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Meidaninikjeh S, Mohammadi P, Elikaei A. Bacteriophages and bacterial extracellular vesicles, threat or opportunity? Life Sci 2024; 350:122749. [PMID: 38821215 DOI: 10.1016/j.lfs.2024.122749] [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: 12/04/2023] [Revised: 03/25/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
Emergence of antimicrobial-resistant bacteria (AMR) is one of the health major problems worldwide. The scientists are looking for a novel method to treat infectious diseases. Phage therapy is considered a suitable approach for treating infectious diseases. However, there are different challenges in this way. Some biological aspects can probably influence on therapeutic results and further investigations are necessary to reach a successful phage therapy. Bacteriophage activity can influence by bacterial defense system. Bacterial extracellular vesicles (BEVs) are one of the bacterial defense mechanisms which can modify the results of bacteriophage activity. BEVs have the significant roles in the gene transferring, invasion, escape, and spreading of bacteriophages. In this review, the defense mechanisms of bacteria against bacteriophages, especially BEVs secretion, the hidden linkage of BEVs and bacteriophages, and its possible consequences on the bacteriophage activity as well phage therapy will be discussed.
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Affiliation(s)
- Sepideh Meidaninikjeh
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Parisa Mohammadi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
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2
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Meidaninikjeh S, Mohammadi P, Elikaei A. A simplified method of bacteriophage preparation for transmission electron microscope. J Virol Methods 2024; 328:114951. [PMID: 38750823 DOI: 10.1016/j.jviromet.2024.114951] [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: 12/09/2023] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/21/2024]
Abstract
Bacteriophages are viruses that infect bacteria. Researchers use different methods to study the characteristics of bacteriophages. Transmission electron microscope (TEM) is considered the best method to analyze these characteristics. However, the quality of TEM micrographs is significantly influenced by the preparation methods used to prepare the bacteriophages sample. In this study, researchers compared two different methods for preparing the bacteriophage samples. In one method was used SM buffer, while in the other used deionized water. The results were analyzed by TEM and compared with each other. Additionally, the viability of bacteriophage in deionized water and SM buffer at 4°C was determined through plaque assay within 72 hours. TEM micrographs showed that the quality of bacteriophage sample prepared with deionized water is superior to those prepared with SM buffer. Furthermore, the titer of the bacteriophages did not show a significant reduction during 72 hours in both SM and deionized water. In conclusion, the results suggested that preparation method can significantly impact the quality of TEM micrographs. Using sterile deionized water for the preparation of bacteriophages is a simple way to improve the quality of TEM micrographs and it is advisable to send the samples to the laboratory within 72 hours.
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Affiliation(s)
- Sepideh Meidaninikjeh
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Parisa Mohammadi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran
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3
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Zheng K, Liang Y, Paez-Espino D, Zou X, Gao C, Shao H, Sung YY, Mok WJ, Wong LL, Zhang YZ, Tian J, Chen F, Jiao N, Suttle CA, He J, McMinn A, Wang M. Identification of hidden N4-like viruses and their interactions with hosts. mSystems 2023; 8:e0019723. [PMID: 37702511 PMCID: PMC10654107 DOI: 10.1128/msystems.00197-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/19/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.
