Viromic studies are just starting to address some of these issues but they still lag behind microbial metagenomics. In recent years, however, higher-throughput analysis and resequencing have rekindled interest in a field that is just starting to show its true potential. In this review, we take a look at the scientific and technological developments that led to the advent of viral and bacterial metagenomics with a particular, but not exclusive, focus on human viromics from an ecological perspective. We also address some of the most relevant challenges that current viral studies face and ponder on the future directions of the field.
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Affiliation(s)
- Rodrigo García-López
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
| | - Vicente Pérez-Brocal
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
| | - Andrés Moya
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
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8
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Dąbrowska K. Phage therapy: What factors shape phage pharmacokinetics and bioavailability? Systematic and critical review. Med Res Rev 2019; 39:2000-2025. [PMID: 30887551 PMCID: PMC6767042 DOI: 10.1002/med.21572] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 01/23/2019] [Accepted: 02/26/2019] [Indexed: 12/18/2022]
Abstract
Bacteriophages are not forgotten viruses anymore: scientists and practitioners seek to understand phage pharmacokinetics in animals and humans, investigating bacteriophages as therapeutics, nanocarriers or microbiome components. This review provides a comprehensive overview of factors that determine phage circulation, penetration, and clearance, and that in consequence determine phage applicability for medicine. It makes use of experimental data collected by the phage community so far (PubMed 1924‐2016, including non‐English reports), combining elements of critical and systematic review. This study covers phage ability to enter a system by various routes of administration, how (and if) the phage may access various tissues and organs, and finally what mechanisms determine the courses of phage clearance. The systematic review method was applied to analyze (i) phage survival in the gut (gut transit) and (ii) phage ability to enter the mammalian system by many administration routes. Aspects that have not yet been covered by a sufficient number of reports for mathematical analysis, as well as mechanisms underlying trends, are discussed in the form of a critical review. In spite of the extraordinary diversity of bacteriophages and possible phage applications, the analysis revealed that phage morphology, phage specificity, phage dose, presence of sensitive bacteria or the characteristics of treated individuals (age, taxonomy) may affect phage bioavailability in animals and humans. However, once phages successfully enter the body, they reach most organs, including the central nervous system. Bacteriophages are cleared mainly by the immune system: innate immunity removes phages even when no specific response to bacteriophages has yet developed.
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Affiliation(s)
- Krystyna Dąbrowska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Research and Development Center, Regional Specialized Hospital, Wrocław, Poland
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9
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Akhwale JK, Rohde M, Rohde C, Bunk B, Spröer C, Klenk HP, Boga HI, Wittmann J. Comparative genomic analysis of eight novel haloalkaliphilic bacteriophages from Lake Elmenteita, Kenya. PLoS One 2019; 14:e0212102. [PMID: 30763364 PMCID: PMC6375668 DOI: 10.1371/journal.pone.0212102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/28/2019] [Indexed: 12/17/2022] Open
Abstract
We report complete genome sequences of eight bacteriophages isolated from Haloalkaline Lake Elmenteita found on the floor of Kenyan Rift Valley. The bacteriophages were sequenced, annotated and a comparative genomic analysis using various Bioinformatics tools carried out to determine relatedness of the bacteriophages to each other, and to those in public databases. Basic genome properties like genome size, percentage coding density, number of open reading frames, percentage GC content and gene organizations revealed the bacteriophages had no relationship to each other. Comparison to other nucleotide sequences in GenBank database showed no significant similarities hence novel. At the amino acid level, phages of our study revealed mosaicism to genes with conserved domains to already described phages. Phylogenetic analyses of large terminase gene responsible for DNA packaging and DNA polymerase gene for replication further showed diversity among the bacteriophages. Our results give insight into diversity of bacteriophages in Lake Elmenteita and provide information on their evolution. By providing primary sequence information, this study not only provides novel sequences for biotechnological exploitation, but also sets stage for future studies aimed at better understanding of virus diversity and genomes from haloalkaline lakes in the Rift Valley.
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Affiliation(s)
- Juliah Khayeli Akhwale
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
- Department of Zoology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Manfred Rohde
- Helmholtz Centre for Infection Research, Central Facility for Microscopy, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Christine Rohde
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Johannes Wittmann
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, Germany
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10
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Liu Q, Han Y, Wang D, Wang Q, Liu X, Li Y, Song X, Wang M, Jiang Y, Meng Z, Shao H, McMinn A. Complete genomic sequence of bacteriophage J2-1: A novel Pseudoalteromonas phenolica phage isolated from the coastal water of Qingdao, China. Mar Genomics 2018. [DOI: 10.1016/j.margen.2017.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Wang X, Liu J, Yu Z, Jin J, Liu X, Wang G. Novel groups of cyanobacterial podovirus DNA polymerase (pol) genes exist in paddy waters in northeast China. FEMS Microbiol Ecol 2016; 92:fiw192. [DOI: 10.1093/femsec/fiw192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 11/12/2022] Open
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12
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Maat DS, van Bleijswijk JDL, Witte HJ, Brussaard CPD. Virus production in phosphorus-limitedMicromonas pusillastimulated by a supply of naturally low concentrations of different phosphorus sources, far into the lytic cycle. FEMS Microbiol Ecol 2016; 92:fiw136. [DOI: 10.1093/femsec/fiw136] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2016] [Indexed: 11/13/2022] Open
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13
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Betts A, Gifford DR, MacLean RC, King KC. Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system. Evolution 2016; 70:969-78. [PMID: 27005577 PMCID: PMC4982092 DOI: 10.1111/evo.12909] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 03/02/2016] [Accepted: 03/11/2016] [Indexed: 12/01/2022]
Abstract
Host–parasite evolutionary interactions are typically considered in a pairwise species framework. However, natural infections frequently involve multiple parasites. Altering parasite diversity alters ecological and evolutionary dynamics as parasites compete and hosts resist multiple infection. We investigated the effects of parasite diversity on host–parasite population dynamics and evolution using the pathogen Pseudomonas aeruginosa and five lytic bacteriophage parasites. To manipulate parasite diversity, bacterial populations were exposed for 24 hours to either phage monocultures or diverse communities containing up to five phages. Phage communities suppressed host populations more rapidly but also showed reduced phage density, likely due to interphage competition. The evolution of resistance allowed rapid bacterial recovery that was greater in magnitude with increases in phage diversity. We observed no difference in the extent of resistance with increased parasite diversity, but there was a profound impact on the specificity of resistance; specialized resistance evolved to monocultures through mutations in a diverse set of genes. In summary, we demonstrate that parasite diversity has rapid effects on host–parasite population dynamics and evolution by selecting for different resistance mutations and affecting the magnitude of bacterial suppression and recovery. Finally, we discuss the implications of phage diversity for their use as biological control agents.
