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Wang H, Xie G, Huang J. Genome-based characterization of a novel prophage of Vibrio parahaemolyticus, VPS05ph1, a novel member of Peduoviridae. Virology 2024; 595:110087. [PMID: 38636362 DOI: 10.1016/j.virol.2024.110087] [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: 11/20/2023] [Revised: 03/08/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
Vibrio parahaemolyticus is a globally important bacterium related to climate warming and health threat to human and marine animals. Yet, there is limited knowledge about its polylysogeny harboring multiple prophages and the genetic information. In this study, two prophages (VPS05ph1 and VPS05ph2) were identified in a V. parahaemolyticus isolate through genomic and transcriptional analyses. Both prophages were determined as HP1-like phages, located in a novel phylogenetic lineage of Peduoviridae. They shared a moderate genome-wide sequence similarity with each other and high synteny with the closest relatives, but showed low identities to the repressor counterparts of the representative phages within the family. In addition, no bacterial virulence genes, antibiotic resistance genes and known phage-encoded lytic proteins were identified on both prophage genomes. Moreover, the V. parahaemolyticus isolate was induced with mitomycin, which caused aberrant cellular morphology and nonviability of bacterial cells and excision of prophage VPS05ph1, accompanied by the respective inhibition and promotion of transcriptions of the cI-like and cox-like regulator genes for phage decision making. Results in this study provide the genetic context of polylysogeny in the V. parahaemolyticus isolate, support the diversity and prevalence of HP1-like phages in vibrios, and promote to explore interactions between the HP1-like prophage and its vibrio host.
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Affiliation(s)
| | - Guosi Xie
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Jie Huang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, 266237, China; Network of Aquaculture Centres in Asia-Pacific, Bangkok, 10900, Thailand.
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Wang F, Ghonimy A, Wang X. Whole-genome sequencing of Pseudoalteromonas piscicida 2515 revealed its antibacterial potency against Vibrio anguillarum: a preliminary invitro study. Antonie Van Leeuwenhoek 2024; 117:84. [PMID: 38809302 DOI: 10.1007/s10482-024-01974-w] [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: 05/24/2023] [Accepted: 04/26/2024] [Indexed: 05/30/2024]
Abstract
Pseudoalteromonas piscicida 2515, isolated from Litopenaeus vannamei culture water, is a potential marine probiotic with broad anti-Vibrio properties. However, genomic information on P. piscicida 2515 is scarce. In this study, the general genomic characteristics and probiotic properties of the P. piscicida 2515 strain were analysed. In addition, we determined the antibacterial mechanism of this bacterial strain by scanning electron microscopy (SEM). The results indicated that the whole-genome sequence of P. piscicida 2515 contained one chromosome and one plasmid, including a total length of 5,541,406 bp with a G + C content of 43.24%, and 4679 protein-coding genes were predicted. Various adhesion-related genes, amino acid and vitamin metabolism and biosynthesis genes, and stress-responsive genes were found with genome mining tools. The presence of genes encoding chitin, bromocyclic peptides, lantibiotics, and sactipeptides showed the strong antibacterial activity of the P. piscicida 2515 strain. Moreover, in coculture with Vibrio anguillarum, P. piscicida 2515 displayed vesicle/pilus-like structures located on its surface that possibly participated in its bactericidal activity, representing an antibacterial mechanism. Additionally, 16 haemolytic genes and 3 antibiotic resistance genes, including tetracycline, fluoroquinolone, and carbapenem were annotated, but virulence genes encoding enterotoxin FM (entFM), cereulide (ces), and cytotoxin K were not detected. Further tests should be conducted to confirm the safety characteristics of P. piscicida 2515, including long-term toxicology tests, ecotoxicological assessment, and antibiotic resistance transfer risk assessment. Our results here revealed a new understanding of the probiotic properties and antibacterial mechanism of P. piscicida 2515, in addition to theoretical information for its application in aquaculture.
