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Zhang Y, Shao Y, You H, Shen Y, Miao F, Yuan C, Chen X, Zhai M, Shen Y, Zhang J. Characterization and therapeutic potential of MRABP9, a novel lytic bacteriophage infecting multidrug-resistant Acinetobacter baumannii clinical strains. Virology 2024; 595:110098. [PMID: 38705084 DOI: 10.1016/j.virol.2024.110098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/13/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024]
Abstract
Acinetobacter baumannii is one of the most important pathogens of healthcare-associated infections. The rising prevalence of multidrug-resistant A. baumannii (MRAB) strains and biofilm formation impact the outcome of conventional treatment. Phage-related therapy is a promising strategy to tame troublesome multidrug-resistant bacteria. Here, we isolated and evaluated a highly efficient lytic phage called MRABP9 from hospital sewage. The phage was a novel species within the genus Friunavirus and exhibited lytic activity against 2 other identified MRAB strains. Genomic analysis revealed it was a safe virulent phage and a pectate lyase domain was identified within its tail spike protein. MRABP9 showed potent bactericidal and anti-biofilm activity against MRAB, significantly delaying the time point of bacterial regrowth in vitro. Phage administration could rescue the mice from acute lethal MRAB infection. Considering its features, MRABP9 has the potential as an efficient candidate for prophylactic and therapeutic use against acute infections caused by MRAB strains.
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Affiliation(s)
- Ying Zhang
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, 210009, China; Department of Critical Care Medicine, Zhongda Hospital, Jiangsu Provincial Key Laboratory of Critical Care Medicine, Medical School, Southeast University, Nanjing, 210009, China.
| | - Yong Shao
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, 210018, China
| | - Hongyang You
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, 210018, China
| | - Yuqing Shen
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, 210009, China; Department of Critical Care Medicine, Zhongda Hospital, Jiangsu Provincial Key Laboratory of Critical Care Medicine, Medical School, Southeast University, Nanjing, 210009, China
| | - Fengqin Miao
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, 210009, China
| | - Chenyan Yuan
- Department of Clinical Laboratory, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Xin Chen
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, 210009, China
| | - Mengyan Zhai
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, 210009, China
| | - Yi Shen
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, 210018, China
| | - Jianqiong Zhang
- Department of Microbiology and Immunology, Medical School, Southeast University, Nanjing, 210009, China; Department of Critical Care Medicine, Zhongda Hospital, Jiangsu Provincial Key Laboratory of Critical Care Medicine, Medical School, Southeast University, Nanjing, 210009, China; Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, 210018, China
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2
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Zheng K, Liang Y, Paez-Espino D, Zou X, Gao C, Shao H, Sung YY, Mok WJ, Wong LL, Zhang YZ, Tian J, Chen F, Jiao N, Suttle CA, He J, McMinn A, Wang M. Identification of hidden N4-like viruses and their interactions with hosts. mSystems 2023; 8:e0019723. [PMID: 37702511 PMCID: PMC10654107 DOI: 10.1128/msystems.00197-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/19/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.
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Affiliation(s)
- Kaiyang Zheng
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yantao Liang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - David Paez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Mammoth Biosciences Inc., South San Francisco, California, USA
| | - Xiao Zou
- Qingdao Central Hospital, Qingdao, China
| | - Chen Gao
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Hongbing Shao
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Yu-Zhong Zhang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jianfeng He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Andrew McMinn
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Min Wang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
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3
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Gonzalez-Serrano R, Rosselli R, Roda-Garcia JJ, Martin-Cuadrado AB, Rodriguez-Valera F, Dunne M. Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps. Nat Commun 2023; 14:6517. [PMID: 37845226 PMCID: PMC10579305 DOI: 10.1038/s41467-023-42114-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/27/2023] [Indexed: 10/18/2023] Open
Abstract
The host recognition modules encoding the injection machinery and receptor binding proteins (RBPs) of bacteriophages are predisposed to mutation and recombination to maintain infectivity towards co-evolving bacterial hosts. In this study, we reveal how Alteromonas mediterranea schitovirus A5 shares its host recognition module, including tail fiber and cognate chaperone, with phages from distantly related families including Alteromonas myovirus V22. While the V22 chaperone is essential for producing active tail fibers, here we demonstrate production of functional A5 tail fibers regardless of chaperone co-expression. AlphaFold-generated models of tail fiber and chaperone pairs from phages A5, V22, and other Alteromonas phages reveal how amino acid insertions within both A5-like proteins results in a knob domain duplication in the tail fiber and a chaperone β-hairpin "tentacle" extension. These structural modifications are linked to differences in chaperone dependency between the A5 and V22 tail fibers. Structural similarity between the chaperones and intramolecular chaperone domains of other phage RBPs suggests an additional function of these chaperones as transient fiber "caps". Finally, our identification of homologous host recognition modules from morphologically distinct phages implies that horizontal gene transfer and recombination events between unrelated phages may be a more common process than previously thought among Caudoviricetes phages.
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Affiliation(s)
- Rafael Gonzalez-Serrano
- Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain
- Centro de Biología Molecular Severo Ochoa, CBMSO-CSIC, Madrid, Spain
| | - Riccardo Rosselli
- Research & Development Department, LABAQUA S.A. Las Atalayas, Alicante, Spain
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | | | | | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Switzerland.