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Affiliation(s)
- Alex Betts
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom.
| | - Danna R Gifford
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - R Craig MacLean
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - Kayla C King
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
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14
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Complete Genomic Sequence of Bacteriophage H188: A Novel Vibrio kanaloae Phage Isolated from Yellow Sea. Curr Microbiol 2016; 72:628-33. [DOI: 10.1007/s00284-015-0984-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/04/2015] [Indexed: 11/29/2022]
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15
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Garcia-Heredia I, Rodriguez-Valera F, Martin-Cuadrado AB. Novel group of podovirus infecting the marine bacterium Alteromonas macleodii.. BACTERIOPHAGE 2014; 3:e24766. [PMID: 24228219 PMCID: PMC3821669 DOI: 10.4161/bact.24766] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 04/22/2013] [Accepted: 04/22/2013] [Indexed: 12/29/2022]
Abstract
Four novel, closely related podoviruses, which displayed lytic activity against the gamma-proteobacterium Alteromonas macleodii, have been isolated and sequenced. Alterophages AltAD45-P1 to P4 were obtained from water recovered near a fish farm in the Mediterranean Sea. Their morphology indicates that they belong to the Podoviridae. Their linear and dsDNA genomes are 100–104 kb in size, remarkably larger than any other described podovirus. The four AltAD45-phages share 99% nucleotide sequence identity over 97% of their ORFs, although an insertion was found in AltAD45-P1 and P2 and some regions were slightly more divergent. Despite the high overall sequence similarity among these four phages, the group with the insertion and the group without it, have different host ranges against the A. macleodii strains tested. The AltAD45-P1 to P4 phages have genes for DNA replication and transcription as well as structural genes, which are similar to the N4-like Podoviridae genus that is widespread in proteobacteria. However, in terms of their genomic structure, AltAD45-P1 to P4 differ from that of the N4-like phages. Some distinguishing features include the lack of a large virion encapsidated RNA polymerase gene, very well conserved among all the previously described N4-like phages, a single-stranded DNA binding protein and different tail protein genes. We conclude that the AltAD45 phages characterized in this study constitute a new genus within the Podoviridae.
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Affiliation(s)
- Inmaculada Garcia-Heredia
- Evolutionary Genomics Group; División de Microbiología; Universidad Miguel Hernández; San Juan, Alicante Spain
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Clokie MR, Millard AD, Letarov AV, Heaphy S. Phages in nature. BACTERIOPHAGE 2014; 1:31-45. [PMID: 21687533 DOI: 10.4161/bact.1.1.14942] [Citation(s) in RCA: 633] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/17/2011] [Accepted: 01/18/2011] [Indexed: 12/28/2022]
Abstract
Bacteriophages or phages are the most abundant organisms in the biosphere and they are a ubiquitous feature of prokaryotic existence. A bacteriophage is a virus which infects a bacterium. Archaea are also infected by viruses, whether these should be referred to as 'phages' is debatable, but they are included as such in the scope this article. Phages have been of interest to scientists as tools to understand fundamental molecular biology, as vectors of horizontal gene transfer and drivers of bacterial evolution, as sources of diagnostic and genetic tools and as novel therapeutic agents. Unraveling the biology of phages and their relationship with their hosts is key to understanding microbial systems and their exploitation. In this article we describe the roles of phages in different host systems and show how modeling, microscopy, isolation, genomic and metagenomic based approaches have come together to provide unparalleled insights into these small but vital constituents of the microbial world.
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Affiliation(s)
- Martha Rj Clokie
- Department of Infection, Immunity and Inflammation; Medical Sciences Building; University of Leicester; Leicester, UK
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Wang G, Liu J, Yu Z, Jin J, Liu X. Unique distribution of cyanobacterial podoviruses and their potential hosts in a paddy field of northeast China. FEMS Microbiol Ecol 2014; 90:331-4. [PMID: 25088984 DOI: 10.1111/1574-6941.12401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 07/13/2014] [Accepted: 07/31/2014] [Indexed: 11/29/2022] Open
Abstract
We first surveyed the DNA polymerase (pol) gene of cyanopodoviruses and the 16S-23S rRNA gene internal transcribed spacer (ITS) region of picocyanobacteria in a paddy field of northeast China. A total of 49 DNA pol clones and 76 ITS clones were obtained. The blast search results showed that all DNA pol clones and nearly 50% of the ITS clones had up to 76% and 50% identity/similarity to known sequences, respectively. Phylogenetic analyses showed that the DNA pol clones were narrowly distributed in the phylogenetic tree, and two new subclusters of cyanopodoviruses (PG-Pol-I and PG-Pol-II) specific to paddy field were discovered. In contrast, the distribution of ITS clones was very broad, and seven paddy-specific groups of picocyanobacteria (PG-Picocya-I-VII) were identified. In general, novel groups of cyanopodoviruses and picocyanobacteria were observed in this study, suggesting that coevolution between cyanopodoviruses and their hosts occurs in the paddy field.
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Affiliation(s)
- Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Jing R, Liu J, Yu Z, Liu X, Wang G. Phylogenetic distribution of the capsid assembly protein gene (g20) of cyanophages in paddy floodwaters in Northeast China. PLoS One 2014; 9:e88634. [PMID: 24533125 PMCID: PMC3922986 DOI: 10.1371/journal.pone.0088634] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 01/13/2014] [Indexed: 12/03/2022] Open
Abstract
Numerous studies have revealed the high diversity of cyanophages in marine and freshwater environments, but little is currently known about the diversity of cyanophages in paddy fields, particularly in Northeast (NE) China. To elucidate the genetic diversity of cyanophages in paddy floodwaters in NE China, viral capsid assembly protein gene (g20) sequences from five floodwater samples were amplified with the primers CPS1 and CPS8. Denaturing gradient gel electrophoresis (DGGE) was applied to distinguish different g20 clones. In total, 54 clones differing in g20 nucleotide sequences were obtained in this study. Phylogenetic analysis showed that the distribution of g20 sequences in this study was different from that in Japanese paddy fields, and all the sequences were grouped into Clusters α, β, γ and ε. Within Clusters α and β, three new small clusters (PFW-VII∼-IX) were identified. UniFrac analysis of g20 clone assemblages demonstrated that the community compositions of cyanophage varied among marine, lake and paddy field environments. In paddy floodwater, community compositions of cyanophage were also different between NE China and Japan.
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Affiliation(s)
- Ruiyong Jing
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Harbin, China
- Graduate University of Chinese Academy of Science, Beijing, China
- Heilongjiang BaYi Agricultural University, College of Life and Sci-technology, Daqing, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Harbin, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Harbin, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Harbin, China
- * E-mail:
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Virulence Changes to Harveyi Clade Bacteria Infected with Bacteriophage from Vibrio owensii. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2013; 24:180-7. [PMID: 24426274 DOI: 10.1007/s13337-013-0136-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 05/02/2013] [Indexed: 10/26/2022]
Abstract
Vibrio owensii is one of the most virulent vibrios known being able to kill crustacean larvae at 10(2) CFU ml(-1). This study describes virulence changes to naïve strains of Vibrio harveyi and Vibrio campbellii when infected with the bacteriophage VOB from a closely related species V. owensii 47666-1. The bacteriophage from V. owensii was induced into lytic phase by using mitomycin C at 100 ng ml(-1). One strain of V. harveyi and two strains of V. campbellii from 29 tested containing no prophage were susceptible to lysogenic conversion with VOB. Virulence changes induced in Harveyi clade bacteria included the up-regulation of protein secretion, statistically significant increased haemolysin and chitinase production and increased mortality to nauplii of Penaeus monodon. No change in siderophore production was observed. Bacteriophage VOB is likely to be responsible for some of the virulence factors expressed by V. owensii. As this bacteriophage is able to infect strains of V. harveyi and V. campbellii this phage may contribute to increased virulence of other vibrios in aquaculture and in the natural environment.