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Affiliation(s)
- Kaiyang Zheng
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yantao Liang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - David Paez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Mammoth Biosciences Inc., South San Francisco, California, USA
| | - Xiao Zou
- Qingdao Central Hospital, Qingdao, China
| | - Chen Gao
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Hongbing Shao
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Yu-Zhong Zhang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jianfeng He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Andrew McMinn
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Min Wang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
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4
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Jia HJ, Jia PP, Yin S, Bu LK, Yang G, Pei DS. Engineering bacteriophages for enhanced host range and efficacy: insights from bacteriophage-bacteria interactions. Front Microbiol 2023; 14:1172635. [PMID: 37323893 PMCID: PMC10264812 DOI: 10.3389/fmicb.2023.1172635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
Bacteriophages, the most abundant organisms on earth, have the potential to address the rise of multidrug-resistant bacteria resulting from the overuse of antibiotics. However, their high specificity and limited host range can hinder their effectiveness. Phage engineering, through the use of gene editing techniques, offers a means to enhance the host range of bacteria, improve phage efficacy, and facilitate efficient cell-free production of phage drugs. To engineer phages effectively, it is necessary to understand the interaction between phages and host bacteria. Understanding the interaction between the receptor recognition protein of bacteriophages and host receptors can serve as a valuable guide for modifying or replacing these proteins, thereby altering the receptor range of the bacteriophage. Research and development focused on the CRISPR-Cas bacterial immune system against bacteriophage nucleic acids can provide the necessary tools to promote recombination and counter-selection in engineered bacteriophage programs. Additionally, studying the transcription and assembly functions of bacteriophages in host bacteria can facilitate the engineered assembly of bacteriophage genomes in non-host environments. This review highlights a comprehensive summary of phage engineering methods, including in-host and out-of-host engineering, and the use of high-throughput methods to understand their role. The main aim of these techniques is to harness the intricate interactions between bacteriophages and hosts to inform and guide the engineering of bacteriophages, particularly in the context of studying and manipulating the host range of bacteriophages. By employing advanced high-throughput methods to identify specific bacteriophage receptor recognition genes, and subsequently introducing modifications or performing gene swapping through in-host recombination or out-of-host synthesis, it becomes possible to strategically alter the host range of bacteriophages. This capability holds immense significance for leveraging bacteriophages as a promising therapeutic approach against antibiotic-resistant bacteria.
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Affiliation(s)
- Huang-Jie Jia
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Supei Yin
- Urinary Nephropathy Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ling-Kang Bu
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Guan Yang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, China
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5
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Sun M, Chen F. Distribution of rare N4-like viruses in temperate estuaries unveiled by viromics. Environ Microbiol 2022; 24:6100-6111. [PMID: 36054739 DOI: 10.1111/1462-2920.16172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/11/2022] [Indexed: 01/12/2023]
Abstract
The relative abundance of N4-like viruses in two temperate estuaries was assessed using four different methods, read mapping to known N4-like virus isolates, read mapping to native viral contigs, reciprocal blast search based on core genes, and read taxonomy classification using Kaiju. Overall, N4-like viruses were found to be of low abundance in the estuarine viromes. When mapping reads to only known N4-like virus genomes, high occurrences of N4-like viruses infecting Roseobacter were found, with their diversity consisting mostly of locally isolated Roseobacter N4-like virus species. Both contig-based methods and Kaiju classification showed similar seasonal patterns for N4-like viruses, and redundancy analysis revealed a negative correlation between N4-like viruses and temperature, suggesting that N4-like viruses may be more abundant in colder water. The discrepancy of relative abundance estimates using different methods indicates that N4-like viruses are best represented by native viral sequences. Our study indicates that N4-like viruses are rare in the marine environment and also provide insight into the importance of including local viral sequences in reference databases.
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Affiliation(s)
- Mengqi Sun
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
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6
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Alharbi NM, Ziadi MM. Wastewater as a fertility source for novel bacteriophages against multi-drug resistant bacteria. Saudi J Biol Sci 2021; 28:4358-4364. [PMID: 34354420 PMCID: PMC8324929 DOI: 10.1016/j.sjbs.2021.04.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 01/21/2023] Open
Abstract
Antibiotic resistance is a common and serious public health worldwide. As an alternative to antibiotics, bacteriophage (phage) therapy offers one of the best solutions to antibiotic resistance. Bacteriophages survive where their bacterial hosts are found; thus, they exist in almost all environments and their applications are quite varied in the medical, environmental, and industrial fields. Moreover, a single phage or a mixture of phages can be used in phage therapy; mixed phages tend to be more effective in reducing the number and/or activity of pathogenic bacteria than that of a single phage.