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Affiliation(s)
- Fenglin Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Abdallah Ghonimy
- Key Laboratory of Sustainable Development of Marine Fisheries, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiuhua Wang
- Key Laboratory of Marine Aquaculture Disease Control, Ministry of Agriculture, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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Patel ZZ, Joshi H, Puvar A, Pandit R, Joshi C, Joshi M, Tipre DR. A study into the diversity of coral-associated bacteria using culture-dependent and culture-independent approaches in coral Dipsastraea favus from the Gulf of Kutch. MARINE POLLUTION BULLETIN 2024; 201:116172. [PMID: 38394797 DOI: 10.1016/j.marpolbul.2024.116172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/03/2023] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Corals harbour ~25 % of the marine diversity referring to biodiversity hotspots in marine ecosystems. Global efforts to find ways to restore the coral reef ecosystem from various threats can be complemented by studying coral-associated bacteria. Coral-associated bacteria are vital components of overall coral wellbeing. We explored the bacterial diversity associated with coral Dipsastraea favus (D. favus) collected from the Gulf of Kutch, India, using both culture-dependent and metagenomic approaches. In both approaches, phylum Proteobacteria, Firmicutes, and Actinobacteria predominated, comprising the genera Vibrio, Bacillus, Shewanella, Pseudoalteromonas, Exiguobacterium and Streptomyces. Moreover, the majority of culturable isolates showed multiple antibiotic resistance index ≥0.2. In this study, specific bacterial diversity associated with coral sp. D. favus and its possible role in managing coral health was established. Almost 43 strains from the samples were successfully cultured, creating a base for exploring these microbes for their potential use in coral conservation methods.
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Affiliation(s)
- Zarna Z Patel
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad 380009, India; Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Himanshu Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Apurvasinh Puvar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), Government of Gujarat, Gandhinagar 382011, India.
| | - Devayani R Tipre
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad 380009, India.
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Ren Y, Wang L, Chen R, Li X, Li S, Li J, Li Q, Wang Z, Xu Y. Isolation and characterization of a novel phage vB_ValP_VA-RY-3 infecting Vibrio alginolyticus. Virus Res 2022; 322:198945. [PMID: 36181974 DOI: 10.1016/j.virusres.2022.198945] [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: 07/17/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2022]
Abstract
Vibrio alginolyticus is a common foodborne pathogen existing both in contaminated seafood and the environment and can cause serious mortality in aquaculture facilities. Bacteriophages can be used as an alternative bio-control agent to eliminate and reduce pathogens. In this study, a novel lytic phage, designated vB_ValP_VA-RY-3 (referred to as S1R3Y), was isolated from sewage collected in Dalian, China. The linear double-stranded DNA genome of phage S1R3Y is 40.271 kb, which has a mol% G + C content of 43.98, containing 51 ORFs with a T7-like genomic organization. It shared the closest relationship with phage vB_CsaP_Ss1, but the homology coverage is just 6%. S1R3Y lacks tRNA and no known virulence or lysogenic genes were found. S1R3Y had a burst size of 147 PFU/cell and is stable under different temperatures (4-56 °C) and pH (5.0-7.0). A comparison of its genomic features and phylogenetic analysis revealed that phage S1R3Y is a novel member of the order Caudovirales, family Podoviridae. Our results suggest that phage S1R3Y may represent a potential therapeutic agent against Vibrio alginolyticus.
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Affiliation(s)
- Yuan Ren
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Renjie Chen
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Shuying Li
- Technology Innovation Center for Phage Application of Liaoning Province, Dalian 116620, China; Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China
| | - Jibin Li
- Technology Innovation Center for Phage Application of Liaoning Province, Dalian 116620, China; Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China
| | - Qiang Li
- College of Marine and Biology Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Zhenhui Wang
- College of Marine and Biology Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China; Technology Innovation Center for Phage Application of Liaoning Province, Dalian 116620, China; Dalian SEM Bio-Engineering Technology Co. Ltd., Dalian 116620, China.