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4
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Cui JQ, Liu WH, Zhang C, Zou L, Ren HY. Genomic characterization of three bacteriophages infecting donkey-derived Escherichia coli. Virus Genes 2023; 59:752-762. [PMID: 37322310 DOI: 10.1007/s11262-023-02008-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/13/2023] [Indexed: 06/17/2023]
Abstract
Bacteriophages are an important source of novel genetic diversity. Sequencing of phage genomes can reveal new proteins with potential uses in phage therapy and help unravel the diversity of biological mechanisms by which phages take over the machinery of the host during infection. To expand the available collection of phage genomes, we have isolated, sequenced, and assembled the genome sequences of three phages that infect three pathogenic Escherichia coli strains: vB_EcoM_DE15, vB_EcoM_DE16, and vB_EcoM_DE17. Morphological characterization and genomic analysis indicated that all three phages were strictly lytic and free from integrases, virulence factors, toxins, and antimicrobial resistance genes. All three phages contained tRNAs, and especially, vB_EcoM_DE17 contained 25 tRNAs. The genomic features of these phages indicate that natural phages are capable of lysing pathogenic E.coli and have great potential in the biocontrol of bacteria.
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Affiliation(s)
- Jia-Qi Cui
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wen-Hua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ling Zou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Hui-Ying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China.
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5
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Jia K, Peng Y, Chen X, Jian H, Jin M, Yi Z, Su M, Dong X, Yi M. A Novel Inovirus Reprograms Metabolism and Motility of Marine Alteromonas. Microbiol Spectr 2022; 10:e0338822. [PMID: 36301121 PMCID: PMC9769780 DOI: 10.1128/spectrum.03388-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/09/2022] [Indexed: 01/10/2023] Open
Abstract
Members from the Inoviridae family with striking features are widespread, highly diverse, and ecologically pervasive across multiple hosts and environments. However, a small number of inoviruses have been isolated and studied. Here, a filamentous phage infecting Alteromonas abrolhosensis, designated ϕAFP1, was isolated from the South China Sea and represented a novel genus of Inoviridae. ϕAFP1 consisted of a single-stranded DNA genome (5986 bp), encoding eight putative ORFs. Comparative analyses revealed ϕAFP1 could be regarded as genetic mosaics having homologous sequences with Ralstonia and Stenotrophomonas phages. The temporal transcriptome analysis of A. abrolhosensis to ϕAFP1 infection revealed that 7.78% of the host genes were differentially expressed. The genes involved in translation processes, ribosome pathways, and degradation of multiple amino acid pathways at the plateau period were upregulated, while host material catabolic and bacterial motility-related genes were downregulated, indicating that ϕAFP1 might hijack the energy of the host for the synthesis of phage proteins. ϕAFP1 exerted step-by-step control on host genes through the appropriate level of utilizing host resources. Our study provided novel information for a better understanding of filamentous phage characteristics and phage-host interactions. IMPORTANCE Alteromonas is widely distributed and plays a vital role in biogeochemical in marine environments. However, little information about Alteromonas phages is available. Here, we isolated and characterized the biological characteristics and genome sequence of a novel inovirus infecting Alteromonas abrolhosensis, designated ϕAFP1, representing a novel viral genus of Inoviridae. We then presented a comprehensive view of the ϕAFP1 phage-Alteromonas abrolhosensis interactions, elucidating reprogramed host metabolism and motility. Our study provided novel information for better comprehension of filamentous phage characteristics and phage-host interactions.
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Affiliation(s)
- Kuntong Jia
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Yongyi Peng
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xueji Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Min Jin
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Zhiwei Yi
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Meisheng Yi
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
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6
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Cui JQ, Liu WH, Zang YX, Zhang C, Zou L, Sun HZ, Pan Q, Ren HY. Characterization and complete genome analysis of a bacteriophage vB_EcoM_DE7 infecting donkey-derived Escherichia coli. Virus Res 2022; 321:198913. [PMID: 36064043 DOI: 10.1016/j.virusres.2022.198913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022]
Abstract
A lytic bacteriophage vB_EcoM_DE7 (hereafter designated DE7) that could infect donkey-derived Escherichia coli was isolated. The bacteriophage was examined by transmission electron microscopy, and the result showed that DE7 belonged to the family Myoviridae. The microbiological characterization revealed that DE7 was stable over a broad range of pHs (3 ∼10) at 40-50 °C. The latent period was 10 min, and the burst size was 43 PFUs/infected cell. The whole-genome sequencing showed that DE7 was a dsDNA virus and had a genome of 86,130 bp. The genome contained 124 predicted open reading frames (ORFs), 35 of which had known functions, including DNA replication and modification, transcriptional regulation, structural and packaging proteins, and host cell lysis. Twenty tRNA genes were identified, but no genes associated with bacterial pathogenicity, lysogeny and drug resistance were identified. BLASTN analysis revealed that phage DE7 had a high sequence identity (96%) with Salmonella phage vB_SPuM_SP116, but it could not lyse any Salmonella strain tested in this study. DE7 was classified as a Felix O1-like virus based on its general characterization and genomic information. Since phage DE7 exhibited high efficacy in lysing E. coli and lacked genes associated with bacterial virulence, antimicrobial resistance and lysogeny, it could be potentially used to control foal diarrhoea caused by E. coli.
