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Zhou Q, Li D, Lin W, Pan L, Qian M, Wang F, Cai R, Qu C, Tong Y. Genomic Analysis of a New Freshwater Cyanophage Lbo240-yong1 Suggests a New Taxonomic Family of Bacteriophages. Viruses 2023; 15:v15040831. [PMID: 37112811 PMCID: PMC10140849 DOI: 10.3390/v15040831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
A worldwide ecological issue, cyanobacterial blooms in marine and freshwater have caused enormous losses in both the economy and the environment. Virulent cyanophages-specifically, infecting and lysing cyanobacteria-are key ecological factors involved in limiting the overall extent of the population development of cyanobacteria. Over the past three decades, reports have mainly focused on marine Prochlorococcus and Synechococcus cyanophages, while information on freshwater cyanophages remained largely unknown. In this study, a novel freshwater cyanophage, named Lbo240-yong1, was isolated via the double-layer agar plate method using Leptolyngbya boryana FACHB-240 as a host. Transmission electron microscopy observation illustrated the icosahedral head (50 ± 5 nm in diameter) and short tail (20 ± 5 nm in length) of Lbo240-yong1. Experimental infection against 37 cyanobacterial strains revealed that host-strain-specific Lbo240-yong1 could only lyse FACHB-240. The complete genome of Lbo240-yong1 is a double-stranded DNA of 39,740 bp with a G+C content of 51.99%, and it harbors 44 predicted open reading frames (ORFs). A Lbo240-yong1 ORF shared the highest identity with a gene of a filamentous cyanobacterium, hinting at a gene exchange between the cyanophage and cyanobacteria. A BLASTn search illustrated that Lbo240-yong1 had the highest sequence similarity with the Phormidium cyanophage Pf-WMP4 (89.67% identity, 84% query coverage). In the proteomic tree based on genome-wide sequence similarities, Lbo240-yong1, three Phormidium cyanophages (Pf-WMP4, Pf-WMP3, and PP), one Anabaena phage (A-4L), and one unclassified Arthronema cyanophage (Aa-TR020) formed a monophyletic group that was more deeply diverging than several other families. Pf-WMP4 is the only member of the independent genus Wumpquatrovirus that belongs to the Caudovircetes class. Pf-WMP3 and PP formed the independent genus Wumptrevirus. Anabaena phage A-4L is the only member of the independent Kozyakovvirus genus. The six cyanopodoviruses share similar gene arrangements. Eight core genes were found in them. We propose, here, to set up a new taxonomic family comprising the six freshwater cyanopodoviruses infecting filamentous cyanobacteria. This study enriched the field's knowledge of freshwater cyanophages.
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Affiliation(s)
- Qin Zhou
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Wei Lin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Linting Pan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Minhua Qian
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Fei Wang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Ruqian Cai
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Chenxin Qu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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2
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Zhang X, Liang Y, Jiang J, Lu C, Shi F, Cao Q, Zhang Y, Diao H. A High-Salt Diet Exacerbates Liver Fibrosis through Enterococcus-Dependent Macrophage Activation. Microbiol Spectr 2023; 11:e0340322. [PMID: 36786636 PMCID: PMC10100947 DOI: 10.1128/spectrum.03403-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/14/2023] [Indexed: 02/15/2023] Open
Abstract
People consume more salt than the recommended levels due to poor dietary practices. The effects of long-term consumption of high-salt diets (HSD) on liver fibrosis are unclear. This study aimed to explore the impact of HSD on liver fibrosis. In this study, a carbon tetrachloride (CCL4)-induced liver fibrosis mouse model was used to evaluate fibrotic changes in the livers of mice fed a normal diet (ND) and an HSD. The HSD exacerbated liver injury and fibrosis. Moreover, the protein expression levels of transforming growth factor β (TGF-β), tumor necrosis factor alpha (TNF-α), and monocyte chemoattractant protein 1 (MCP-1) were significantly higher in the HSD group than in the normal group. The proportion of macrophages and activation significantly increased in the livers of HSD-fed mice. Meanwhile, the number of macrophages significantly increased in the small intestinal lamina propria of HSD-fed mice. The levels of profibrotic factors also increased in the small intestine of HSD-fed mice. Additionally, HSD increased the profibrotic chemokines and monocyte chemoattractant levels in the portal vein blood. Further characterization suggested that the HSD decreased the expression of tight junction proteins (ZO-1 and CLDN1), enhancing the translocation of bacteria. Enterococcus promoted liver injury and inflammation. In vitro experiments demonstrated that Enterococcus induced macrophage activation through the NF-κB pathway, thus promoting the expression of fibrosis-related genes, leading to liver fibrogenesis. Similarly, Enterococcus disrupted the gut microbiome in vivo and significantly increased the fibrotic markers, TGF-β, and alpha smooth muscle actin (α-SMA) expression in the liver. IMPORTANCE This study further confirms that Enterococcus induce liver fibrosis in mice. These results indicate that an HSD can exacerbate liver fibrosis by altering the gut microbiota composition, thus impairing intestinal barrier function. Therefore, this may serve as a new target for liver fibrosis therapy and gut microbiota management.