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Affiliation(s)
- Najwa M. Alharbi
- College of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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7
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Ullah A, Qamash T, Khan FA, Sultan A, Ahmad S, Abbas M, Khattak MAK, Begum N, Din SU, Jamil J, Kalsoom. Characterization of a Coliphage AS1 isolated from sewage effluent in Pakistan. BRAZ J BIOL 2021; 82:e240943. [PMID: 34259715 DOI: 10.1590/1519-6984.240943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/14/2020] [Indexed: 01/21/2023] Open
Abstract
The emergence of multi-drug resistant (MDR) bacterial strains, which are posing a global health threat has developed the interest of scientists to use bacteriophages instead of conventional antibiotics therapy. In light of an increased interest in the use of phage as a bacterial control agent, the study aimed to isolate and characterize lytic phages from sewage effluent. During the current study, bacteriophage AS1 was isolated from sewage effluent against E.coli S2. The lytic activity of phageAS1 was limited to E.coli S2 strain showing monovalent behavior. The calculated phage titer was 3.5×109 pfu/ml. PhageAS1 was stable at a wide range of pH and temperature. The maximum stability was recorded at 37ºC and pH 7.0, while showing its normal lytic activity at temperature 60ºC and from pH 5.0 to11.0 respectively. At temperature 70ºC, phage activity was somewhat reduced whereas, further increase in temperature and decrease or increase in pH completely inactivated the phage. From the current study, it was concluded that waste water is a best source for finding bacteriophages against multi-drug resistant bacterial strains and can be used as bacterial control agent.
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Affiliation(s)
- A Ullah
- University of Swabi, Department of Microbiology, Swabi, KP, Pakistan
| | - T Qamash
- University of Swabi, Department of Microbiology, Swabi, KP, Pakistan
| | - F A Khan
- University of Okara, Department of Microbiology and Molecular Genetics, Okara, Pakistan
| | - A Sultan
- University of Swabi, Department of Microbiology, Swabi, KP, Pakistan
| | - S Ahmad
- University of Swabi, Department of Microbiology, Swabi, KP, Pakistan
| | - M Abbas
- Abdul Wali Khan University, Department of Pharmacy, Mardan, KP, Pakistan
| | - M A K Khattak
- University of Swabi, Department of Microbiology, Swabi, KP, Pakistan
| | - N Begum
- University of Swabi, Department of Microbiology, Swabi, KP, Pakistan
| | - S U Din
- Quaid E Azam University, Department of Microbiology, Islamabad, Pakistan
| | - J Jamil
- University of Swabi, Department of Microbiology, Swabi, KP, Pakistan
| | - Kalsoom
- University of Swabi, Department of Microbiology, Swabi, KP, Pakistan
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8
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Silva Batalha L, Pardini Gontijo MT, Vianna Novaes de Carvalho Teixeira A, Meireles Gouvêa Boggione D, Soto Lopez ME, Renon Eller M, Santos Mendonça RC. Encapsulation in alginate-polymers improves stability and allows controlled release of the UFV-AREG1 bacteriophage. Food Res Int 2020; 139:109947. [PMID: 33509500 DOI: 10.1016/j.foodres.2020.109947] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/21/2020] [Accepted: 11/28/2020] [Indexed: 11/16/2022]
Abstract
The bacteriophage UFV-AREG1 was used as a model organism to evaluate the encapsulation via extrusion using different hydrocolloids. Pure alginate [0.75%, 1.0%, 1.5% and 2.0% (m/v)] and mixtures of alginate [0.75% or 1.0% (m/v)] with carrageenan [1.25% (m/v)], chitosan [0.5% (m/v)], or whey protein [1.5% (m/v)] were used to produce bacteriophage-loaded beads. The encapsulating solutions presented flow behavior of non-Newtonian pseudoplastic fluids and the concentration of hydrocolloid did not influence (p > 0.05) the morphology of the beads, except for alginate-chitosan solutions, which presented the higher flow consistency index (K) and the lower flow behavior index (n). The encapsulation efficiency was about 99% and the confocal photomicrography of the encapsulated bacteriophages labeled with fluorescein isothiocyanate showed homogenous distribution of the viral particles within the beads. The phages remained viable in the beads of alginate-whey protein even when submitted to pH 2.5 for 2 h. Beads incubated directly in simulated intestinal fluid (pH 6.8) resulted in a minimal of 50% release