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González-Gómez JP, Rodríguez-Arellano SN, Gomez-Gil B, Vergara-Jiménez MDJ, Chaidez C. Genomic and biological characterization of bacteriophages against Enterobacter cloacae, a high-priority pathogen. Virology 2024; 595:110100. [PMID: 38714025 DOI: 10.1016/j.virol.2024.110100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
Enterobacter cloacae is a clinically significant pathogen due to its multi-resistance to antibiotics, presenting a challenge in the treatment of infections. As concerns over antibiotic resistance escalate, novel therapeutic approaches have been explored. Bacteriophages, characterized by their remarkable specificity and ability to self-replicate within target bacteria, are emerging as a promising alternative therapy. In this study, we isolated and partially characterized nine lytic bacteriophages targeting E. cloacae, with two selected for comprehensive genomic analysis based on their host range and bacteriolytic activity. All identified phages exhibited a narrow host range, demonstrated stability within a temperature range of 30-60 °C, displayed pH tolerance from 3 to 10, and showed an excellent bacteriolytic capacity for up to 18 h. Notably, the fully characterized phage genomes revealed an absence of lysogenic, virulence, or antibiotic-resistance genes, positioning them as promising candidates for therapeutic intervention against E. cloacae-related diseases. Nonetheless, translating this knowledge into practical therapeutic applications mandates a deeper understanding of bacteriophage interactions within complex biological environments.
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Affiliation(s)
- Jean Pierre González-Gómez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico
| | | | - Bruno Gomez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Unidad Mazatlán en Acuicultura y Manejo Ambiental, AP 711, Mazatlan, Sinaloa, Mexico
| | | | - Cristobal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacan, Sinaloa, Mexico.
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2
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Schmid N, Brandt D, Walasek C, Rolland C, Wittmann J, Fischer D, Müsken M, Kalinowski J, Thormann K. An autonomous plasmid as an inovirus phage satellite. Appl Environ Microbiol 2024; 90:e0024624. [PMID: 38597658 DOI: 10.1128/aem.00246-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/11/2024] Open
Abstract
Bacterial viruses (phages) are potent agents of lateral gene transfer and thus are important drivers of evolution. A group of mobile genetic elements, referred to as phage satellites, exploits phages to disseminate their own genetic material. Here, we isolated a novel member of the family Inoviridae, Shewanella phage Dolos, along with an autonomously replicating plasmid, pDolos. Dolos causes a chronic infection in its host Shewanella oneidensis by phage production with only minor effects on the host cell proliferation. When present, plasmid pDolos hijacks Dolos functions to be predominantly packaged into phage virions and released into the environment and, thus, acts as a phage satellite. pDolos can disseminate further genetic material encoding, e.g., resistances or fluorophores to host cells sensitive to Dolos infection. Given the rather simple requirements of a plasmid for takeover of an inovirus and the wide distribution of phages of this group, we speculate that similar phage-satellite systems are common among bacteria.IMPORTANCEPhage satellites are mobile genetic elements, which hijack phages to be transferred to other host cells. The vast majority of these phage satellites integrate within the host's chromosome, and they all carry remaining phage genes. Here, we identified a novel phage satellite, pDolos, which uses an inovirus for dissemination. pDolos (i) remains as an autonomously replicating plasmid within its host, (ii) does not carry recognizable phage genes, and (iii) is smaller than any other phage satellites identified so far. Thus, pDolos is the first member of a new class of phage satellites, which resemble natural versions of phagemids.
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Affiliation(s)
- Nicole Schmid
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - David Brandt
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Claudia Walasek
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Clara Rolland
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Dorian Fischer
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research GmbH, Braunschweig, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Kai Thormann
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
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3
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Warwick-Dugdale J, Tian F, Michelsen ML, Cronin DR, Moore K, Farbos A, Chittick L, Bell A, Zayed AA, Buchholz HH, Bolanos LM, Parsons RJ, Allen MJ, Sullivan MB, Temperton B. Long-read powered viral metagenomics in the oligotrophic Sargasso Sea. Nat Commun 2024; 15:4089. [PMID: 38744831 PMCID: PMC11094077 DOI: 10.1038/s41467-024-48300-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.
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Affiliation(s)
- Joanna Warwick-Dugdale
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK.
- Plymouth Marine Laboratory, Plymouth, Devon, PL1 3DH, UK.
| | - Funing Tian
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | | | - Dylan R Cronin
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | - Karen Moore
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Audrey Farbos
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Lauren Chittick
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Ashley Bell
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Ahmed A Zayed
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
| | - Holger H Buchholz
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Luis M Bolanos
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Rachel J Parsons
- Bermuda Institute of Ocean Sciences, St.George's, GE, 01, Bermuda
- School of Ocean Futures, Arizona State University, Tempe, AZ, US
| | - Michael J Allen
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK
| | - Matthew B Sullivan
- Center of Microbiome Science and Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH, 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, Devon, EX4 4SB, UK.
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An N, Wu Q, Fang Z, Xiang L, Liu Q, Tan L, Weng Q. Genome analysis and classification of Xanthomonas bacteriophage AhaSv, a new member of the genus Salvovirus. Arch Virol 2024; 169:117. [PMID: 38739272 DOI: 10.1007/s00705-024-06047-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024]
Abstract
Xanthomonas phage AhaSv was isolated from lake water. Genome sequencing showed that its genome is a linear dsDNA molecule with a length of 55,576 bp and a G+C content of 63.23%. Seventy-one open reading frames (ORFs) were predicted, and no tRNAs were found in the genome. Phylogenetic analysis showed that AhaSv is closely related to members of the genus Salvovirus of the family Casjensviridae. Intergenomic similarity values between phage AhaSv and homologous phages were up to 90.6%, suggesting that phage AhaSv should be considered a member of a new species in the genus Salvovirus.
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Affiliation(s)
- Ni An
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Lan Xiang
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China.
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China.
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Kobakhidze S, Koulouris S, Kakabadze N, Kotetishvili M. Genetic recombination-mediated evolutionary interactions between phages of potential industrial importance and prophages of their hosts within or across the domains of Escherichia, Listeria, Salmonella, Campylobacter, and Staphylococcus. BMC Microbiol 2024; 24:155. [PMID: 38704526 PMCID: PMC11069274 DOI: 10.1186/s12866-024-03312-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND The in-depth understanding of the role of lateral genetic transfer (LGT) in phage-prophage interactions is essential to rationalizing phage applications for human and animal therapy, as well as for food and environmental safety. This in silico study aimed to detect LGT between phages of potential industrial importance and their hosts. METHODS A large array of genetic recombination detection algorithms, implemented in SplitsTree and RDP4, was applied to detect LGT between various Escherichia, Listeria, Salmonella, Campylobacter, Staphylococcus, Pseudomonas, and Vibrio phages and their hosts. PHASTER and RAST were employed respectively to identify prophages across the host genome and to annotate LGT-affected genes with unknown functions. PhageAI was used to gain deeper insights into the life cycle history of recombined phages. RESULTS The split decomposition inferences (bootstrap values: 91.3-100; fit: 91.433-100), coupled with the Phi (0.0-2.836E-12) and RDP4 (P being well below 0.05) statistics, provided strong evidence for LGT between certain Escherichia, Listeria, Salmonella, and Campylobacter virulent phages and prophages of their hosts. The LGT events entailed mainly the phage genes encoding for hypothetical proteins, while some of these genetic loci appeared to have been affected even by intergeneric recombination in specific E. coli and S. enterica virulent phages when interacting with their host prophages. Moreover, it is shown that certain L. monocytogenes virulent phages could serve at least as the donors of the gene loci, involved in encoding for the basal promoter specificity factor, for L. monocytogenes. In contrast, the large genetic clusters were determined to have been simultaneously exchanged by many S. aureus prophages and some Staphylococcus temperate phages proposed earlier as potential therapeutic candidates (in their native or modified state). The above genetic clusters were found to encompass multiple genes encoding for various proteins, such as e.g., phage tail proteins, the capsid and scaffold proteins, holins, and transcriptional terminator proteins. CONCLUSIONS It is suggested that phage-prophage interactions, mediated by LGT (including intergeneric recombination), can have a far-reaching impact on the co-evolutionary trajectories of industrial phages and their hosts especially when excessively present across microbially rich environments.
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Affiliation(s)
- Saba Kobakhidze
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia
- Faculty of Medicine, Iv. Javakhishvili Tbilisi State University, 1 Ilia Chavchavadze Ave. 0179, Tbilisi, Georgia
| | - Stylianos Koulouris
- Directorate General for Health and Food Safety (DG-SANTE), European Commission, 1049, Bruxelles/Brussel, Belgium
| | - Nata Kakabadze
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia
| | - Mamuka Kotetishvili
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitary, 78 D. Uznadze St. 0102, Tbilisi, Georgia.
- Scientific Research Institute, School of Science and Technology, the University of Georgia, 77a M. Kostava St., 0171, Tbilisi, Georgia.
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Wang Z, Yang X, Wang H, Wang S, Fang R, Li X, Xing J, Wu Q, Li Z, Song N. Characterization and efficacy against carbapenem-resistant Acinetobacter baumannii of a novel Friunavirus phage from sewage. Front Cell Infect Microbiol 2024; 14:1382145. [PMID: 38736748 PMCID: PMC11086170 DOI: 10.3389/fcimb.2024.1382145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/08/2024] [Indexed: 05/14/2024] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) has become a new threat in recent years, owing to its rapidly increasing resistance to antibiotics and new effective therapies are needed to combat this pathogen. Phage therapy is considered to be the most promising alternative for treating CRAB infections. In this study, a novel phage, Ab_WF01, which can lyse clinical CRAB, was isolated and characterized from hospital sewage. The multiplicity of infection, morphology, one-step growth curve, stability, sensitivity, and lytic activity of the phage were also investigated. The genome of phage Ab_WF01 was 41, 317 bp in size with a GC content of 39.12% and encoded 51 open reading frames (ORFs). tRNA, virulence, and antibiotic resistance genes were not detected in the phage genome. Comparative genomic and phylogenetic analyses suggest that phage Ab_WF01 is a novel species of the genus Friunavirus, subfamily Beijerinckvirinae, and family Autographiviridae. The in vivo results showed that phage Ab_WF01 significantly increased the survival rate of CRAB-infected Galleria mellonella (from 0% to 70% at 48 h) and mice (from 0% to 60% for 7 days). Moreover, after day 3 post-infection, phage Ab_WF01 reduced inflammatory response, with strongly ameliorated histological damage and bacterial clearance in infected tissue organs (lungs, liver, and spleen) in mouse CRAB infection model. Taken together, these results show that phage Ab_WF01 holds great promise as a potential alternative agent with excellent stability for against CRAB infections.