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Affiliation(s)
- Xujun Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yan Liang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jingjing Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Chong Lu
- Department of Gastroenterology, Jinhua Hospital of Zhejiang University, Jinhua, Zhejiang, China
| | - Fan Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Qingyi Cao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Yanhui Zhang
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Hongyan Diao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
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3
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Wang X, Xiong K, Huang F, Huang J, Liu Q, Duan N, Ruan H, Jiang H, Zhu Y, Lin L, Song Y, Zhao M, Zheng L, Ye P, Qian Y, Hu Q, Yan F, Wang W. A metagenome-wide association study of the gut microbiota in recurrent aphthous ulcer and regulation by thalidomide. Front Immunol 2022; 13:1018567. [PMID: 36341405 PMCID: PMC9626999 DOI: 10.3389/fimmu.2022.1018567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/30/2022] [Indexed: 12/04/2022] Open
Abstract
Recurrent aphthous ulcer (RAU), one of the most common diseases in humans, has an unknown etiology and is difficult to treat. Thalidomide is an important immunomodulatory and antitumor drug and its effects on the gut microbiota still remain unclear. We conducted a metagenomic sequencing study of fecal samples from a cohort of individuals with RAU, performed biochemical assays of cytokines, immunoglobulins and antimicrobial peptides in serum and saliva, and investigated the regulation effects of thalidomide administration and withdrawal. Meanwhile we constructed the corresponding prediction models. Our metagenome-wide association results indicated that gut dysbacteriosis, microbial dysfunction and immune imbalance occurred in RAU patients. Thalidomide regulated gut dysbacteriosis in a species-specific manner and had different sustainable effects on various probiotics and pathogens. A previously unknown association between gut microbiota alterations and RAU was found, and the specific roles of thalidomide in modulating the gut microbiota and immunity were determined, suggesting that RAU may be affected by targeting gut dysbacteriosis and modifying immune imbalance. In-depth insights into sophisticated networks consisting of the gut microbiota and host cells may lead to the development of emerging treatments, including prebiotics, probiotics, synbiotics, and postbiotics.
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Affiliation(s)
- Xiang Wang
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Kexu Xiong
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fan Huang
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jinqun Huang
- Beijing Genomics Institute (BGI)-genomics, BGI-Shenzhen, Shenzhen, China
| | - Qin Liu
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Ning Duan
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Huanhuan Ruan
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Hongliu Jiang
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yanan Zhu
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Lin Lin
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yuefeng Song
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Maomao Zhao
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Lichun Zheng
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Pei Ye
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yajie Qian
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Qingang Hu
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Fuhua Yan
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wenmei Wang
- Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
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Pan L, Li D, Lin W, Liu W, Qin W, Xu L, Tong Y. Genomic analysis of a novel active prophage of Hafnia paralvei. Arch Virol 2022; 167:2027-2034. [PMID: 35752683 DOI: 10.1007/s00705-022-05498-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/20/2022] [Indexed: 11/30/2022]
Abstract
Little is known about the prophages in Hafniaceae bacteria. A novel Hafnia phage, yong2, was induced from Hafnia paralvei by treatment with mitomycin C. The phage has an elliptical head with dimensions of approximately 45 × 38 nm and a long noncontractile tail of approximately 157 × 4 nm. The complete genome of Hafnia phage yong2 is a 39,546-bp double-stranded DNA with a G+C content of 49.9%, containing 59 open reading frames (ORFs) and having at least one fixed terminus (GGGGCAGCGACA). In phylogenetic analysis, Hafnia phage yong2 clustered with four predicted Hafnia prophages and one predicted Enterobacteriaceae prophage. These prophages and members of the family Drexlerviridae together formed two distinct subclades nested within a clade, suggesting the existence of a novel class of prophages with conserved sequences and a unique evolutionary status not yet studied before in Hafniaceae and Enterobacteriaceae bacteria.
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Affiliation(s)
- Lingting Pan
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Wei Lin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Wencai Liu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Weinan Qin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Lihua Xu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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5
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Isolation and Characterization of a Novel Cyanophage Encoding Multiple Auxiliary Metabolic Genes. Viruses 2022; 14:v14050887. [PMID: 35632629 PMCID: PMC9146016 DOI: 10.3390/v14050887] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023] Open
Abstract
As significant drivers of cyanobacteria mortality, cyanophages have been known to regulate the population dynamics, metabolic activities, and community structure of this most important marine autotrophic picoplankton and, therefore, influence the global primary production and biogeochemical cycle in aquatic ecosystems. In the present study, a lytic Synechococcus phage, namely S-SZBM1, was isolated and identified. Cyanophage S-SZBM1 has a double-stranded DNA genome of 177,834 bp with a G+C content of 43.31% and contains a total of 218 predicted ORFs and six tRNA genes. Phylogenetic analysis and nucleotide-based intergenomic similarity suggested that cyanophage S-SZBM1 belongs to a new genus under the family Kyanoviridae. A variety of auxiliary metabolic genes (AMGs) that have been proved or speculated to relate to photosynthesis, carbon metabolism, nucleotide synthesis and metabolism, cell protection, and other cell metabolism were identified in cyanophage S-SZBM1 genome and may affect host processes during infection. In addition, 24 of 32 predicted structural proteins were identified by a high-throughput proteome analysis which were potentially involved in the assembly processes of virion. The genomic and proteomic analysis features of cyanophage S-SZBM1 offer a valuable insight into the interactions between cyanophages and their hosts during infection.
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6
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Pan L, Li D, Sun Z, Lin W, Hong B, Qin W, Xu L, Liu W, Zhou Q, Wang F, Cai R, Qian M, Tong Y. First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism. Front Microbiol 2022; 12:754331. [PMID: 35211099 PMCID: PMC8861465 DOI: 10.3389/fmicb.2021.754331] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/20/2021] [Indexed: 01/25/2023] Open
Abstract
A unique lytic phage infecting Hafnia paralvei was isolated and identified. Hafnia phage Ca belongs to the family Autographiviridae, possessing an icosahedral head with a diameter of 55 nm and a short non-contractile tail. Unusually, the burst size of Hafnia phage Ca of 10,292 ± 1,097 plaque-forming units (PFUs)/cell is much larger than other dsDNA phages reported before. Compared to the genome of the related phage, Hafnia phage Ca genome contains extra genes including DNA mimic ocr, dGTP triphosphohydrolase inhibitor, endonuclease, endonuclease VII, and HNH homing endonuclease gene. Extraordinarily, the phage developed different sizes of plaques when a single plaque was picked out and inoculated on a double-layer Luria broth agar plate with its host. Furthermore, varied packaging tightness for the tails of Hafnia phage Ca was observed (tail length: 4.35–45.92 nm). Most of the tails appeared to be like a cone with appendages, some were dot-like, bun-like, table tennis racket handle-like, and ponytail-like. Although the complete genome of Hafnia phage Ca is 40,286 bp, an incomplete genome with a deletion of a 397-bp fragment, containing one ORF predicted as HNH homing endonuclease gene (HEG), was also found by high throughput sequencing. Most of the genome of the virus particles in large plaques is complete (>98%), while most of the genome of the virus particles in small plaques is incomplete (>98%), and the abundance of both of them in medium-sized plaques is similar (complete, 40%; incomplete, 60%). In an experiment to see if the phage could be protective to brocade carps intramuscularly injected with H. paralvei LY-23 and phage Ca, the protection rate of Hafnia phage Ca to brocade carp (Cyprinus aka Koi) against H. paralvei was 33.38% (0.01 < p < 0.05). This study highlights some new insights into the peculiar biological and genomic characteristics of phage.