of the UFV-AREG1 phages after 5 min, even when previously submitted to the simulated gastric fluid (pH 2.5). Encapsulation enabled phages to remain viable under refrigeration for five months. Encapsulated UFV-AREG1 phages were sensitive to dehydration, suggesting the need for protective agents. In this study, for the first-time bacteriophages were encapsulated in alginate-carrageenan beads, as well as alginate-chitosan as a bead-forming hydrocolloid. In addition, a novel procedure for encapsulating bacteriophages in alginate-whey protein was proposed. The assembled system showed efficiency in the encapsulation of UFV-AREG1 bacteriophages using different hydrocolloids and has potential to be used for the entrapment of a variety of bioactive compounds.
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Affiliation(s)
- Laís Silva Batalha
- Department of Food Technology, Universidade Federal de Viçosa (UFV), Viçosa, 36570-900 Minas Gerais, Brazil
| | - Marco Túlio Pardini Gontijo
- Department of Food Technology, Universidade Federal de Viçosa (UFV), Viçosa, 36570-900 Minas Gerais, Brazil; Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas, 13083-970, São Paulo, Brazil
| | | | | | - Maryoris Elisa Soto Lopez
- Department of Food Technology, Universidade Federal de Viçosa (UFV), Viçosa, 36570-900 Minas Gerais, Brazil; Department of Food Engineering, Universidad de Córdoba (UNICORDOBA), Montería 230002, Colombia
| | - Monique Renon Eller
- Department of Food Technology, Universidade Federal de Viçosa (UFV), Viçosa, 36570-900 Minas Gerais, Brazil.
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Liao Y, Lavenburg VM, Lennon M, Salvador A, Hsu AL, Wu VCH. The effects of environmental factors on the prevalence and diversity of bacteriophages lytic against the top six
non‐O157
Shiga toxin‐producing
Escherichia coli
on an organic farm. J Food Saf 2020. [DOI: 10.1111/jfs.12865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yen‐Te Liao
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service Western Regional Research Center Albany California USA
| | - Valerie M. Lavenburg
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service Western Regional Research Center Albany California USA
| | - Marion Lennon
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service Western Regional Research Center Albany California USA
| | - Alexandra Salvador
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service Western Regional Research Center Albany California USA
| | - Angeline L. Hsu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service Western Regional Research Center Albany California USA
| | - Vivian C. H. Wu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service Western Regional Research Center Albany California USA
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10
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Latino L, Midoux C, Vergnaud G, Pourcel C. Investigation of Pseudomonas aeruginosa strain PcyII-10 variants resisting infection by N4-like phage Ab09 in search for genes involved in phage adsorption. PLoS One 2019; 14:e0215456. [PMID: 30990839 PMCID: PMC6467409 DOI: 10.1371/journal.pone.0215456] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/02/2019] [Indexed: 12/20/2022] Open
Abstract
Bacteria and their bacteriophages coexist and coevolve for the benefit of both in a mutualistic association. Multiple mechanisms are used by bacteria to resist phages in a trade-off between survival and maintenance of fitness. In vitro studies allow inquiring into the fate of virus and host in different conditions aimed at mimicking natural environment. We analyse here the mutations emerging in a clinical Pseudomonas aeruginosa strain in response to infection by Ab09, a N4-like lytic podovirus and describe a variety of chromosomal deletions and mutations conferring resistance. Some deletions result from illegitimate recombination taking place during long-term maintenance of the phage genome. Phage variants with mutations in a tail fiber gene are selected during pseudolysogeny with the capacity to infect resistant cells and produce large plaques. These results highlight the complex host/phage association and suggest that phage Ab09 promotes bacterial chromosome rearrangements. Finally this study points to the possible role of two bacterial genes in Ab09 phage adhesion to the cell, rpsB encoding protein S2 of the 30S ribosomal subunit and ORF1587 encoding a Wzy-like membrane protein involved in LPS biosynthesis.
