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Passeri I, Vaccaro F, Mengoni A, Fagorzi C. Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges. Int J Mol Sci 2024; 25:4425. [PMID: 38674013 PMCID: PMC11050019 DOI: 10.3390/ijms25084425] [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: 02/17/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The universality of DNA methylation as an epigenetic regulatory mechanism belongs to all biological kingdoms. However, while eukaryotic systems have been the primary focus of DNA methylation studies, the molecular mechanisms in prokaryotes are less known. Nevertheless, DNA methylation in prokaryotes plays a pivotal role in many cellular processes such as defense systems against exogenous DNA, cell cycle dynamics, and gene expression, including virulence. Thanks to single-molecule DNA sequencing technologies, genome-wide identification of methylated DNA is becoming feasible on a large scale, providing the possibility to investigate more deeply the presence, variability, and roles of DNA methylation. Here, we present an overview of the multifaceted roles of DNA methylation in prokaryotes and suggest research directions and tools which can enable us to better understand the contribution of DNA methylation to prokaryotic genome evolution and adaptation. In particular, we emphasize the need to understand the presence and role of transgenerational inheritance, as well as the impact of epigenomic signatures on adaptation and genome evolution. Research directions and the importance of novel computational tools are underlined.
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Affiliation(s)
| | | | - Alessio Mengoni
- Department of Biology, University of Florence, 50121 Firenze, Italy; (I.P.); (F.V.); (C.F.)
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2
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Sterzi L, Nodari R, Di Marco F, Ferrando ML, Saluzzo F, Spitaleri A, Allahverdi H, Papaleo S, Panelli S, Rimoldi SG, Batisti Biffignandi G, Corbella M, Cavallero A, Prati P, Farina C, Cirillo DM, Zuccotti G, Bandi C, Comandatore F. Genetic barriers more than environmental associations explain Serratia marcescens population structure. Commun Biol 2024; 7:468. [PMID: 38632370 PMCID: PMC11023947 DOI: 10.1038/s42003-024-06069-w] [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: 11/02/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis.
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Affiliation(s)
- Lodovico Sterzi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Riccardo Nodari
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Federico Di Marco
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Laura Ferrando
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Saluzzo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Hamed Allahverdi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Stella Papaleo
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Simona Panelli
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
| | - Sara Giordana Rimoldi
- Laboratorio di Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze, ASST Fatebenefratelli Sacco, Milan, Italy
| | | | - Marta Corbella
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100, Pavia, Italy
| | | | - Paola Prati
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Pavia, Italy
| | - Claudio Farina
- Laboratory of Microbiology and Virology, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, Bergamo, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy
- Department of Paediatrics, Children's Hospital "V. Buzzi", Milano, Italy
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center "Romeo Ed Enrica Invernizzi", University of Milan, 20133, Milan, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Università Di Milano, 20157, Milan, Italy.
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3
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Flores-Fernández CN, Lin D, Robins K, O'Callaghan CA. DNA methylases for site-selective inhibition of type IIS restriction enzyme activity. Appl Microbiol Biotechnol 2024; 108:174. [PMID: 38270650 PMCID: PMC10810934 DOI: 10.1007/s00253-024-13015-7] [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: 01/08/2024] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
DNA methylases of the restriction-modifications (R-M) systems are promising enzymes for the development of novel molecular and synthetic biology tools. Their use in vitro enables the deployment of independent and controlled catalytic reactions. This work aimed to produce recombinant DNA methylases belonging to the R-M systems, capable of in vitro inhibition of the type IIS restriction enzymes BsaI, BpiI, or LguI. Non-switchable methylases are those whose recognition sequences fully overlap the recognition sequences of their associated endonuclease. In switch methylases, the methylase and endonuclease recognition sequences only partially overlap, allowing sequence engineering to alter methylation without altering restriction. In this work, ten methylases from type I and II R-M systems were selected for cloning and expression in E. coli strains tolerant to methylation. Isopropyl β-D-1-thiogalactopyranoside (IPTG) concentrations and post-induction temperatures were tested to optimize the soluble methylases expression, which was achieved with 0.5 mM IPTG at 20 °C. The C-terminal His6-Tag versions showed better expression than the N-terminal tagged versions. DNA methylation was analyzed using purified methylases and custom test plasmids which, after the methylation reactions, were digested using the corresponding associated type IIS endonuclease. The non-switchable methylases M2.Eco31I, M2.BsaI, M2.HpyAII, and M1.MboII along with the switch methylases M.Osp807II and M2.NmeMC58II showed the best activity for site-selective inhibition of type IIS restriction enzyme activity. This work demonstrates that our recombinant methylases were able to block the activity of type IIS endonucleases in vitro, allowing them to be developed as valuable tools in synthetic biology and DNA assembly techniques. KEY POINTS: • Non-switchable methylases always inhibit the relevant type IIS endonuclease activity • Switch methylases inhibit the relevant type IIS endonuclease activity depending on the sequence engineering of their recognition site • Recombinant non-switchable and switch methylases were active in vitro and can be deployed as tools in synthetic biology and DNA assembly.