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Affiliation(s)
- Lingting Pan
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhitong Sun
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wei Lin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Binxin Hong
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Weinan Qin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Lihua Xu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wencai Liu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Qin Zhou
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Fei Wang
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Ruqian Cai
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Minhua Qian
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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7
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Zhang S, He X, Cao L, Tong Y, Zhao B, An W. A Novel Wide-Range Freshwater Cyanophage MinS1 Infecting the Harmful Cyanobacterium Microcystis aeruginosa. Viruses 2022; 14:v14020433. [PMID: 35216026 PMCID: PMC8876498 DOI: 10.3390/v14020433] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 01/07/2023] Open
Abstract
Microcystis aeruginosa, as one of the major players in algal bloom, produces microcystins, which are strongly hepatotoxic, endangering human health and damaging the ecological environment. Biological control of the overgrowth of Microcystis with cyanophage has been proposed to be a promising solution for algal bloom. In this study, a novel strain of Microcystis cyanophage, MinS1, was isolated. MinS1 contains an icosahedral head approximately 54 nm in diameter and a 260 nm-long non-contractile tail. The phage genome consists of a linear, double-stranded 49,966 bp DNA molecule, which shares very low homology with known phages in the NCBI database (only 1% of the genome showed weak homology with known phages when analyzed by megablast). The phage contains 75 ORFs, of which 23 ORFs were predicted to code for proteins of known function, 39 ORFs were predicted to code for proteins of unknown function, and 13 ORFs showed no similarity to any protein sequences. Transmission electron microscopy and phylogenetic analysis showed that MinS1 belongs to the family Siphoviridae. Various experiments confirmed that the phage could infect several different orders of cyanobacteria, including Chroococcales, Nostocales, Oscillatoriales, Hormogonales, and Synechococcales, indicating that it has a very broad host range. In addition, MinS1 has no known antibiotic tolerance genes, virulence genes, and tRNAs, and it is tolerant to temperature, pH, UV, and salinity, suggesting that MinS1 has good potential for application as a biological control agent against cyanobacterial blooms. This study expands the diversity and knowledge of cyanophages, and it provides useful information for the development of novel prevention and control measures against cyanobacterial blooms.
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Affiliation(s)
- Shanshan Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China;
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (X.H.); (L.C.)
| | - Xiaoqi He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (X.H.); (L.C.)
| | - Lei Cao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (X.H.); (L.C.)
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (X.H.); (L.C.)
- Correspondence: (Y.T.); (B.Z.); (W.A.); Tel.: +86-010-64451781 (Y.T.); +86-0311-80789731 (B.Z.); +86-010-52245228 (W.A.)
| | - Baohua Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, China;
- Correspondence: (Y.T.); (B.Z.); (W.A.); Tel.: +86-010-64451781 (Y.T.); +86-0311-80789731 (B.Z.); +86-010-52245228 (W.A.)
| | - Wenlin An
- Department of Scientific Research Management, National Vaccine and Serum Institute, Beijing 100176, China
- Correspondence: (Y.T.); (B.Z.); (W.A.); Tel.: +86-010-64451781 (Y.T.); +86-0311-80789731 (B.Z.); +86-010-52245228 (W.A.)
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8
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Qian M, Li D, Lin W, Pan L, Liu W, Zhou Q, Cai R, Wang F, Zhu J, Tong Y. A Novel Freshwater Cyanophage, Mae-Yong924-1, Reveals a New Family. Viruses 2022; 14:v14020283. [PMID: 35215876 PMCID: PMC8875630 DOI: 10.3390/v14020283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Cyanobacterial blooms are a worldwide ecological issue. Cyanophages are aquatic viruses specifically infecting cyanobacteria. Little is known about freshwater cyanophages. In this study, a freshwater cyanophage, Mae-Yong924-1, was isolated by the double-layer agar plate method using Microcystis aeruginosa FACHB-924 as an indicator host. Mae-Yong924-1 has several unusual characteristics: a unique shape, cross-taxonomic order infectivity and a very unique genome sequence. Mae-Yong924-1 contains a nearly spherical head of about 100 nm in diameter. The tail or tail-like structure (approximately 40 nm in length) is like the tassel of a round Chinese lantern. It could lyse six diverse cyanobacteria strains across three orders including Chroococcales, Nostocales and Oscillatoriales. The genome of the cyanophage is 40,325 bp in length, with a G + C content of 48.32%, and 59 predicted open reading frames (ORFs), only 12 (20%) of which were functionally annotated. Both BLASTn and BLASTx scanning resulted in “No significant similarity found”, i.e., the Mae-Yong924-1 genome shared extremely low homology with sequences in NCBI databases. Mae-Yong924-1 formed a root node alone and monopolized a root branch in the proteomic tree based on genome-wide sequence similarities. The results suggest that Mae-Yong924-1 may reveal a new unknown family apparently distinct from other viruses.