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Affiliation(s)
- Jia-Qi Cui
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wen-Hua Liu
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ya-Xin Zang
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Can Zhang
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ling Zou
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Hu-Zhi Sun
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Hui-Ying Ren
- College of Veterinary medicine, Qingdao Agricultural University, Qingdao, Shandong, China.
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Abstract
Alteromonas is an opportunistic marine bacterium that persists in the global ocean and has important ecological significance. However, current knowledge about the diversity and ecology of alterophages (phages that infect Alteromonas) is lacking. Here, three similar phages infecting Alteromonas macleodii ATCC 27126T were isolated and physiologically characterized. Transmission electron microscopy revealed Siphoviridae morphology, with an oblate icosahedral head and a long noncontractile tail. Notably, these members displayed a small burst size (15–19 plaque-forming units/cell) yet an extensively broad host spectrum when tested on 175 Alteromonas strains. Such unique infection kinetics are potentially associated with discrepancies in codon usage bias from the host tRNA inventory. Phylogenetic analysis indicated that the three phages are closely evolutionarily related; they clustered at the species level and represent a novel genus. Three auxiliary metabolic genes with roles in nucleotide metabolism and putative biofilm dispersal were found in these phage genomes, which revealed important biogeochemical significance of these alterophages in marine ecosystems. Our isolation and characterization of these novel phages expand the current understanding of alterophage diversity, evolution, and phage–host interactions. IMPORTANCE The marine bacterium Alteromonas is prevalent in the global ocean with crucial ecological significance; however, little is known about the diversity and evolution of its bacteriophages that profoundly affect the bacterial communities. Our study characterized a novel genus of three newly isolated Alteromonas phages that exhibited a distinct infection strategy of broad host spectrum and small burst size. This strategy is likely a consequence of the viral trade-off between virulence and lysis profiles during phage–host coevolution, and our work provides new insight into viral evolution and infection strategies.
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8
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Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus. Microbiol Spectr 2021; 9:e0046321. [PMID: 34643440 PMCID: PMC8515928 DOI: 10.1128/spectrum.00463-21] [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] [Indexed: 12/27/2022] Open
Abstract
Alteromonas is a ubiquitous, abundant, copiotrophic and phytoplankton-associated marine member of the Gammaproteobacteria with a range extending from tropical waters to polar regions and including hadal zones. Here, we describe a novel Alteromonas phage, ZP6, that was isolated from surface coastal waters of Qingdao, China. ZP6 contains a linear, double-stranded, 38,080-bp DNA molecule with 50.1% G+C content and 47 putative open reading frames (ORFs). Three auxiliary metabolic genes were identified, encoding metal-dependent phosphohydrolase, diaminopurine synthetase, and nucleotide pyrophosphohydrolase. The first two ORFs facilitate the replacement of adenine (A) by diaminopurine (Z) in phage genomes and help phages to evade attack from host restriction enzymes. The nucleotide pyrophosphohydrolase enables the host cells to stop programmed cell death and improves the survival rate of the host in a nutrient-depleted environment. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis revealed that ZP6 is most closely related to Enhodamvirus but with low similarity (shared genes, <30%, and average nucleotide sequence identity, <65%); it is distinct from other bacteriophages. Together, these results suggest that ZP6 could represent a novel viral genus, here named Mareflavirus. Combining its ability to infect Alteromonas, its harboring of a diaminopurine genome-biosynthetic system, and its representativeness of an understudied viral group, ZP6 could be an important and novel model system for marine virus research. IMPORTANCEAlteromonas is an important symbiotic bacterium of phytoplankton, but research on its bacteriophages is still at an elementary level. Our isolation and genome characterization of a novel Alteromonas podovirus, ZP6, identified a new viral genus of podovirus, namely, Mareflavirus. The ZP6 genome, with a diaminopurine genome-biosynthetic system, is different from those of other isolated Alteromonas phages and will bring new impetus to the development of virus classification and provide important insights into novel viral sequences from metagenomic data sets.
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Ma R, Lai J, Chen X, Wang L, Yang Y, Wei S, Jiao N, Zhang R. A Novel Phage Infecting Alteromonas Represents a Distinct Group of Siphophages Infecting Diverse Aquatic Copiotrophs. mSphere 2021; 6:e0045421. [PMID: 34106770 PMCID: PMC8265664 DOI: 10.1128/msphere.00454-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
Bacteriophages play critical roles in impacting microbial community succession both ecologically and evolutionarily. Although the majority of phage genetic diversity has been increasingly unveiled, phages infecting members of the ecologically important genus Alteromonas remain poorly understood. Here, we present a comprehensive analysis of a newly isolated alterophage, vB_AcoS-R7M (R7M), to characterize its life cycle traits, genomic features, and putative evolutionary origin. R7M harbors abundant genes identified as host-like auxiliary metabolic genes facilitating viral propagation. Genomic analysis suggested that R7M is distinct from currently known alterophages. Interestingly, R7M was found to share a set of similar characteristics with a number of siphophages infecting diverse aquatic opportunistic copiotrophs. We therefore proposed the creation of one new subfamily (Queuovirinae) to group with these evolutionarily related phages. Notably, tail genes were less likely to be shared among them, and baseplate-related genes varied the most. In-depth analyses indicated that R7M has replaced its distal tail with a Rhodobacter capsulatus gene transfer agent (RcGTA)-like baseplate and further acquired a putative receptor interaction site targeting Alteromonas. These findings suggest that horizontal exchanges of viral tail adsorption apparatuses are widespread and vital for phages to hunt new hosts and to adapt to new niches. IMPORTANCE The evolution and ecology of phages infecting members of Alteromonas, a marine opportunistic genus that is widely distributed and of great ecological significance, remain poorly understood. The present study integrates physiological and genomic evidence to characterize the properties and putative phage-host interactions of a newly isolated Alteromonas phage, vB_AcoS-R7M (R7M). A taxonomic study reveals close evolutionary relationships among R7M and a number of siphophages infecting various aquatic copiotrophs. Their similar head morphology and overall genetic framework suggest their putative common ancestry and the grouping of a new viral subfamily. However, their major difference lies in the viral tail adsorption apparatuses and the horizontal exchanges of which possibly account for variations in host specificity. These findings outline an evolutionary scenario for the emergence of diverse viral lineages of a shared genetic pool and give insights into the genetics and ecology of viral host jumps.