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Affiliation(s)
- Zhitao Wang
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Xue Yang
- School of Pharmacy, Shandong Second Medical University, Weifang, China
| | - Hui Wang
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Shuxian Wang
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Ren Fang
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Xiaotian Li
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Jiayin Xing
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Qianqian Wu
- Department of Clinical Laboratory, Affiliated Hospital of Shandong Second Medical University, Weifang, China
| | - Zhaoli Li
- SAFE Pharmaceutical Technology Co. Ltd., Beijing, China
| | - Ningning Song
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
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Ely B, Hils M, Clarke A, Albert M, Holness N, Lenski J, Mohammadi T. New Genera and Species of Caulobacter and Brevundimonas Bacteriophages Provide Insights into Phage Genome Evolution. Viruses 2024; 16:641. [PMID: 38675982 PMCID: PMC11053796 DOI: 10.3390/v16040641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Previous studies have identified diverse bacteriophages that infect Caulobacter vibrioides strain CB15 ranging from small RNA phages to four genera of jumbo phages. In this study, we focus on 20 bacteriophages whose genomes range from 40 to 60 kb in length. Genome comparisons indicated that these diverse phages represent six Caulobacter phage genera and one additional genus that includes both Caulobacter and Brevundimonas phages. Within species, comparisons revealed that both single base changes and inserted or deleted genetic material cause the genomes of closely related phages to diverge. Among genera, the basic gene order and the orientation of key genes were retained with most of the observed variation occurring at ends of the genomes. We hypothesize that the nucleotide sequences of the ends of these phage genomes are less important than the need to maintain the size of the genome and the stability of the corresponding mRNAs.
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Affiliation(s)
- Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA (A.C.); (M.A.); (T.M.)
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Zhao H, Yang M, Fan X, Gui Q, Yi H, Tong Y, Xiao W. A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants. Viruses 2024; 16:535. [PMID: 38675877 PMCID: PMC11054999 DOI: 10.3390/v16040535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
The concentration of viruses in sewage sludge is significantly higher (10-1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions.
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Affiliation(s)
- Haozhe Zhao
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China; (H.Z.); (M.Y.); (X.F.); (Q.G.); (H.Y.)
| | - Mingfei Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China; (H.Z.); (M.Y.); (X.F.); (Q.G.); (H.Y.)
| | - Xiang Fan
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China; (H.Z.); (M.Y.); (X.F.); (Q.G.); (H.Y.)
| | - Qian Gui
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China; (H.Z.); (M.Y.); (X.F.); (Q.G.); (H.Y.)
| | - Hao Yi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China; (H.Z.); (M.Y.); (X.F.); (Q.G.); (H.Y.)
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Xiao
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China; (H.Z.); (M.Y.); (X.F.); (Q.G.); (H.Y.)
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Babkin IV, Tikunov AY, Baykov IK, Morozova VV, Tikunova NV. Genome Analysis of Epsilon CrAss-like Phages. Viruses 2024; 16:513. [PMID: 38675856 PMCID: PMC11054128 DOI: 10.3390/v16040513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon crAss-like phage genomes was found. Comparative analysis indicated that epsilon crAss-like phages are divided into two putative genera, which were proposed to be named Epsilonunovirus and Epsilonduovirus; CrAssE-Sib belongs to the former. The crAssE-Sib genome contains a diversity-generating retroelement (DGR) cassette with all essential elements, including the reverse transcriptase (RT) and receptor binding protein (RBP) genes. However, this RT contains the GxxxSP motif in its fourth domain instead of the usual GxxxSQ motif found in all known phage and bacterial DGRs. RBP encoded by CrAssE-Sib and other Epsilonunoviruses has an unusual structure, and no similar phage proteins were found. In addition, crAssE-Sib and other Epsilonunoviruses encode conserved prophage repressor and anti-repressors that could be involved in lysogenic-to-lytic cycle switches. Notably, DNA primase sequences of epsilon crAss-like phages are not included in the monophyletic group formed by the DNA primases of all other crAss-like phages. Therefore, epsilon crAss-like phage substantially differ from other crAss-like phages, indicating the need to classify these phages into a separate family.
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Affiliation(s)
- Igor V. Babkin
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Artem Y. Tikunov
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Ivan K. Baykov
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
- Shared Research Facility “Siberian Circular Photon Source” (SRF “SKIF”) of Boreskov Institute of Catalysis SB RAS, 630090 Novosibirsk, Russia
| | - Vera V. Morozova
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Nina V. Tikunova
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
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10
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Xi H, Fu B, Sheng Q, Luo M, Sun L. Isolation and Characterization of a Lytic Bacteriophage RH-42-1 of Erwinia amylovora from Orchard Soil in China. Viruses 2024; 16:509. [PMID: 38675852 PMCID: PMC11054837 DOI: 10.3390/v16040509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Fire blight, caused by the bacterium Erwinia amylovora, is a major threat to pear production worldwide. Bacteriophages, viruses that infect bacteria, are a promising alternative to antibiotics for controlling fire blight. In this study, we isolated a novel bacteriophage, RH-42-1, from Xinjiang, China. We characterized its biological properties, including host range, plaque morphology, infection dynamics, stability, and sensitivity to various chemicals. RH-42-1 infected several E. amylovora strains but not all. It produced clear, uniform plaques and exhibited optimal infectivity at a multiplicity of infection (MOI) of 1, reaching a high titer of 9.6 × 109 plaque-forming units (PFU)/mL. The bacteriophage had a short latent period (10 min), a burst size of 207 PFU/cell, and followed a sigmoidal one-step growth curve. It was stable at temperatures up to 60 °C but declined rapidly at higher temperatures. RH-42-1 remained viable within a pH range of 5 to 9 and was sensitive to extreme pH values. The bacteriophage demonstrates sustained activity upon exposure to ultraviolet radiation for 60 min, albeit with a marginal reduction. In our assays, it exhibited a certain level of resistance to 5% chloroform (CHCl3), 5% isopropanol (C3H8O), and 3% hydrogen peroxide (H2O2), which had little effect on its activity, whereas it showed sensitivity to 75% ethanol (C2H5OH). Electron microscopy revealed that RH-42-1 has a tadpole-shaped morphology. Its genome size is 14,942 bp with a GC content of 48.19%. Based on these characteristics, RH-42-1 was identified as a member of the Tectiviridae family, Alphatectivirus genus. This is the first report of a bacteriophage in this genus with activity against E. amylovora.
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Affiliation(s)
- Haishen Xi
- The Department of Plant Pathology, College of Agronomy at Xinjiang Agricultural University/Key Laboratory of Detection and Control of Agricultural and Forest Pests, Urumqi 830052, China; (H.X.); (B.F.)
- Ministry of Agriculture and Rural Affairs Key Laboratory for Pests and Diseases Control of Northwest Arid Oasis Agricultural Foreign Invasion Species, Urumqi 830052, China
| | - Benzhong Fu
- The Department of Plant Pathology, College of Agronomy at Xinjiang Agricultural University/Key Laboratory of Detection and Control of Agricultural and Forest Pests, Urumqi 830052, China; (H.X.); (B.F.)
- Ministry of Agriculture and Rural Affairs Key Laboratory for Pests and Diseases Control of Northwest Arid Oasis Agricultural Foreign Invasion Species, Urumqi 830052, China
| | - Qiang Sheng
- Xinjiang Bayingolin Mongolian Autonomous Prefecture Academy of Agricultural Sciences, Korla 841003, China;
| | - Ming Luo
- The Department of Plant Pathology, College of Agronomy at Xinjiang Agricultural University/Key Laboratory of Detection and Control of Agricultural and Forest Pests, Urumqi 830052, China; (H.X.); (B.F.)
- Ministry of Agriculture and Rural Affairs Key Laboratory for Pests and Diseases Control of Northwest Arid Oasis Agricultural Foreign Invasion Species, Urumqi 830052, China
| | - Liying Sun
- The Department of Plant Pathology, College of Plant Protection, Northwest A&F University, Yangling 712100, China
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Zhu C, Li J, Liu Y, Jin F, Wang Z, Tong Y, Qin J, Fang B. Genomic analysis and characterization of bacteriophage vB_SpuS_NX263 infecting Salmonella enterica subsp. enterica serovar Pullorum. Arch Virol 2023; 168:216. [PMID: 37525023 DOI: 10.1007/s00705-023-05841-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 06/20/2023] [Indexed: 08/02/2023]
Abstract
In this study, a new Salmonella phage, NX263, was isolated from sewage. This phage could lyse 90.57% (48/53) of the bacterial strains tested and showed good activity over a wide range of temperature (up to 60°C) and pH (5-10). Phylogenetic analysis showed that it should be classified as a member of the genus Skatevirus. The genome of phage NX263 is 46,574 bp in length with a GC content of 45.52%. It contains 89 open reading frames and two tRNA genes. No lysogeny, drug resistance, or virulence-associated genes were identified in the genome sequence, suggesting that this phage could potentially be used to treat Salmonella Pullorum infections.
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Affiliation(s)
- Chunyang Zhu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Jing Li
- Beijing Advanced Innovation Centre for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Yang Liu
- Wen's Foodstuffs Group Co., Ltd, Yunfu, 527439, China
| | - Fenhua Jin
- Guangdong Wens Dahuanong Biotechnology Co., Ltd, 527400, Yunfu, China
| | - Zhanxin Wang
- Wen's Foodstuffs Group Co., Ltd, Yunfu, 527439, China
| | - Yigang Tong
- Beijing Advanced Innovation Centre for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, 100029, Beijing, China
| | - Jianping Qin
- Wen's Foodstuffs Group Co., Ltd, Yunfu, 527439, China.
| | - Binghu Fang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.
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Zhao X, Sun C, Jin M, Chen J, Xing L, Yan J, Wang H, Liu Z, Chen WH. Enrichment Culture but Not Metagenomic Sequencing Identified a Highly Prevalent Phage Infecting Lactiplantibacillus plantarum in Human Feces. Microbiol Spectr 2023; 11:e0434022. [PMID: 36995238 PMCID: PMC10269749 DOI: 10.1128/spectrum.04340-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/07/2023] [Indexed: 03/31/2023] Open
Abstract
Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human diseases, but its phages in the human gut remain unexplored. Here, we report its first gut phage, Gut-P1, which we systematically screened using metagenomic sequencing, virus-like particle (VLP) sequencing, and enrichment culture from 35 fecal samples. Gut-P1 is virulent, belongs to the Douglaswolinvirus genus, and is highly prevalent in the gut (~11% prevalence); it has a genome of 79,928 bp consisting of 125 protein coding genes and displaying low sequence similarities to public L. plantarum phages. Physiochemical characterization shows that it has a short latent period and adapts to broad ranges of temperatures and pHs. Furthermore, Gut-P1 strongly inhibits the growth of L. plantarum strains at a multiplicity of infection (MOI) of 1e-6. Together, these results indicate that Gut-P1 can greatly impede the application of L. plantarum in humans. Strikingly, Gut-P1 was identified only in the enrichment culture, not in our metagenomic or VLP sequencing data nor in any public human phage databases, indicating the inefficiency of bulk sequencing in recovering low-abundance but highly prevalent phages and pointing to the unexplored hidden diversity of the human gut virome despite recent large-scale sequencing and bioinformatics efforts. IMPORTANCE As Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human gut-related diseases, its bacteriophages may pose a certain threat to their further application and should be identified and characterized more often from the human intestine. Here, we isolated and identified the first gut L. plantarum phage that is prevalent in a Chinese population. This phage, Gut-P1, is virulent and can strongly inhibit the growth of multiple L. plantarum strains at low MOIs. Our results also show that bulk sequencing is inefficient at recovering low-abundance but highly prevalent phages such as Gut-P1, suggesting that the hidden diversity of human enteroviruses has not yet been explored. Our results call for innovative approaches to isolate and identify intestinal phages from the human gut and to rethink our current understanding of the enterovirus, particularly its underestimated diversity and overestimated individual specificity.