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Affiliation(s)
- Minhua Qian
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Dengfeng Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
- Correspondence: (D.L.); (Y.T.); Tel.: +86-13819823176 (D.L.); +86-13611272813 (Y.T.)
| | - Wei Lin
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingting Pan
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Wencai Liu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Qin Zhou
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Ruqian Cai
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Fei Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Junquan Zhu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Correspondence: (D.L.); (Y.T.); Tel.: +86-13819823176 (D.L.); +86-13611272813 (Y.T.)
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9
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Lin W, Li D, Gao M, Qin W, Xu L, Pan L, Liu W, Fan H, Mi Z, Tong Y. Isolation, characterization and biocontrol efficacy of a T4-like phage virulent to multidrug-resistant Enterobacter hormaechei. DISEASES OF AQUATIC ORGANISMS 2021; 147:97-109. [PMID: 34913439 DOI: 10.3354/dao03622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enterobacter hormaechei is an important emerging pathogen, often exhibiting resistance to multiple clinically important antibiotics. In this study, E. hormaechei was found, for the first time, to be lethal to fish. Bacteriophages are considered potential treatments for bacterial infections. The lytic phage vB_EhoM-IME523 (abbreviated 'IME523') infecting multidrug-resistant E. hormaechei was isolated from hospital sewage. IME523 exhibits T4-like morphology, including a prolate icosahedral head 110 ± 1.89 nm (mean ± SD) long and 82 ± 0.75 nm wide, and a contractile tail of ca. 110 ± 0.91 nm in length. The complete genome length of phage IME523 is 172763 bp, with a G + C content of 39.97%. The whole genome sequence of IME523 has a 93.10% average nucleotide identity (ANI) and a 53.3% in silico DNA-DNA hybridization (isDDH) value with the closest-related Enterobacter phage vB_EclM_CIP9 ('CIP9'). ANI and isDDH values between IME523 and other phages were lower than 78 and 22%, respectively. IME523 and CIP9 formed a monophyletic branch in a phylogenetic tree based on the terminase large subunit, DNA polymerase protein and whole genome phylogenetic analysis. Results suggest that IME523 is a novel species in the subfamily Tevenvirinae and forms a novel genus together with CIP9. No IME523 open reading frame was found to be associated with virulence factors or antibiotic resistance genes. IME523 showed promising protection to zebrafish and brocade carp against E. hormaechei challenge.
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Affiliation(s)
- Wei Lin
- Zhejiang Key Laboratory of Marine Biotechnology, Ningbo University, Ningbo 315832, Zhejiang, PR China
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10
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Characterization of a Novel Bacteriophage Henu2 and Evaluation of the Synergistic Antibacterial Activity of Phage-Antibiotics. Antibiotics (Basel) 2021; 10:antibiotics10020174. [PMID: 33572473 PMCID: PMC7916345 DOI: 10.3390/antibiotics10020174] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus phage Henu2 was isolated from a sewage sample collected in Kaifeng, China, in 2017. In this study, Henu2, a linear double-stranded DNA virus, was sequenced and found to be 43,513 bp long with 35% G + C content and 63 putative open reading frames (ORFs). Phage Henu2 belongs to the family Siphoviridae and possesses an isometric head (63 nm in diameter). The latent time and burst size of Henu2 were approximately 20 min and 7.8 plaque forming unit (PFU)/infected cells. The Henu2 maintained infectivity over a wide range of temperature (10–60 °C) and pH values (4–12). Phylogenetic and comparative genomic analyses indicate that Staphylococcus aureus phage Henu2 should be a new member of the family of Siphoviridae class-II. In this paper, Phage Henu2 alone exhibited weak inhibitory activity on the growth of S. aureus. However, the combination of phage Henu2 and some antibiotics or oxides could effectively inhibit the growth of S. aureus, with a decrease of more than three logs within 24 h in vitro. These results provide useful information that phage Henu2 can be combined with antibiotics to increase the production of phage Henu2 and thus enhance the efficacy of bacterial killing.
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11
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Huang S, Sun Y, Zhang S, Long L. Temporal transcriptomes of a marine cyanopodovirus and its Synechococcus host during infection. Microbiologyopen 2020; 10:e1150. [PMID: 33377630 PMCID: PMC7885011 DOI: 10.1002/mbo3.1150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/01/2020] [Accepted: 12/07/2020] [Indexed: 12/24/2022] Open
Abstract
Marine picocyanobacteria belonging to genera Synechococcus and Prochlorococcus are genetically diverged and distributed into distinct biogeographical patterns, and both are infected by genetically closely related cyanopodoviruses. Previous studies have not fully explored whether the two virus–host systems share similar gene expression patterns during infection. Whole‐genome expression dynamics of T7‐like cyanopodovirus P‐SSP7 and its host Prochlorococcus strain MED4 have already been reported. Here, we conducted genomic and transcriptomic analyses on T7‐like cyanopodovirus S‐SBP1 during its infection on Synechococcus strain WH7803. S‐SBP1 has a latent period of 8 h and phage DNA production of 30 copies per cell. In terms of whole‐genome phylogenetic relationships and average nucleotide identity, S‐SBP1 was most similar to cyanopodovirus S‐RIP2, which also infects Synechococcus WH7803. Three hypervariable genomic islands were identified when comparing the genomes of S‐SBP1 and S‐RIP2. Single nucleotide variants were also observed in three S‐SBP1 genes, which were located within the island regions. Based on RNA‐seq analysis, S‐SBP1 genes clustered into three temporal expression classes, whose gene content was similar to that of P‐SSP7. Thirty‐two host genes were upregulated during phage infection, including those involved in carbon metabolism, ribosome components, and stress response. These upregulated genes were similar to those upregulated by Prochlorococcus MED4 in response to infection by P‐SSP7. Our study demonstrates a programmed temporal expression pattern of cyanopodoviruses and hosts during infection.