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Zheng C, Wang G, Liu J, Song C, Gao H, Liu X. Characterization of the major capsid genes (g23) of T4-type bacteriophages in the wetlands of northeast China. MICROBIAL ECOLOGY 2013; 65:616-25. [PMID: 23306393 DOI: 10.1007/s00248-012-0158-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 12/09/2012] [Indexed: 05/08/2023]
Abstract
To obtain genetic information and to evaluate the composition of T4-type bacteriophage (phage) communities in wetlands, environmental soil and water DNAs were obtained from two natural wetlands dominated by Carex lasiocarpa and Deyeuxia angustifolia plant species, and a neighboring paddy field in Sanjiang plain of northeast China. The biomarker gene of g23, which encodes the major capsid protein of T4-type phages, was amplified with primers MZIA1bis and MZIA6, and the PCR products were cloned and sequenced. In total, 96 and 50 different g23 clones were obtained from natural wetlands and a paddy field, respectively. A larger number of clones with low levels of identity to known sequences were found in water than in soil both in the natural wetlands and the paddy field, suggesting that many of T4-type phages in wetland water and paddy floodwater in Sanjiang plain are uncharacterized. Phylogenetic analyses showed that the g23 clones in natural wetlands, irrespective of water and soil, were distinctly different from those in marine waters, lake waters, and upland black soils, but were similar to those in paddy fields. The UniFrac analysis of g23 assemblages indicated that T4-type phage community compositions were different between soils and waters, and also were different between the natural wetlands and the paddy field. In general, the global analysis of g23 clone assemblages demonstrated that T4-type phage community compositions were different among natural wetlands, marines, lakes, paddy fields, and upland black soils.
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Affiliation(s)
- Chunyu Zheng
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Matteson AR, Rowe JM, Ponsero AJ, Pimentel TM, Boyd PW, Wilhelm SW. High abundances of cyanomyoviruses in marine ecosystems demonstrate ecological relevance. FEMS Microbiol Ecol 2013; 84:223-34. [PMID: 23240688 DOI: 10.1111/1574-6941.12060] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 09/11/2012] [Accepted: 12/03/2012] [Indexed: 12/01/2022] Open
Abstract
The distribution of cyanomyoviruses was estimated using a quantitative PCR (qPCR) approach that targeted the g20 gene as a proxy for phage. Samples were collected spatially during a > 3000 km transect through the Sargasso Sea and temporally during a gyre-constrained phytoplankton bloom within the southern Pacific Ocean. Cyanomyovirus abundances were lower in the Sargasso Sea than in the southern Pacific Ocean, ranging from 2.75 × 10(3) to 5.15 × 10(4) mL(-1) and correlating with the abundance of their potential hosts (Prochlorococcus and Synechococcus). Cyanomyovirus abundance in the southern Pacific Ocean (east of New Zealand) followed Synechococcus host populations in the system: this included a decrease in g20 gene copies (from 4.3 × 10(5) to 9.6 × 10(3) mL(-1) ) following the demise of a Synechococcus bloom. When compared with direct counts of viruses, observations suggest that the cyanomyoviruses comprised 0.5 to >25% of the total virus community. We estimated daily lysis rates of 0.2-46% of the standing stock of Synechococcus in the Pacific Ocean compared with c. < 1.0% in the Sargasso Sea. In total, our observations confirm this family of viruses is abundant in marine systems and that they are an important source of cyanobacterial mortality.
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Affiliation(s)
- Audrey R Matteson
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996-0845, USA
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22
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Boujelben I, Yarza P, Almansa C, Villamor J, Maalej S, Antón J, Santos F. Virioplankton community structure in Tunisian solar salterns. Appl Environ Microbiol 2012; 78:7429-37. [PMID: 22904045 PMCID: PMC3457115 DOI: 10.1128/aem.01793-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 08/06/2012] [Indexed: 11/20/2022] Open
Abstract
The microbial community inhabiting Sfax solar salterns on the east coast of Tunisia has been studied by means of different molecular and culture-dependent tools that have unveiled the presence of novel microbial groups as well as a community structure different from that of other coastal hypersaline environments. We have focused on the study of the viral assemblages of these salterns and their changes along the salinity gradient and over time. Viruses from three ponds (C4, M1, and TS) encompassing salinities from moderately hypersaline to saturated (around 14, 19, and 35%, respectively) were sampled in May and October 2009 and analyzed by transmission electron microscopy (TEM) and pulsed-field gel electrophoresis (PFGE). Additionally, for all three October samples and the May TS sample, viral metagenomic DNA was cloned in fosmids, end sequenced, and analyzed. Viral concentration, as well as virus-to-cell ratios, increased along the salinity gradient, with around 10(10) virus-like particles (VLPs)/ml in close-to-saturation ponds, which represents the highest viral concentration reported so far for aquatic systems. Four distinct morphologies could be observed with TEM (spherical, tailed, spindled, and filamentous) but with various proportions in the different samples. Metagenomic analyses indicated that every pond harbored a distinct viral assemblage whose G+C content could be roughly correlated with that of the active part of the microbial community that may have constituted the putative hosts. As previously reported for hypersaline metaviromes, most sequences did not have matches in the databases, although some were conserved among the Sfax metaviromes. BLASTx, BLASTp, and dinucleotide frequency analyses indicated that (i) factors additional to salinity could be structuring viral communities and (ii) every metavirome had unique gene contents and dinucleotide frequencies. Comparison with hypersaline metaviromes available in the databases indicated that the viral assemblages present in close-to-saturation environments located thousands of kilometers apart presented some common traits among them in spite of their differences regarding the putative hosts. A small core metavirome for close-to-saturation systems was found that contained 7 sequences of around 100 nucleotides (nt) whose function was not hinted at by in silico search results, although it most likely represents properties essential for hyperhalophilic viruses.