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Affiliation(s)
- Carol N Flores-Fernández
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Da Lin
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Current address: Triple Helix Biotechnology Ltd, Moneta Building (B280), Babraham Research Campus, Babraham, Cambridge, CB22 3AT, UK
| | - Katherine Robins
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Current address: Complete Regulatory, 19-20 King Edward Street, Macclesfield, SK10 1AQ, UK
| | - Chris A O'Callaghan
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
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Manzer HS, Doran KS. Complete m6A and m4C methylomes for group B streptococcal clinical isolates CJB111, A909, COH1, and NEM316. Microbiol Resour Announc 2024; 13:e0073323. [PMID: 38099685 PMCID: PMC10793328 DOI: 10.1128/mra.00733-23] [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: 08/08/2023] [Accepted: 11/17/2023] [Indexed: 01/18/2024] Open
Abstract
Group B Streptococcus (GBS) is known to colonize the female reproductive tract and causes adverse pregnancy outcomes and neonatal disease. DNA methylation is a common mechanism for both phage defense and transcriptional regulation. Here, we report the m6A and m4C methylomes of four clinical GBS isolates, CJB111, A909, COH1, and NEM316.
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Affiliation(s)
- Haider S. Manzer
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kelly S. Doran
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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5
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Bin Hafeez A, Pełka K, Worobo R, Szweda P. In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates. Int J Mol Sci 2024; 25:666. [PMID: 38203838 PMCID: PMC10780176 DOI: 10.3390/ijms25010666] [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: 12/11/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.
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Affiliation(s)
- Ahmer Bin Hafeez
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Karolina Pełka
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Randy Worobo
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
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Yuan P, Chen Z, Xu M, Cai W, Liu Z, Sun D. Microbial cell factories using Paenibacillus: status and perspectives. Crit Rev Biotechnol 2023:1-17. [PMID: 38105503 DOI: 10.1080/07388551.2023.2289342] [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: 12/06/2022] [Accepted: 04/22/2023] [Indexed: 12/19/2023]
Abstract
Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium Paenibacillus has been widely applied in: agriculture, medicine, industry, and environmental remediation. Paenibacillus species not only accelerate plant growth and degrade toxic substances in wastewater and soil but also produce industrially-relevant enzymes and antimicrobial peptides. Due to a lack of genetic manipulation tools and methods, exploitation of the bioresources of naturally isolated Paenibacillus species has long been limited. Genetic manipulation tools and methods continue to improve in Paenibacillus, such as shuttle plasmids, promoters, and genetic tools of CRISPR. Furthermore, genetic transformation systems develop gradually, including: penicillin-mediated transformation, electroporation, and magnesium amino acid-mediated transformation. As genetic manipulation methods of homologous recombination and CRISPR-mediated editing system have developed gradually, Paenibacillus has come to be regarded as a promising microbial chassis for biomanufacturing, expanding its application scope, such as: industrial enzymes, bioremediation and bioadsorption, surfactants, and antibacterial agents. In this review, we describe the applications of Paenibacillus bioproducts, and then discuss recent advances and future challenges in the development of genetic manipulation systems in this genus. This work highlights the potential of Paenibacillus as a new microbial chassis for mining bioresources.