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Affiliation(s)
- Sijun Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yingting Sun
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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12
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Biological characteristics and genome analysis of a novel phage vB_KpnP_IME279 infecting Klebsiella pneumoniae. Folia Microbiol (Praha) 2020; 65:925-936. [PMID: 33064268 DOI: 10.1007/s12223-020-00775-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/19/2020] [Indexed: 10/23/2022]
Abstract
Klebsiella pneumoniae (family Enterobacteriaceae) is a gram-negative bacterium that has strong pathogenicity to humans and can cause sepsis, pneumonia, and urinary tract infection. In recent years, the unreasonable use of antibacterial drugs has led to an increase in drug-resistant strains of K. pneumoniae, a serious threat to public health. Bacteriophages, viruses that infect bacteria, are ubiquitous in the natural environment. They are considered to be the most promising substitute for antibiotics because of their high specificity, high efficiency, high safety, low cost, and short development cycle. In this study, a novel phage designated vB_KpnP_IME279 was successfully isolated from hospital sewage using a multidrug-resistant strain of K. pneumoniae as an indicator. A one-step growth curve showed that vB_KpnP_IME279 has a burst size of 140 plaque-forming units/cell and a latent period of 20 min at its optimal multiplicity of infection (MOI = 0.1). Phage vB_KpnP_IME279 survives in a wide pH range between 3 and 11 and is stable at temperatures ranging from 40 to 60 °C. Ten of the 20 strains of K. pneumoniae including the host bacteria were lysed by the phage vB_KpnP_IME279, and the multilocus sequence typing and wzi typing of the 10 strains were ST11, ST37, ST375, wzi209, wzi52, and wzi72, respectively. The genome of vB_KpnP_IME279 is 42,518 bp long with a G + C content of 59.3%. Electron microscopic observation showed that the phage belongs to the family Podoviridae. BLASTN alignment showed that the genome of the phage has low similarity with currently known phages. The evolutionary relationship between phage vB_KpnP_IME279 and other Podoviridae was analyzed using a phylogenetic tree based on sequences of phage major capsid protein and indicates that the phage vB_KpnP_IME279 belongs to the Podoviridae subfamily. These data enhance understanding of K. pneumoniae phages and will help in development of treatments for multidrug-resistant bacteria using phages.
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13
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Lin W, Li D, Sun Z, Tong Y, Yan X, Wang C, Zhang X, Pei G. A novel freshwater cyanophage vB_MelS-Me-ZS1 infecting bloom-forming cyanobacterium Microcystis elabens. Mol Biol Rep 2020; 47:7979-7989. [PMID: 33025507 DOI: 10.1007/s11033-020-05876-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/29/2020] [Indexed: 11/28/2022]
Abstract
Blooms of cyanobacteria cause enormous losses in both the economy and environment. Cyanophages are of great potential for fighting blooming cyanobacteria. Research report on cyanophage of bloom-forming cyanobacterium, Microcystis elabens is deficient. vB_MelS-Me-ZS1 (abbreviated as Me-ZS1) was isolated from fresh water by double-layer agar plate method using M. elabens. TEM exhibited that cyanosiphovirus Me-ZS1 has an icosahedral head about 60 nm in diameter, and a noncontractile tail approximately 260 nm. Experimental infection against 15 cyanobacterial strains showed that Me-ZS1 can infect 12 strains across taxonomic orders (Chroococcales, Nostocales and Oscillatoriales). High-throughput sequencing and bioinformatics analysis revealed that Me-ZS1 has a double-stranded DNA genome of 49,665 bp, with a G + C content of 58.22%, and 73 predicted open reading frames (ORFs). BLASTn and ORF comparisons showed that Me-ZS1 shares very low homology with the public sequences, and the phylogenetic tree based on TerL indicated that Me-ZS1 may delegate a novel and genetically distinct clade of Siphoviridae phages. In microcosm experiment, Me-ZS1 represented apparent effect on reducing relative abundance of cyanobacteria, increasing relative abundance of Saprospiraceae and protecting brocade carp (Carassius auratus) in cyanobacterial bloom water. This study isolated and characterized a novel broad-host-range Microcystis phage Me-ZS1 presenting a genetically distinct clade of freshwater cyanophage. The features of cyanophage Me-ZS1 provide a potential solution to the loss caused by cyanobacterial bloom.
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Affiliation(s)
- Wei Lin
- Key Laboratory of Marine Biotechnology of Zhejiang, Ningbo University, Ningbo, 315832, Zhejiang, People's Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology of Zhejiang, Ningbo University, Ningbo, 315832, Zhejiang, People's Republic of China.
| | - Zhitong Sun
- Key Laboratory of Marine Biotechnology of Zhejiang, Ningbo University, Ningbo, 315832, Zhejiang, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Xiaojun Yan
- Key Laboratory of Marine Biotechnology of Zhejiang, Ningbo University, Ningbo, 315832, Zhejiang, People's Republic of China
| | - Chunlin Wang
- Key Laboratory of Marine Biotechnology of Zhejiang, Ningbo University, Ningbo, 315832, Zhejiang, People's Republic of China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Guangqian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
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14
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Cui H, Zhang J, Cong C, Wang L, Li X, Murtaza B, Xu Y. Complete genome analysis of the novel Edwardsiella tarda phage vB_EtaM_ET-ABTNL-9. Arch Virol 2020; 165:1241-1244. [PMID: 32219545 DOI: 10.1007/s00705-020-04600-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 02/26/2020] [Indexed: 10/24/2022]
Abstract
This work describes the characterization and genome annotation of a new lytic phage, vB_EtaM_ET-ABTNL-9 (referred to as PETp9), isolated from waste water samples collected in Dalian, China, that can kill bacteria of the species Edwardsiella tarda. The genome of phage PETp9 is a circular double-stranded DNA molecule that is 89,762 bp in length with a G+C content of 37.26%, contains 132 ORFs, and encodes one tRNA. Phylogenetic analysis indicated that phage PETp9 should be considered a novel phage.
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Affiliation(s)
- Huijing Cui
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jiancheng Zhang
- Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian, 116620, China
| | - Cong Cong
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.,Ministry of Education Center for Food Safety of Animal Origin, Dalian, 116600, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.,Ministry of Education Center for Food Safety of Animal Origin, Dalian, 116600, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China. .,Ministry of Education Center for Food Safety of Animal Origin, Dalian, 116600, China.