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Affiliation(s)
- Xueyang Zhao
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Menglu Jin
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jingchao Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lulu Xing
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jin Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hailei Wang
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Zhi Liu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, China
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d’Acapito A, Roret T, Zarkadas E, Mocaër PY, Lelchat F, Baudoux AC, Schoehn G, Neumann E. Structural Study of the Cobetia marina Bacteriophage 1 (Carin-1) by Cryo-EM. J Virol 2023; 97:e0024823. [PMID: 36943070 PMCID: PMC10134823 DOI: 10.1128/jvi.00248-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/23/2023] Open
Abstract
Most of studied bacteriophages (phages) are terrestrial viruses. However, marine phages are shown to be highly involved in all levels of oceanic regulation. They are, however, still largely overlooked by the scientific community. By inducing cell lysis on half of the bacterial population daily, their role and influence on the bacterial biomass and evolution, as well as their impact in the global biogeochemical cycles, is undeniable. Cobetia marina virus 1 (Carin-1) is a member of the Podoviridae family infecting the γ-protoabacteria C. marina. Here, we present the almost complete, nearly-atomic resolution structure of Carin-1 comprising capsid, portal, and tail machineries at 3.5 Å, 3.8 Å and 3.9 Å, respectively, determined by cryo-electron microscopy (cryo-EM). Our experimental results, combined with AlphaFold2 (AF), allowed us to obtain the nearly-atomic structure of Carin-1 by fitting and refining the AF atomic models in the high resolution cryo-EM map, skipping the bottleneck of de-novo manual building and speeding up the structure determination process. Our structural results highlighted the T7-like nature of Carin1, as well as several novel structural features like the presence of short spikes on the capsid, reminiscent those described for Rhodobacter capsulatus gene transfer agent (RcGTA). This is, to our knowledge, the first time such assembly is described for a bacteriophage, shedding light into the common evolution and shared mechanisms between gene transfer agents and phages. This first full structure determined for a marine podophage allowed to propose an infection mechanism different than the one proposed for the archetypal podophage T7. IMPORTANCE Oceans play a central role in the carbon cycle on Earth and on the climate regulation (half of the planet's CO2 is absorbed by phytoplankton photosynthesis in the oceans and just as much O2 is liberated). The understanding of the biochemical equilibriums of marine biology represents a major goal for our future. By lysing half of the bacterial population every day, marine bacteriophages are key actors of these equilibriums. Despite their importance, these marine phages have, so far, only been studied a little and, in particular, structural insights are currently lacking, even though they are fundamental for the understanding of the molecular mechanisms of their mode of infection. The structures described in our manuscript allow us to propose an infection mechanism that differs from the one proposed for the terrestrial T7 virus, and might also allow us to, in the future, better understand the way bacteriophages shape the global ecosystem.
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Affiliation(s)
| | - Thomas Roret
- Station Biologique de Roscoff (SBR), CNRS FR2424, Sorbonne Université, Roscoff, France
| | | | - Pierre-Yves Mocaër
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
| | | | - Anne-Claire Baudoux
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
| | - Guy Schoehn
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
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Vera-Mansilla J, Sánchez P, Silva-Valenzuela CA, Molina-Quiroz RC. Isolation and Characterization of Novel Lytic Phages Infecting Multidrug-Resistant Escherichia coli. Microbiol Spectr 2022; 10:e0167821. [PMID: 35171030 PMCID: PMC8849078 DOI: 10.1128/spectrum.01678-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/07/2021] [Indexed: 12/26/2022] Open
Abstract
Urinary tract infections (UTIs) are the second most frequent bacterial infections worldwide, with Escherichia coli being the main causative agent. The increase of antibiotic-resistance determinants among isolates from clinical samples, including UTIs, makes the development of novel therapeutic strategies a necessity. In this context, the use of bacteriophages as a therapeutic alternative has been proposed, due to their ability to efficiently kill bacteria. In this work, we isolated and characterized three novel bacteriophages, microbes laboratory phage 1 (MLP1), MLP2, and MLP3, belonging to the Chaseviridae, Myoviridae, and Podoviridae families, respectively. These phages efficiently infect and kill laboratory reference strains and multidrug-resistant clinical E. coli isolates from patients with diagnosed UTIs. Interestingly, these phages are also able to infect intestinal pathogenic Escherichia coli strains, such as enteroaggregative E. coli and diffusely adherent E. coli. Our data show that the MLP phages recognize different regions of the lipopolysaccharide (LPS) molecule, an important virulence factor in bacteria that is also highly variable among different E. coli strains. Altogether, our results suggest that these phages may represent an interesting alternative for the treatment of antibiotic-resistant E. coli. IMPORTANCE Urinary tract infections affect approximately 150 million people annually. The current antibiotic resistance crisis demands the development of novel therapeutic alternatives. Our results show that three novel phages, MLP1, MLP2, and MLP3 are able to infect both laboratory and multidrug-resistant clinical isolates of Escherichia coli. Since these phages (i) efficiently kill antibiotic-resistant clinical isolates of uropathogenic Escherichia coli (UPEC), (ii) recognize different portions of the LPS molecule, and (iii) are able to efficiently infect intestinal pathogenic Escherichia coli hosts, we believe that these novel phages are good candidates to be used as a therapeutic alternative to treat antibiotic-resistant E. coli strains generating urinary tract and/or intestinal infections.
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Liao YT, Zhang Y, Salvador A, Harden LA, Wu VCH. Characterization of a T4-like Bacteriophage vB_EcoM-Sa45lw as a Potential Biocontrol Agent for Shiga Toxin-Producing Escherichia coli O45 Contaminated on Mung Bean Seeds. Microbiol Spectr 2022; 10:e0222021. [PMID: 35107386 PMCID: PMC8809338 DOI: 10.1128/spectrum.02220-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/29/2021] [Indexed: 01/21/2023] Open
Abstract
Application of lytic bacteriophages is a promising and alternative intervention technology to relieve antibiotic resistance pressure and control bacterial pathogens in the food industry. Despite the increase of produce-associated outbreaks caused by non-O157 Shiga toxin-producing E. coli (STEC) serogroups, the information of phage application on sprouts to mitigate these pathogens is lacking. Therefore, the objective of this study was to characterize a T4-like Escherichia phage vB_EcoM-Sa45lw (or Sa45lw) for the biocontrol potential of STEC O45 on mung bean seeds. Phage Sa45lw belongs to the Tequatrovirus genus under the Myoviridae family and displays a close evolutionary relationship with a STEC O157-infecting phage AR1. Sa45lw contains a long-tail fiber gene (gp37), sharing high genetic similarity with the counterpart of Escherichia phage KIT03, and a unique tail lysozyme (gp5) to distinguish its host range (STEC O157, O45, ATCC 13706, and Salmonella Montevideo and Thompson) from phage KIT03 (O157 and Salmonella enterica). No stx, antibiotic resistance, and lysogenic genes were found in the Sa45lw genome. The phage has a latent period of 27 min with an estimated burst size of 80 PFU/CFU and is stable at a wide range of pH (pH 3 to pH 10.5) and temperatures (-80°C to 50°C). Phage Sa45lw is particularly effective in reducing E. coli O45:H16 both in vitro (MOI = 10) by 5 log and upon application (MOI = 1,000) on the contaminated mung bean seeds for 15 min by 2 log at 25°C. These findings highlight the potential of phage application against non-O157 STEC on sprout seeds. IMPORTANCE Seeds contaminated with foodborne pathogens, such as Shiga toxin-producing E. coli, are the primary sources of contamination in produce and have contributed to numerous foodborne outbreaks. Antibiotic resistance has been a long-lasting issue that poses a threat to human health and the food industry. Therefore, developing novel antimicrobial interventions, such as bacteriophage application, is pivotal to combat these pathogens. This study characterized a lytic bacteriophage Sa45lw as an alternative antimicrobial agent to control pathogenic E. coli on the contaminated mung bean seeds. The phage exhibited antimicrobial effects against both pathogenic E. coli and Salmonella without containing virulent or lysogenic genes that could compromise the safety of phage application. In addition, after 15 min of phage treatment, Sa45lw mitigated E. coli O45:H16 on the contaminated mung bean seeds by a 2-log reduction at room temperature, demonstrating the biocontrol potential of non-O157 Shiga toxin-producing E. coli on sprout seeds.
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Affiliation(s)
- Yen-Te Liao
- Produce Safety and Microbiology Research Unit, Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States
| | - Yujie Zhang
- Produce Safety and Microbiology Research Unit, Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States
| | - Alexandra Salvador
- Produce Safety and Microbiology Research Unit, Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States
| | - Leslie A. Harden
- Produce Safety and Microbiology Research Unit, Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States
| | - Vivian C. H. Wu
- Produce Safety and Microbiology Research Unit, Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States
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Qian M, Li D, Lin W, Pan L, Liu W, Zhou Q, Cai R, Wang F, Zhu J, Tong Y. A Novel Freshwater Cyanophage, Mae-Yong924-1, Reveals a New Family. Viruses 2022; 14:v14020283. [PMID: 35215876 PMCID: PMC8875630 DOI: 10.3390/v14020283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Cyanobacterial blooms are a worldwide ecological issue. Cyanophages are aquatic viruses specifically infecting cyanobacteria. Little is known about freshwater cyanophages. In this study, a freshwater cyanophage, Mae-Yong924-1, was isolated by the double-layer agar plate method using Microcystis aeruginosa FACHB-924 as an indicator host. Mae-Yong924-1 has several unusual characteristics: a unique shape, cross-taxonomic order infectivity and a very unique genome sequence. Mae-Yong924-1 contains a nearly spherical head of about 100 nm in diameter. The tail or tail-like structure (approximately 40 nm in length) is like the tassel of a round Chinese lantern. It could lyse six diverse cyanobacteria strains across three orders including Chroococcales, Nostocales and Oscillatoriales. The genome of the cyanophage is 40,325 bp in length, with a G + C content of 48.32%, and 59 predicted open reading frames (ORFs), only 12 (20%) of which were functionally annotated. Both BLASTn and BLASTx scanning resulted in “No significant similarity found”, i.e., the Mae-Yong924-1 genome shared extremely low homology with sequences in NCBI databases. Mae-Yong924-1 formed a root node alone and monopolized a root branch in the proteomic tree based on genome-wide sequence similarities. The results suggest that Mae-Yong924-1 may reveal a new unknown family apparently distinct from other viruses.
