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Sprotte S, Brinks E, Neve H, Franz CM. Complete genome sequence of the novel virulent phage PMBT24 infecting Enterocloster bolteae from the human gut. Heliyon 2024; 10:e28813. [PMID: 38655313 PMCID: PMC11035940 DOI: 10.1016/j.heliyon.2024.e28813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
PMBT24, the first reported virulent bacteriophage infecting the anaerobic human gut bacterium Enterocloster bolteae strain MBT-21, was isolated from a municipal sewage sample and its genome was sequenced and analysed. Transmission electron microscopy revealed a phage with an icosahedral head and a long, non-contractile tail. The circularly permutated, 99,962-bp dsDNA genome of the pac-type phage has a mol% G + C content of 32.1 and comprises 173 putative ORFs. Using amino acid sequence-based phylogeny, phage PMBT24 showed similarity to other, hitherto non-published phage genomes in the databases. Our data suggested phage PMBT24 to present the type phage of a novel genus (proposed name Kielvirus) and novel family of phages (proposed name Kielviridae).
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Affiliation(s)
- Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
| | | | - Charles M.A.P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
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2
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Rodea M GE, González-Villalobos E, Espinoza-Mellado MDR, Hernández-Chiñas U, Eslava-Campos CA, Balcázar JL, Molina-López J. Genomic analysis of a novel phage vB_SenS_ST1UNAM with lytic activity against Salmonella enterica serotypes. Diagn Microbiol Infect Dis 2024; 109:116305. [PMID: 38643675 DOI: 10.1016/j.diagmicrobio.2024.116305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/09/2024] [Accepted: 04/12/2024] [Indexed: 04/23/2024]
Abstract
In this study, we present the complete annotated genome of a novel Salmonella phage, vB_SenS_ST1UNAM. This phage exhibits lytic activity against several Salmonella enterica serotypes, such as S. Typhi, S. Enteritidis, and S. Typhimurium strains, which are major causes of foodborne illness worldwide. Its genome consists of a linear, double-stranded DNA of 47,877 bp with an average G+C content of 46.6%. A total of 85 coding regions (CDS) were predicted, of which only 43 CDS were functionally assigned. Neither genes involved in the regulation of lysogeny, nor antibiotic resistance genes were identified. This phage harbors a lytic cassette that encodes a type II-holin and a Rz/Rz1-like spanin complex, along with a restriction-modification evasion system and a depolymerase that degrades Salmonella exopolysaccharide. Moreover, the comparative analysis with closely related phage genomes revealed that vB_SenS_ST1UNAM represents a novel genus, for which the genus "Gomezvirus" within the subfamily "ST1UNAM-like" is proposed.
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Affiliation(s)
- Gerardo E Rodea M
- Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación. Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720 Mexico City, Mexico; Unidad de Investigación en Enfermedades Infecciosas Área de Genética Bacteriana, Hospital Infantil de México Federico Gómez, Ciudad de México, México
| | - Edgar González-Villalobos
- Laboratorio de Epidemiología Molecular División de Investigación, departamento de Salud Pública, Facultad de Medicina UNAM, C.P. 06720 Mexico City, Mexico
| | - María Del Rosario Espinoza-Mellado
- Central de Instrumentación de Microscopía, Depto. Investigación, Instituto Politécnico Nacional-Escuela Nacional de Ciencias Biológicas (IPN-ENCB), Prolongación de Carpio y Plan de Ayala, Mexico City 11340, México
| | - Ulises Hernández-Chiñas
- Unidad Periférica de Investigación Básica y Clínica en Enfermedades Infecciosas; Departamento de Salud Pública/División de Investigación, Facultad de Medicina, UNAM, C.P. 04510. Mexico City, Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación. Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720 Mexico City, Mexico
| | - Carlos Alberto Eslava-Campos
- Unidad Periférica de Investigación Básica y Clínica en Enfermedades Infecciosas; Departamento de Salud Pública/División de Investigación, Facultad de Medicina, UNAM, C.P. 04510. Mexico City, Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación. Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720 Mexico City, Mexico
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA). 17003, Girona, Spain; University of Girona. 17004 Girona, Spain
| | - José Molina-López
- Unidad Periférica de Investigación Básica y Clínica en Enfermedades Infecciosas; Departamento de Salud Pública/División de Investigación, Facultad de Medicina, UNAM, C.P. 04510. Mexico City, Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación. Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720 Mexico City, Mexico.
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3
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Nazir A, Li L, Li F, Tong Y, Liu Y, Chen Y. Characterization, taxonomic classification, and genomic analysis of two newly isolated bacteriophages with potential to infect Escherichia coli. Microbiol Spectr 2024:e0223023. [PMID: 38376266 DOI: 10.1128/spectrum.02230-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Escherichia coli is a pathogenic bacterium that is widely distributed and can lead to serious illnesses in both humans and animals. As there is rising incidence of multidrug resistance among these bacteria, it has become imperative to discover alternative therapies beyond antibiotics to effectively treat such infections. Bacteriophage (phage) therapy has the potential to treat infections caused by E. coli, as phages contain enzymes that can cause lysis or destruction of bacterial cells. Simultaneously, the easy accessibility and cost-effectiveness of next-generation sequencing technologies have led to the accumulation of a vast amount of phage sequence data. Here, phages IME177 and IME267 were isolated from sewage water of a hospital in China. Modern phylogenetic approaches and key findings from the genomic analysis revealed that phages IME177 and IME267 are classified as members of the Kayfunavirus genus, Autographiviridae family, and a newly proposed Suseptimavirus genus under subfamily Gordonclarkvirinae, respectively. Further, the Kuravirus genus reshaped into three different genera: Kuravirus, Nieuwekanaalvirus, and Suspeptimavirus, which are classified together under a higher taxonomic rank (subfamily) named Gordonclarkvirinae. No genes related to virulence were detected in the genomes of the phages IME177 and IME267. Both phages exhibited a high degree of resilience to a wide range of conditions, including pH, temperature, exposure to chloroform, and UV radiation. Phages IME177 and IME267 are promising biological agents that can infect E. coli, making them suitable candidates for use in phage therapies.IMPORTANCEBiological and taxonomic characterization of phages is essential for facilitating the development of effective strategies for phage therapy and disease control. Escherichia coli phages are incredibly diverse, and their isolation and classification help us understand the scope and nature of this diversity. By identifying new phages and grouping them into families, we can better understand the genetic and structural variations between phages and how they affect their infectivity and interactions with bacteria. Overall, the isolation and classification of E. coli phages have broad implications for both basic and applied research, clinical practice, and public health.