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Affiliation(s)
- Libera Latino
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Cédric Midoux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
- * E-mail: ,
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11
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Zhan Y, Chen F. Bacteriophages that infect marine roseobacters: genomics and ecology. Environ Microbiol 2019; 21:1885-1895. [DOI: 10.1111/1462-2920.14504] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 12/01/2018] [Accepted: 12/11/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Yuanchao Zhan
- Institute of Marine and Environmental TechnologyUniversity of Maryland Center for Environmental Science Baltimore MD USA
| | - Feng Chen
- Institute of Marine and Environmental TechnologyUniversity of Maryland Center for Environmental Science Baltimore MD USA
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12
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Shende RK, Hirpurkar SD, Sannat C, Rawat N, Pandey V. Isolation and characterization of bacteriophages with lytic activity against common bacterial pathogens. Vet World 2017; 10:973-978. [PMID: 28919692 PMCID: PMC5591488 DOI: 10.14202/vetworld.2017.973-978] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/25/2017] [Indexed: 12/12/2022] Open
Abstract
Aim: Present investigation was conducted to isolate and characterize bacteriophages with lytic activity against common bacterial pathogens. Materials and Methods: A total of 60 samples of animal waste disposal from cattle (42) and buffalo (18) farms were collected from three different strata, i.e., top, mid, and bottom of collection tank. Samples were primarily subjected to rapid detection methods, and then isolation of phage was done by double agar layer method using Bacillus subtilis (BsH) and Escherichia coli (EH) as host system. Phages were characterized on the basis of plaque morphology, temperature, pH susceptibility, and host range. Results: Recovery of phages was higher from dairy cattle farm waste (78.57%) as compared to buffalo farm waste (72.22%) and bottom layer of tank showed maximum recovery. Bacillus subtilis (91%) supported the growth of more phages as compared to E. coli (9%). Three different phage morphotypes were observed each against Bacillus subtilis (BsHR1, BsHR2, and BsHR3) and E. coli (EHR1, EHR2, and EHR3). Mean phage titer of above six phage isolates ranged between 3×1010 and 5×1012 plaque forming units/ml. Viability of phages was by, and large unaffected at 70°C within 2-3 min, and phage isolates were completely inactivated below pH 3 and above 11. Coliphage EHR1 had widest host range followed by BsHR1 and BsHR2 while EHR2, EHR3, and BsHR3 had low lytic activity. Conclusion: It could be concluded from the present study that the Bacillus and Coli phage has wide host range and thus exhibits the potential to be used as drug substitute tool against common bacterial pathogens.