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Affiliation(s)
- Minhua Qian
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Dengfeng Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
- Correspondence: (D.L.); (Y.T.); Tel.: +86-13819823176 (D.L.); +86-13611272813 (Y.T.)
| | - Wei Lin
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingting Pan
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Wencai Liu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Qin Zhou
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Ruqian Cai
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Fei Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Junquan Zhu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China; (M.Q.); (W.L.); (L.P.); (W.L.); (Q.Z.); (R.C.); (F.W.); (J.Z.)
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Correspondence: (D.L.); (Y.T.); Tel.: +86-13819823176 (D.L.); +86-13611272813 (Y.T.)
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Forero-Junco LM, Alanin KWS, Djurhuus AM, Kot W, Gobbi A, Hansen LH. Bacteriophages Roam the Wheat Phyllosphere. Viruses 2022; 14:v14020244. [PMID: 35215838 PMCID: PMC8876510 DOI: 10.3390/v14020244] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/13/2022] Open
Abstract
The phyllosphere microbiome plays an important role in plant fitness. Recently, bacteriophages have been shown to play a role in shaping the bacterial community composition of the phyllosphere. However, no studies on the diversity and abundance of phyllosphere bacteriophage communities have been carried out until now. In this study, we extracted, sequenced, and characterized the dsDNA and ssDNA viral community from a phyllosphere for the first time. We sampled leaves from winter wheat (Triticum aestivum), where we identified a total of 876 virus operational taxonomic units (vOTUs), mostly predicted to be bacteriophages with a lytic lifestyle. Remarkably, 848 of these vOTUs corresponded to new viral species, and we estimated a minimum of 2.0 × 106 viral particles per leaf. These results suggest that the wheat phyllosphere harbors a large and active community of novel bacterial viruses. Phylloviruses have potential applications as biocontrol agents against phytopathogenic bacteria or as microbiome modulators to increase plant growth-promoting bacteria.
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Affiliation(s)
- Laura Milena Forero-Junco
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
- Correspondence: (L.M.F.-J.); (L.H.H.)
| | - Katrine Wacenius Skov Alanin
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
- Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
| | - Amaru Miranda Djurhuus
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
| | - Alex Gobbi
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
- Correspondence: (L.M.F.-J.); (L.H.H.)
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Nakonieczna A, Rutyna P, Fedorowicz M, Kwiatek M, Mizak L, Łobocka M. Three Novel Bacteriophages, J5a, F16Ba, and z1a, Specific for Bacillus anthracis, Define a New Clade of Historical Wbeta Phage Relatives. Viruses 2022; 14:v14020213. [PMID: 35215807 PMCID: PMC8878798 DOI: 10.3390/v14020213] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus anthracis is a potent biowarfare agent, able to be highly lethal. The bacteria dwell in the soil of certain regions, as natural flora. Bacteriophages or their lytic enzymes, endolysins, may be an alternative for antibiotics and other antibacterials to fight this pathogen in infections and to minimize environmental contamination with anthrax endospores. Upon screening environmental samples from various regions in Poland, we isolated three new siphophages, J5a, F16Ba, and z1a, specific for B. anthracis. They represent new species related to historical anthrax phages Gamma, Cherry, and Fah, and to phage Wbeta of Wbetavirus genus. We show that the new phages and their closest relatives, phages Tavor_SA, Negev_SA, and Carmel_SA, form a separate clade of the Wbetavirus genus, designated as J5a clade. The most distinctive feature of J5a clade phages is their cell lysis module. While in the historical phages it encodes a canonical endolysin and a class III holin, in J5a clade phages it encodes an endolysin with a signal peptide and two putative holins. We present the basic characteristic of the isolated phages. Their comparative genomic analysis indicates that they encode two receptor-binding proteins, of which one may bind a sugar moiety of B. anthracis cell surface.
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Affiliation(s)
- Aleksandra Nakonieczna
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
- Correspondence: (A.N.); (M.Ł.)
| | - Paweł Rutyna
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Magdalena Fedorowicz
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Magdalena Kwiatek
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Lidia Mizak
- Biological Threats Identification and Countermeasure Center, Military Institute of Hygiene and Epidemiology, 24-100 Pulawy, Poland; (P.R.); (M.F.); (M.K.); (L.M.)
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106 Warsaw, Poland
- Correspondence: (A.N.); (M.Ł.)
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19
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Oliveira H, Domingues R, Evans B, Sutton JM, Adriaenssens EM, Turner D. Genomic Diversity of Bacteriophages Infecting the Genus Acinetobacter. Viruses 2022; 14:v14020181. [PMID: 35215775 PMCID: PMC8878043 DOI: 10.3390/v14020181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 01/21/2023] Open
Abstract
The number of sequenced Acinetobacter phage genomes in the International Nucleotide Sequence Database Collaboration has increased significantly in recent years, from 37 in 2017 to a total of 139 as of January 2021 with genome sizes ranging from 31 to 378 kb. Here, we explored the genetic diversity of the Acinetobacter phages using comparative genomics approaches that included assessment of nucleotide similarity, shared gene content, single gene phylogeny, and the network-based classification tool vConTACT2. Phages infecting Acinetobacter sp. are genetically diverse and can be grouped into 8 clusters (subfamilies) and 46 sub-clusters (genera), of which 8 represent genomic singletons (additional genera). We propose the creation of five new subfamilies and suggest a reorganisation of the genus Obolenskvirus. These results provide an updated view of the viruses infecting Acinetobacter species, providing insights into their diversity.
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Affiliation(s)
- Hugo Oliveira
- Centre of Biological Engineering, University of Minho, Campus de Gualtar Braga, 4710-057 Braga, Portugal; (H.O.); (R.D.)
| | - Rita Domingues
- Centre of Biological Engineering, University of Minho, Campus de Gualtar Braga, 4710-057 Braga, Portugal; (H.O.); (R.D.)
| | - Benjamin Evans
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK;
| | - J. Mark Sutton
- United Kingdom Health Security Agency, Research and Evaluation, Porton Down, Salisbury SP4 OJG, UK;
| | | | - Dann Turner
- Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol BS16 1QY, UK
- Correspondence:
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20
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Kapinos A, Aghamalian P, Capehart E, Alag A, Angel H, Briseno E, Corado Perez B, Farag E, Foster H, Hakim A, Hernandez-Casas D, Huang C, Lam D, Mendez M, Min A, Nguyen N, Omholt AL, Ortiz E, Saldivar LS, Shannon JA, Smith R, Sridhar MV, Ta A, Theophilus MC, Ngo R, Torres C, Reddi K, Freise AC, Moberg Parker J. Novel Cluster AZ Arthrobacter phages Powerpuff, Lego, and YesChef exhibit close functional relationships with Microbacterium phages. PLoS One 2022; 17:e0262556. [PMID: 35025964 PMCID: PMC8758107 DOI: 10.1371/journal.pone.0262556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/28/2021] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages exhibit a vast spectrum of relatedness and there is increasing evidence of close genomic relationships independent of host genus. The variability in phage similarity at the nucleotide, amino acid, and gene content levels confounds attempts at quantifying phage relatedness, especially as more novel phages are isolated. This study describes three highly similar novel Arthrobacter globiformis phages-Powerpuff, Lego, and YesChef-which were assigned to Cluster AZ using a nucleotide-based clustering parameter. Phages in Cluster AZ, Microbacterium Cluster EH, and the former Microbacterium singleton Zeta1847 exhibited low nucleotide similarity. However, their gene content similarity was in excess of the recently adopted Microbacterium clustering parameter, which ultimately resulted in the reassignment of Zeta1847 to Cluster EH. This finding further highlights the importance of using multiple metrics to capture phage relatedness. Additionally, Clusters AZ and EH phages encode a shared integrase indicative of a lysogenic life cycle. In the first experimental verification of a Cluster AZ phage's life cycle, we show that phage Powerpuff is a true temperate phage. It forms stable lysogens that exhibit immunity to superinfection by related phages, despite lacking identifiable repressors typically required for lysogenic maintenance and superinfection immunity. The ability of phage Powerpuff to undergo and maintain lysogeny suggests that other closely related phages may be temperate as well. Our findings provide additional evidence of significant shared phage genomic content spanning multiple actinobacterial host genera and demonstrate the continued need for verification and characterization of life cycles in newly isolated phages.
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Affiliation(s)
- Andrew Kapinos
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Pauline Aghamalian
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Erika Capehart
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Anya Alag
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Heather Angel
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Eddie Briseno
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Byron Corado Perez
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Emily Farag
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Hilory Foster
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Abbas Hakim
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Daisy Hernandez-Casas
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Calvin Huang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Derek Lam
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Maya Mendez
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Ashley Min
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Nikki Nguyen
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Alexa L. Omholt
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Emily Ortiz
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Lizbeth Shelly Saldivar
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Jack Arthur Shannon
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Rachel Smith
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Mihika V. Sridhar
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - An Ta
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Malavika C. Theophilus
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Ryan Ngo
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Canela Torres
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Krisanavane Reddi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Amanda C. Freise
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
| | - Jordan Moberg Parker
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, United States of America
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21
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Dewanggana MN, Evangeline C, Ketty MD, Waturangi DE, Yogiara, Magdalena S. Isolation, characterization, molecular analysis and application of bacteriophage DW-EC to control Enterotoxigenic Escherichia coli on various foods. Sci Rep 2022; 12:495. [PMID: 35017610 PMCID: PMC8752677 DOI: 10.1038/s41598-021-04534-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/22/2021] [Indexed: 12/24/2022] Open
Abstract
Among food preservation methods, bacteriophage treatment can be a viable alternative method to overcome the drawbacks of traditional approaches. Bacteriophages are naturally occurring viruses that are highly specific to their hosts and have the capability to lyse bacterial cells, making them useful as biopreservation agents. This study aims to characterize and determine the application of bacteriophage isolated from Indonesian traditional Ready-to-Eat (RTE) food to control Enterotoxigenic Escherichia coli (ETEC) population in various foods. Phage DW-EC isolated from Indonesian traditional RTE food called dawet with ETEC as its host showed a positive result by the formation of plaques (clear zone) in the bacterial host lawn. Transmission electron microscopy (TEM) results also showed that DW-EC can be suspected to belong to the Myoviridae family. Molecular characterization and bioinformatic analysis showed that DW-EC exhibited characteristics as promising biocontrol agents in food samples. Genes related to the lytic cycle, such as lysozyme and tail fiber assembly protein, were annotated. There were also no signs of lysogenic genes among the annotation results. The resulting PHACTS data also indicated that DW-EC was leaning toward being exclusively lytic. DW-EC significantly reduced the ETEC population (P ≤ 0.05) in various food samples after two different incubation times (1 day and 6 days) in chicken meat (80.93%; 87.29%), fish meat (63.78%; 87.89%), cucumber (61.42%; 71.88%), tomato (56.24%; 74.51%), and lettuce (46.88%; 43.38%).