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Affiliation(s)
- Amina Nazir
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lulu Li
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Fei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yuqing Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Yibao Chen
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
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Putzeys L, Wicke L, Brandão A, Boon M, Pires DP, Azeredo J, Vogel J, Lavigne R, Gerovac M. Exploring the transcriptional landscape of phage-host interactions using novel high-throughput approaches. Curr Opin Microbiol 2024; 77:102419. [PMID: 38271748 PMCID: PMC10884466 DOI: 10.1016/j.mib.2023.102419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
In the last decade, powerful high-throughput sequencing approaches have emerged to analyse microbial transcriptomes at a global scale. However, to date, applications of these approaches to microbial viruses such as phages remain scarce. Tailoring these techniques to virus-infected bacteria promises to obtain a detailed picture of the underexplored RNA biology and molecular processes during infection. In addition, transcriptome study of stress and perturbations induced by phages in their infected bacterial hosts is likely to reveal new fundamental mechanisms of bacterial metabolism and gene regulation. Here, we provide references and blueprints to implement emerging transcriptomic approaches towards addressing transcriptome architecture, RNA-RNA and RNA-protein interactions, RNA modifications, structures and heterogeneity of transcription profiles in infected cells that will provide guides for future directions in phage-centric therapeutic applications and microbial synthetic biology.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium; Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Ana Brandão
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Diana P Pires
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
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5
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Zheng L, Shen J, Chen R, Hu Y, Zhao W, Leung ELH, Dai L. Genome engineering of the human gut microbiome. J Genet Genomics 2024:S1673-8527(24)00003-1. [PMID: 38218395 DOI: 10.1016/j.jgg.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
The human gut microbiome, a complex ecosystem, significantly influences host health, impacting crucial aspects such as metabolism and immunity. To deepen our comprehension and control of the molecular mechanisms orchestrating the intricate interplay between gut commensal bacteria and human health, the exploration of genome engineering for gut microbes is a promising frontier. Nevertheless, the complexities and diversities inherent in the gut microbiome pose substantial challenges to the development of effective genome engineering tools for human gut microbes. In this comprehensive review, we provide an overview of the current progress and challenges in genome engineering of human gut commensal bacteria, whether executed in vitro or in situ. A specific focus is directed towards the advancements and prospects in cargo DNA delivery and high-throughput techniques. Additionally, we elucidate the immense potential of genome engineering methods to deepen our understanding of the human gut microbiome and engineer the microorganisms to enhance human health.
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Affiliation(s)
- Linggang Zheng
- Dr Neher's Biophysics Laboratory for Innovative Drug Discovery/State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Juntao Shen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ruiyue Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yucan Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Elaine Lai-Han Leung
- Cancer Center, Faculty of Health Science, University of Macau, Macau, China; MOE Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China.
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Montso PK, Kropinski AM, Mokoena F, Pierneef RE, Mlambo V, Ateba CN. Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces. Sci Rep 2023; 13:21426. [PMID: 38052835 PMCID: PMC10698182 DOI: 10.1038/s41598-023-48788-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
The increasing prevalence of antimicrobial-resistant (AMR) pathogens has become a major global health concern. To address this challenge, innovative strategies such as bacteriophage therapy must be optimised. Genomic characterisation is a crucial step in identifying suitable phage candidates for combating AMR pathogens. The aim of this study was to characterise seven phages that infect the Escherichia coli O177 strain using a whole genome sequencing. The analysis of genome sequences revealed that these phages had linear dsDNA, with genome sizes spanning from 136, 483 to 166,791 bp and GC content varying from 35.39 to 43.63%. Taxonomically, the phages were classified under three different subfamilies (Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae) and three genera (Phapecoctavirus, Tequatrovirus, and Vequintavirus) within the class Caudoviricetes. In silico PhageAI analysis predicted that all the phages were virulent, with confidence levels between 96.07 and 97.26%. The phage genomes contained between 66 and 82 ORFs, which encode hypothetical and putative functional proteins. In addition, the phage genomes contained core genes associated with molecular processes such as DNA replication, transcription modulation, nucleotide metabolism, phage structure (capsid and tail), and lysis. None of the genomes carried genes associated with undesirable traits such as integrase, antimicrobial resistance, virulence, and toxins. The study revealed high genome and proteome homology among E. coli O177 phages and other known Escherichia phages. The results suggest that the seven phages are new members of the genera Phapecoctavirus, Tequatrovirus, and Vequintavirus under the subfamilies Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae, respectively.