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Affiliation(s)
- R K Shende
- Department of Veterinary Microbiology, College of Veterinary Science & Animal Husbandry, Anjora Chhattisgarh Kamdhenu Vishwavidyalaya, Durg, Chhattisgarh, India
| | - S D Hirpurkar
- Department of Veterinary Microbiology, College of Veterinary Science & Animal Husbandry, Anjora Chhattisgarh Kamdhenu Vishwavidyalaya, Durg, Chhattisgarh, India
| | - C Sannat
- Department of Veterinary Microbiology, College of Veterinary Science & Animal Husbandry, Anjora Chhattisgarh Kamdhenu Vishwavidyalaya, Durg, Chhattisgarh, India
| | - Nidhi Rawat
- Department of Veterinary Microbiology, College of Veterinary Science & Animal Husbandry, Anjora Chhattisgarh Kamdhenu Vishwavidyalaya, Durg, Chhattisgarh, India
| | - Vinay Pandey
- Department of Animal Nutrition, College of Veterinary Science & Animal Husbandry, Anjora, Chhattisgarh Kamdhenu Vishwavidyalaya, Durg, Chhattisgarh, India
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13
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Prokhorov NS, Riccio C, Zdorovenko EL, Shneider MM, Browning C, Knirel YA, Leiman PG, Letarov AV. Function of bacteriophage G7C esterase tailspike in host cell adsorption. Mol Microbiol 2017; 105:385-398. [PMID: 28513100 DOI: 10.1111/mmi.13710] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2017] [Indexed: 12/29/2022]
Abstract
Bacteriophages recognize and bind to their hosts with the help of receptor-binding proteins (RBPs) that emanate from the phage particle in the form of fibers or tailspikes. RBPs show a great variability in their shapes, sizes, and location on the particle. Some RBPs are known to depolymerize surface polysaccharides of the host while others show no enzymatic activity. Here we report that both RBPs of podovirus G7C - tailspikes gp63.1 and gp66 - are essential for infection of its natural host bacterium E. coli 4s that populates the equine intestinal tract. We characterize the structure and function of gp63.1 and show that unlike any previously described RPB, gp63.1 deacetylates surface polysaccharides of E. coli 4s leaving the backbone of the polysaccharide intact. We demonstrate that gp63.1 and gp66 form a stable complex, in which the N-terminal part of gp66 serves as an attachment site for gp63.1 and anchors the gp63.1-gp66 complex to the G7C tail. The esterase domain of gp63.1 as well as domains mediating the gp63.1-gp66 interaction is widespread among all three families of tailed bacteriophages.
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Affiliation(s)
- Nikolai S Prokhorov
- Research Center of Biotechnology, Russian Academy of Sciences, Winogradsky Institute of Microbiology, 7b2 pr. 60-letiya Oktyabrya, Moscow, 117312, Russia
| | - Cristian Riccio
- École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, Lausanne, 1015, Switzerland
| | - Evelina L Zdorovenko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky pr, Moscow, 119991, Russia
| | - Mikhail M Shneider
- École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, Lausanne, 1015, Switzerland.,Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya St, Moscow, 117997, Russia
| | - Christopher Browning
- École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, Lausanne, 1015, Switzerland
| | - Yuriy A Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky pr, Moscow, 119991, Russia
| | - Petr G Leiman
- École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, Lausanne, 1015, Switzerland
| | - Andrey V Letarov
- Research Center of Biotechnology, Russian Academy of Sciences, Winogradsky Institute of Microbiology, 7b2 pr. 60-letiya Oktyabrya, Moscow, 117312, Russia.,Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, 119991, Russia
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14
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Jończyk-Matysiak E, Weber-Dąbrowska B, Żaczek M, Międzybrodzki R, Letkiewicz S, Łusiak-Szelchowska M, Górski A. Prospects of Phage Application in the Treatment of Acne Caused by Propionibacterium acnes. Front Microbiol 2017; 8:164. [PMID: 28228751 PMCID: PMC5296327 DOI: 10.3389/fmicb.2017.00164] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 01/23/2017] [Indexed: 12/11/2022] Open
Abstract
Propionibacterium acnes is associated with purulent skin infections, and it poses a global problem for both patients and doctors. Acne vulgaris (acne) remains a problem due to its chronic character and difficulty of treatment, as well as its large impact on patients' quality of life. Due to the chronic course of the disease, treatment is long lasting, and often ineffective. Currently there are data regarding isolation of P. acnes phages, and there have been numerous studies on phage killing of P. acnes, but no data are available on phage application specifically in acne treatment. In this review, we have summarized the current knowledge on the phages active against P. acnes described so far and their potential application in the treatment of acne associated with P. acnes. The treatment of acne with phages may be important in order to reduce the overuse of antibiotics, which are currently the main acne treatment. However, more detailed studies are first needed to understand phage functioning in the skin microbiome and the possibility to use phages to combat P. acnes.