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Affiliation(s)
- Ines Boujelben
- Département des Sciences de la Vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Pablo Yarza
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Cristina Almansa
- Servicios Técnicos de Investigación (SSTTI), Unidad de Microscopía, Universidad de Alicante, Alicante, Spain
| | - Judith Villamor
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Sami Maalej
- Département des Sciences de la Vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
| | - Josefa Antón
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
- Instituto Multidisciplinar para el Estudio del Medio Ramón Margalef, Universidad de Alicante, Alicante, Spain
| | - Fernando Santos
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
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Ray J, Dondrup M, Modha S, Steen IH, Sandaa RA, Clokie M. Finding a needle in the virus metagenome haystack--micro-metagenome analysis captures a snapshot of the diversity of a bacteriophage armoire. PLoS One 2012; 7:e34238. [PMID: 22509283 PMCID: PMC3324506 DOI: 10.1371/journal.pone.0034238] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 02/24/2012] [Indexed: 12/12/2022] Open
Abstract
Viruses are ubiquitous in the oceans and critical components of marine microbial communities, regulating nutrient transfer to higher trophic levels or to the dissolved organic pool through lysis of host cells. Hydrothermal vent systems are oases of biological activity in the deep oceans, for which knowledge of biodiversity and its impact on global ocean biogeochemical cycling is still in its infancy. In order to gain biological insight into viral communities present in hydrothermal vent systems, we developed a method based on deep-sequencing of pulsed field gel electrophoretic bands representing key viral fractions present in seawater within and surrounding a hydrothermal plume derived from Loki's Castle vent field at the Arctic Mid-Ocean Ridge. The reduction in virus community complexity afforded by this novel approach enabled the near-complete reconstruction of a lambda-like phage genome from the virus fraction of the plume. Phylogenetic examination of distinct gene regions in this lambdoid phage genome unveiled diversity at loci encoding superinfection exclusion- and integrase-like proteins. This suggests the importance of fine-tuning lyosgenic conversion as a viral survival strategy, and provides insights into the nature of host-virus and virus-virus interactions, within hydrothermal plumes. By reducing the complexity of the viral community through targeted sequencing of prominent dsDNA viral fractions, this method has selectively mimicked virus dominance approaching that hitherto achieved only through culturing, thus enabling bioinformatic analysis to locate a lambdoid viral "needle" within the greater viral community "haystack". Such targeted analyses have great potential for accelerating the extraction of biological knowledge from diverse and poorly understood environmental viral communities.
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Affiliation(s)
- Jessica Ray
- Department of Biology, University of Bergen, Bergen, Norway
| | | | - Sejal Modha
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | | | - Ruth-Anne Sandaa
- Department of Biology, University of Bergen, Bergen, Norway
- * E-mail:
| | - Martha Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
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Bohlin J, van Passel MWJ, Snipen L, Kristoffersen AB, Ussery D, Hardy SP. Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands. BMC Genomics 2012; 13:66. [PMID: 22325062 PMCID: PMC3305612 DOI: 10.1186/1471-2164-13-66] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 02/10/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure. RESULTS Relative entropy was highest in bacterial chromosomes and had the sequence chromosomes > GI > phage > plasmid. There was an association between relative entropy and AT content in chromosomes, phages, plasmids and GIs with the strongest association being in phages. Relative entropy was also found to be lower in the obligate intracellular Mycobacterium leprae than in the related M. tuberculosis when measured on a shared set of highly conserved genes. CONCLUSIONS We argue that relative entropy differences reflect how plasmids, phages and GIs interact with microbial host chromosomes and that all these biological entities are, or have been, subjected to different selective pressures. The rate at which amelioration of horizontally acquired DNA occurs within the chromosome is likely to account for the small differences between chromosomes and stably incorporated GIs compared to the transient or independent replicons such as phages and plasmids.
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Affiliation(s)
- Jon Bohlin
- Norwegian School of Veterinary Science, EpiCentre, Department of Food Safety and Infection biology, Ullevålsveien 72, Oslo, Norway.
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Characterization of the ELPhiS prophage from Salmonella enterica serovar Enteritidis strain LK5. Appl Environ Microbiol 2012; 78:1785-93. [PMID: 22247173 DOI: 10.1128/aem.07241-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Phages are a primary driving force behind the evolution of bacterial pathogens by transferring a variety of virulence genes into their hosts. Similar to other bacterial genomes, the Salmonella enterica serovar Enteritidis LK5 genome contains several regions that are homologous to phages. Although genomic analysis demonstrated the presence of prophages, it was unable to confirm which phage elements within the genome were viable. Genetic markers were used to tag one of the prophages in the genome to allow monitoring of phage induction. Commonly used laboratory strains of Salmonella were resistant to phage infection, and therefore a rapid screen was developed to identify susceptible hosts. This approach showed that a genetically tagged prophage, ELPhiS (Enteritidis lysogenic phage S), was capable of infecting Salmonella serovars that are diverse in host range and virulence and has the potential to laterally transfer genes between these serovars via lysogenic conversion. The rapid screen approach is adaptable to any system with a large collection of isolates and may be used to test the viability of prophages found by sequencing the genomes of various bacterial pathogens.
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26
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Jameson E, Mann NH, Joint I, Sambles C, Mühling M. The diversity of cyanomyovirus populations along a North-South Atlantic Ocean transect. THE ISME JOURNAL 2011; 5:1713-21. [PMID: 21633395 PMCID: PMC3197166 DOI: 10.1038/ismej.2011.54] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 03/24/2011] [Accepted: 03/26/2011] [Indexed: 11/08/2022]
Abstract
Viruses that infect the marine cyanobacterium Prochlorococcus have the potential to impact the growth, productivity, diversity and abundance of their hosts. In this study, changes in the microdiversity of cyanomyoviruses were investigated in 10 environmental samples taken along a North-South Atlantic Ocean transect using a myoviral-specific PCR-sequencing approach. Phylogenetic analyses of 630 viral g20 clones from this study, with 786 published g20 sequences, revealed that myoviral populations in the Atlantic Ocean had higher diversity than previously reported, with several novel putative g20 clades. Some of these clades were detected throughout the Atlantic Ocean. Multivariate statistical analyses did not reveal any significant correlations between myoviral diversity and environmental parameters, although myoviral diversity appeared to be lowest in samples collected from the north and south of the transect where Prochlorococcus diversity was also lowest. The results were correlated to the abundance and diversity of the co-occurring Prochlorococcus and Synechococcus populations, but revealed no significant correlations to either of the two potential host genera. This study provides evidence that cyanophages have extremely high and variable diversity and are distributed over large areas of the Atlantic Ocean.
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Affiliation(s)
- Eleanor Jameson
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, UK.
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27
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Danovaro R, Corinaldesi C, Dell'Anno A, Fuhrman JA, Middelburg JJ, Noble RT, Suttle CA. Marine viruses and global climate change. FEMS Microbiol Rev 2011; 35:993-1034. [DOI: 10.1111/j.1574-6976.2010.00258.x] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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28
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Zsak L, Day JM, Oakley BB, Seal BS. The complete genome sequence and genetic analysis of ΦCA82 a novel uncultured microphage from the turkey gastrointestinal system. Virol J 2011; 8:331. [PMID: 21714899 PMCID: PMC3135560 DOI: 10.1186/1743-422x-8-331] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 06/29/2011] [Indexed: 12/18/2022] Open
Abstract
The genomic DNA sequence of a novel enteric uncultured microphage, ΦCA82 from a turkey gastrointestinal system was determined utilizing metagenomics techniques. The entire circular, single-stranded nucleotide sequence of the genome was 5,514 nucleotides. The ΦCA82 genome is quite different from other microviruses as indicated by comparisons of nucleotide similarity, predicted protein similarity, and functional classifications. Only three genes showed significant similarity to microviral proteins as determined by local alignments using BLAST analysis. ORF1 encoded a predicted phage F capsid protein that was phylogenetically most similar to the Microviridae ΦMH2K member's major coat protein. The ΦCA82 genome also encoded a predicted minor capsid protein (ORF2) and putative replication initiation protein (ORF3) most similar to the microviral bacteriophage SpV4. The distant evolutionary relationship of ΦCA82 suggests that the divergence of this novel turkey microvirus from other microviruses may reflect unique evolutionary pressures encountered within the turkey gastrointestinal system.