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Affiliation(s)
- Peter Kotsoana Montso
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
| | - Andrew M Kropinski
- Department Food Science, and Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Fortunate Mokoena
- Department of Biochemistry, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Rian Ewald Pierneef
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0001, South Africa
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, 0001, South Africa
- SARChI Chair: Marine Microbiomics, Microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
| | - Victor Mlambo
- Faculty of Agriculture and Natural Sciences, School of Agricultural Sciences, University of Mpumalanga, Mbombela, 1200, South Africa
| | - Collins Njie Ateba
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
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Lopez MES, Gontijo MTP, Cardoso RR, Batalha LS, Eller MR, Bazzolli DMS, Vidigal PMP, Mendonça RCS. Complete genome analysis of Tequatrovirus ufvareg1, a Tequatrovirus species inhibiting Escherichia coli O157:H7. Front Cell Infect Microbiol 2023; 13:1178248. [PMID: 37274318 PMCID: PMC10236363 DOI: 10.3389/fcimb.2023.1178248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/27/2023] [Indexed: 06/06/2023] Open
Abstract
Introduction Bacteriophages infecting human pathogens have been considered potential biocontrol agents, and studying their genetic content is essential to their safe use in the food industry. Tequatrovirus ufvareg1 is a bacteriophage named UFV-AREG1, isolated from cowshed wastewater and previously tested for its ability to inhibit Escherichia coli O157:H7. Methods T. ufvareg1 was previously isolated using E. coli O157:H7 (ATCC 43895) as a bacterial host. The same strain was used for bacteriophage propagation and the one-step growth curve. The genome of the T. ufvareg1 was sequenced using 305 Illumina HiSeq, and the genome comparison was calculated by VIRIDIC and VIPTree. Results Here, we characterize its genome and compare it to other Tequatrovirus. T. ufvareg1 virions have an icosahedral head (114 x 86 nm) and a contracted tail (117 x 23 nm), with a latent period of 25 min, and an average burst size was 18 phage particles per infected E. coli cell. The genome of the bacteriophage T. ufvareg1 contains 268 coding DNA sequences (CDS) and ten tRNA genes distributed in both negative and positive strains. T. ufvareg1 genome also contains 40 promoters on its regulatory regions and two rho-independent terminators. T. ufvareg1 shares an average intergenomic similarity (VIRIDC) of 88.77% and an average genomic similarity score (VipTree) of 88.91% with eight four reference genomes for Tequatrovirus available in the NCBI RefSeq database. The pan-genomic analysis confirmed the high conservation of Tequatrovirus genomes. Among all CDS annotated in the T. ufvareg1 genome, there are 123 core genes, 38 softcore genes, 94 shell genes, and 13 cloud genes. None of 268 CDS was classified as being exclusive of T. ufvareg1. Conclusion The results in this paper, combined with other previously published findings, indicate that T. ufvareg1 bacteriophage is a potential candidate for food protection against E. coli O157:H7 in foods.
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Affiliation(s)
- Maryoris Elisa Soto Lopez
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Departamento de Ingeniería de Alimentos, Universidad de Córdoba, Montería, Colombia
| | - Marco Tulio Pardini Gontijo
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Duke University, Durham, NC, United States
| | - Rodrigo Rezende Cardoso
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Laís Silva Batalha
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Monique Renon Eller
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Peters DL, Davis CM, Harris G, Zhou H, Rather PN, Hrapovic S, Lam E, Dennis JJ, Chen W. Characterization of Virulent T4-Like Acinetobacter baumannii Bacteriophages DLP1 and DLP2. Viruses 2023; 15:v15030739. [PMID: 36992448 PMCID: PMC10051250 DOI: 10.3390/v15030739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
The world is currently facing a global health crisis due to the rapid increase in antimicrobial-resistant bacterial infections. One of the most concerning pathogens is Acinetobacter baumannii, which is listed as a Priority 1 pathogen by the World Health Organization. This Gram-negative bacterium has many intrinsic antibiotic resistance mechanisms and the ability to quickly acquire new resistance determinants from its environment. A limited number of effective antibiotics against this pathogen complicates the treatment of A. baumannii infections. A potential treatment option that is rapidly gaining interest is “phage therapy”, or the clinical application of bacteriophages to selectively kill bacteria. The myoviruses DLP1 and DLP2 (vB_AbaM-DLP_1 and vB_AbaM-DLP_2, respectively) were isolated from sewage samples using a capsule minus variant of A. baumannii strain AB5075. Host range analysis of these phages against 107 A. baumannii strains shows a limited host range, infecting 15 and 21 for phages DLP1 and DLP2, respectively. Phage DLP1 has a large burst size of 239 PFU/cell, a latency period of 20 min, and virulence index of 0.93. In contrast, DLP2 has a smaller burst size of 24 PFU/cell, a latency period of 20 min, and virulence index of 0.86. Both phages show potential for use as therapeutics to combat A. baumannii infections.
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Affiliation(s)
- Danielle L. Peters
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
- Correspondence:
| | - Carly M. Davis
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Greg Harris
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Hongyan Zhou
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
| | - Philip N. Rather
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
- Research Service, Atlanta VA Medical Center, Decatur, GA 30033, USA
| | - Sabahudin Hrapovic
- Aquatic and Crop Resource Development (ACRD) Research Center, National Research Council Canada, Montreal, QC H4P 2R2, Canada
| | - Edmond Lam
- Aquatic and Crop Resource Development (ACRD) Research Center, National Research Council Canada, Montreal, QC H4P 2R2, Canada
| | - Jonathan J. Dennis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Wangxue Chen
- Human Health Therapeutics (HHT) Research Center, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
- Department of Biology, Brock University, St. Catharines, ON L2S 3A1, Canada
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9
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Vidigal PMP, Hungaro HM. Genome sequencing of Pseudomonas fluorescens phage UFJF_PfSW6: a novel lytic Pijolavirus specie with potential for biocontrol in the dairy industry. 3 Biotech 2023; 13:67. [PMID: 36726557 PMCID: PMC9884711 DOI: 10.1007/s13205-023-03485-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 01/18/2023] [Indexed: 01/31/2023] Open
Abstract
The genomic characterization of phages with biocontrol potential against food-related bacteria is essential to future commercial applications. Here, we report the genome sequence of P. fluorescens phage UFJF_PfSW6 and a taxonomy proposal framing it as a novel phage species with great potential for biocontrol in the dairy industry. It showed a short linear double-stranded DNA genome (~ 39 kb) with a GC content of 21.2% and short DTR sequences of 215 bp. The genome of the UFJF_PfSW6 phage contains 48 genes with a unidirectional organization into three functional modules: DNA replication and metabolism, structural proteins, and DNA packing and host lysis. Thirteen promoters from phage and nine from host regulate these genes, and six Rho-independent terminators control their transcription. Twenty-seven genes of the UFJF_PfSW6 encode proteins with predicted functions. Comparative genome analysis revealed that the UFJF_PfSW6 genome shares 84% of genomic similarity with the genome sequence of the Pijolavirus PspYZU08, the only representative of the genus recognized so far. Therefore, our findings indicate that both phages are of the same genus, but UFJF_PfSW6 a is a novel Pijolavirus specie belonging to the Studiervirinae subfamily. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03485-3.