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Affiliation(s)
- Marta Nisita Dewanggana
- Biotechnology Department, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jenderal Sudirman 51 Street, South Jakarta, DKI Jakarta, 12930, Indonesia
| | - Clare Evangeline
- Biotechnology Department, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jenderal Sudirman 51 Street, South Jakarta, DKI Jakarta, 12930, Indonesia
- Food Technology Department, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Maurita Delia Ketty
- Biotechnology Department, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jenderal Sudirman 51 Street, South Jakarta, DKI Jakarta, 12930, Indonesia
- Food Technology Department, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Diana Elizabeth Waturangi
- Biotechnology Department, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jenderal Sudirman 51 Street, South Jakarta, DKI Jakarta, 12930, Indonesia.
| | - Yogiara
- Biotechnology Department, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jenderal Sudirman 51 Street, South Jakarta, DKI Jakarta, 12930, Indonesia
| | - Stella Magdalena
- Biotechnology Department, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jenderal Sudirman 51 Street, South Jakarta, DKI Jakarta, 12930, Indonesia
- Food Technology Department, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
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22
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Jin H, You L, Zhao F, Li S, Ma T, Kwok LY, Xu H, Sun Z. Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome. Gut Microbes 2022; 14:2021790. [PMID: 35067170 PMCID: PMC8786330 DOI: 10.1080/19490976.2021.2021790] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/03/2021] [Accepted: 12/13/2021] [Indexed: 02/04/2023] Open
Abstract
A large number of microbial genomes have already been identified from the human gut microbiome, but the understanding of the role of the low-abundance species at the individual level remains challenging, largely due to the relatively shallow sequencing depth used in most studies. To improve genome assembling performance, a HiSeq-PacBio hybrid, ultra-deep metagenomic sequencing approach was used to reconstruct metagenomic-assembled genomes (MAGs) from 12 fecal samples. Such approach combined third-generation sequencing with ultra-deep second-generation sequencing to improve the sequencing coverage of the low-abundance subpopulation in the gut microbiome. Our study generated a total of 44 megabase-scale scaffolds, achieving four single-scaffolds of complete (circularized, no gaps) MAGs (CMAGs) that were the first circular genomes of their species. Moreover, 475 high-quality MAGs were assembled across all samples. Among them, 234 MAGs were currently uncultured, including 24 MAGs that were not found in any public genome database. Additionally, 287 and 77 MAGs were classified as low-abundance (0.1-1%) and extra-low-abundance (<0.1%) gut species in each individual, respectively. Our results also revealed individual-specific genomic features in the MAG profiles, including microbial genome growth rate, selective pressure, and frequency of chromosomal mobile genetic elements. Finally, thousands of extrachromosomal mobile genetic elements were identified from the metagenomic data, including 5097 bacteriophages and 79 novel plasmid genomes. Overall, our strategy represents an important step toward comprehensive genomic and functional characterization of the human gut microbiome at an individual level.
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Affiliation(s)
- Hao Jin
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Lijun You
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Feiyan Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Shenghui Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Teng Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
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23
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Kazantseva OA, Buzikov RM, Pilipchuk TA, Valentovich LN, Kazantsev AN, Kalamiyets EI, Shadrin AM. The Bacteriophage Pf-10-A Component of the Biopesticide "Multiphage" Used to Control Agricultural Crop Diseases Caused by Pseudomonas syringae. Viruses 2021; 14:42. [PMID: 35062246 PMCID: PMC8779105 DOI: 10.3390/v14010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Phytopathogenic pseudomonads are widespread in the world and cause a wide range of plant diseases. In this work, we describe the Pseudomonas phage Pf-10, which is a part of the biopesticide "Multiphage" used for bacterial diseases of agricultural crops caused by Pseudomonas syringae. The Pf-10 chromosome is a dsDNA molecule with two direct terminal repeats (DTRs). The phage genomic DNA is 39,424 bp long with a GC-content of 56.5%. The Pf-10 phage uses a packaging mechanism based on T7-like short DTRs, and the length of each terminal repeat is 257 bp. Electron microscopic analysis has shown that phage Pf-10 has the podovirus morphotype. Phage Pf-10 is highly stable at pH values from 5 to 10 and temperatures from 4 to 60 °C and has a lytic activity against Pseudomonas strains. Phage Pf-10 is characterized by fast adsorption rate (80% of virions attach to the host cells in 10 min), but has a relatively small number of progeny (37 ± 8.5 phage particles per infected cell). According to the phylogenetic analysis, phage Pf-10 can be classified as a new phage species belonging to the genus Pifdecavirus, subfamily Studiervirinae, family Autographiviridae, order Caudovirales.
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Affiliation(s)
- Olesya A. Kazantseva
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
| | - Rustam M. Buzikov
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
| | - Tatsiana A. Pilipchuk
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
| | - Leonid N. Valentovich
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
- Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus
| | - Andrey N. Kazantsev
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Pushchino Radio Astronomy Observatory, 142290 Pushchino, Russia;
| | - Emilia I. Kalamiyets
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
| | - Andrey M. Shadrin
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
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24
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Biosca EG, Català-Senent JF, Figàs-Segura À, Bertolini E, López MM, Álvarez B. Genomic Analysis of the First European Bacteriophages with Depolymerase Activity and Biocontrol Efficacy against the Phytopathogen Ralstonia solanacearum. Viruses 2021; 13:v13122539. [PMID: 34960808 PMCID: PMC8703784 DOI: 10.3390/v13122539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/28/2022] Open
Abstract
Ralstonia solanacearum is the causative agent of bacterial wilt, one of the most destructive plant diseases. While chemical control has an environmental impact, biological control strategies can allow sustainable agrosystems. Three lytic bacteriophages (phages) of R. solanacearum with biocontrol capacity in environmental water and plants were isolated from river water in Europe but not fully analysed, their genomic characterization being fundamental to understand their biology. In this work, the phage genomes were sequenced and subjected to bioinformatic analysis. The morphology was also observed by electron microscopy. Phylogenetic analyses were performed with a selection of phages able to infect R. solanacearum and the closely related phytopathogenic species R. pseudosolanacearum. The results indicated that the genomes of vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 range from 40,688 to 41,158 bp with almost 59% GC-contents, 52 ORFs in vRsoP-WF2 and vRsoP-WM2, and 53 in vRsoP-WR2 but, with only 22 or 23 predicted proteins with functional homologs in databases. Among them, two lysins and one exopolysaccharide (EPS) depolymerase, this type of depolymerase being identified in R. solanacearum phages for the first time. These three European phages belong to the same novel species within the Gyeongsanvirus, Autographiviridae family (formerly Podoviridae). These genomic data will contribute to a better understanding of the abilities of these phages to damage host cells and, consequently, to an improvement in the biological control of R. solanacearum.
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Affiliation(s)
- Elena G. Biosca
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Correspondence:
| | - José Francisco Català-Senent
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Centro de Investigación Príncipe Felipe, Unidad de Bioinformática y Bioestadística, 46012 Valencia, Spain
| | - Àngela Figàs-Segura
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
| | - Edson Bertolini
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil
| | - María M. López
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain;
| | - Belén Álvarez
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Departamento de Investigación Aplicada y Extensión Agraria, Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), 28800 Alcalá de Henares, Spain
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25
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Cui N, Yang F, Zhang JT, Sun H, Chen Y, Yu RC, Chen ZP, Jiang YL, Han SJ, Xu X, Li Q, Zhou CZ. Capsid Structure of Anabaena Cyanophage A-1(L). J Virol 2021; 95:e0135621. [PMID: 34549983 PMCID: PMC8610606 DOI: 10.1128/jvi.01356-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/19/2021] [Indexed: 01/09/2023] Open
Abstract
A-1(L) is a freshwater cyanophage with a contractile tail that specifically infects Anabaena sp. PCC 7120, one of the model strains for molecular studies of cyanobacteria. Although isolated for half a century, its structure remains unknown, which limits our understanding on the interplay between A-1(L) and its host. Here we report the 3.35 Å cryo-EM structure of A-1(L) capsid, representing the first near-atomic resolution structure of a phage capsid with a T number of 9. The major capsid gp4 proteins assemble into 91 capsomers, including 80 hexons: 20 at the center of the facet and 60 at the facet edge, in addition to 11 identical pentons. These capsomers further assemble into the icosahedral capsid, via gradually increasing curvatures. Different from the previously reported capsids of known-structure, A-1(L) adopts a noncovalent chainmail structure of capsid stabilized by two kinds of mortise-and-tenon inter-capsomer interactions: a three-layered interface at the pseudo 3-fold axis combined with the complementarity in shape and electrostatic potential around the 2-fold axis. This unique capsomer construction enables A-1(L) to possess a rigid capsid, which is solely composed of the major capsid proteins with an HK97 fold. IMPORTANCE Cyanobacteria are the most abundant photosynthetic bacteria, contributing significantly to the biomass production, O2 generation, and CO2 consumption on our planet. Their community structure and homeostasis in natural aquatic ecosystems are largely regulated by the corresponding cyanophages. In this study, we solved the structure of cyanophage A-1(L) capsid at near-atomic resolution and revealed a unique capsid construction. This capsid structure provides the molecular details for better understanding the assembly of A-1(L), and a structural platform for future investigation and application of A-1(L) in combination with its host Anabaena sp. PCC 7120. As the first isolated freshwater cyanophage that infects the genetically tractable model cyanobacterium, A-1(L) should become an ideal template for the genetic engineering and synthetic biology studies.
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Affiliation(s)
- Ning Cui
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Feng Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Jun-Tao Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Hui Sun
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yu Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Rong-Cheng Yu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhi-Peng Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Shu-Jing Han
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Xudong Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiong Li
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
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Wójcicki M, Średnicka P, Błażejak S, Gientka I, Kowalczyk M, Emanowicz P, Świder O, Sokołowska B, Juszczuk-Kubiak E. Characterization and Genome Study of Novel Lytic Bacteriophages against Prevailing Saprophytic Bacterial Microflora of Minimally Processed Plant-Based Food Products. Int J Mol Sci 2021; 22:12460. [PMID: 34830335 PMCID: PMC8624825 DOI: 10.3390/ijms222212460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
The food industry is still searching for novel solutions to effectively ensure the microbiological safety of food, especially fresh and minimally processed food products. Nowadays, the use of bacteriophages as potential biological control agents in microbiological food safety and preservation is a promising strategy. The aim of the study was the isolation and comprehensive characterization of novel bacteriophages with lytic activity against saprophytic bacterial microflora of minimally processed plant-based food products, such as mixed leaf salads. From 43 phages isolated from municipal sewage, four phages, namely Enterobacter phage KKP 3263, Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 have lytic activity against Enterobacter ludwigii KKP 3083, Citrobacter freundii KKP 3655, Enterobacter cloacae KKP 3082, and Serratia fonticola KKP 3084 bacterial strains, respectively. Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) identified Enterobacter phage KKP 3263 as an Autographiviridae, and Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 as members of the Myoviridae family. Genome sequencing revealed that these phages have linear double-stranded DNA (dsDNA) with sizes of 39,418 bp (KKP 3263), 61,608 bp (KKP 3664), 84,075 bp (KKP 3262), and 148,182 bp (KKP 3264). No antibiotic resistance genes, virulence factors, integrase, recombinase, or repressors, which are the main markers of lysogenic viruses, were annotated in phage genomes. Serratia phage KKP 3264 showed the greatest growth inhibition of Serratia fonticola KKP 3084 strain. The use of MOI 1.0 caused an almost 5-fold decrease in the value of the specific growth rate coefficient. The phages retained their lytic activity in a wide range of temperatures (from -20 °C to 50 °C) and active acidity values (pH from 4 to 11). All phages retained at least 70% of lytic activity at 60 °C. At 80 °C, no lytic activity against tested bacterial strains was observed. Serratia phage KKP 3264 was the most resistant to chemical factors, by maintaining high lytic activity across a broader range of pH from 3 to 11. The results indicated that these phages could be a potential biological control agent against saprophytic bacterial microflora of minimally processed plant-based food products.