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Affiliation(s)
- Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Jiayong Lai
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Long Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yahui Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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10
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Feng X, Yan W, Wang A, Ma R, Chen X, Lin TH, Chen YL, Wei S, Jin T, Jiao N, Zhang R. A Novel Broad Host Range Phage Infecting Alteromonas. Viruses 2021; 13:v13060987. [PMID: 34073246 PMCID: PMC8228385 DOI: 10.3390/v13060987] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
Bacteriophages substantially contribute to bacterial mortality in the ocean and play critical roles in global biogeochemical processes. Alteromonas is a ubiquitous bacterial genus in global tropical and temperate waters, which can cross-protect marine cyanobacteria and thus has important ecological benefits. However, little is known about the biological and ecological features of Alteromonas phages (alterophages). Here, we describe a novel alterophage vB_AmeP-R8W (R8W), which belongs to the Autographiviridae family and infects the deep-clade Alteromonas mediterranea. R8W has an equidistant and icosahedral head (65 ± 1 nm in diameter) and a short tail (12 ± 2 nm in length). The genome size of R8W is 48,825 bp, with a G + C content of 40.55%. R8W possesses three putative auxiliary metabolic genes encoding proteins involved in nucleotide metabolism and DNA binding: thymidylate synthase, nucleoside triphosphate pyrophosphohydrolase, and PhoB. R8W has a rapid lytic cycle with a burst size of 88 plaque-forming units/cell. Notably, R8W has a wide host range, such that it can infect 35 Alteromonas strains; it exhibits a strong specificity for strains isolated from deep waters. R8W has two specific receptor binding proteins and a compatible holin-endolysin system, which contribute to its wide host range. The isolation of R8W will contribute to the understanding of alterophage evolution, as well as the phage-host interactions and ecological importance of alterophages.
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Affiliation(s)
- Xuejin Feng
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Wei Yan
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- College of Marine Science and Technology, China University of Geosciences, Wuhan 430074, China
| | - Anan Wang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Ta-Hui Lin
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Yi-Lung Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Tao Jin
- Guangzhou Magigene Biotechnology Co., Ltd., Guangzhou 510000, China;
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- Correspondence: (N.J.); (R.Z.)
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
- Correspondence: (N.J.); (R.Z.)
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11
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Huang X, Jiao N, Zhang R. The genomic content and context of auxiliary metabolic genes in roseophages. Environ Microbiol 2021; 23:3743-3757. [PMID: 33511765 DOI: 10.1111/1462-2920.15412] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/24/2021] [Indexed: 11/26/2022]
Abstract
Marine bacteriophages frequently possess auxiliary metabolic genes (AMGs) that accelerate host metabolism during phage infection. The significance of AMGs in phage infecting the ecologically important Roseobacter clade, found predominantly in marine environments, remains to be determined. Here, we analysed the distribution and genomic context of 180 AMGs, annotated into 20 types, across 50 roseophage genomes. Roseophages share seven high-frequency AMGs (trx, grx, RNR, thyX, DCD, phoH, and mazG), most of them involved in the nucleotide biosynthesis pathway that represent conserved intra and inter operational taxonomic units (OTUs), and share ≥97% full-length DNA sequence similarity. Sporadic AMGs (dUTPase, lexA, degS, Que, NAPRT, AHL, pcnB, ctrA, RTX, RNR-nrdA, RNR-nrdE, wclP, and flgJ), present in only one or two OTUs, show high functional diversity. The roseophage AMG repertoire weakly correlates with environmental factors, while host range partially explains the sporadic AMG distribution. Locally co-linear blocks distribution index (LDI) analysis indicated that high-frequency roseopodovirus AMGs are restricted to particular genomic islands, possibly originating from limited historical acquisition events. Low-frequency roseopodovirus AMGs and all roseosiphovirus AMGs have high LDI values, implying multiple historical acquisition events. In summary, roseophages have acquired a range of AMGs through horizontal gene transfer, and the forces shaping the evolution of roseophages are described.