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Affiliation(s)
- Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Campus da UFV, Universidade Federal de Viçosa (UFV), Viçosa, MG 36570-900 Brazil
| | - Humberto Moreira Hungaro
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora, MG 36036-900 Brazil
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10
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Grami E, Badawy S, Kiljunen S, Saidi N, Skurnik M. Characterization and genome analysis of Escherichia phage fBC-Eco01, isolated from wastewater in Tunisia. Arch Virol 2023; 168:44. [PMID: 36609878 DOI: 10.1007/s00705-022-05680-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/01/2022] [Indexed: 01/09/2023]
Abstract
The rise of antibiotic resistance in bacterial strains has led to vigorous exploration for alternative treatments. To this end, phage therapy has been revisited, and it is gaining increasing attention, as it may represent an efficient alternative for treating multiresistant pathogenic bacteria. Phage therapy is considered safe, and phages do not infect eukaryotic cells. There have been many studies investigating phage-host bacteria interactions and the ability of phages to target specific hosts. Escherichia coli is the causative agent of a multitude of infections, ranging from urinary tract infections to sepsis, with growing antibiotic resistance. In this study, we characterized the Escherichia phage fBC-Eco01, which was isolated from a water sample collected at Oued, Tunis. Electron microscopy showed that fBC-Eco01 phage particles have siphovirus morphology, with an icosahedral head of 61 ± 3 nm in diameter and a non-contractile tail of 94 ± 2 nm in length and 12 ± 0.9 nm in width. The genome of fBC-Eco01 is a linear double-stranded DNA of 43.466 bp with a GC content of 50.4%. Comparison to databases allowed annotation of the functions to 39 of the 78 predicted gene products. A single-step growth curve revealed that fBC-Eco01 has a latent period of 30 minutes and a burst size of 175 plaque-forming units (PFU) per infected cell. Genomic analysis indicated that fBC-Eco01 is a member of the subfamily Guernseyvirinae. It is most closely related to a group of phages of the genus Kagunavirus that infect Enterobacter, Raoultella, and Escherichia strains.
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11
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Shujaat M, Jin JS, Tayara H, Chong KT. iProm-phage: A two-layer model to identify phage promoters and their types using a convolutional neural network. Front Microbiol 2022; 13:1061122. [PMID: 36406389 PMCID: PMC9672459 DOI: 10.3389/fmicb.2022.1061122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/18/2022] [Indexed: 04/26/2024] Open
Abstract
The increased interest in phages as antibacterial agents has resulted in a rise in the number of sequenced phage genomes, necessitating the development of user-friendly bioinformatics tools for genome annotation. A promoter is a DNA sequence that is used in the annotation of phage genomes. In this study we proposed a two layer model called "iProm-phage" for the prediction and classification of phage promoters. Model first layer identify query sequence as promoter or non-promoter and if the query sequence is predicted as promoter then model second layer classify it as phage or host promoter. Furthermore, rather than using non-coding regions of the genome as a negative set, we created a more challenging negative dataset using promoter sequences. The presented approach improves discrimination while decreasing the frequency of erroneous positive predictions. For feature selection, we investigated 10 distinct feature encoding approaches and utilized them with several machine-learning algorithms and a 1-D convolutional neural network model. We discovered that the one-hot encoding approach and the CNN model outperformed based on performance metrics. Based on the results of the 5-fold cross validation, the proposed predictor has a high potential. Furthermore, to make it easier for other experimental scientists to obtain the results they require, we set up a freely accessible and user-friendly web server at http://nsclbio.jbnu.ac.kr/tools/iProm-phage/.
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Affiliation(s)
- Muhammad Shujaat
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, South Korea
| | - Joe Sung Jin
- Graduate School of Integrated Energy AI, Jeonbuk National University, Jeonju, South Korea
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju, South Korea
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, South Korea
- Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju, South Korea
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12
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Hungaro HM, Vidigal PMP, do Nascimento EC, Gomes da Costa Oliveira F, Gontijo MTP, Lopez MES. Genomic Characterisation of UFJF_PfDIW6: A Novel Lytic Pseudomonas fluorescens-Phage with Potential for Biocontrol in the Dairy Industry. Viruses 2022; 14:v14030629. [PMID: 35337036 PMCID: PMC8951688 DOI: 10.3390/v14030629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/12/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
In this study, we have presented the genomic characterisation of UFJF_PfDIW6, a novel lytic Pseudomonas fluorescens-phage with potential for biocontrol in the dairy industry. This phage showed a short linear double-stranded DNA genome (~42 kb) with a GC content of 58.3% and more than 50% of the genes encoding proteins with unknown functions. Nevertheless, UFJF_PfDIW6’s genome was organised into five functional modules: DNA packaging, structural proteins, DNA metabolism, lysogenic, and host lysis. Comparative genome analysis revealed that the UFJF_PfDIW6’s genome is distinct from other viral genomes available at NCBI databases, displaying maximum coverages of 5% among all alignments. Curiously, this phage showed higher sequence coverages (38–49%) when aligned with uncharacterised prophages integrated into Pseudomonas genomes. Phages compared in this study share conserved locally collinear blocks comprising genes of the modules’ DNA packing and structural proteins but were primarily differentiated by the composition of the DNA metabolism and lysogeny modules. Strategies for taxonomy assignment showed that UFJF_PfDIW6 was clustered into an unclassified genus in the Podoviridae clade. Therefore, our findings indicate that this phage could represent a novel genus belonging to the Podoviridae family.
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Affiliation(s)
- Humberto Moreira Hungaro
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
- Correspondence: (H.M.H.); (M.E.S.L.); Tel.: +55-32-2102-3804 (H.M.H.); +57-310-469-02-04 (M.E.S.L.)
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Campus da UFV, Universidade Federal de Viçosa (UFV), Viçosa 36570-900, MG, Brazil;
| | - Edilane Cristina do Nascimento
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
| | - Felipe Gomes da Costa Oliveira
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
| | - Marco Túlio Pardini Gontijo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-872, SP, Brazil;
| | - Maryoris Elisa Soto Lopez
- Departamento de Engenharia de Alimentos, Universidade de Córdoba (UNICORDOBA), Córdoba 230002, Colombia
- Correspondence: (H.M.H.); (M.E.S.L.); Tel.: +55-32-2102-3804 (H.M.H.); +57-310-469-02-04 (M.E.S.L.)
