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Maciel-Guerra A, Babaarslan K, Baker M, Rahman A, Hossain M, Sadique A, Alam J, Uzzaman S, Ferdous Rahman Sarker M, Sultana N, Islam Khan A, Ara Begum Y, Hassan Afrad M, Senin N, Hossain Habib Z, Shirin T, Qadri F, Dottorini T. Core and accessory genomic traits of Vibrio cholerae O1 drive lineage transmission and disease severity. Nat Commun 2024; 15:8231. [PMID: 39313510 PMCID: PMC11420230 DOI: 10.1038/s41467-024-52238-0] [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: 03/28/2024] [Accepted: 08/30/2024] [Indexed: 09/25/2024] Open
Abstract
In Bangladesh, Vibrio cholerae lineages are undergoing genomic evolution, with increased virulence and spreading ability. However, our understanding of the genomic determinants influencing lineage transmission and disease severity remains incomplete. Here, we developed a computational framework using machine-learning, genome scale metabolic modelling (GSSM) and 3D structural analysis, to identify V. cholerae genomic traits linked to lineage transmission and disease severity. We analysed in-patients isolates from six Bangladeshi regions (2015-2021), and uncovered accessory genes and core SNPs unique to the most recent dominant lineage, with virulence, motility and bacteriophage resistance functions. We also found a strong correlation between V. cholerae genomic traits and disease severity, with some traits overlapping those driving lineage transmission. GSMM and 3D structure analysis unveiled a complex interplay between transcription regulation, protein interaction and stability, and metabolic networks, associated to lifestyle adaptation, intestinal colonization, acid tolerance and symptom severity. Our findings support advancing therapeutics and targeted interventions to mitigate cholera spread.
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Affiliation(s)
- Alexandre Maciel-Guerra
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Kubra Babaarslan
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
| | - Aura Rahman
- NSU Genome Research Institute (NGRI), North South University, Baridhara, Bashundhara, Dhaka, 1229, Bangladesh
| | - Maqsud Hossain
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK
- NSU Genome Research Institute (NGRI), North South University, Baridhara, Bashundhara, Dhaka, 1229, Bangladesh
| | - Abdus Sadique
- NSU Genome Research Institute (NGRI), North South University, Baridhara, Bashundhara, Dhaka, 1229, Bangladesh
| | - Jahidul Alam
- NSU Genome Research Institute (NGRI), North South University, Baridhara, Bashundhara, Dhaka, 1229, Bangladesh
| | - Salim Uzzaman
- Institute of Epidemiology, Disease Control and Research (IEDCR), 44, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Mohammad Ferdous Rahman Sarker
- Institute of Epidemiology, Disease Control and Research (IEDCR), 44, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Nasrin Sultana
- Institute of Epidemiology, Disease Control and Research (IEDCR), 44, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Ashraful Islam Khan
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), 68, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Yasmin Ara Begum
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), 68, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Mokibul Hassan Afrad
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), 68, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Nicola Senin
- Department of Engineering, University of Perugia, 06125, Perugia, Italy
| | - Zakir Hossain Habib
- Institute of Epidemiology, Disease Control and Research (IEDCR), 44, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), 44, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), 68, Shaheed Tajuddin Ahmed Sarani Mohakhali, Dhaka, 1212, Bangladesh
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Loughborough, Leicestershire, LE12 5RD, UK.
- Centre for Smart Food Research, Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, 315100, P. R. China.
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Kumari K, Sharma PK, Singh RP. The transcriptome response of Enterobacter sp. S-33 is modulated by low pH-stress. Genes Genomics 2024; 46:671-687. [PMID: 38687436 DOI: 10.1007/s13258-024-01513-x] [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: 06/13/2023] [Accepted: 03/26/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Acidic environments naturally occur worldwide and uncontrolled use of agricultural practices may also cause acidification of soils. The development of acidic conditions disturbs the establishment of efficient microbial populations in their natural niches. The survival of Enterobacter species under acidic stress remains poorly understood. OBJECTIVE This study aimed to investigate the survival of an environmental isolate Enterobacter sp. S-33 under acidic stress and to identify the various genes involved in stress protection at the global gene transcription level. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to environmental pH changes. METHODS We used the next-generation sequencing (NGS) method to analyze the expression (up-regulation & down-regulation) of genes under varying pH conditions. RESULTS A total of 4214 genes were differentially expressed under acidic conditions (pH 5.0), with 294 up-regulated and 167 down-regulated. At pH 6.0, 50 genes were significantly expressed, of which 34 and 16 were identified as up-regulated and down-regulated, respectively. Many of the up-regulated genes were involved in carbohydrate metabolism, amino acid transport & metabolism, and the most down-regulated genes were related to post-translational modification, lipid transport & metabolism, etc. The observed transcriptomic regulation of genes and pathways identified that Enterobacter reduced its post-translational modification, lipid transport & metabolism, and increased carbohydrate metabolism, amino acid metabolism & transport, energy production & conversion to adapt and grow in acidic stress. CONCLUSIONS The present work provides in-depth information on the characterization of genes associated with tolerance or adaptation to acidic stress of Enterobacter bacterium.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Rajnish Prakash Singh
- Department of Biotechnlogy, Jaypee Insttute of Information Technology, Noida, 201309, India.