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15
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Gao M, Wang C, Qiang X, Liu H, Li P, Pei G, Zhang X, Mi Z, Huang Y, Tong Y, Bai C. Isolation and Characterization of a Novel Bacteriophage Infecting Carbapenem-Resistant Klebsiella pneumoniae. Curr Microbiol 2020; 77:722-729. [PMID: 31912220 DOI: 10.1007/s00284-019-01849-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/13/2019] [Indexed: 01/13/2023]
Abstract
A novel virulent phage, vB_KpnP_IME337, isolated from a hospital sewage in Beijing, China, that infects carbapenem-resistant Klebsiella pneumoniae KN2 capsular type was identified and characterized. Next-generation sequencing and genome analysis revealed that vB_KpnP_IME337 had a linear double-stranded genome with a length of 44,266 base pairs and G+C content of 53.7%. Fifty-two putative open reading frames were identified, and no transfer RNA-encoding genes were detected. BLASTn analysis revealed that phage vB_KpnP_IME337 had the highest sequence similarity with Klebsiella phage phiBO1E, with genome coverage of 79%. Based on morphology, phage vB_KpnP_IME337 was determined to belong to the family Podoviridae of the order Caudovirales. It was shown that phage vB_KpnP_IME337 had an infection duration of ~ 90 min and 10 min latent period, and a highly specific to host strain. In conclusion, phage vB_KpnP_IME337 may be a promising alternative candidate to antibiotic treatment for controlling diseases caused by drug-resistant K. pneumoniae.
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Affiliation(s)
- Mingming Gao
- Department of Graduate, Hebei North University, Zhangjiakou, 075000, China
| | - Can Wang
- Department of Respiratory and Critical Care Diseases, The Fifth Medical Center, Chinese General Hospital of the PLA, Beijing, 100071, China
| | - Xin Qiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Huiying Liu
- Department of Respiratory and Critical Care Diseases, The Fifth Medical Center, Chinese General Hospital of the PLA, Beijing, 100071, China
| | - Puyuan Li
- Department of Respiratory and Critical Care Diseases, The Fifth Medical Center, Chinese General Hospital of the PLA, Beijing, 100071, China
| | - Guangqian Pei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Zhiqiang Mi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yong Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China. .,Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Changqing Bai
- Department of Graduate, Hebei North University, Zhangjiakou, 075000, China. .,Department of Respiratory and Critical Care Diseases, The Fifth Medical Center, Chinese General Hospital of the PLA, Beijing, 100071, China. .,Shenzhen University General Hospital, Shenzhen, 518055, China.
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16
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Wang Z, Zhao J, Wang L, Li C, Liu J, Zhang L, Zhang Y. A Novel Benthic Phage Infecting Shewanella with Strong Replication Ability. Viruses 2019; 11:v11111081. [PMID: 31752437 PMCID: PMC6893657 DOI: 10.3390/v11111081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 11/17/2019] [Indexed: 12/31/2022] Open
Abstract
The coastal sediments were considered to contain diverse phages playing important roles in driving biogeochemical cycles based on genetic analysis. However, till now, benthic phages in coastal sediments were very rarely isolated, which largely limits our understanding of their biological characteristics. Here, we describe a novel lytic phage (named Shewanella phage S0112) isolated from the coastal sediments of the Yellow Sea infecting a sediment bacterium of the genus Shewanella. The phage has a very high replication capability, with the burst size of ca. 1170 phage particles per infected cell, which is 5–10 times higher than that of most phages isolated before. Meanwhile, the latent period of this phage is relatively longer, which might ensure adequate time for phage replication. The phage has a double-stranded DNA genome comprising 62,286 bp with 102 ORFs, ca. 60% of which are functionally unknown. The expression products of 16 ORF genes, mainly structural proteins, were identified by LC-MS/MS analysis. Besides the general DNA metabolism and structure assembly genes in the phage genome, there is a cluster of auxiliary metabolic genes that may be involved in 7-cyano-7-deazaguanine (preQ0) biosynthesis. Meanwhile, a pyrophosphohydrolase (MazG) gene being considered as a regulator of programmed cell death or involving in host stringer responses is inserted in this gene cluster. Comparative genomic and phylogenetic analysis both revealed a great novelty of phage S0112. This study represents the first report of a benthic phage infecting Shewanella, which also sheds light on the phage–host interactions in coastal sediments.
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Affiliation(s)
- Zengmeng Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (Z.W.); (J.Z.); (L.W.); (C.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiulong Zhao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (Z.W.); (J.Z.); (L.W.); (C.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (Z.W.); (J.Z.); (L.W.); (C.L.)
| | - Chengcheng Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (Z.W.); (J.Z.); (L.W.); (C.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhui Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (J.L.); (L.Z.)
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; (J.L.); (L.Z.)
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (Z.W.); (J.Z.); (L.W.); (C.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-532-80662680
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17
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Yang M, Liang Y, Su R, Chen H, Wang J, Zhang J, Ding Y, Kong L, Zeng H, Xue L, Wu H, Wu Q. Genome characterization of the novel lytic Vibrio parahaemolyticus phage vB_VpP_BA6. Arch Virol 2019; 164:2627-2630. [PMID: 31363923 DOI: 10.1007/s00705-019-04351-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/24/2019] [Indexed: 11/30/2022]
Abstract
A lytic bacteriophage, designated Vibrio phage vB_VpP_BA6, was isolated from sewage collected in Guangzhou, China. The double-stranded DNA genome of phage BA6 is composed of 50,520 bp with a G+C content of 41.77%. It possesses 64 open reading frames relating to phage structure, packaging, host lysis, DNA metabolism, and additional functions. Three tRNAs genes (encoding Pro, Ile and Trp) were detected. Comparison of its genomic features and phylogenetic analysis revealed that phage BA6 is a novel member of the family Podoviridae. This phage may represent a potential therapeutic agent against multidrug-resistant Vibrio parahaemolyticus.