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Affiliation(s)
- Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland
| | - Maciej Żaczek
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Ryszard Międzybrodzki
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Department of Clinical Immunology, Transplantation Institute, Medical University of WarsawWarsaw, Poland
| | - Sławomir Letkiewicz
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Medical Sciences Institute, Katowice School of EconomicsKatowice, Poland
| | - Marzanna Łusiak-Szelchowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Department of Clinical Immunology, Transplantation Institute, Medical University of WarsawWarsaw, Poland
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15
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Weber-Dąbrowska B, Jończyk-Matysiak E, Żaczek M, Łobocka M, Łusiak-Szelachowska M, Górski A. Bacteriophage Procurement for Therapeutic Purposes. Front Microbiol 2016; 7:1177. [PMID: 27570518 PMCID: PMC4981656 DOI: 10.3389/fmicb.2016.01177] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/18/2016] [Indexed: 01/05/2023] Open
Abstract
Bacteriophages (phages), discovered 100 years ago, are able to infect and destroy only bacterial cells. In the current crisis of antibiotic efficacy, phage therapy is considered as a supplementary or even alternative therapeutic approach. Evolution of multidrug-resistant and pandrug-resistant bacterial strains poses a real threat, so it is extremely important to have the possibility to isolate new phages for therapeutic purposes. Our phage laboratory and therapy center has extensive experience with phage isolation, characterization, and therapeutic application. In this article we present current progress in bacteriophages isolation and use for therapeutic purposes, our experience in this field and its practical implications for phage therapy. We attempt to summarize the state of the art: properties of phages, the methods for their isolation, criteria of phage selection for therapeutic purposes and limitations of their use. Perspectives for the use of genetically engineered phages to specifically target bacterial virulence-associated genes are also briefly presented.
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Affiliation(s)
- Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Maciej Żaczek
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland; Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life SciencesWarsaw, Poland
| | - Marzanna Łusiak-Szelachowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences Wroclaw, Poland
| | - Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWroclaw, Poland; Department of Clinical Immunology, Transplantation Institute, Medical University of WarsawWarsaw, Poland
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16
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A novel roseobacter phage possesses features of podoviruses, siphoviruses, prophages and gene transfer agents. Sci Rep 2016; 6:30372. [PMID: 27460944 PMCID: PMC4961962 DOI: 10.1038/srep30372] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/30/2016] [Indexed: 11/09/2022] Open
Abstract
Bacteria in the Roseobacter lineage have been studied extensively due to their significant biogeochemical roles in the marine ecosystem. However, our knowledge on bacteriophage which infects the Roseobacter clade is still very limited. Here, we report a new bacteriophage, phage DSS3Φ8, which infects marine roseobacter Ruegeria pomeroyi DSS-3. DSS3Φ8 is a lytic siphovirus. Genomic analysis showed that DSS3Φ8 is most closely related to a group of siphoviruses, CbK-like phages, which infect freshwater bacterium Caulobacter crescentus. DSS3Φ8 contains a smaller capsid and has a reduced genome size (146 kb) compared to the CbK-like phages (205-279 kb). DSS3Φ8 contains the DNA polymerase gene which is closely related to T7-like podoviruses. DSS3Φ8 also contains the integrase and repressor genes, indicating its potential to involve in lysogenic cycle. In addition, four GTA (gene transfer agent) genes were identified in the DSS3Φ8 genome. Genomic analysis suggests that DSS3Φ8 is a highly mosaic phage that inherits the genetic features from siphoviruses, podoviruses, prophages and GTAs. This is the first report of CbK-like phages infecting marine bacteria. We believe phage isolation is still a powerful tool that can lead to discovery of new phages and help interpret the overwhelming unknown sequences in the viral metagenomics.
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