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13
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Vera-Mansilla J, Sánchez P, Silva-Valenzuela CA, Molina-Quiroz RC. Isolation and Characterization of Novel Lytic Phages Infecting Multidrug-Resistant Escherichia coli. Microbiol Spectr 2022; 10:e0167821. [PMID: 35171030 PMCID: PMC8849078 DOI: 10.1128/spectrum.01678-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/07/2021] [Indexed: 12/26/2022] Open
Abstract
Urinary tract infections (UTIs) are the second most frequent bacterial infections worldwide, with Escherichia coli being the main causative agent. The increase of antibiotic-resistance determinants among isolates from clinical samples, including UTIs, makes the development of novel therapeutic strategies a necessity. In this context, the use of bacteriophages as a therapeutic alternative has been proposed, due to their ability to efficiently kill bacteria. In this work, we isolated and characterized three novel bacteriophages, microbes laboratory phage 1 (MLP1), MLP2, and MLP3, belonging to the Chaseviridae, Myoviridae, and Podoviridae families, respectively. These phages efficiently infect and kill laboratory reference strains and multidrug-resistant clinical E. coli isolates from patients with diagnosed UTIs. Interestingly, these phages are also able to infect intestinal pathogenic Escherichia coli strains, such as enteroaggregative E. coli and diffusely adherent E. coli. Our data show that the MLP phages recognize different regions of the lipopolysaccharide (LPS) molecule, an important virulence factor in bacteria that is also highly variable among different E. coli strains. Altogether, our results suggest that these phages may represent an interesting alternative for the treatment of antibiotic-resistant E. coli. IMPORTANCE Urinary tract infections affect approximately 150 million people annually. The current antibiotic resistance crisis demands the development of novel therapeutic alternatives. Our results show that three novel phages, MLP1, MLP2, and MLP3 are able to infect both laboratory and multidrug-resistant clinical isolates of Escherichia coli. Since these phages (i) efficiently kill antibiotic-resistant clinical isolates of uropathogenic Escherichia coli (UPEC), (ii) recognize different portions of the LPS molecule, and (iii) are able to efficiently infect intestinal pathogenic Escherichia coli hosts, we believe that these novel phages are good candidates to be used as a therapeutic alternative to treat antibiotic-resistant E. coli strains generating urinary tract and/or intestinal infections.
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14
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Ford S, Moeskjær S, Young P, Santamaría RI, Harrison E. Introducing a Novel, Broad Host Range Temperate Phage Family Infecting Rhizobium leguminosarum and Beyond. Front Microbiol 2021; 12:765271. [PMID: 34858375 PMCID: PMC8631192 DOI: 10.3389/fmicb.2021.765271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/13/2021] [Indexed: 02/01/2023] Open
Abstract
Temperate phages play important roles in bacterial communities but have been largely overlooked, particularly in non-pathogenic bacteria. In rhizobia the presence of temperate phages has the potential to have significant ecological impacts but few examples have been described. Here we characterize a novel group of 5 Rhizobium leguminosarum prophages, capable of sustaining infections across a broad host range within their host genus. Genome comparisons identified further putative prophages infecting multiple Rhizobium species isolated globally, revealing a wider family of 10 temperate phages including one previously described lytic phage, RHEph01, which appears to have lost the ability to form lysogens. Phylogenetic discordance between prophage and host phylogenies suggests a history of active mobilization between Rhizobium lineages. Genome comparisons revealed conservation of gene content and order, with the notable exception of an approximately 5 kb region of hypervariability, containing almost exclusively hypothetical genes. Additionally, several horizontally acquired genes are present across the group, including a putative antirepressor present only in the RHEph01 genome, which may explain its apparent inability to form lysogens. In summary, both phenotypic and genomic comparisons between members of this group of phages reveals a clade of viruses with a long history of mobilization within and between Rhizobium species.
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Affiliation(s)
- Sam Ford
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Sara Moeskjær
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Peter Young
- Department of Biology, University of York, York, United Kingdom
| | - Rosa I Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, México City, Mexico
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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15
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Abstract
All sequencing projects of bacteriophages (phages) should seek to report an accurate and comprehensive annotation of their genomes. This article defines 14 questions for those new to phage genomics that should be addressed before submitting a genome sequence to the International Nucleotide Sequence Database Collaboration or writing a publication.
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Affiliation(s)
- Dann Turner
- Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom
| | | | - Igor Tolstoy
- Viral Resources, National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, Maryland, USA
| | - Andrew M Kropinski
- Department of Food Science, and University of Guelph, Guelph, Ontario, Canada.,Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
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16
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Martinez-Hernandez F, Diop A, Garcia-Heredia I, Bobay LM, Martinez-Garcia M. Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth. ISME J 2021; 16:1025-1035. [PMID: 34775488 DOI: 10.1038/s41396-021-01150-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 11/09/2022]
Abstract
Viral genetic microdiversity drives adaptation, pathogenicity, and speciation and has critical consequences for the viral-host arms race occurring at the strain and species levels, which ultimately impact microbial community structure and biogeochemical cycles. Despite the fact that most efforts have focused on viral macrodiversity, little is known about the microdiversity of ecologically important viruses on Earth. Recently, single-virus genomics discovered the putatively most abundant ocean virus in temperate and tropical waters: the uncultured dsDNA virus vSAG 37-F6 infecting Pelagibacter, the most abundant marine bacteria. In this study, we report the cooccurrence of up to ≈1,500 different viral strains (>95% nucleotide identity) and ≈30 related species (80-95% nucleotide identity) in a single oceanic sample. Viral microdiversity was maintained over space and time, and most alleles were the result of synonymous mutations without any apparent adaptive benefits to cope with host translation codon bias and efficiency. Gene flow analysis used to delimitate species according to the biological species concept (BSC) revealed the impact of recombination in shaping vSAG 37-F6 virus and Pelagibacter speciation. Data demonstrated that this large viral microdiversity somehow mirrors the host species diversity since ≈50% of the 926 analyzed Pelagibacter genomes were found to belong to independent BSC species that do not significantly engage in gene flow with one another. The host range of this evolutionarily successful virus revealed that a single viral species can infect multiple Pelagibacter BSC species, indicating that this virus crosses not only formal BSC barriers but also biomes since viral ancestors are found in freshwater.