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Affiliation(s)
- Laszlo Zsak
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA.
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29
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Rowe JM, Fabre MF, Gobena D, Wilson WH, Wilhelm SW. Application of the major capsid protein as a marker of the phylogenetic diversity of Emiliania huxleyi viruses. FEMS Microbiol Ecol 2011; 76:373-80. [PMID: 21255053 DOI: 10.1111/j.1574-6941.2011.01055.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Studies of the Phycodnaviridae have traditionally relied on the DNA polymerase (pol) gene as a biomarker. However, recent investigations have suggested that the major capsid protein (MCP) gene may be a reliable phylogenetic biomarker. We used MCP gene amplicons gathered across the North Atlantic to assess the diversity of Emiliania huxleyi-infecting Phycodnaviridae. Nucleotide sequences were examined across >6000 km of open ocean, with comparisons between concentrates of the virus-size fraction of seawater and of lysates generated by exposing host strains to these same virus concentrates. Analyses revealed that many sequences were only sampled once, while several were over-represented. Analyses also revealed nucleotide sequences distinct from previous coastal isolates. Examination of lysed cultures revealed a new richness in phylogeny, as MCP sequences previously unrepresented within the existing collection of E. huxleyi viruses (EhV) were associated with viruses lysing cultures. Sequences were compared with previously described EhV MCP sequences from the North Sea and a Norwegian Fjord, as well as from the Gulf of Maine. Principal component analysis indicates that location-specific distinctions exist despite the presence of sequences common across these environments. Overall, this investigation provides new sequence data and an assessment on the use of the MCP gene.
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Affiliation(s)
- Janet M Rowe
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996-0845, USA
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30
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Wang G, Asakawa S, Kimura M. Spatial and temporal changes of cyanophage communities in paddy field soils as revealed by the capsid assembly protein gene g20. FEMS Microbiol Ecol 2011; 76:352-9. [PMID: 21255050 DOI: 10.1111/j.1574-6941.2011.01052.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Bacteriophages are ubiquitous in various environments. Our previous study revealed the diversity of the cyanophage community in paddy floodwater. In this study, the phylogeny and genetic diversity of cyanophage communities in paddy field soils were reported. The viral capsid assembly protein gene (g20) of cyanophage was amplified with the primers CPS1 and CPS8 from soil DNA extracted during two different sampling times at three sampling sites in Japan. The sequencing results indicated that about 93% of the clones were g20 genes. In total, 70 clones of g20 genes were obtained in this study, of which 69 clones were of cyanophage origin. As evaluated by g20 sequence assemblages in paddy field soils, the unifrac analyses results indicated that cyanophage communities changed among the sampling sites and times and differed from those communities detected in paddy floodwater. The phylogenetic analysis showed that the g20 sequences in paddy field soils were very diverse and distributed into Clusters α, β and ɛ, as well as four newly formed clusters. Within Clusters β and ɛ, four unique subclusters were formed from the g20 clones that were only observed in this study. These findings suggested that the cyanophage communities in paddy field soils are different from those found in freshwater, marine water and paddy floodwater.
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Affiliation(s)
- Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
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31
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Dittmar T, Zänker KS. Horizontal gene transfers with or without cell fusions in all categories of the living matter. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 714:5-89. [PMID: 21506007 PMCID: PMC7120942 DOI: 10.1007/978-94-007-0782-5_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.
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Affiliation(s)
- Thomas Dittmar
- Inst. Immunologie, Universität Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
| | - Kurt S. Zänker
- Institute of Immunologie, University of Witten/Herdecke, Stockumer Str. 10, Witten, 58448 Germany
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Seal BS, Fouts DE, Simmons M, Garrish JK, Kuntz RL, Woolsey R, Schegg KM, Kropinski AM, Ackermann HW, Siragusa GR. Clostridium perfringens bacteriophages ΦCP39O and ΦCP26F: genomic organization and proteomic analysis of the virions. Arch Virol 2011; 156:25-35. [PMID: 20963614 PMCID: PMC4127328 DOI: 10.1007/s00705-010-0812-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 08/27/2010] [Indexed: 10/18/2022]
Abstract
Poultry intestinal material, sewage and poultry processing drainage water were screened for virulent Clostridium perfringens bacteriophages. Viruses isolated from broiler chicken offal washes (O) and poultry feces (F), designated ΦCP39O and ΦCP26F, respectively, produced clear plaques on host strains. Both bacteriophages had isometric heads of 57 nm in diameter with 100-nm non-contractile tails characteristic of members of the family Siphoviridae in the order Caudovirales. The double-strand DNA genome of bacteriophage ΦCP39O was 38,753 base pairs (bp), while the ΦCP26F genome was 39,188 bp, with an average GC content of 30.3%. Both viral genomes contained 62 potential open reading frames (ORFs) predicted to be encoded on one strand. Among the ORFs, 29 predicted proteins had no known similarity while others encoded putative bacteriophage capsid components such as a pre-neck/appendage, tail, tape measure and portal proteins. Other genes encoded a predicted DNA primase, single-strand DNA-binding protein, terminase, thymidylate synthase and a transcription factor. Potential lytic enzymes such as a fibronectin-binding autolysin, an amidase/hydrolase and a holin were encoded in the viral genomes. Several ORFs encoded proteins that gave BLASTP matches with proteins from Clostridium spp. and other Gram-positive bacterial and bacteriophage genomes as well as unknown putative Collinsella aerofaciens proteins. Proteomics analysis of the purified viruses resulted in the identification of the putative pre-neck/appendage protein and a minor structural protein encoded by large open reading frames. Variants of the portal protein were identified, and several mycobacteriophage gp6-like protein variants were detected in large amounts relative to other virion proteins. The predicted amino acid sequences of the pre-neck/appendage proteins had major differences in the central portion of the protein between the two phage gene products. Based on phylogenetic analysis of the large terminase protein, these phages are predicted to be pac-type, using a head-full DNA packaging strategy.
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Affiliation(s)
- Bruce S Seal
- Richard B. Russell Agricultural Research Center, USDA, Athens, GA 30605, USA.