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Affiliation(s)
- Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Paulina Średnicka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Stanisław Błażejak
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland; (S.B.); (I.G.)
| | - Iwona Gientka
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland; (S.B.); (I.G.)
| | - Monika Kowalczyk
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Paulina Emanowicz
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland;
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland;
| | - Edyta Juszczuk-Kubiak
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (M.W.); (P.Ś.); (M.K.); (P.E.)
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Kumar P, Meghvansi MK, Kamboj DV. Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage. Sci Rep 2021; 11:22197. [PMID: 34772986 PMCID: PMC8590004 DOI: 10.1038/s41598-021-01419-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Shigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controlling Shigella infections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity against Shigella dysenteriae, Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticus and Enterococcus faecium. The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genus Hanrivervirus of subfamily Tempevirinae under the family Drexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members of Drexlerviridae taking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genus Hanrivervirus. The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.
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Affiliation(s)
- Prince Kumar
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- Regional Ayurveda Research Institute, Gwalior, Madhya Pradesh, 474009, India
| | - Mukesh K Meghvansi
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- Bioprocess Technology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - D V Kamboj
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India.
- Defence Research Laboratory, Tezpur, Assam, 784001, India.
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Hosseini N, Paquet VE, Chehreghani M, Moineau S, Charette SJ. Phage Cocktail Development against Aeromonas salmonicida subsp. salmonicida Strains Is Compromised by a Prophage. Viruses 2021; 13:2241. [PMID: 34835047 PMCID: PMC8621227 DOI: 10.3390/v13112241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/22/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Aquaculture is a rapidly growing food production sector. Fish farmers are experiencing increasing problems with antibiotic resistance when fighting against pathogenic bacteria such as Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis. Phage therapy may provide an alternative, but effective use must be determined. Here, we studied the inhibition of A. salmonicida subsp. salmonicida strains by five phages (HER98 [44RR2.8t.2], HER110 [65.2], SW69-9, L9-6 and Riv-10) used individually or as combinations of two to five phages. A particular combination of four phages (HER98 [44RR2.8t.2], SW69-9, Riv-10, and HER110 [65.2]) was found to be the most effective when used at an initial multiplicity of infection (MOI) of 1 against the A. salmonicida subsp. salmonicida strain 01-B526. The same phage cocktail is effective against other strains except those bearing a prophage (named Prophage 3), which is present in 2/3 of the strains from the province of Quebec. To confirm the impact of this prophage, we tested the effectiveness of the same cocktail on strains that were either cured or lysogenized with Prophage 3. While the parental strains were sensitive to the phage cocktail, the lysogenized ones were much less sensitive. These data indicate that the prophage content of A. salmonicida subsp. salmonicida can affect the efficacy of a cocktail of virulent phages for phage therapy purposes.
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Affiliation(s)
- Nava Hosseini
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC G1V 4G5, Canada
| | - Valérie E. Paquet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC G1V 4G5, Canada
| | - Mahdi Chehreghani
- Department of Mechanical Engineering, McGill University, Montreal, QC H3A 0C3, Canada;
| | - Sylvain Moineau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de Médecine Dentaire, Université Laval, Quebec City, QC G1V 0A6, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve J. Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, QC G1V 0A6, Canada; (N.H.); (V.E.P.); (S.M.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC G1V 4G5, Canada
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Thomas GH. Microbial Musings - September 2021. Microbiology (Reading) 2021; 167. [PMID: 34672917 PMCID: PMC8698185 DOI: 10.1099/mic.0.001115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Gavin H. Thomas
- Department of Biology, University of York, YO10 5YW, UK
- *Correspondence: Gavin H. Thomas,
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Martino G, Holtappels D, Vallino M, Chiapello M, Turina M, Lavigne R, Wagemans J, Ciuffo M. Molecular Characterization and Taxonomic Assignment of Three Phage Isolates from a Collection Infecting Pseudomonas syringae pv. actinidiae and P. syringae pv. phaseolicola from Northern Italy. Viruses 2021; 13:2083. [PMID: 34696512 PMCID: PMC8537276 DOI: 10.3390/v13102083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/27/2022] Open
Abstract
Bacterial kiwifruit vine disease (Pseudomonas syringae pv. actinidiae, Psa) and halo blight of bean (P. syringae pv. phaseolicola, Pph) are routinely treated with copper, leading to environmental pollution and bacterial copper resistance. An alternative sustainable control method could be based on bacteriophages, as phage biocontrol offers high specificity and does not result in the spread of toxic residues into the environment or the food chain. In this research, specific phages suitable for phage-based biocontrol strategies effective against Psa and Pph were isolated and characterized. In total, sixteen lytic Pph phage isolates and seven lytic Psa phage isolates were isolated from soil in Piedmont and Veneto in northern Italy. Genome characterization of fifteen selected phages revealed that the isolated Pph phages were highly similar and could be considered as isolates of a novel species, whereas the isolated Psa phages grouped into four distinct clades, two of which represent putative novel species. No lysogeny-, virulence- or toxin-related genes were found in four phages, making them suitable for potential biocontrol purposes. A partial biological characterization including a host range analysis was performed on a representative subset of these isolates. This analysis was a prerequisite to assess their efficacy in greenhouse and in field trials, using different delivery strategies.
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Affiliation(s)
- Gabriele Martino
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Dominique Holtappels
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, 3001 Leuven, Belgium; (D.H.); (R.L.); (J.W.)
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National Research Council of Italy, I-10135 Torino, Italy; (G.M.); (M.V.); (M.C.); (M.T.)
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Wu Z, Zhang Y, Xu X, Ahmed T, Yang Y, Loh B, Leptihn S, Yan C, Chen J, Li B. The Holin-Endolysin Lysis System of the OP2-Like Phage X2 Infecting Xanthomonas oryzae pv. oryzae. Viruses 2021; 13:v13101949. [PMID: 34696380 PMCID: PMC8541568 DOI: 10.3390/v13101949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/18/2021] [Accepted: 09/21/2021] [Indexed: 01/01/2023] Open
Abstract
Most endolysins of dsDNA phages are exported by a holin-dependent mechanism, while in some cases endolysins are exported via a holin-independent mechanism. However, it is still unclear whether the same endolysins can be exported by both holin-dependent and holin-independent mechanisms. This study investigated the lysis system of OP2-like phage X2 infecting Xanthomonas oryzae pv. oryzae, causing devastating bacterial leaf blight disease in rice. Based on bioinformatics and protein biochemistry methods, we show that phage X2 employs the classic "holin-endolysin" lysis system. The endolysin acts on the cell envelope and exhibits antibacterial effects in vitro, while the holin facilitates the release of the protein into the periplasm. We also characterized the role of the transmembrane domain (TMD) in the translocation of the endolysin across the inner membrane. We found that the TMD facilitated the translocation of the endolysin via the Sec secretion system. The holin increases the efficiency of protein release, leading to faster and more efficient lysis. Interestingly, in E. coli, the expression of either holin or endolysin with TMDs resulted in the formation of long rod shaped cells. We conclude that the TMD of X2-Lys plays a dual role: One is the transmembrane transport while the other is the inhibition of cell division, resulting in larger cells and thus in a higher number of released viruses per cell.
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Affiliation(s)
- Zhifeng Wu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.W.); (Y.Z.); (X.X.); (T.A.)
| | - Yang Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.W.); (Y.Z.); (X.X.); (T.A.)
| | - Xinyang Xu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.W.); (Y.Z.); (X.X.); (T.A.)
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.W.); (Y.Z.); (X.X.); (T.A.)
| | - Yong Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.Y.)
| | - Belinda Loh
- University of Edinburgh Institute, Zhejiang University, Hangzhou 314400, China; (B.L.); (S.L.)
| | - Sebastian Leptihn
- University of Edinburgh Institute, Zhejiang University, Hangzhou 314400, China; (B.L.); (S.L.)
| | - Chenqi Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.Y.)
- Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.Y.)
- Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Correspondence: (J.C.); (B.L.); Tel.: +86-571-8898-2412 (B.L.)
| | - Bin Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.W.); (Y.Z.); (X.X.); (T.A.)
- Correspondence: (J.C.); (B.L.); Tel.: +86-571-8898-2412 (B.L.)
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Crippen CS, Zhou B, Andresen S, Patry RT, Muszyński A, Parker CT, Cooper KK, Szymanski CM. RNA and Sugars, Unique Properties of Bacteriophages Infecting Multidrug Resistant Acinetobacter radioresistens Strain LH6. Viruses 2021; 13:1652. [PMID: 34452516 PMCID: PMC8402811 DOI: 10.3390/v13081652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteriophages (phages) are predicted to be the most ubiquitous biological entity on earth, and yet, there are still vast knowledge gaps in our understanding of phage diversity and phage-host interactions. Approximately one hundred Acinetobacter-infecting DNA viruses have been identified, and in this report, we describe eight more. We isolated two typical dsDNA lytic podoviruses (CAP1-2), five unique dsRNA lytic cystoviruses (CAP3-7), and one dsDNA lysogenic siphovirus (SLAP1), all capable of infecting the multidrug resistant isolate Acinetobacter radioresistens LH6. Using transmission electron microscopy, bacterial mutagenesis, phage infectivity assays, carbohydrate staining, mass-spectrometry, genomic sequencing, and comparative studies, we further characterized these phages. Mutation of the LH6 initiating glycosyltransferase homolog, PglC, necessary for both O-linked glycoprotein and capsular polysaccharide (CPS) biosynthesis, prevented infection by the lytic podovirus CAP1, while mutation of the pilin protein, PilA, prevented infection by CAP3, representing the lytic cystoviruses. Genome sequencing of the three dsRNA segments of the isolated cystoviruses revealed low levels of homology, but conserved synteny with the only other reported cystoviruses that infect Pseudomonas species. In Pseudomonas, the cystoviruses are known to be enveloped phages surrounding their capsids with the inner membrane from the infected host. To characterize any membrane-associated glycoconjugates in the CAP3 cystovirus, carbohydrate staining was used to identify a low molecular weight lipid-linked glycoconjugate subsequently identified by mutagenesis and mass-spectrometry as bacterial lipooligosaccharide. Together, this study demonstrates the isolation of new Acinetobacter-infecting phages and the determination of their cell receptors. Further, we describe the genomes of a new genus of Cystoviruses and perform an initial characterization of membrane-associated glycoconjugates.