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Application and challenge of bacteriophage in the food protection. Int J Food Microbiol 2022; 380:109872. [PMID: 35981493 DOI: 10.1016/j.ijfoodmicro.2022.109872] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022]
Abstract
In recent years, foodborne diseases caused by pathogens have been increasing. Therefore, it is essential to control the growth and transmission of pathogens. Bacteriophages (phages) have the potential to play an important role in the biological prevention, control, and treatment of these foodborne diseases due to their favorable advantages. Phages not only effectively inhibit pathogenic bacteria and prolong the shelf life of food, but also possess the advantages of specificity and an absence of chemical residues. Currently, there are many cases of phage applications in agriculture, animal disease prevention and control, food safety, and the treatment of drug-resistant disease. In this review, we summarize the recent research progress on phages against foodborne pathogenic bacteria, including Escherichia coli, Salmonella, Campylobacter, Listeria monocytogenes, Shigella, Vibrio parahaemolyticus, and Staphylococcus aureus. We also discuss the main issues and their corresponding solutions in the application of phages in the food industry. In recent years, although researchers have discovered more phages with potential applications in the food industry, most researchers use these phages based on their host spectrum, and the application environment is mostly in the laboratory. Therefore, the practical application of these phages in different aspects of the food industry may be unsatisfactory and even have some negative effects. Thus, we suggest that before using these phages, it is necessary to identify their specific receptors. Using their specific receptors as the selection basis for their application and combining phages with other phages or phages with traditional antibacterial agents may further improve their safety and application efficiency. Collectively, this review provides a theoretical reference for the basic research and application of phages in the food industry.
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Ge H, Lin C, Xu Y, Hu M, Xu Z, Geng S, Jiao X, Chen X. A phage for the controlling of Salmonella in poultry and reducing biofilms. Vet Microbiol 2022; 269:109432. [DOI: 10.1016/j.vetmic.2022.109432] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/05/2022] [Accepted: 04/10/2022] [Indexed: 12/12/2022]
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Guan J, Bao C, Wang P, Jing Y, Wang L, Li X, Mu X, Li B, Zhou D, Guo X, Yin Z. Genetic Characterization of Four Groups of Chromosome-Borne Accessory Genetic Elements Carrying Drug Resistance Genes in Providencia. Infect Drug Resist 2022; 15:2253-2270. [PMID: 35510160 PMCID: PMC9058013 DOI: 10.2147/idr.s354934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose The aim of this study was to gain a deeper genomics and bioinformatics understanding of diversification of accessory genetic elements (AGEs) in Providencia. Methods Herein, the complete genome sequences of five Providencia isolates from China were determined, and seven AGEs were identified from the chromosomes. Detailed genetic dissection and sequence comparison were applied to these seven AGEs, together with additional 10 chromosomal ones from GenBank (nine of them came from Providencia). Results These 17 AGEs were divided into four groups: Tn6512 and its six derivatives, Tn6872 and its two derivatives, Tn6875 and its one derivative, and Tn7 and its four derivatives. These AGEs display high-level diversification in modular structures that had complex mosaic natures, and particularly different multidrug resistance (MDR) regions were presented in these AGEs. At least 52 drug resistance genes, involved in resistance to 15 different categories of antimicrobials and heavy metal, were found in 15 of these 17 AGEs. Conclusion Integration of these AGEs into the Providencia chromosomes would contribute to the accumulation and distribution of drug resistance genes and enhance the ability of Providencia isolates to survive under drug selection pressure.
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Affiliation(s)
- Jiayao Guan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China
| | - Chunmei Bao
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, People’s Republic of China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Lingling Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xinyue Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xiaofei Mu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Boan Li
- Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, People’s Republic of China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
| | - Xuejun Guo
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China
- Xuejun Guo, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130122, People’s Republic of China, Tel +86-431-86985931, Email
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China
- Correspondence: Zhe Yin, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People’s Republic of China, Tel +86-10-66948557, Email
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