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Affiliation(s)
- Xingyu Huang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean & Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean & Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean & Earth Sciences, Xiamen University, Xiamen, 361102, China
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12
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Zhang X, Liu Y, Wang M, Wang M, Jiang T, Sun J, Gao C, Jiang Y, Guo C, Shao H, Liang Y, McMinn A. Characterization and Genome Analysis of a Novel Marine Alteromonas Phage P24. Curr Microbiol 2020; 77:2813-2820. [PMID: 32588135 DOI: 10.1007/s00284-020-02077-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/04/2020] [Indexed: 10/24/2022]
Abstract
Although Alteromonas is ubiquitous in the marine environment, very little is known about Alteromonas phages, with only ten, thus far, being isolated and reported on. In this study, a novel double-stranded DNA phage, Alteromonas phage P24, which infects Alteromonas macleodii, was isolated from the coastal waters off Qingdao. Alteromonas phage P24 has a siphoviral morphology, with an icosahedral head, 61 ± 1 nm in diameter, and a tail length of 105 ± 1 nm. Alteromonas phage P24 contains lipids. It has an optimal temperature and pH for growth of 20℃ and 5-7, respectively. A one-step growth curve shows a latent period of 55 min, a rise period of 65 min, and an average burst size of approximately 147 virions per cell. Alteromonas phage P24 has the genome of 46,945 bp with 43.80% GC content and 74 open reading frames (ORFs) without tRNA. The results of the phylogenetic tree, based on the mcp and terL genes, show that Alteromonas phage P24 is closely related to Aeromonas phage phiARM81ld. Meanwhile, phylogenetic analysis based on the whole genome of P24 indicates that it forms a unique viral sub-cluster within Siphoviridae. This study contributes to the understanding of the genomic characteristics and the virus-host interactions of Alteromonas phages.
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Affiliation(s)
- Xinran Zhang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China
| | - Yundan Liu
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, People's Republic of China.,Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, People's Republic of China
| | - Meiwen Wang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China
| | - Tong Jiang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China
| | - Jianhua Sun
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China
| | - Chen Gao
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, People's Republic of China.,Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, People's Republic of China
| | - Cui Guo
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, People's Republic of China.,Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, People's Republic of China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China. .,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, People's Republic of China. .,Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, People's Republic of China.
| | - Yantao Liang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China. .,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, People's Republic of China. .,Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, People's Republic of China.
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Shinan District, Qingdao, 266071, People's Republic of China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, People's Republic of China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
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13
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Alteromonas Myovirus V22 Represents a New Genus of Marine Bacteriophages Requiring a Tail Fiber Chaperone for Host Recognition. mSystems 2020; 5:5/3/e00217-20. [PMID: 32518192 PMCID: PMC7289586 DOI: 10.1128/msystems.00217-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Marine phages play a variety of critical roles in regulating the microbial composition of our oceans. Despite constituting the majority of genetic diversity within these environments, there are relatively few isolates with complete genome sequences or in-depth analyses of their host interaction mechanisms, such as characterization of their receptor binding proteins (RBPs). Here, we present the 92,760-bp genome of the Alteromonas-targeting phage V22. Genomic and morphological analyses identify V22 as a myovirus; however, due to a lack of sequence similarity to any other known myoviruses, we propose that V22 be classified as the type phage of a new Myoalterovirus genus within the Myoviridae family. V22 shows gene homology and synteny with two different subfamilies of phages infecting enterobacteria, specifically within the structural region of its genome. To improve our understanding of the V22 adsorption process, we identified putative RBPs (gp23, gp24, and gp26) and tested their ability to decorate the V22 propagation strain, Alteromonas mediterranea PT11, as recombinant green fluorescent protein (GFP)-tagged constructs. Only GFP-gp26 was capable of bacterial recognition and identified as the V22 RBP. Interestingly, production of functional GFP-gp26 required coexpression with the downstream protein gp27. GFP-gp26 could be expressed alone but was incapable of host recognition. By combining size-exclusion chromatography with fluorescence microscopy, we reveal how gp27 is not a component of the final RBP complex but instead is identified as a new type of phage-encoded intermolecular chaperone that is essential for maturation of the gp26 RBP.IMPORTANCE Host recognition by phage-encoded receptor binding proteins (RBPs) constitutes the first step in all phage infections and the most critical determinant of host specificity. By characterizing new types of RBPs and identifying their essential chaperones, we hope to expand the repertoire of known phage-host recognition machineries. Due to their genetic plasticity, studying RBPs and their associated chaperones can shed new light onto viral evolution affecting phage-host interactions, which is essential for fields such as phage therapy or biotechnology. In addition, since marine phages constitute one of the most important reservoirs of noncharacterized genetic diversity on the planet, their genomic and functional characterization may be of paramount importance for the discovery of novel genes with potential applications.
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14
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Ji J, Liu Q, Wang R, Luo T, Guo X, Xu M, Yin Q, Wang X, Zhou M, Li M, He P. Identification of a novel phage targeting methicillin-resistant Staphylococcus aureus In vitro and In vivo. Microb Pathog 2020; 149:104317. [PMID: 32512153 DOI: 10.1016/j.micpath.2020.104317] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/31/2020] [Accepted: 05/31/2020] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Staphylococcus aureus is a common human pathogen that causes various diseases including infections on the skin, in the bloodstream and the lower respiratory tracts. The emergence of methicillin-resistant S. aureus (MRSA) made the treatment of the bacterial infection more difficult, calling for development of new therapeutics. Compared with conventional antibiotic therapy, phage therapy offers a promising alternative to combat infections caused by MRSA. RESULTS Here we showed that phage VB_SauS_SH-St 15644 isolated from sewage inhibited MRSA isolates in vitro and in the murine skin infection model. Phage VB_SauS_SH-St 15644 belongs to Siphoviridae. The genome of the phage is a linear, 45,111 bp double-stranded DNA with GC content of 33.35%. Among the 37 clinical MRSA isolates tested, 12 (32%) were lysed by the phage in vitro. The phage was relatively stable at temperatures up to 40 °C or between pH 6 and 9. However, the phage was sensitive to UV light. 80% of the phage was approximately adsorbed to the host MRSA isolate in 4 min. The one-step growth curve showed that the latent period was about 12 min followed by the growth period (about 9 min). The burst size was estimated at 13 PFU per infected cell. Furthermore, in a murine skin infection model, the phage significantly inhibited MRSA infection. CONCLUSIONS Our study suggested that phage VB_SauS_SH-St 15644 has a potential to inhibit MRSA skin infection.