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Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1. ISME JOURNAL 2010; 5:107-21. [PMID: 20613791 DOI: 10.1038/ismej.2010.94] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Marine phages have an astounding global abundance and ecological impact. However, little knowledge is derived from phage genomes, as most of the open reading frames in their small genomes are unknown, novel proteins. To infer potential functional and ecological relevance of sequenced marine Pseudoalteromonas phage H105/1, two strategies were used. First, similarity searches were extended to include six viral and bacterial metagenomes paired with their respective environmental contextual data. This approach revealed 'ecogenomic' patterns of Pseudoalteromonas phage H105/1, such as its estuarine origin. Second, intrinsic genome signatures (phylogenetic, codon adaptation and tetranucleotide (tetra) frequencies) were evaluated on a resolved intra-genomic level to shed light on the evolution of phage functional modules. On the basis of differential codon adaptation of Phage H105/1 proteins to the sequenced Pseudoalteromonas spp., regions of the phage genome with the most 'host'-adapted proteins also have the strongest bacterial tetra signature, whereas the least 'host'-adapted proteins have the strongest phage tetra signature. Such a pattern may reflect the evolutionary history of the respective phage proteins and functional modules. Finally, analysis of the structural proteome identified seven proteins that make up the mature virion, four of which were previously unknown. This integrated approach combines both novel and classical strategies and serves as a model to elucidate ecological inferences and evolutionary relationships from phage genomes that typically abound with unknown gene content.
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Zegans ME, Wagner JC, Cady KC, Murphy DM, Hammond JH, O'Toole GA. Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa. J Bacteriol 2009; 191:210-9. [PMID: 18952788 PMCID: PMC2612449 DOI: 10.1128/jb.00797-08] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Accepted: 10/17/2008] [Indexed: 01/24/2023] Open
Abstract
Bacteriophage infection has profound effects on bacterial biology. Clustered regular interspaced short palindromic repeats (CRISPRs) and cas (CRISPR-associated) genes are found in most archaea and many bacteria and have been reported to play a role in resistance to bacteriophage infection. We observed that lysogenic infection of Pseudomonas aeruginosa PA14 with bacteriophage DMS3 inhibits biofilm formation and swarming motility, both important bacterial group behaviors. This inhibition requires the CRISPR region in the host. Mutation or deletion of five of the six cas genes and one of the two CRISPRs in this region restored biofilm formation and swarming to DMS3 lysogenized strains. Our observations suggest a role for CRISPR regions in modifying the effects of lysogeny on P. aeruginosa.
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Affiliation(s)
- Michael E Zegans
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, NH 03755, USA
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Sullivan MB, Coleman ML, Quinlivan V, Rosenkrantz JE, Defrancesco AS, Tan G, Fu R, Lee JA, Waterbury JB, Bielawski JP, Chisholm SW. Portal protein diversity and phage ecology. Environ Microbiol 2008; 10:2810-23. [PMID: 18673386 PMCID: PMC2657995 DOI: 10.1111/j.1462-2920.2008.01702.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Oceanic phages are critical components of the global ecosystem, where they play a role in microbial mortality and evolution. Our understanding of phage diversity is greatly limited by the lack of useful genetic diversity measures. Previous studies, focusing on myophages that infect the marine cyanobacterium Synechococcus, have used the coliphage T4 portal-protein-encoding homologue, gene 20 (g20), as a diversity marker. These studies revealed 10 sequence clusters, 9 oceanic and 1 freshwater, where only 3 contained cultured representatives. We sequenced g20 from 38 marine myophages isolated using a diversity of Synechococcus and Prochlorococcus hosts to see if any would fall into the clusters that lacked cultured representatives. On the contrary, all fell into the three clusters that already contained sequences from cultured phages. Further, there was no obvious relationship between host of isolation, or host range, and g20 sequence similarity. We next expanded our analyses to all available g20 sequences (769 sequences), which include PCR amplicons from wild uncultured phages, non-PCR amplified sequences identified in the Global Ocean Survey (GOS) metagenomic database, as well as sequences from cultured phages, to evaluate the relationship between g20 sequence clusters and habitat features from which the phage sequences were isolated. Even in this meta-data set, very few sequences fell into the sequence clusters without cultured representatives, suggesting that the latter are very rare, or sequencing artefacts. In contrast, sequences most similar to the culture-containing clusters, the freshwater cluster and two novel clusters, were more highly represented, with one particular culture-containing cluster representing the dominant g20 genotype in the unamplified GOS sequence data. Finally, while some g20 sequences were non-randomly distributed with respect to habitat, there were always numerous exceptions to general patterns, indicating that phage portal proteins are not good predictors of a phage's host or the habitat in which a particular phage may thrive.
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Affiliation(s)
- Matthew B Sullivan
- Departments of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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Sandaa RA. Burden or benefit? Virus-host interactions in the marine environment. Res Microbiol 2008; 159:374-81. [PMID: 18571902 DOI: 10.1016/j.resmic.2008.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 04/23/2008] [Accepted: 04/23/2008] [Indexed: 10/22/2022]
Abstract
Viruses are the most numerous and diverse biological entities in the oceans. We are now beginning to understand the ecological role of viruses in the marine environment. As a result, we believe that viruses have important roles in both biochemical cycling and structuring of marine communities.
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Affiliation(s)
- Ruth-Anne Sandaa
- Department of Biology, University of Bergen, Post Box 7800, N-5020 Bergen, Norway.
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Abstract
In the last 30 years, the study of virus evolution has undergone a transformation. Originally concerned with disease and its emergence, virus evolution had not been well integrated into the general study of evolution. This chapter reviews the developments that have brought us to this new appreciation for the general significance of virus evolution to all life. We now know that viruses numerically dominate all habitats of life, especially the oceans. Theoretical developments in the 1970s regarding quasispecies, error rates, and error thresholds have yielded many practical insights into virus–host dynamics. The human diseases of HIV-1 and hepatitis C virus cannot be understood without this evolutionary framework. Yet recent developments with poliovirus demonstrate that viral fitness can be the result of a consortia, not one fittest type, a basic Darwinian concept in evolutionary biology. Darwinian principles do apply to viruses, such as with Fisher population genetics, but other features, such as reticulated and quasispecies-based evolution distinguish virus evolution from classical studies. The available phylogenetic tools have greatly aided our analysis of virus evolution, but these methods struggle to characterize the role of virus populations. Missing from many of these considerations has been the major role played by persisting viruses in stable virus evolution and disease emergence. In many cases, extreme stability is seen with persisting RNA viruses. Indeed, examples are known in which it is the persistently infected host that has better survival. We have also recently come to appreciate the vast diversity of phage (DNA viruses) of prokaryotes as a system that evolves by genetic exchanges across vast populations (Chapter 10). This has been proposed to be the “big bang” of biological evolution. In the large DNA viruses of aquatic microbes we see surprisingly large, complex and diverse viruses. With both prokaryotic and eukaryotic DNA viruses, recombination is the main engine of virus evolution, and virus host co-evolution is common, although not uniform. Viral emergence appears to be an unending phenomenon and we can currently witness a selective sweep by retroviruses that infect and become endogenized in koala bears.