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Affiliation(s)
- Panhong Yuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Ziyan Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Mengtao Xu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Wenfeng Cai
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Zhizhi Liu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
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Dekham K, Jones SM, Jitrakorn S, Charoonnart P, Thadtapong N, Intuy R, Dubbs P, Siripattanapipong S, Saksmerprome V, Chaturongakul S. Functional and genomic characterization of a novel probiotic Lactobacillus johnsonii KD1 against shrimp WSSV infection. Sci Rep 2023; 13:21610. [PMID: 38062111 PMCID: PMC10703779 DOI: 10.1038/s41598-023-47897-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
White Spot syndrome virus (WSSV) causes rapid shrimp mortality and production loss worldwide. This study demonstrates potential use of Lactobacillus johnsonii KD1 as an anti-WSSV agent for post larva shrimp cultivation and explores some potential mechanisms behind the anti-WSSV properties. Treatment of Penaeus vannamei shrimps with L. johnsonii KD1 prior to oral challenge with WSSV-infected tissues showed a significantly reduced mortality. In addition, WSSV copy numbers were not detected and shrimp immune genes were upregulated. Genomic analysis of L. johnsonii KD1 based on Illumina and Nanopore platforms revealed a 1.87 Mb chromosome and one 15.4 Kb plasmid. Only one antimicrobial resistance gene (ermB) in the chromosome was identified. Phylogenetic analysis comparing L. johnsonii KD1 to other L. johnsonii isolates revealed that L. johnsonii KD1 is closely related to L. johnsonii GHZ10a isolated from wild pigs. Interestingly, L. johnsonii KD1 contains isolate-specific genes such as genes involved in a type I restriction-modification system and CAZymes belonging to the GT8 family. Furthermore, genes coding for probiotic survival and potential antimicrobial/anti-viral metabolites such as a homolog of the bacteriocin helveticin-J were found. Protein-protein docking modelling suggests the helveticin-J homolog may be able to block VP28-PmRab7 interactions and interrupt WSSV infection.
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Affiliation(s)
- Kanokwan Dekham
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Samuel Merryn Jones
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, CT2 7NZ, UK
| | - Sarocha Jitrakorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Patai Charoonnart
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Nalumon Thadtapong
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathum Thani, 12120, Thailand
| | - Rattanaporn Intuy
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Padungsri Dubbs
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | | | - Vanvimon Saksmerprome
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Soraya Chaturongakul
- Molecular Medical Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand.
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Kar P, Ghosh S, Payra P, Chakrabarti S, Pradhan S, Mondal KC, Ghosh K. Characterization of a novel lytic bacteriophage VPMCC14 which efficiently controls Vibrio harveyi in Penaeus monodon culture. Int Microbiol 2023:10.1007/s10123-023-00456-9. [PMID: 38044417 DOI: 10.1007/s10123-023-00456-9] [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: 08/15/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 12/05/2023]
Abstract
Vibrio harveyi causes luminous vibriosis diseases in shrimp, which lead to shrimp mortalities. Considering the emergence of antibiotic-resistant bacteria, a Vibrio-infecting bacteriophage, VPMCC14, was characterized, and its lysis ability was evaluated on a laboratory scale. VPMCC14 was shown to infect V. harveyi S5A and V. harveyi ATCC 14126. VPMCC14 also exhibited a latent period of 30 min, with a burst size of 38 PFU/cell on its propagation strain. The bacteriophage was stable at a wide range of pHs (3-9), temperatures (0-45°C), and salinities (up to 40 ppt). VPMCC14 exhibited strict virulence properties as the bacteriophage entirely lysed V. harveyi S5A in liquid culture inhibition after 5 h and 4 h at very low MOIs such as MOI 0.1 and MOI 1, respectively. VPMCC14 could control V. harveyi infection in aquariums at MOI 1 and decrease the mortality of Penaeus monodon challenged by V. harveyi. VPMCC14 genome was 134,472 bp long with a 34.5 G+C% content, and 240 open reading frames. A unique characteristic of VPMCC14 was the presence of the HicB family antitoxin-coding open reading frame. Comparative genomic analyses suggested that VPMCC14 could be a representative of a new genus in the Caudoviricetes class. This novel bacteriophage, VPMCC14, could be applied as a biocontrol agent for controlling V. harveyi infection.
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Affiliation(s)
- Priyanka Kar
- Department of Biological Sciences, Midnapore City College, Midnapore, West Bengal, 721129, India
- Biodiversity and Environmental Studies Research Center, Midnapore City College affiliated to Vidyasagar University, Midnapore, West Bengal, India
| | - Smita Ghosh
- Department of Biological Sciences, Midnapore City College, Midnapore, West Bengal, 721129, India
- Biodiversity and Environmental Studies Research Center, Midnapore City College affiliated to Vidyasagar University, Midnapore, West Bengal, India
| | - Pijush Payra
- Department of Industrial Fish & Fisheries, Ramnagar College, Depal, Ramnagar, West Bengal, India
| | - Sudipta Chakrabarti
- Department of Biological Sciences, Midnapore City College, Midnapore, West Bengal, 721129, India
| | - Shrabani Pradhan
- Department of Biological Sciences, Midnapore City College, Midnapore, West Bengal, 721129, India
| | - Keshab Ch Mondal
- Department of Microbiology, Vidyasagar University, Midnapore, West Bengal, India
| | - Kuntal Ghosh
- Department of Biological Sciences, Midnapore City College, Midnapore, West Bengal, 721129, India.
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