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Affiliation(s)
| | - Awa Diop
- Department of Biology, University of North Carolina at Greensboro, Greensboro, USA
| | | | - Louis-Marie Bobay
- Department of Biology, University of North Carolina at Greensboro, Greensboro, USA
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain.
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17
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Koonjan S, Cooper CJ, Nilsson AS. Complete Genome Sequence of vB_EcoP_SU7, a Podoviridae Coliphage with the Rare C3 Morphotype. Microorganisms 2021; 9:microorganisms9081576. [PMID: 34442655 PMCID: PMC8399022 DOI: 10.3390/microorganisms9081576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) strains are an important cause of bacterial diarrheal illness in humans and animals. Infections arising from ETEC could potentially be treated through the use of bacteriophage (phage) therapy, as phages encode for enzymes capable of bacterial cell lysis. vB_EcoP_SU7 was isolated from the Käppala wastewater treatment plant in Stockholm, Sweden, and propagated on an ETEC strain exhibiting the O:139 serovar. Transmission electron microscopy confirmed that vB_EcoP_SU7 belongs to the Podoviridae family and has the rare C3 morphotype of an elongated head. Bioinformatic analyses showed that the genome was 76,626 base pairs long and contained 35 genes with predicted functions. A total of 81 open reading frames encoding proteins with hypothetical function and two encoding proteins of no significant similarity were also found. A putative tRNA gene, which may aid in vB_EcoP_SU7’s translation, was also identified. Phylogenetic analyses showed that compared to other Podoviridae, vB_EcoP_SU7 is a rare Kuravirus and is closely related to E. coli phages with the uncommon C3 morphotype, such as ECBP2, EK010, vB_EcoP_EcoN5, and vB_EcoP_SU10. Phage vB_EcoP_SU7 has a narrow host range, infecting 11 out of the 137 E. coli strains tested, a latency period of 30 min, a burst size of 12 PFU/cell, and an adsorption rate of 8.78 × 10−9 mL/min five minutes post infection. With a limited host range and poor infection kinetics, it is unlikely that SU7 can be a standalone phage used for therapeutic purposes; rather, it must be used in combination with other phages for broad-spectrum therapeutic success.
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Affiliation(s)
- Shazeeda Koonjan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden;
- Correspondence:
| | - Callum J. Cooper
- School of Pharmacy, Pharmaceutical and Cosmetic Sciences, Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland SR13SD, UK;
| | - Anders S. Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden;
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18
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Abdelsattar AS, Dawoud A, Makky S, Nofal R, Aziz RK, El-Shibiny A. Bacteriophages: from isolation to application. Curr Pharm Biotechnol 2021; 23:337-360. [PMID: 33902418 DOI: 10.2174/1389201022666210426092002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/29/2021] [Accepted: 03/11/2021] [Indexed: 11/22/2022]
Abstract
Bacteriophages are considered as a potential alternative to fight pathogenic bacteria during the antibiotic resistance era. With their high specificity, they are being widely used in various applications: medicine, food industry, agriculture, animal farms, biotechnology, diagnosis, etc. Many techniques have been designed by different researchers for phage isolation, purification, and amplification, each of which has strengths and weaknesses. However, all aim at having a reasonably pure phage sample that can be further characterized. Phages can be characterized based on their physiological, morphological or inactivation tests. Microscopy, in particular, has opened a wide gate not only for visualizing phage morphological structure, but also for monitoring biochemistry and behavior. Meanwhile, computational analysis of phage genomes provides more details about phage history, lifestyle, and potential for toxigenic or lysogenic conversion, which translate to safety in biocontrol and phage therapy applications. This review summarizes phage application pipelines at different levels and addresses specific restrictions and knowledge gaps in the field. Recently developed computational approaches, which are used in phage genome analysis, are critically assessed. We hope that this assessment provides researchers with useful insights for selection of suitable approaches for Phage-related research aims and applications.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Salsabil Makky
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Rana Nofal
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Qasr El-Ainy St, Cairo. Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
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19
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Kornienko M, Fisunov G, Bespiatykh D, Kuptsov N, Gorodnichev R, Klimina K, Kulikov E, Ilina E, Letarov A, Shitikov E. Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1. Viruses 2020; 12:E1320. [PMID: 33213043 PMCID: PMC7698491 DOI: 10.3390/v12111320] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022] Open
Abstract
The Twort-like myoviruses (Kayvirus genus) of S. aureus are promising agents for bacteriophage therapy due to a broad host range and high killing activity against clinical isolates. This work improves the current understanding of the phage infection physiology by transcriptome analysis. The expression profiles of a typical member of the Kayvirus genus (vB_SauM-515A1) were obtained at three time-points post-infection using RNA sequencing. A total of 35 transcription units comprising 238 ORFs were established. The sequences for 58 early and 12 late promoters were identified in the phage genome. The early promoters represent the strong sigma-70 promoters consensus sequence and control the host-dependent expression of 26 transcription units (81% of genes). The late promoters exclusively controlled the expression of four transcription units, while the transcription of the other five units was directed by both types of promoters. The characteristic features of late promoters were long -10 box of TGTTATATTA consensus sequence and the absence of -35 boxes. The data obtained are also of general interest, demonstrating a strategy of the phage genome expression with a broad overlap of the early and late transcription phases without any middle transcription, which is unusual for the large phage genomes (>100 kbp).