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Affiliation(s)
- Jiawei Ji
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China; Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Qian Liu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Rui Wang
- Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Tingting Luo
- Department of Pharmaceutical Engineering, Zhejiang Pharmaceutical College, Ningbo, China
| | - Xiaokui Guo
- Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Mengsha Xu
- Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Qian Yin
- Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xuetong Wang
- Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Min Zhou
- Institute of Respiratory Diseases, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
| | - Ping He
- Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
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15
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Luo E, Eppley JM, Romano AE, Mende DR, DeLong EF. Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column. ISME JOURNAL 2020; 14:1304-1315. [PMID: 32060418 PMCID: PMC7174320 DOI: 10.1038/s41396-020-0604-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/17/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022]
Abstract
Microbial communities are critical to ecosystem dynamics and biogeochemical cycling in the open oceans. Viruses are essential elements of these communities, influencing the productivity, diversity, and evolution of cellular hosts. To further explore the natural history and ecology of open-ocean viruses, we surveyed the spatiotemporal dynamics of double-stranded DNA (dsDNA) viruses in both virioplankton and bacterioplankton size fractions in the North Pacific Subtropical Gyre, one of the largest biomes on the planet. Assembly and clustering of viral genomes revealed a peak in virioplankton diversity at the base of the euphotic zone, where virus populations and host species richness both reached their maxima. Simultaneous characterization of both extracellular and intracellular viruses suggested depth-specific reproductive strategies. In particular, analyses indicated elevated lytic interactions in the mixed layer, more temporally variable temperate phage interactions at the base of the euphotic zone, and increased lysogeny in the mesopelagic ocean. Furthermore, the depth variability of auxiliary metabolic genes suggested habitat-specific strategies for viral influence on light-energy, nitrogen, and phosphorus acquisition during host infection. Most virus populations were temporally persistent over several years in this environment at the 95% nucleic acid identity level. In total, our analyses revealed variable distributional patterns and diverse reproductive and metabolic strategies of virus populations in the open-ocean water column.
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Affiliation(s)
- Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - Anna E Romano
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI, 96822, USA.
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16
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Wu Y, Wang R, Xu M, Liu Y, Zhu X, Qiu J, Liu Q, He P, Li Q. A Novel Polysaccharide Depolymerase Encoded by the Phage SH-KP152226 Confers Specific Activity Against Multidrug-Resistant Klebsiella pneumoniae via Biofilm Degradation. Front Microbiol 2019; 10:2768. [PMID: 31849905 PMCID: PMC6901502 DOI: 10.3389/fmicb.2019.02768] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/13/2019] [Indexed: 01/09/2023] Open
Abstract
The increasing prevalence of infections caused by multidrug-resistant Klebsiella pneumoniae necessitates the development of alternative therapies. Here, we isolated, characterized, and sequenced a K. pneumoniae bacteriophage (SH-KP152226) that specifically infects and lyses K. pneumoniae capsular type K47. The phage SH-KP152226 contains a genome of 41,420 bp that encodes 48 predicted proteins. Among these proteins, Dep42, the gene product of ORF42, is a putative tail fiber protein and hypothetically possesses depolymerase activity. We demonstrated that recombinant Dep42 showed specific enzymatic activities in the depolymerization of the K47 capsule of K. pneumoniae and was able to significantly inhibit biofilm formation and/or degrade formed biofilms. We also showed that Dep42 could enhance polymyxin activity against K. pneumoniae biofilms when used in combination with antibiotics. These results suggest that combination of the identified novel depolymerase Dep42, encoded by the phage SH-KP152226, with antibiotics may represent a promising strategy to combat infections caused by drug-resistant and biofilm-forming K. pneumoniae.
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Affiliation(s)
- Yunqiang Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Wang
- Department of Research, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengsha Xu
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanan Liu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xianchao Zhu
- Department of Gastrointestinal Surgery, Shanghai Ruizhou Biotech Co. Ltd., Shanghai, China
| | - Jiangfeng Qiu
- Department of Research, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiming Liu
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping He
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingtian Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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17
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Wang D, Jiang Y, Xiao S, Wang M, Liu Q, Huang L, Xue C, Wang Q, Lin T, Shao H, McMinn A. Characterization and Genome Analysis of a Novel Alteromonas Phage JH01 Isolated from the Qingdao Coast of China. Curr Microbiol 2019; 76:1256-1263. [PMID: 31372731 DOI: 10.1007/s00284-019-01751-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/31/2019] [Accepted: 07/26/2019] [Indexed: 12/27/2022]
Abstract
A novel Alteromonas phage JH01, with the host strain identified to be Alteromonas marina SW-47(T), was isolated from the Qingdao coast during the summer of 2017. Transmission electron microscopy analysis showed that phage JH01 can be categorized into the Siphoviridae family, with an icosahedral head of 62 ± 5 nm and a long contractile tail of 254 ± 10 nm. The bioinformatic analysis shows that this phage consists of a linear, double-stranded 46,500 bp DNA molecule with a GC content of 44.39%, and 58 ORFs with no tRNA genes. The ORFs are classified into four groups, including phage packaging, phage structure, DNA replication and regulation, and hypothetical protein. The phylogenetic tree, constructed using neighbor-joining analysis, shows that phage JH01 has altitudinal homology with some Vibrio and Pseudoalteromonas phage B8b. Comparative analysis reveals the high similarity between phage JH01 and phage B8b. Additionally, our study of phage JH01 provides useful information for further research on the interaction between Alteromonas phages and their hosts.