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Affiliation(s)
- Clay S. Crippen
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (C.S.C.); (B.Z.); (S.A.); (R.T.P.)
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA;
| | - Bibi Zhou
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (C.S.C.); (B.Z.); (S.A.); (R.T.P.)
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA;
| | - Silke Andresen
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (C.S.C.); (B.Z.); (S.A.); (R.T.P.)
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA;
| | - Robert T. Patry
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (C.S.C.); (B.Z.); (S.A.); (R.T.P.)
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA;
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA;
| | - Craig T. Parker
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA 94710, USA;
| | - Kerry K. Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA;
| | - Christine M. Szymanski
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (C.S.C.); (B.Z.); (S.A.); (R.T.P.)
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA;
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Petrzik K, Brázdová S, Krawczyk K. Novel Viruses That Lyse Plant and Human Strains of Kosakonia cowanii. Viruses 2021; 13:1418. [PMID: 34452284 PMCID: PMC8402661 DOI: 10.3390/v13081418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 12/02/2022] Open
Abstract
Kosakonia cowanii (syn. Enterobacter cowanii) is a highly competitive bacterium that lives with plant, insect, fish, bird, and human organisms. It is pathogenic on some plants and an opportunistic pathogen of human. Nine novel viruses that lyse plant pathogenic strains and/or human strains of K. cowanii were isolated, sequenced, and characterized. Kc166A is a novel kayfunavirus, Kc261 is a novel bonnellvirus, and Kc318 is a new cronosvirus (all Autographiviridae). Kc237 is a new sortsnevirus, but Kc166B and Kc283 are members of new genera within Podoviridae. Kc304 is a new winklervirus, and Kc263 and Kc305 are new myoviruses. The viruses differ in host specificity, plaque phenotype, and lysis kinetics. Some of them should be suitable also as pathogen control agents.
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Affiliation(s)
- Karel Petrzik
- Biology Centre, Department of Plant Virology, Institute of Plant Molecular Biology, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - Sára Brázdová
- Biology Centre, Department of Plant Virology, Institute of Plant Molecular Biology, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - Krzysztof Krawczyk
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection-National Research Institute, Władislawa Węgorka 20, 60-318 Poznań, Poland;
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Kupritz J, Martin J, Fischer K, Curtis KC, Fauver JR, Huang Y, Choi YJ, Beatty WL, Mitreva M, Fischer PU. Isolation and characterization of a novel bacteriophage WO from Allonemobius socius crickets in Missouri. PLoS One 2021; 16:e0250051. [PMID: 34197460 PMCID: PMC8248633 DOI: 10.1371/journal.pone.0250051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/15/2021] [Indexed: 11/19/2022] Open
Abstract
Wolbachia are endosymbionts of numerous arthropod and some nematode species, are important for their development and if present can cause distinct phenotypes of their hosts. Prophage DNA has been frequently detected in Wolbachia, but particles of Wolbachia bacteriophages (phage WO) have been only occasionally isolated. Here, we report the characterization and isolation of a phage WO of the southern ground cricket, Allonemobius socius, and provided the first whole-genome sequence of phage WO from this arthropod family outside of Asia. We screened A. socius abdomen DNA extracts from a cricket population in eastern Missouri by quantitative PCR for Wolbachia surface protein and phage WO capsid protein and found a prevalence of 55% and 50%, respectively, with many crickets positive for both. Immunohistochemistry using antibodies against Wolbachia surface protein showed many Wolbachia clusters in the reproductive system of female crickets. Whole-genome sequencing using Oxford Nanopore MinION and Illumina technology allowed for the assembly of a high-quality, 55 kb phage genome containing 63 open reading frames (ORF) encoding for phage WO structural proteins and host lysis and transcriptional manipulation. Taxonomically important regions of the assembled phage genome were validated by Sanger sequencing of PCR amplicons. Analysis of the nucleotides sequences of the ORFs encoding the large terminase subunit (ORF2) and minor capsid (ORF7) frequently used for phage WO phylogenetics showed highest homology to phage WOAu of Drosophila simulans (94.46% identity) and WOCin2USA1 of the cherry fruit fly, Rhagoletis cingulata (99.33% identity), respectively. Transmission electron microscopy examination of cricket ovaries showed a high density of phage particles within Wolbachia cells. Isolation of phage WO revealed particles characterized by 40–62 nm diameter heads and up to 190 nm long tails. This study provides the first detailed description and genomic characterization of phage WO from North America that is easily accessible in a widely distributed cricket species.
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Affiliation(s)
- Jonah Kupritz
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John Martin
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kerstin Fischer
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kurt C. Curtis
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Joseph R. Fauver
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yuefang Huang
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Young-Jun Choi
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Wandy L. Beatty
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Makedonka Mitreva
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Peter U. Fischer
- Infectious Disease Division, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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Ma R, Lai J, Chen X, Wang L, Yang Y, Wei S, Jiao N, Zhang R. A Novel Phage Infecting Alteromonas Represents a Distinct Group of Siphophages Infecting Diverse Aquatic Copiotrophs. mSphere 2021; 6:e0045421. [PMID: 34106770 PMCID: PMC8265664 DOI: 10.1128/msphere.00454-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
Bacteriophages play critical roles in impacting microbial community succession both ecologically and evolutionarily. Although the majority of phage genetic diversity has been increasingly unveiled, phages infecting members of the ecologically important genus Alteromonas remain poorly understood. Here, we present a comprehensive analysis of a newly isolated alterophage, vB_AcoS-R7M (R7M), to characterize its life cycle traits, genomic features, and putative evolutionary origin. R7M harbors abundant genes identified as host-like auxiliary metabolic genes facilitating viral propagation. Genomic analysis suggested that R7M is distinct from currently known alterophages. Interestingly, R7M was found to share a set of similar characteristics with a number of siphophages infecting diverse aquatic opportunistic copiotrophs. We therefore proposed the creation of one new subfamily (Queuovirinae) to group with these evolutionarily related phages. Notably, tail genes were less likely to be shared among them, and baseplate-related genes varied the most. In-depth analyses indicated that R7M has replaced its distal tail with a Rhodobacter capsulatus gene transfer agent (RcGTA)-like baseplate and further acquired a putative receptor interaction site targeting Alteromonas. These findings suggest that horizontal exchanges of viral tail adsorption apparatuses are widespread and vital for phages to hunt new hosts and to adapt to new niches. IMPORTANCE The evolution and ecology of phages infecting members of Alteromonas, a marine opportunistic genus that is widely distributed and of great ecological significance, remain poorly understood. The present study integrates physiological and genomic evidence to characterize the properties and putative phage-host interactions of a newly isolated Alteromonas phage, vB_AcoS-R7M (R7M). A taxonomic study reveals close evolutionary relationships among R7M and a number of siphophages infecting various aquatic copiotrophs. Their similar head morphology and overall genetic framework suggest their putative common ancestry and the grouping of a new viral subfamily. However, their major difference lies in the viral tail adsorption apparatuses and the horizontal exchanges of which possibly account for variations in host specificity. These findings outline an evolutionary scenario for the emergence of diverse viral lineages of a shared genetic pool and give insights into the genetics and ecology of viral host jumps.
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Affiliation(s)
- Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Jiayong Lai
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Long Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yahui Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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Cadwell K, Wang D. Editorial overview: The virome in health and disease. Curr Opin Virol 2021; 49:139-141. [PMID: 34130041 DOI: 10.1016/j.coviro.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Ken Cadwell
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Langone Health, New York, NY 10016, USA.
| | - David Wang
- Departments of Molecular Microbiology and Pathology&Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA.
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Gabashvili E, Kobakhidze S, Koulouris S, Robinson T, Kotetishvili M. Bi- and Multi-directional Gene Transfer in the Natural Populations of Polyvalent Bacteriophages, and Their Host Species Spectrum Representing Foodborne Versus Other Human and/or Animal Pathogens. Food Environ Virol 2021; 13:179-202. [PMID: 33484405 DOI: 10.1007/s12560-021-09460-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Unraveling the trends of phage-host versus phage-phage coevolution is critical for avoiding possible undesirable outcomes from the use of phage preparations intended for therapeutic, food safety or environmental safety purposes. We aimed to investigate a phenomenon of intergeneric recombination and its trajectories across the natural populations of phages predominantly linked to foodborne pathogens. The results from the recombination analyses, using a large array of the recombination detection algorithms imbedded in SplitsTree, RDP4, and Simplot software packages, provided strong evidence (fit: 100; P ≤ 0.014) for both bi- and multi-directional intergeneric recombination of the genetic loci involved collectively in phage morphogenesis, host specificity, virulence, replication, and persistence. Intergeneric recombination was determined to occur not only among conspecifics of the virulent versus temperate phages but also between the phages with these different lifestyles. The recombining polyvalent phages were suggested to interact with fairly large host species networks, including sometimes genetically very distinct species, such as e.g., Salmonella enterica and/or Escherichia coli versus Staphylococcus aureus or Yersinia pestis. Further studies are needed to understand whether phage-driven intergeneric recombination can lead to undesirable changes of intestinal and other microbiota in humans and animals.
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Affiliation(s)
- Ekaterine Gabashvili
- School of Natural Sciences and Medicine, Ilia State University, 1 Giorgi Tsereteli exit, 0162, Tbilisi, Georgia
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia
| | - Saba Kobakhidze
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia
| | - Stylianos Koulouris
- Engagement and Cooperation Unit, European Food Safety Authority, Via Carlo Magno 1A, 43126, Parma, Italy
| | - Tobin Robinson
- Scientific Committee, and Emerging Risks Unit, European Food Safety Authority, Via Carlo Magno 1A, 43126, Parma, Italy
| | - Mamuka Kotetishvili
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia.
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitation, 78 D. Uznadze St., 0102, Tbilisi, Georgia.