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Affiliation(s)
- Maria Kornienko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Gleb Fisunov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Dmitry Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Nikita Kuptsov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Roman Gorodnichev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Ksenia Klimina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Eugene Kulikov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, 117312 Moscow, Russia; (E.K.); (A.L.)
| | - Elena Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Andrey Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, 117312 Moscow, Russia; (E.K.); (A.L.)
| | - Egor Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
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20
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Evseev PV, Lukianova AA, Shneider MM, Korzhenkov AA, Bugaeva EN, Kabanova AP, Miroshnikov KK, Kulikov EE, Toshchakov SV, Ignatov AN, Miroshnikov KA. Origin and Evolution of Studiervirinae Bacteriophages Infecting Pectobacterium: Horizontal Transfer Assists Adaptation to New Niches. Microorganisms 2020; 8:E1707. [PMID: 33142811 PMCID: PMC7693777 DOI: 10.3390/microorganisms8111707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 01/25/2023] Open
Abstract
Black leg and soft rot are devastating diseases causing up to 50% loss of potential potato yield. The search for, and characterization of, bacterial viruses (bacteriophages) suitable for the control of these diseases is currently a sought-after task for agricultural microbiology. Isolated lytic Pectobacterium bacteriophages Q19, PP47 and PP81 possess a similar broad host range but differ in their genomic properties. The genomic features of characterized phages have been described and compared to other Studiervirinae bacteriophages. Thorough phylogenetic analysis has clarified the taxonomy of the phages and their positioning relative to other genera of the Autographiviridae family. Pectobacterium phage Q19 seems to represent a new genus not described previously. The genomes of the phages are generally similar to the genome of phage T7 of the Teseptimavirus genus but possess a number of specific features. Examination of the structure of the genes and proteins of the phages, including the tail spike protein, underlines the important role of horizontal gene exchange in the evolution of these phages, assisting their adaptation to Pectobacterium hosts. The results provide the basis for the development of bacteriophage-based biocontrol of potato soft rot as an alternative to the use of antibiotics.
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Affiliation(s)
- Peter V. Evseev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
| | - Anna A. Lukianova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Mikhail M. Shneider
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
| | | | - Eugenia N. Bugaeva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Anastasia P. Kabanova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Kirill K. Miroshnikov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Eugene E. Kulikov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Stepan V. Toshchakov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Alexander N. Ignatov
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Konstantin A. Miroshnikov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
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21
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Dias C, Almeida C, Łobocka M, Oliveira H. Genome Sequences of Four Potentially Therapeutic Bacteriophages Infecting Shiga Toxin-Producing Escherichia coli. Microbiol Resour Announc 2020; 9:e00749-20. [PMID: 32883785 DOI: 10.1128/MRA.00749-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Four phages infecting Shiga toxin-producing Escherichia coli (STEC) strains of different serotypes were isolated from wastewater samples. Their virion DNAs range from 51 to 170 kbp, are circularly permuted or have defined terminal repeats, and can encode 82 to 279 proteins. Despite their high similarity to other phages, only about 30% of their genes have a predicted function. Four phages infecting Shiga toxin-producing Escherichia coli (STEC) strains of different serotypes were isolated from wastewater samples. Their virion DNAs range from 51 to 170 kbp, are circularly permuted or have defined terminal repeats, and can encode 82 to 279 proteins. Despite their high similarity to other phages, only about 30% of their genes have a predicted function.
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22
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Topka-Bielecka G, Bloch S, Nejman-Faleńczyk B, Grabski M, Jurczak-Kurek A, Górniak M, Dydecka A, Necel A, Węgrzyn G, Węgrzyn A. Characterization of the Bacteriophage vB_EfaS-271 Infecting Enterococcus faecalis. Int J Mol Sci 2020; 21:ijms21176345. [PMID: 32882938 PMCID: PMC7503890 DOI: 10.3390/ijms21176345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022] Open
Abstract
A newly isolated bacteriophage infecting Enterococcus faecalis strains has been characterized, including determination of its molecular features. This phage, named vB_EfaS-271, has been classified as a Siphoviridae member, according to electron microscopy characterization of the virions, composed of a 50 nm-diameter head and a long, flexible, noncontractable tail (219 × 12.5 nm). Analysis of the whole dsDNA genome of this phage showed that it consists of 40,197 bp and functional modules containing genes coding for proteins that are involved in DNA replication (including DNA polymerase/primase), morphogenesis, packaging and cell lysis. Mass spectrometry analysis allowed us to identify several phage-encoded proteins. vB_EfaS-271 reveals a relatively narrow host range, as it is able to infect only a few E. faecalis strains. On the other hand, it is a virulent phage (unable to lysogenize host cells), effectively and quickly destroying cultures of sensitive host bacteria, with a latent period as short as 8 min and burst size of approximately 70 phages per cell at 37 °C. This phage was also able to destroy biofilms formed by E. faecalis. These results contribute to our understanding of the biodiversity of bacteriophages, confirming the high variability among these viruses and indicating specific genetic and functional features of vB_EfaS-271.
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Affiliation(s)
- Gracja Topka-Bielecka
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
| | - Sylwia Bloch
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland;
| | - Bożena Nejman-Faleńczyk
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
| | - Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
- Laboratory of Marine Biogeochemistry, Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Agata Jurczak-Kurek
- Department of Molecular Evolution, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (A.J.-K.); (M.G.)
| | - Marcin Górniak
- Department of Molecular Evolution, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (A.J.-K.); (M.G.)
| | - Aleksandra Dydecka
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
| | - Agnieszka Necel
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (G.T.-B.); (B.N.-F.); (M.G.); (A.D.); (A.N.); (G.W.)
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland;
- Correspondence: ; Tel.: +48-58-523-6040
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23
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Friedersdorff JCA, Kingston-Smith AH, Pachebat JA, Cookson AR, Rooke D, Creevey CJ. The Isolation and Genome Sequencing of Five Novel Bacteriophages From the Rumen Active Against Butyrivibrio fibrisolvens. Front Microbiol 2020; 11:1588. [PMID: 32760371 PMCID: PMC7372960 DOI: 10.3389/fmicb.2020.01588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 06/17/2020] [Indexed: 01/21/2023] Open
Abstract
Although the prokaryotic communities of the rumen microbiome are being uncovered through genome sequencing, little is known about the resident viral populations. Whilst temperate phages can be predicted as integrated prophages when analyzing bacterial and archaeal genomes, the genetics underpinning lytic phages remain poorly characterized. To the five genomes of bacteriophages isolated from rumen-associated samples sequenced and analyzed previously, this study adds a further five novel genomes and predictions gleaned from them to further the understanding of the rumen phage population. Lytic bacteriophages isolated from fresh ovine and bovine fecal and rumen fluid samples were active against the predominant fibrolytic ruminal bacterium Butyrivibrio fibrisolvens. The double stranded DNA genomes were sequenced and reconstructed into single circular complete contigs. Based on sequence similarity and genome distances, the five phages represent four species from three separate genera, consisting of: (1) Butyrivibrio phages Arian and Bo-Finn; (2) Butyrivibrio phages Idris and Arawn; and (3) Butyrivibrio phage Ceridwen. They were predicted to all belong to the Siphoviridae family, based on evidence in the genomes such as size, the presence of the tail morphogenesis module, genes that share similarity to those in other siphovirus isolates and phylogenetic analysis using phage proteomes. Yet, phylogenomic analysis and sequence similarity of the entire phage genomes revealed that these five phages are unique and novel. These phages have only been observed undergoing the lytic lifecycle, but there is evidence in the genomes of phages Arawn and Idris for the potential to be temperate. However, there is no evidence in the genome of the bacterial host Butyrivibrio fibrisolvens of prophage genes or genes that share similarity with the phage genomes.