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Affiliation(s)
- Dongxu Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China. .,Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003, China.
| | - Shicong Xiao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China. .,Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003, China.
| | - Qian Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Liyang Huang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Chenglong Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Qi Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Tongtong Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Private Bag 129, Hobart, 7001, Australia
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18
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Characterization and genome analysis of a novel bacteriophage vB_SpuP_Spp16 that infects Salmonella enterica serovar pullorum. Virus Genes 2019; 55:532-540. [PMID: 31004278 DOI: 10.1007/s11262-019-01664-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 04/14/2019] [Indexed: 10/27/2022]
Abstract
A novel virulent bacteriophage vB_SpuP_Spp16 (hereafter designated Spp16) that infects Salmonella enterica serovar pullorum was isolated. Transmission electron microscopy showed that Spp16 possessed an isometric polyhedral head (60 nm in diameter) and a short tail (10 nm in length) belonging to the family Podoviridae. Its complete genome was determined to be 41,832 bp, with a 39.46% GC content by next-generation sequencing. The genome contains 53 proposed open reading frames that are involved in DNA replication and modification, transcriptional regulation, phage structural and packaging proteins and bacterial lysis. No transfer RNA genes were identified. The termini of genome were determined using our previously proposed termini identification method, which suggests that this phage has redundant termini with 421 bp direct terminal repeats. BLASTn analysis revealed the highest sequence similarity with Yersinia phage phi80-18, with a genome coverage of 33% and highest sequence identity of 69%. The phylogenetic analysis indicated that Spp16 forms a distinct branch of the subfamily Autographivirinae. Comparative genomics analysis showed that the phage Spp16 should be regarded as a new subcluster within the GAP227-like cluster in the Autographivirinae subfamily. The phage Spp16 has an obligate lytic life cycle demonstrated by experimental data and genomic analysis. These results suggest that Spp16 may be a proper candidate to control diseases caused by Salmonella enterica serovar pullorum.
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Hua Y, Luo T, Yang Y, Dong D, Wang R, Wang Y, Xu M, Guo X, Hu F, He P. Phage Therapy as a Promising New Treatment for Lung Infection Caused by Carbapenem-Resistant Acinetobacter baumannii in Mice. Front Microbiol 2018; 8:2659. [PMID: 29375524 PMCID: PMC5767256 DOI: 10.3389/fmicb.2017.02659] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/20/2017] [Indexed: 12/15/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) which is noted as a major pathogen associated with healthcare-associated infections has steadily developed beyond antibiotic control. Lytic bacteriophages with the characteristics of infecting and lysing specific bacteria have been used as a potential alternative to traditional antibiotics to solve multidrug-resistant bacterial infections. Here, we isolated A. baumannii-specific lytic phages and evaluated their potential therapeutic effect against lung infection caused by CRAB clinical strains. The combined lysis spectrum of four lytic phages' ranges was 87.5% (42 of 48) against CRAB clinical isolates. Genome sequence and analysis indicated that phage SH-Ab15519 is a novel phage which does not contain the virulence or antibiotic resistance genes. In vivo study indicated that phage SH-Ab15519 administered intranasally can effectively rescue mice from lethal A. baumannii lung infection without deleterious side effects. Our work explores the potential use of phages as an alternative therapeutic agent against the lung infection caused by CRAB strains.
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Affiliation(s)
- Yunfen Hua
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China.,Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tingting Luo
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China.,Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiqi Yang
- Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dong Dong
- Institute of Antibiotics, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Rui Wang
- Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjun Wang
- Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mengsha Xu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China.,Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaokui Guo
- Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ping He
- Department of Medical Microbiology and Immunology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Abstract
Bacteriophages are numerically the most abundant DNA-containing entities in the oligotrophic ocean, yet how specific phage populations vary over time and space remains to be fully explored. Here, we conducted a metagenomic time-series survey of double-stranded DNA phages throughout the water column in the North Pacific Subtropical Gyre, encompassing 1.5 years from depths of 25 to 1,000 m. Viral gene sequences were identified in assembled metagenomic samples, yielding an estimated 172,385 different viral gene families. Viral marker gene distributions suggested that lysogeny was more prevalent at mesopelagic depths than in surface waters, consistent with prior prophage induction studies using mitomycin C. A total of 129 ALOHA viral genomes and genome fragments from 20 to 108 kbp were selected for further study, which represented the most abundant phages in the water column. Phage genotypes displayed discrete population structures. Most phages persisted throughout the time-series and displayed a strong depth structure that mirrored the stratified depth distributions of co-occurring bacterial taxa in the water column. Mesopelagic phages were distinct from surface water phages with respect to diversity, gene content, putative life histories, and temporal persistence, reflecting depth-dependent differences in host genomic architectures and phage reproductive strategies. The spatiotemporal distributions of the most abundant open-ocean bacteriophages that we report here provide new insight into viral temporal persistence, life history, and virus-host-environment interactions throughout the open-ocean water column. The North Pacific Subtropical Gyre represents one of the largest biomes on the planet, where microbial communities are central mediators of ecosystem dynamics and global biogeochemical cycles. Critical members of these communities are the viruses of marine bacteria, which can alter microbial metabolism and significantly influence their survival and productivity. To better understand these viral assemblages, we conducted genomic analyses of planktonic viruses over a seasonal cycle to ocean depths of 1,000 m. We identified 172,385 different viral gene families and 129 unique virus genotypes in this open-ocean setting. The spatiotemporal distributions of the most abundant open-ocean viruses that we report here provide new insights into viral temporal variability, life history, and virus-host-environment interactions throughout the water column.