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3
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Dominguez SR, Doan PN, Rivera-Chávez F. The intersection between host-pathogen interactions and metabolism during Vibrio cholerae infection. Curr Opin Microbiol 2024; 77:102421. [PMID: 38215547 DOI: 10.1016/j.mib.2023.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 01/14/2024]
Abstract
Vibrio cholerae (V. cholerae), the etiological agent of cholera, uses cholera toxin (CT) to cause severe diarrheal disease. Cholera is still a significant cause of mortality worldwide with about half of all cholera cases and deaths occurring in children under five. Owing to the lack of cost-effective vaccination and poor vaccine efficacy in children, there is a need for alternative preventative and therapeutic strategies. Recent advances in our knowledge of the interplay between CT-induced disease and host-pathogen metabolism have opened the door for investigating how modulation of intestinal metabolism by V. cholerae during disease impacts host intestinal immunity, the gut microbiota, and pathogen-phage interactions. In this review article, we examine recent progress in our understanding of host-pathogen interactions during V. cholerae infection and discuss future work deciphering how modulation of gut metabolism during cholera intersects these processes to enable successful fecal-oral transmission of the pathogen.
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Affiliation(s)
- Sedelia R Dominguez
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Phillip N Doan
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Fabian Rivera-Chávez
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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Jones LO, Willms RJ, Xu X, Graham RDV, Eklund M, Shin M, Foley E. Single-cell resolution of the adult zebrafish intestine under conventional conditions and in response to an acute Vibrio cholerae infection. Cell Rep 2023; 42:113407. [PMID: 37948182 DOI: 10.1016/j.celrep.2023.113407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/08/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Vibrio cholerae is an aquatic bacterium that causes severe and potentially deadly diarrheal disease. Despite the impact on global health, our understanding of host mucosal responses to Vibrio remains limited, highlighting a knowledge gap critical for the development of effective prevention and treatment strategies. Using a natural infection model, we combine physiological and single-cell transcriptomic studies to characterize conventionally reared adult zebrafish guts and guts challenged with Vibrio. We demonstrate that Vibrio causes a mild mucosal immune response characterized by T cell activation and enhanced antigen capture; Vibrio suppresses host interferon signaling; and ectopic activation of interferon alters the course of infection. We show that the adult zebrafish gut shares similarities with mammalian counterparts, including the presence of Best4+ cells, tuft cells, and a population of basal cycling cells. These findings provide important insights into host-pathogen interactions and emphasize the utility of zebrafish as a natural model of Vibrio infection.
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Affiliation(s)
- Lena O Jones
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Reegan J Willms
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Xinyue Xu
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Ralph Derrick V Graham
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Mckenna Eklund
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Minjeong Shin
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Edan Foley
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada; Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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5
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Moraskie M, Roshid MHO, O'Connor G, Artola Zavala T, Dikici E, Zingg JM, Deo S, Daunert S. Engineered biosensors for the quorum sensing molecule 3,5-dimethyl-pyrazine-2-ol (DPO) reveal its presence in humans, animals, and bacterial species beyond Vibrio cholerae. Biosens Bioelectron 2023; 237:115494. [PMID: 37419073 DOI: 10.1016/j.bios.2023.115494] [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: 05/05/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/09/2023]
Abstract
A biosensor was engineered to enable the study of the novel quorum sensing molecule (QSM), 3,5-dimethylpyrazin-2-ol (DPO), employed by Vibrio cholerae to regulate biofilm formation and virulence factor production. Investigations into bacterial quorum sensing (QS), a form of communication based on the production and detection of QSMs to coordinate gene expression in a population dependent manner, offer a unique window to study the molecular underpinnings of microbial behavior and host interactions. Herein, we report the construction of an engineered microbial whole-cell bioluminescent biosensing system that incorporates the recognition of the VqmA regulatory protein of Vibrio cholerae with the bioluminescent reporting signal of luciferase for the selective, sensitive, stable, and reproducible detection of DPO in a variety of samples. Importantly, using our newly developed biosensor our studies demonstrate the detection of DPO in rodent and human samples. Employing our developed biosensor should help enable elucidation of microbial behavior at the molecular level and its impact in health and disease.
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Affiliation(s)
- Michael Moraskie
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Md Harun Or Roshid
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA
| | - Gregory O'Connor
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Teresa Artola Zavala
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA; Universidad Francisco de Vitoria, Madrid, Spain
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Jean-Marc Zingg
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sapna Deo
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA; The Miami Clinical and Translational Science Institute, University of Miami, Miami, FL, 33146, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33146, USA.