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Affiliation(s)
- Jessica C A Friedersdorff
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom.,Institute for Global Food Security (IGFS), Queen's University, Belfast, United Kingdom
| | - Alison H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Justin A Pachebat
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Alan R Cookson
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - David Rooke
- Dynamic Extractions Ltd., Tredegar, United Kingdom
| | - Christopher J Creevey
- Institute for Global Food Security (IGFS), Queen's University, Belfast, United Kingdom
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24
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Oliveira H, Pinto G, Mendes B, Dias O, Hendrix H, Akturk E, Noben JP, Gawor J, Łobocka M, Lavigne R, Azeredo J. A Tailspike with Exopolysaccharide Depolymerase Activity from a New Providencia stuartii Phage Makes Multidrug-Resistant Bacteria Susceptible to Serum-Mediated Killing. Appl Environ Microbiol 2020; 86:e00073-20. [PMID: 32357999 DOI: 10.1128/AEM.00073-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/13/2020] [Indexed: 12/12/2022] Open
Abstract
Providencia stuartii is emerging as a significant drug-resistant nosocomial pathogen, which encourages the search for alternative therapies. Here, we have isolated Providencia stuartii phage Stuart, a novel podovirus infecting multidrug-resistant hospital isolates of this bacterium. Phage Stuart is a proposed member of a new Autographivirinae subfamily genus, with a 41,218-bp genome, direct 345-bp repeats at virion DNA ends, and limited sequence similarity of proteins to proteins in databases. Twelve out of the 52 predicted Stuart proteins are virion components. We found one to be a tailspike with depolymerase activity. The tailspike could form a highly thermostable oligomeric β-structure migrating close to the expected trimer in a nondenaturing gel. It appeared to be essential for the infection of three out of four P. stuartii hosts infected by phage Stuart. Moreover, it degraded the exopolysaccharide of relevant phage Stuart hosts, making the bacteria susceptible to serum killing. Prolonged exposure of a sensitive host to the tailspike did not cause the emergence of bacteria resistant to the phage or to serum killing, opposite to the prolonged exposure to the phage. This indicates that phage tail-associated depolymerases are attractive antivirulence agents that could complement the immune system in the fight with P. stuartii IMPORTANCE The pace at which multidrug-resistant strains emerge has been alarming. P. stuartii is an infrequent but relevant drug-resistant nosocomial pathogen causing local to systemic life-threatening infections. We propose an alternative approach to fight this bacterium based on the properties of phage tailspikes with depolymerase activity that degrade the surface bacterial polymers, making the bacteria susceptible to the immune system. Unlike antibiotics, phage tailspikes have narrow and specific substrate spectra, and by acting as antivirulent but not bactericidal agents they do not cause the selection of resistant bacteria.
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25
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Yu X, Xu J, Gu Y, Zhang R, Zhu Y, Liu X. Molecular Characterization and Comparative Genomic Analysis of vB_PaeP_YA3, a Novel Temperate Bacteriophage of Pseudomonas aeruginosa. Front Microbiol 2020; 11:947. [PMID: 32655502 PMCID: PMC7326022 DOI: 10.3389/fmicb.2020.00947] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/20/2020] [Indexed: 01/21/2023] Open
Abstract
It is well known that bacteriophages play crucial roles in many aspects, such as controlling the number and the diversity of bacteria and participating in horizontal gene transfer, which is a key process in the evolution of bacteria. However, so far, the number of temperate bacteriophages is still limited, and their life processes are severely unknown, except for members of the lambdoid family of coliphages. In this study, a novel temperate phage of Pseudomonas aeruginosa, YA3 (vB_PaeP_YA3), was isolated from waste water. The morphology of YA3 suggested that it is a Podoviridae. The YA3 genome is a circular double-stranded DNA of 45,253 bp, with an average G + C content of 57.2%. A total of 65 open reading frames (ORFs) were predicted according to the sequence of YA3’s genome, of which only 32 (49.2%) ORFs were assigned with putative functions and 13 ORFs were confirmed by the structural proteome. Genome and proteome analyses confirmed the lysogenic nature of this phage, which encodes the typical lysogen-related proteins integrase, CI, Cro, and Q protein. The genome of YA3 is most closely related with that of temperate phage vB_PaeP_Tr60_Ab31, whereas the homology coverage is just 48%. There are many critical differences between their genomes, involving promoters, lysis pathways, and regulation patterns. YA3 is capable of stably lysogenizing its host P. aeruginosa PA14, targeting the integration site within the serine tRNA gene (PA14_RS20820), which is similar with phage vB_PaeP_Tr60_Ab31. The phylogenetic analysis is more complicated than we thought. Based on phage terminase large subunit (TerL) and CI proteins, phage YA3 is related with phage lambda, while their genome coverage is extremely low (<1%). Therefore, phage YA3 is a considerably novel lambda-like temperate phage, and a further study of its genome may deepen our understanding of the interaction between lysogenic phages and their bacterial hosts.
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Affiliation(s)
- Xinyan Yu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Jing Xu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Yu Gu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Ruiyang Zhang
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Yefei Zhu
- Laboratory Medicine Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoqiu Liu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, China
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