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Affiliation(s)
- Meiyan Yang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China.,College of Agriculture, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Yongjian Liang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China.,College of Agriculture, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Runbin Su
- College of Agriculture, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Hanfang Chen
- College of Agriculture, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Jing Wang
- College of Agriculture, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Yu Ding
- Department of Food Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Li Kong
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Haiyan Zeng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Liang Xue
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Haoming Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Xianlie Zhong Road 100, Guangzhou, 510070, Guangdong, China.
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18
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Yuan Y, Zhao F, Wang L, Tan D, Cong C, Li X, Xu Y. Complete genome analysis of the novel Enterococcus faecalis phage vB_EfaS_AL3. Arch Virol 2019; 164:2599-2603. [PMID: 31278422 DOI: 10.1007/s00705-019-04341-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 06/04/2019] [Indexed: 10/26/2022]
Abstract
This work describes the characterization and genome annotation of a new lytic Enterococcus faecalis siphovirus, vB_EfaS_AL3 (referred to as AL3), isolated from wastewater samples collected in Liaoning Province, China. The genome of phage AL3 is composed of linear double-stranded DNA that is 40,789 bp in length with a G + C content of 34.84% and 61 putative protein-coding genes. Phylogenetic and comparative genomic analyses indicate that phage AL3 should be considered a novel phage.
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Affiliation(s)
- Yuyu Yuan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Feiyang Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.,Ministry of Education Center for Food Safety of Animal Origin, Dalian, 116600, China
| | - Demeng Tan
- Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian, 116620, China
| | - Cong Cong
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.,Ministry of Education Center for Food Safety of Animal Origin, Dalian, 116600, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China. .,Ministry of Education Center for Food Safety of Animal Origin, Dalian, 116600, China.
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19
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Abstract
High-throughput sequencing (HTS) is an effective tool for bacteriophage genome and its termini analysis. HTS technology parallelizes the sequencing process, producing thousands to millions of reads concurrently. Terminal information of a bacteriophage genome is important and basic knowledge for understanding the biology of the bacteriophage. We have created a high-occurrence reads as termini theory and developed practical methods to determine the bacteriophage genome termini, which is based on the large data of HTS. With this method, the termini of the bacteriophage genome can be efficiently and reliably identified as a by-product of bacteriophage genome sequencing, by solely analyzing the sequence statistics of the raw sequencing data (reads), without any further lab experiments.
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20
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Su J, Sun H, Liu J, Guo Z, Fan G, Gu G, Wang G. Complete genome sequence of a novel lytic bacteriophage isolated from Ralstonia solanacearum. Arch Virol 2017; 162:3919-3923. [PMID: 28929273 DOI: 10.1007/s00705-017-3555-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/31/2017] [Indexed: 10/18/2022]
Abstract
A lytic podophage RSPI1 was isolated from tobacco field soil collected in Fujian Province, South China using host bacterium Ralstonia solanacearum Tb15-14. Whole genome sequencing of this phage was performed using the high-throughput Ion Torrent PGM Sequencer. The complete genome of RSPI1 was 43,211 bp in length with a mean DNA G + C content of 61.5%. A total of 48 open reading frames were identified with lengths ranging from 132 bp to 5,061 bp, of which, 11, 12 and 25 were identified as functional, structural and unknown genes, respectively. A BLAST analysis revealed that this phage genome had a query cover of 78-79% and a highest identity of 84% with four podophages that infect Burkholderia pseudomallei. Two neighbor-joining phylogenetic trees were constructed using phage DNA polymerase I and tail fiber protein sequences and showed that this phage is closely related to Burkholderia phage Bp-AMP1, and also related to several phages that infect Ralstonia solanacearum. These findings indicate that RSPI1 is a novel phage that infects the notorious plant pathogen Ralstonia solanacearum.
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Affiliation(s)
- Jingfang Su
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Hongwei Sun
- Mudanjiang Tobacco Research Institute, Heilongjiang Branch of China National Tobacco Corporation, Mudangjiang, 157011, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Zhaokui Guo
- Mudanjiang Tobacco Research Institute, Heilongjiang Branch of China National Tobacco Corporation, Mudangjiang, 157011, China
| | - Guoquan Fan
- Virus-free Seedling, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Gang Gu
- Tobacco Agricultural Institute of Fujian Tobacco Monopoly Bureau, Fuzhou, 350003, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
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PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data. Sci Rep 2017; 7:8292. [PMID: 28811656 PMCID: PMC5557969 DOI: 10.1038/s41598-017-07910-5] [Citation(s) in RCA: 392] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/04/2017] [Indexed: 02/04/2023] Open
Abstract
The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cycle, phage-host interactions, and evolution. In this work, we demonstrate how it is possible to recover more information from sequencing data than just the phage genome. We developed a theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data. Our method relies on the detection of biases in the number of reads, which are observable at natural DNA termini compared with the rest of the phage genome. We implemented our method with the creation of the software PhageTerm and validated it using a set of phages with well-established packaging mechanisms representative of the termini diversity, i.e. 5′cos (Lambda), 3′cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, we determined the termini of nine Clostridium difficile phages and six phages whose sequences were retrieved from the Sequence Read Archive. PhageTerm is freely available (https://sourceforge.net/projects/phageterm), as a Galaxy ToolShed and on a Galaxy-based server (https://galaxy.pasteur.fr).