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Isolation and molecular characterisation of Achromobacter phage phiAxp-3, an N4-like bacteriophage. Sci Rep 2016; 6:24776. [PMID: 27094846 PMCID: PMC4837373 DOI: 10.1038/srep24776] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/05/2016] [Indexed: 02/07/2023] Open
Abstract
Achromobacter xylosoxidans, an opportunistic pathogen, is responsible for various nosocomial and community-acquired infections. We isolated phiAxp-3, an N4-like bacteriophage that infects A. xylosoxidans, from hospital waste and studied its genomic and biological properties. Transmission electron microscopy revealed that, with a 67-nm diameter icosahedral head and a 20-nm non-contractile tail, phiAxp-3 has features characteristic of Podoviridae bacteriophages (order Caudovirales). With a burst size of 9000 plaque-forming units and a latent period of 80 min, phiAxp-3 had a host range limited to only four A. xylosoxidans strains of the 35 strains that were tested. The 72,825 bp phiAxp-3 DNA genome, with 416-bp terminal redundant ends, contains 80 predicted open reading frames, none of which are related to virulence or drug resistance. Genome sequence comparisons place phiAxp-3 more closely with JWAlpha and JWDelta Achromobacter phages than with other N4 viruses. Using proteomics, we identified 25 viral proteins from purified phiAxp-3 particles. Notably, investigation of the phage phiAxp-3 receptor on the surface of the host cell revealed that lipopolysaccharide serves as the receptor for the adsorption of phage phiAxp-3. Our findings advance current knowledge about A. xylosoxidans phages in an age where alternative therapies to combat antibiotic-resistant bacteria are urgently needed.
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Rodriguez-Valera F, Mizuno CM, Ghai R. Tales from a thousand and one phages. BACTERIOPHAGE 2014; 4:e28265. [PMID: 24616837 DOI: 10.4161/bact.28265] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/17/2014] [Accepted: 02/17/2014] [Indexed: 12/17/2022]
Abstract
The sequencing of marine metagenomic fosmids led to the discovery of several new complete phage genomes. Among the 21 major sequence groups, 10 totally novel groups of marine phages could be identified. Some of these represent the first phages infecting large marine prokaryotic phyla, such as the Verrucomicrobia and the recently described Ca. Actinomarinales. Coming from a single deep photic zone sample the diversity of phages found is astonishing, and the comparison with a metavirome from the same location indicates that only 2% of the real diversity was recovered. In addition to this large macro-diversity, rich micro-diversity was also found, affecting host-recognition modules, mirroring the variation of cell surface components in their host marine microbes.
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Affiliation(s)
| | - Carolina Megumi Mizuno
- Evolutionary Genomics Group; Universidad Miguel Hernandez; Campus de San Juan; Alicante, Spain
| | - Rohit Ghai
- Evolutionary Genomics Group; Universidad Miguel Hernandez; Campus de San Juan; Alicante, Spain
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Mizuno CM, Ghai R, Rodriguez-Valera F. Evidence for metaviromic islands in marine phages. Front Microbiol 2014; 5:27. [PMID: 24550898 PMCID: PMC3909814 DOI: 10.3389/fmicb.2014.00027] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/16/2014] [Indexed: 11/13/2022] Open
Abstract
Metagenomic islands (MGIs) have been defined as genomic regions in prokaryotic genomes that under-recruit from metagenomes where most of the same genome recruits at close to 100% identity over most of its length. The presence of MGIs in prokaryotes has been associated to the diversity of concurrent lineages that vary at this level to disperse the predatory pressure of phages that, reciprocally, maintain high clonal diversity in the population and improve ecosystem performance. This was proposed as a Constant-Diversity (C-D) model. Here we have investigated the regions of phage genomes under-recruiting in a metavirome constructed with a sample from the same habitat where they were retrieved. Some of the genes found to under-recruit are involved in host recognition as would be expected from the C-D model. Furthermore, the recruitment of intragenic regions known to be involved in molecular recognition also had a significant under-recruitment compared to the rest of the gene. However, other genes apparently disconnected from the recognition process under-recruited often, specifically the terminases involved in packaging of the phage genome in the capsid and a few others. In addition, some highly related phage genomes (at nucleotide sequence level) had no metaviromic islands (MVIs). We speculate that the latter might be generalist phages with broad infection range that do not require clone specific lineages.
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Affiliation(s)
- Carolina Megumi Mizuno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández Alicante, Spain
| | - Rohit Ghai
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández Alicante, Spain
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