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Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria. BMC Genomics 2007; 8:236. [PMID: 17634101 PMCID: PMC1950889 DOI: 10.1186/1471-2164-8-236] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 07/16/2007] [Indexed: 02/08/2023] Open
Abstract
Background The origin and evolution of viruses is currently a heavily discussed issue. One element in this discussion is the innate viral "self" concept, which suggests that viral structures and functions can be divided into two categories. The first category consists of genetic determinants that are inherited from a viral ancestor and encode the viral "self". The second group consists of another set of structures and functions, the "nonself", which is interchangeable between different viruses and can be obtained via lateral gene transfer. Comparing the structures and sequences of the "self" elements, we have proposed that viruses can be grouped into lineages regardless of which domain of life (bacteria, archaea, eukarya) they infect. It has also been suggested that viruses are ancient and possibly predate modern cells. Results Here we identified thirteen putative prophages (viral genomes integrated into bacterial chromosome) closely related to the virulent icosahedral tailless lipid-containing bacteriophage PM2. Using the comparative genomics approach, we present evidence to support the viral "self" hypothesis and divide genes of the bacteriophage PM2 and related prophages into "self" and "nonself" categories. Conclusion We show here that the previously proposed most conserved viral "self" determinants, the major coat protein and the packaging ATPase, were the only proteins that could be recognized in all detected corticoviral elements. We also argue here that the genes needed for viral genome replication, as well as for host cell lysis, belong to the "nonself" category of genes. Furthermore, we suggest that abundance of PM2-like viruses in the aquatic environment as well as their importance in the ecology of aquatic microorganisms might have been underestimated.
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Abstract
In contrast to the phages of heterotrophic hosts, light can play a key role in all aspects of the life cycle of phages infecting ecologically important marine unicellular cyanobacteria of the genera Synechococcus and Prochlorococcus. Phage adsorption, replication, modulation of the host cell metabolism, and survival in the environment following lysis, all exhibit light-dependent components. The analysis of cyanophage genomes has revealed the acquisition of key photosynthetic genes during the course of evolution, such as those encoding central components of the light harvesting apparatus. These discoveries are beginning to reveal novel features of the interactions between parasite and host that shape the biology of both.
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Affiliation(s)
- Martha R J Clokie
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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Hambly E, Suttle CA. The viriosphere, diversity, and genetic exchange within phage communities. Curr Opin Microbiol 2005; 8:444-50. [PMID: 15979387 DOI: 10.1016/j.mib.2005.06.005] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Accepted: 06/13/2005] [Indexed: 01/25/2023]
Abstract
Natural phage communities are reservoirs of the greatest uncharacterized genetic diversity on Earth. Yet, identical phage sequences can be found in extremely different environments, which implies that there is wide circulation of viral genes among distantly related host populations. Further evidence of genetic exchange among phage and host communities is the presence in phage of genes coding for proteins that are essential for photosynthesis. These observations support the idea that a primary role of host populations in phage ecology and evolution is to serve as vectors for genetic exchange.
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Affiliation(s)
- Emma Hambly
- Department of Earth and Ocean Sciences, University of British Columbia, 1461 Biological Sciences, 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada
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Abstract
The global ocean is an integrated living system where energy and matter transformations are governed by interdependent physical, chemical and biotic processes. Although the fundamentals of ocean physics and chemistry are well established, comprehensive approaches to describing and interpreting oceanic microbial diversity and processes are only now emerging. In particular, the application of genomics to problems in microbial oceanography is significantly expanding our understanding of marine microbial evolution, metabolism and ecology. Integration of these new genome-enabled insights into the broader framework of ocean science represents one of the great contemporary challenges for microbial oceanographers.
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Affiliation(s)
- Edward F DeLong
- Department of Civil and Environmental Engineering & Division of Biological Engineering, 48-427 Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Paul JH, Sullivan MB. Marine phage genomics: what have we learned? Curr Opin Biotechnol 2005; 16:299-307. [PMID: 15961031 DOI: 10.1016/j.copbio.2005.03.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Revised: 02/20/2005] [Accepted: 03/21/2005] [Indexed: 10/25/2022]
Abstract
Marine phages are the most abundant and diverse form of life on the planet, and their genomes have been described as the largest untapped reservoir of genomic information. To date, however, the complete genome sequences of only 17 marine phage are known. Nevertheless, these genomes have revealed some interesting features, including the presence of photosynthetic genes in cyanophage and common patterns of genomic organization. Intriguing findings are also being made from studies of the uncultivated marine viral community genome ('metavirome'). The greatest challenge in interpreting the biology of these phages, and for making comparisons with their terrestrial counterparts, is the high proportion of unidentifiable open reading frames (approximately 60%). Future studies are likely to focus on sequencing more marine phage genomes from disparate hosts and diverse environments and on further basic studies of the biology of existing marine phages.
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Affiliation(s)
- John H Paul
- College of Marine Science, University of South Florida, St Petersburg, Florida 33701, USA.
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Abstract
The third age of phage has begun with the recognition that phages may be key to the great planetary biogeochemical cycles and represent the greatest potential genetic resource in the biosphere
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Affiliation(s)
- Nicholas H Mann
- Department of Biological Sciences, University of Warwick, Coventry, United Kingdom.
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Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol 2005; 3:e144. [PMID: 15828858 PMCID: PMC1079782 DOI: 10.1371/journal.pbio.0030144] [Citation(s) in RCA: 436] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2004] [Accepted: 02/23/2005] [Indexed: 11/19/2022] Open
Abstract
The oceanic cyanobacteria Prochlorococcus are globally important, ecologically diverse primary producers. It is thought that their viruses (phages) mediate population sizes and affect the evolutionary trajectories of their hosts. Here we present an analysis of genomes from three Prochlorococcus phages: a podovirus and two myoviruses. The morphology, overall genome features, and gene content of these phages suggest that they are quite similar to T7-like (P-SSP7) and T4-like (P-SSM2 and P-SSM4) phages. Using the existing phage taxonomic framework as a guideline, we examined genome sequences to establish “core” genes for each phage group. We found the podovirus contained 15 of 26 core T7-like genes and the two myoviruses contained 43 and 42 of 75 core T4-like genes. In addition to these core genes, each genome contains a significant number of “cyanobacterial” genes, i.e., genes with significant best BLAST hits to genes found in cyanobacteria. Some of these, we speculate, represent “signature” cyanophage genes. For example, all three phage genomes contain photosynthetic genes (psbA, hliP) that are thought to help maintain host photosynthetic activity during infection, as well as an aldolase family gene (talC) that could facilitate alternative routes of carbon metabolism during infection. The podovirus genome also contains an integrase gene (int) and other features that suggest it is capable of integrating into its host. If indeed it is, this would be unprecedented among cultured T7-like phages or marine cyanophages and would have significant evolutionary and ecological implications for phage and host. Further, both myoviruses contain phosphate-inducible genes (phoH and pstS) that are likely to be important for phage and host responses to phosphate stress, a commonly limiting nutrient in marine systems. Thus, these marine cyanophages appear to be variations of two well-known phages—T7 and T4—but contain genes that, if functional, reflect adaptations for infection of photosynthetic hosts in low-nutrient oceanic environments. An analysis of the genome sequences of three phages capable of infecting marine unicellular cyanobacteria Prochlorococcus reveals they are genetically complex with intriguing adaptations related to their oceanic environment
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Affiliation(s)
- Matthew B Sullivan
- 1Joint Program in Biological Oceanography, Woods Hole Oceanographic Institution and Massachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
| | - Maureen L Coleman
- 2Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
| | - Peter Weigele
- 3Department of Biology, Massachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
| | - Forest Rohwer
- 4Department of Biology, San Diego State UniversitySan Diego, CaliforniaUnited States of America
| | - Sallie W Chisholm
- 2Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
- 3Department of Biology, Massachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
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Van Dessel W, Van Mellaert L, Liesegang H, Raasch C, De Keersmaeker S, Geukens N, Lammertyn E, Streit W, Anné J. Complete genomic nucleotide sequence and analysis of the temperate bacteriophage VWB. Virology 2005; 331:325-37. [PMID: 15629775 DOI: 10.1016/j.virol.2004.10.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Revised: 09/21/2004] [Accepted: 10/16/2004] [Indexed: 11/24/2022]
Abstract
The entire double-stranded DNA genome of the Streptomyces venezuelae bacteriophage VWB was sequenced and analyzed. Its size is 49,220 bp with an overall molar G + C content of 71.2 mol%. Sixty-one potential open reading frames were identified and annotated using several complementary bioinformatics tools. Clusters of functionally related putative genes were defined, supporting a refined version of the modular theory of phage evolution.
