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Nguyen HM, Watanabe S, Sharmin S, Kawaguchi T, Tan XE, Wannigama DL, Cui L. RNA and Single-Stranded DNA Phages: Unveiling the Promise from the Underexplored World of Viruses. Int J Mol Sci 2023; 24:17029. [PMID: 38069353 PMCID: PMC10707117 DOI: 10.3390/ijms242317029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
RNA and single-stranded DNA (ssDNA) phages make up an understudied subset of bacteriophages that have been rapidly expanding in the last decade thanks to advancements in metaviromics. Since their discovery, applications of genetic engineering to ssDNA and RNA phages have revealed their immense potential for diverse applications in healthcare and biotechnology. In this review, we explore the past and present applications of this underexplored group of phages, particularly their current usage as therapeutic agents against multidrug-resistant bacteria. We also discuss engineering techniques such as recombinant expression, CRISPR/Cas-based genome editing, and synthetic rebooting of phage-like particles for their role in tailoring phages for disease treatment, imaging, biomaterial development, and delivery systems. Recent breakthroughs in RNA phage engineering techniques are especially highlighted. We conclude with a perspective on challenges and future prospects, emphasizing the untapped diversity of ssDNA and RNA phages and their potential to revolutionize biotechnology and medicine.
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Affiliation(s)
- Huong Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Sultana Sharmin
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Tomofumi Kawaguchi
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata 990-2292, Yamagata, Japan;
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
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Zaki BM, Mohamed AA, Dawoud A, Essam K, Hammouda ZK, Abdelsattar AS, El-Shibiny A. Isolation, screening and characterization of phage. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:13-60. [PMID: 37739553 DOI: 10.1016/bs.pmbts.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Bacterial resistance threatens public health due to a lack of novel antibacterial classes since the 21st century. Bacteriophages, the most ubiquitous microorganism on Earth and natural predators of bacteria, have the potential to save the world from the post-antibiotic era. Therefore, phage isolation and characterization are in high demand to find suitable phages for therapeutic and bacterial control applications. The chapter presents brief guidance supported by recommendations on the isolation of phages, and initial screening of phage antimicrobial efficacy, in addition to, conducting comprehensive characterization addressing morphological, biological, genomic, and taxonomic features.
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Affiliation(s)
- Bishoy Maher Zaki
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Amira A Mohamed
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Kareem Essam
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Zainab K Hammouda
- Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt
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7
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Krupovic M, Turner D, Morozova V, Dyall-Smith M, Oksanen HM, Edwards R, Dutilh BE, Lehman SM, Reyes A, Baquero DP, Sullivan MB, Uchiyama J, Nakavuma J, Barylski J, Young MJ, Du S, Alfenas-Zerbini P, Kushkina A, Kropinski AM, Kurtböke I, Brister JR, Lood C, Sarkar BL, Yigang T, Liu Y, Huang L, Wittmann J, Chanishvili N, van Zyl LJ, Rumnieks J, Mochizuki T, Jalasvuori M, Aziz RK, Łobocka M, Stedman KM, Shkoporov AN, Gillis A, Peng X, Enault F, Knezevic P, Lavigne R, Rhee SK, Cvirkaite-Krupovic V, Moraru C, Moreno Switt AI, Poranen MM, Millard A, Prangishvili D, Adriaenssens EM. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021. Arch Virol 2021; 166:3239-3244. [PMID: 34417873 PMCID: PMC8497307 DOI: 10.1007/s00705-021-05205-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
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Affiliation(s)
- Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Dann Turner
- Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol, UK
| | - Vera Morozova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Mike Dyall-Smith
- Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Rob Edwards
- Flinders Accelerator for Microbiome Exploration, Adelaide, Australia
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Susan M Lehman
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20903, USA
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | | | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA.,Department Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Jumpei Uchiyama
- School of Veterinary Medicine, Azabu University, Sagamihara, Japan
| | - Jesca Nakavuma
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznan, Collegium Biologicum-Umultowska 89, 61-614, Poznan, Poland
| | - Mark J Young
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Shishen Du
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | | | - Alla Kushkina
- Zabolotny Institute of Microbiology and Virology, NAS of Ukraine, Kyiv, Ukraine
| | - Andrew M Kropinski
- Department of Food Science, University of Guelph, Guelph, Canada.,Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Ipek Kurtböke
- University of the Sunshine Coast, Sippy Downs, Australia
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
| | | | - B L Sarkar
- Emeritus ICMR-National Institute of Cholera and Enteric Diseases (NICED), Kolkata, India
| | - Tong Yigang
- Beijing University of Chemical Technology, Beijing, China
| | - Ying Liu
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Berlin, Germany
| | - Nina Chanishvili
- The Eliava Institute of Bacteriophage, MIcrobiology and Virology, Tbilisi, Georgia
| | | | - Janis Rumnieks
- Latvian Biomedical Research and Study Center, Riga, Latvia
| | - Tomohiro Mochizuki
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University and Microbiology and Immunology Research Program, Children's Cancer Hospital Egypt, Cairo, 57357, Egypt
| | - Małgorzata Łobocka
- Laboratory of Bacteriophage Biology, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Kenneth M Stedman
- Biology Department and Center for Life in Extreme Environments, Portland State University, Portland, USA
| | | | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UC Louvain, Louvain-la-Neuve, Belgium
| | - Xu Peng
- Microbial Immunity Group, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGE, 63000, Clermont-Ferrand, France
| | - Petar Knezevic
- Faculty of Sciences Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | | | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, South Korea
| | | | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Andrea I Moreno Switt
- Escuela de Medicina Veterinaria, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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