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Yang Y, Cai L, Ma R, Xu Y, Tong Y, Huang Y, Jiao N, Zhang R. A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea. Viruses 2017; 9:v9050109. [PMID: 28505134 PMCID: PMC5454422 DOI: 10.3390/v9050109] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/22/2017] [Accepted: 05/10/2017] [Indexed: 12/30/2022] Open
Abstract
The Roseobacter clade is abundant and widespread in marine environments and plays an important role in oceanic biogeochemical cycling. In this present study, a lytic siphophage (labeled vB_DshS-R5C) infecting the strain type of Dinoroseobacter shibae named DFL12T, which is part of the Roseobacter clade, was isolated from the oligotrophic South China Sea. Phage R5C showed a narrow host range, short latent period and low burst size. The genome length of phage R5C was 77, 874 bp with a G+C content of 61.5%. Genomic comparisons detected no genome matches in the GenBank database and phylogenetic analysis based on DNA polymerase I revealed phylogenetic features that were distinct to other phages, suggesting the novelty of R5C. Several auxiliary metabolic genes (e.g., phoH gene, heat shock protein and queuosine biosynthesis genes) were identified in the R5C genome that may be beneficial to the host and/or offer a competitive advantage for the phage. Among siphophages infecting the Roseobacter clade (roseosiphophages), four gene transfer agent-like genes were commonly located with close proximity to structural genes, suggesting that their function may be related to the tail of siphoviruses. The isolation and characterization of R5C demonstrated the high genomic and physiological diversity of roseophages as well as improved our understanding of host-phage interactions and the ecology of the marine Roseobacter.
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Affiliation(s)
- Yunlan Yang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
| | - Lanlan Cai
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
| | - Yongle Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
| | - Yigang Tong
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
| | - Yong Huang
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen 361102, Fujian, China.
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Chung CH, Walter MH, Yang L, Chen SCG, Winston V, Thomas MA. Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data. BMC Genomics 2017; 18:350. [PMID: 28472946 PMCID: PMC5418689 DOI: 10.1186/s12864-017-3744-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/28/2017] [Indexed: 11/10/2022] Open
Abstract
Background Most tailed bacteriophages (phages) feature linear dsDNA genomes. Characterizing novel phages requires an understanding of complete genome sequences, including the definition of genome physical ends. Result We sequenced 48 Bacillus cereus phage isolates and analyzed Next-generation sequencing (NGS) data to resolve the genome configuration of these novel phages. Most assembled contigs featured reads that mapped to both contig ends and formed circularized contigs. Independent assemblies of 31 nearly identical I48-like Bacillus phage isolates allowed us to observe that the assembly programs tended to produce random cleavage on circularized contigs. However, currently available assemblers were not capable of reporting the underlying phage genome configuration from sequence data. To identify the genome configuration of sequenced phage in silico, a terminus prediction method was developed by means of ‘neighboring coverage ratios’ and ‘read edge frequencies’ from read alignment files. Termini were confirmed by primer walking and supported by phylogenetic inference of large DNA terminase protein sequences. Conclusions The Terminus package using phage NGS data along with the contig circularity could efficiently identify the proximal positions of phage genome terminus. Complete phage genome sequences allow a proposed characterization of the potential packaging mechanisms and more precise genome annotation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3744-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cheng-Han Chung
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA.
| | - Michael H Walter
- Department of Biology, University of Northern Iowa, 144 McCollum Science Hall, Cedar Falls, IA, 50614-0421, USA
| | - Luobin Yang
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA
| | - Shu-Chuan Grace Chen
- Department of Mathematics and Statistics, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8085, USA
| | - Vern Winston
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA
| | - Michael A Thomas
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA
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Complete genome sequence of Menghai flavivirus, a novel insect-specific flavivirus from China. Arch Virol 2017; 162:1435-1439. [PMID: 28175982 DOI: 10.1007/s00705-017-3232-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
Abstract
Menghai flavivirus (MFV) was isolated from Aedes albopictus in Menghai county of Yunnan Province, China, during an arboviruses screening program in August 2010. Whole genome sequencing of MFV was performed using an Ion PGM™ Sequencer. The complete genome of MFV was 10897 nucleotides in length and encoded a polyprotein and fairly interesting flavivirus orf (FIFO). The polyprotein contained three flavivirus structural proteins (C, prM/M and E) and seven nonstructural proteins. Nucleotide BLAST analysis revealed that the MFV genome showed highest similarity to Xishuangbanna Aedes flavivirus, a novel insect-specific flavivirus recently isolated from the same area. These species shared a query cover of 99%, but only 71% identity, while FIFO showed no similarity with any of the published sequences. Genomic and phylogenetic analyses suggested that MFV was a novel species of the genus Flavivirus. Our findings enrich our understanding of the genetics and prevalence of the family Flaviviridae.
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Complete genome sequence of Xishuangbanna flavivirus, a novel mosquito-specific flavivirus from China. Arch Virol 2016; 161:1723-7. [DOI: 10.1007/s00705-016-2827-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/12/2016] [Indexed: 10/22/2022]
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Conserved termini and adjacent variable region of Twortlikevirus Staphylococcus phages. Virol Sin 2015; 30:433-40. [PMID: 26670039 DOI: 10.1007/s12250-015-3643-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 11/13/2015] [Indexed: 12/15/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an increasing cause of serious infection, both in the community and hospital settings. Despite sophisticated strategies and efforts, the antibiotic options for treating MRSA infection are narrowing because of the limited number of newly developed antimicrobials. Here, four newly-isolated MRSA-virulent phages, IME-SA1, IMESA2, IME-SA118 and IME-SA119, were sequenced and analyzed. Their genome termini were identified using our previously proposed "termini analysis theory". We provide evidence that remarkable conserved terminus sequences are found in IME-SA1/2/118/119, and, moreover, are widespread throughout Twortlikevirus Staphylococcus phage G1 and K species. Results also suggested that each phage of the two species has conserved 5' terminus while the 3' terminus is variable. More importantly, a variable region with a specific pattern was found to be present near the conserved terminus of Twortlikevirus S. phage G1 species. The clone with the longest variable region had variable terminus lengths in successive generations, while the clones with the shortest variable region and with the average length variable region maintained the same terminal length as themselves during successive generations. IME-SA1 bacterial infection experiments showed that the variation is not derived from adaptation of the phage to different host strains. This is the first study of the conserved terminus and variable region of Twortlikevirus S. phages.
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