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6
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Walton MG, Cubillejo I, Nag D, Withey JH. Advances in cholera research: from molecular biology to public health initiatives. Front Microbiol 2023; 14:1178538. [PMID: 37283925 PMCID: PMC10239892 DOI: 10.3389/fmicb.2023.1178538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/14/2023] [Indexed: 06/08/2023] Open
Abstract
The aquatic bacterium Vibrio cholerae is the etiological agent of the diarrheal disease cholera, which has plagued the world for centuries. This pathogen has been the subject of studies in a vast array of fields, from molecular biology to animal models for virulence activity to epidemiological disease transmission modeling. V. cholerae genetics and the activity of virulence genes determine the pathogenic potential of different strains, as well as provide a model for genomic evolution in the natural environment. While animal models for V. cholerae infection have been used for decades, recent advances in this area provide a well-rounded picture of nearly all aspects of V. cholerae interaction with both mammalian and non-mammalian hosts, encompassing colonization dynamics, pathogenesis, immunological responses, and transmission to naïve populations. Microbiome studies have become increasingly common as access and affordability of sequencing has improved, and these studies have revealed key factors in V. cholerae communication and competition with members of the gut microbiota. Despite a wealth of knowledge surrounding V. cholerae, the pathogen remains endemic in numerous countries and causes sporadic outbreaks elsewhere. Public health initiatives aim to prevent cholera outbreaks and provide prompt, effective relief in cases where prevention is not feasible. In this review, we describe recent advancements in cholera research in these areas to provide a more complete illustration of V. cholerae evolution as a microbe and significant global health threat, as well as how researchers are working to improve understanding and minimize impact of this pathogen on vulnerable populations.
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Affiliation(s)
| | | | | | - Jeffrey H. Withey
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, United States
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7
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Pereira JAM, Berenguer CV, Câmara JS. Delving into Agri-Food Waste Composition for Antibacterial Phytochemicals. Metabolites 2023; 13:metabo13050634. [PMID: 37233675 DOI: 10.3390/metabo13050634] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/20/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023] Open
Abstract
The overuse of antibiotics in the healthcare, veterinary, and agricultural industries has led to the development of antimicrobial resistance (AMR), resulting in significant economic losses worldwide and a growing healthcare problem that urgently needs to be solved. Plants produce a variety of secondary metabolites, making them an area of interest in the search for new phytochemicals to cope with AMR. A great part of agri-food waste is of plant origin, constituting a promising source of valuable compounds with different bioactivities, including those against antimicrobial resistance. Many types of phytochemicals, such as carotenoids, tocopherols, glucosinolates, and phenolic compounds, are widely present in plant by-products, such as citrus peels, tomato waste, and wine pomace. Unveiling these and other bioactive compounds is therefore very relevant and could be an important and sustainable form of agri-food waste valorisation, adding profit for local economies and mitigating the negative impact of these wastes' decomposition on the environment. This review will focus on the potential of agri-food waste from a plant origin as a source of phytochemicals with antibacterial activity for global health benefits against AMR.
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Affiliation(s)
- Jorge A M Pereira
- CQM-Centro de Química da Madeira, Campus da Penteada, Universidade da Madeira, 9020-105 Funchal, Portugal
| | - Cristina V Berenguer
- CQM-Centro de Química da Madeira, Campus da Penteada, Universidade da Madeira, 9020-105 Funchal, Portugal
| | - José S Câmara
- CQM-Centro de Química da Madeira, Campus da Penteada, Universidade da Madeira, 9020-105 Funchal, Portugal
- Departamento de Química, Faculdade de Ciências Exatas e da Engenharia, Campus da Penteada, Universidade da Madeira, 9020-105 Funchal, Portugal
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8
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Zhou S, Liu Z, Song J, Chen Y. Disarm The Bacteria: What Temperate Phages Can Do. Curr Issues Mol Biol 2023; 45:1149-1167. [PMID: 36826021 PMCID: PMC9955262 DOI: 10.3390/cimb45020076] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
In the field of phage applications and clinical treatment, virulent phages have been in the spotlight whereas temperate phages received, relatively speaking, less attention. The fact that temperate phages often carry virulent or drug-resistant genes is a constant concern and drawback in temperate phage applications. However, temperate phages also play a role in bacterial regulation. This review elucidates the biological properties of temperate phages based on their life cycle and introduces the latest work on temperate phage applications, such as on host virulence reduction, biofilm degradation, genetic engineering and phage display. The versatile use of temperate phages coupled with their inherent properties, such as economy, ready accessibility, wide variety and host specificity, make temperate phages a solid candidate in tackling bacterial infections.
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Affiliation(s)
- Shiyue Zhou
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhengjie Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jiaoyang Song
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yibao Chen
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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