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Affiliation(s)
- W Van Dessel
- Laboratorium voor Bacteriologie, Katholieke Universiteit Leuven, Rega Instituut, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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Chibani-Chennoufi S, Dillmann ML, Marvin-Guy L, Rami-Shojaei S, Brüssow H. Lactobacillus plantarum bacteriophage LP65: a new member of the SPO1-like genus of the family Myoviridae. J Bacteriol 2004; 186:7069-83. [PMID: 15489418 PMCID: PMC523202 DOI: 10.1128/jb.186.21.7069-7083.2004] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The virulent Lactobacillus plantarum myophage LP65 was isolated from industrial meat fermentation. Tail contraction led to reorganization of the tail sheath and the baseplate; a tail tube was extruded. In ultrathin section the phage adsorbed via its baseplate to the exterior of the cell, while the tail tube tunneled through the thick bacterial cell wall. Convoluted membrane structures were induced in the infected cell. Progeny phage was detected 100 min postinfection, and lysis occurred after extensive digestion of the cell wall. Sequence analysis revealed a genome of 131,573 bp of nonredundant DNA. Four major genome regions and a large tRNA gene cluster were observed. One module corresponded to DNA replication genes. Helicase/primase and two replication/recombination enzymes represented the only links to T4-like Myoviridae from gram-negative bacteria. Another module corresponded to the structural genes. Sequence relatedness identified links with Listeria phage A511, Staphylococcus phage K, and Bacillus phage SPO1. LP65 structural proteins were identified by two-dimensional proteome analysis and mass spectrometry. The putative tail sheath protein showed a shear-induced change in electrophoretic migration behavior. The genome organization of the structural module in LP65 resembled that of Siphoviridae from the lambda supergroup.
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Serwer P, Hayes SJ, Zaman S, Lieman K, Rolando M, Hardies SC. Improved isolation of undersampled bacteriophages: finding of distant terminase genes. Virology 2004; 329:412-24. [PMID: 15518819 DOI: 10.1016/j.virol.2004.08.021] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Revised: 08/16/2004] [Accepted: 08/20/2004] [Indexed: 11/22/2022]
Abstract
Isolation and characterization of new environmental bacteriophages are performed for (1) analyzing microbial evolution and ecology and (2) delivering biological therapy. The sampling of environmental bacteriophages appears, however, to be limited by the procedure (usually liquid enrichment culture) used to propagate them. An alternative, less competitive procedure is developed here for the purpose of isolating new bacteriophages. This procedure involves extraction directly into and then propagation in a dilute agarose gel. Adaptations of this procedure are used to avoid repeated isolation of the same bacteriophage. Some newly isolated bacteriophages grow so poorly that they appear inaccessible to liquid enrichment culture. Four comparatively high titer bacteriophages were isolated and characterized by a genomic sequence survey. Some had genomes with extremely distant relationships to those of other bacteriophages, based on a tree built from the large terminase genes. These methods find novel genomes by rapidly isolating and screening diverse bacteriophages.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA.
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Sano E, Carlson S, Wegley L, Rohwer F. Movement of viruses between biomes. Appl Environ Microbiol 2004; 70:5842-6. [PMID: 15466522 PMCID: PMC522096 DOI: 10.1128/aem.70.10.5842-5846.2004] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Accepted: 06/17/2004] [Indexed: 11/20/2022] Open
Abstract
Viruses are abundant in all known ecosystems. In the present study, we tested the possibility that viruses from one biome can successfully propagate in another. Viral concentrates were prepared from different near-shore marine sites, lake water, marine sediments, and soil. The concentrates were added to microcosms containing dissolved organic matter as a food source (after filtration to allow 100-kDa particles to pass through) and a 3% (vol/vol) microbial inoculum from a marine water sample (after filtration through a 0.45-microm-pore-size filter). Virus-like particle abundances were then monitored using direct counting. Viral populations from lake water, marine sediments, and soil were able to replicate when they were incubated with the marine microbes, showing that viruses can move between different ecosystems and propagate. These results imply that viruses can laterally transfer DNA between microbes in different biomes.
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Affiliation(s)
- Emiko Sano
- Center for Microbial Sciences, San Diego State University, 5500 Campanile Dr., San Diego, CA 92182, USA
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Espeland EM, Lipp EK, Huq A, Colwell RR. Polylysogeny and prophage induction by secondary infection in Vibrio cholerae. Environ Microbiol 2004; 6:760-3. [PMID: 15186355 DOI: 10.1111/j.1462-2920.2004.00603.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Strains of Vibrio cholerae O1, biotypes El Tor and classical, were infected with a known temperate phage (PhiP15) and monitored over a 15-day period for prophage induction. Over the course of the experiment two morphologically and three genomically distinct virus-like particles were observed from the phage-infected El Tor strain by transmission electron microscopy and field inversion gel electrophoresis, respectively, whereas only one phage, PhiP15, was observed from the infected classical strain. In the uninfected El Tor culture one prophage was spontaneously induced after 6 days. No induction in either strain was observed after treatment with mitomycin C. Data indicate that El Tor biotypes of V. cholerae may be polylysogenic and that secondary infection can promote multiple prophage induction. These traits may be important in the transfer of genetic material among V. cholerae by providing an environmentally relevant route for multiple prophage propagation and transmission.
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Affiliation(s)
- Eric M Espeland
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, 701 E Pratt St, Baltimore MD 21202, USA
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