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Deng S, Xu Q, Fu Y, Liang L, Wu Y, Peng F, Gao M. Genomic Analysis of a Novel Phage Infecting the Turkey Pathogen Escherichia coli APEC O78 and Its Endolysin Activity. Viruses 2021; 13:v13061034. [PMID: 34072620 PMCID: PMC8229158 DOI: 10.3390/v13061034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 01/13/2023] Open
Abstract
Due to the increasing spread of multidrug-resistant (MDR) bacteria, phage therapy is considered one of the most promising methods for addressing MDR bacteria. Escherichia coli lives symbiotically in the intestines of humans and some animals, and most strains are beneficial in terms of maintaining a healthy digestive tract. However, some E. coli strains can cause serious zoonotic diseases, including diarrhea, pneumonia, urinary tract infections, and hemolytic uremic syndrome. In this study, we characterized a newly isolated Myoviridae phage, vB_EcoM_APEC. The phage vB_EcoM_APEC was able to infect E. coli APEC O78, which is the most common MDR E. coli serotype in turkeys. Additionally, the phage's host range included Klebsiella pneumoniae and other E. coli strains. The genome of phage vB_EcoM_APEC (GenBank accession number MT664721) was 35,832 bp in length, with 52 putative open reading frames (ORFs) and a GC content of 41.3%. The genome of vB_EcoM_APEC exhibited low similarity (79.1% identity and 4.0% coverage) to the genome of Acinetobacter phage vB_AbaM_IME284 (GenBank no. MH853787.1) according to the nucleotide Basic Local Alignment Search Tool (BLASTn). Phylogenetic analysis revealed that vB_EcoM_APEC was a novel phage, and its genome sequence showed low similarity to other available phage genomes. Gene annotation indicated that the protein encoded by orf11 was an endolysin designated as LysO78, which exhibited 64.7% identity (91.0% coverage) with the putative endolysin of Acinetobacter baumannii phage vB_AbaM_B9. The LysO78 protein belongs to glycoside hydrolase family 19, and was described as being a chitinase class I protein. LysO78 is a helical protein with 12 α-helices containing a large domain and a small domain in terms of the predicted three-dimensional structure. The results of site-directed mutagenesis indicated that LysO78 contained the catalytic residues E54 and E64. The purified endolysin exhibited broad-spectrum bacteriolytic activity against Gram-negative strains, including the genera Klebsiella, Salmonella, Shigella, Burkholderia, Yersinia, and Pseudomonas, as well as the species Chitinimonas arctica, E. coli, Ralstonia solanacearum, and A. baumannii. An enzymatic assay showed that LysO78 had highly lytic peptidoglycan hydrolases activity (64,620,000 units/mg) against E. coli APEC O78, and that LysO78 had lytic activity in the temperature range of 4-85 °C, with an optimal temperature of 28 °C and optimal pH of 8.0, and was active at pH 3.0-12.0. Overall, the results suggested that LysO78 might be a promising therapeutic agent for controlling MDR E. coli APEC O78 and nosocomial infections caused by multidrug-resistant bacteria.
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Affiliation(s)
- Sangsang Deng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (S.D.); (Y.F.); (L.L.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Qiang Xu
- China Center for Type Culture Collection(CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, China;
| | - Yajuan Fu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (S.D.); (Y.F.); (L.L.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Leiqin Liang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (S.D.); (Y.F.); (L.L.); (Y.W.)
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Wu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (S.D.); (Y.F.); (L.L.); (Y.W.)
| | - Fang Peng
- China Center for Type Culture Collection(CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, China;
- Correspondence: (F.P.); (M.G.)
| | - Meiying Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (S.D.); (Y.F.); (L.L.); (Y.W.)
- Correspondence: (F.P.); (M.G.)
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Mangalea MR, Paez-Espino D, Kieft K, Chatterjee A, Chriswell ME, Seifert JA, Feser ML, Demoruelle MK, Sakatos A, Anantharaman K, Deane KD, Kuhn KA, Holers VM, Duerkop BA. Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential. Cell Host Microbe 2021; 29:726-739.e5. [PMID: 33957082 PMCID: PMC8186507 DOI: 10.1016/j.chom.2021.03.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/12/2021] [Accepted: 03/30/2021] [Indexed: 02/08/2023]
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized in seropositive individuals by the presence of anti-cyclic citrullinated protein (CCP) antibodies. RA is linked to the intestinal microbiota, yet the association of microbes with CCP serology and their contribution to RA is unclear. We describe intestinal phage communities of individuals at risk for developing RA, with or without anti-CCP antibodies, whose first-degree relatives have been diagnosed with RA. We show that at-risk individuals harbor intestinal phage compositions that diverge based on CCP serology, are dominated by Streptococcaceae, Bacteroidaceae, and Lachnospiraceae phages, and may originate from disparate ecosystems. These phages encode unique repertoires of auxiliary metabolic genes, which associate with anti-CCP status, suggesting that these phages directly influence the metabolic and immunomodulatory capability of the microbiota. This work sets the stage for the use of phages as preclinical biomarkers and provides insight into a possible microbial-based causation of RA disease development.
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Affiliation(s)
- Mihnea R Mangalea
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Kristopher Kieft
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Meagan E Chriswell
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jennifer A Seifert
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Marie L Feser
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - M Kristen Demoruelle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Kevin D Deane
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kristine A Kuhn
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - V Michael Holers
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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40
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Song Y, Peters TL, Bryan DW, Hudson LK, Denes TG. Characterization of a Novel Group of Listeria Phages That Target Serotype 4b Listeria monocytogenes. Viruses 2021; 13:v13040671. [PMID: 33919793 PMCID: PMC8070769 DOI: 10.3390/v13040671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/26/2021] [Accepted: 04/10/2021] [Indexed: 12/19/2022] Open
Abstract
Listeria monocytogenes serotype 4b strains are the most prevalent clinical isolates and are widely found in food processing environments. Bacteriophages are natural viral predators of bacteria and are a promising biocontrol agent for L. monocytogenes. The aims of this study were to characterize phages that specifically infect serotype 4b strains and to assess their ability to inhibit the growth of serotype 4b strains. Out of 120 wild Listeria phages, nine phages were selected based on their strong lytic activity against the model serotype 4b strain F2365. These nine phages can be divided into two groups based on their morphological characteristics and host range. Comparison to previously characterized phage genomes revealed one of these groups qualifies to be defined as a novel species. Phages LP-020, LP-027, and LP-094 were selected as representatives of these two groups of phages for further characterization through one-step growth curve and inhibition of serotype 4b L. monocytogenes experiments. Listeria phages that target serotype 4b showed an inhibitory effect on the growth of F2365 and other serotype 4 strains and may be useful for biocontrol of L.monocytogenes in food processing environments.
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41
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Ni P, Wang L, Deng B, Jiu S, Ma C, Zhang C, Almeida A, Wang D, Xu W, Wang S. Characterization of a Lytic Bacteriophage against Pseudomonas syringae pv. actinidiae and Its Endolysin. Viruses 2021; 13:631. [PMID: 33917076 PMCID: PMC8067700 DOI: 10.3390/v13040631] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
Pseudomonas syringae pv. actinidiae (Psa) is a phytopathogen that causes canker in kiwifruit. Few conventional control methods are effective against this bacterium. Therefore, alternative approaches, such as phage therapy are warranted. In this study, a lytic bacteriophage (PN09) of Psa was isolated from surface water collected from a river in Hangzhou, China in 2019. Morphologically, PN09 was classified into the Myoviridae family, and could lyse all 29 Psa biovar 3 strains. The optimal temperature and pH ranges for PN09 activity were determined as 25 to 35 ∘C and 6.0 to 9.0, respectively. The complete genome of PN09 was found to be composed of a linear 99,229 bp double-stranded DNA genome with a GC content of 48.16%. The PN09 endolysin (LysPN09) was expressed in vitro and characterized. LysPN09 was predicted to belong to the Muraidase superfamily domain and showed lytic activity against the outer-membrane-permeabilized Psa strains. The lytic activity of LysPN09 was optimal over temperature and pH ranges of 25 to 40 ∘C and 6.0 to 8.0, respectively. When recombinant endolysin LysPN09 was combined with EDTA, Psa strains were effectively damaged. All these characteristics demonstrate that the phage PN09 and its endolysin, LysPN09, are potential candidates for biocontrol of Psa in the kiwifruit industry.
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Affiliation(s)
- Peien Ni
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Lei Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Bohan Deng
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Songtao Jiu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Chao Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Caixi Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Dapeng Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Wenping Xu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
| | - Shiping Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (P.N.); (L.W.); (B.D.); (S.J.); (C.M.); (C.Z.); (D.W.); (S.W.)
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42
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Abstract
Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy.
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Affiliation(s)
- Dann Turner
- Department of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK;
| | - Andrew M. Kropinski
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
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43
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López-Leal G, Reyes-Muñoz A, Santamaria RI, Cevallos MA, Pérez-Monter C, Castillo-Ramírez S. A novel vieuvirus from multidrug-resistant Acinetobacter baumannii. Arch Virol 2021; 166:1401-1408. [PMID: 33635432 DOI: 10.1007/s00705-021-05010-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/16/2021] [Indexed: 11/26/2022]
Abstract
Bacteriophages are considered the most abundant biological entities on earth, and they are able to modulate the populations of their bacterial hosts. Although the potential of bacteriophages has been accepted as an alternative strategy to combat multidrug-resistant pathogenic bacteria, there still exists a considerable knowledge gap regarding their genetic diversity, which hinders their use as antimicrobial agents. In this study, we undertook a genomic and phylogenetic characterization of the phage Ab11510-phi, which was isolated from a multidrug-resistant Acinetobacter baumannii strain (Ab11510). We found that Ab11510-phi has a narrow host range and belongs to a small group of transposable phages of the genus Vieuvirus that have only been reported to infect Acinetobacter bacteria. Finally, we showed that Ab11510-phi (as well as other vieuvirus phages) has a high level of mosaicism. On a broader level, we demonstrate that comparative genomics and phylogenetic analysis are necessary tools for the proper characterization of phage diversity.
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Affiliation(s)
- Gamaliel López-Leal
- Grupo de Biología Computacional y Ecología Microbiana, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, D.C., Colombia.
| | - Alejandro Reyes-Muñoz
- Grupo de Biología Computacional y Ecología Microbiana, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, D.C., Colombia
| | - Rosa Isela Santamaria
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Carlos Pérez-Monter
- Departamento de Gastroenterología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, México
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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44
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Salem M, Pajunen MI, Jun JW, Skurnik M. T4-like Bacteriophages Isolated from Pig Stools Infect Yersinia pseudotuberculosis and Yersinia pestis Using LPS and OmpF as Receptors. Viruses 2021; 13:v13020296. [PMID: 33668618 PMCID: PMC7917993 DOI: 10.3390/v13020296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/22/2022] Open
Abstract
The Yersinia bacteriophages fPS-2, fPS-65, and fPS-90, isolated from pig stools, have long contractile tails and elongated heads, and they belong to genus Tequatroviruses in the order Caudovirales. The phages exhibited relatively wide host ranges among Yersinia pseudotuberculosis and related species. One-step growth curve experiments revealed that the phages have latent periods of 50-80 min with burst sizes of 44-65 virions per infected cell. The phage genomes consist of circularly permuted dsDNA of 169,060, 167,058, and 167,132 bp in size, respectively, with a G + C content 35.3%. The number of predicted genes range from 267 to 271. The phage genomes are 84-92% identical to each other and ca 85% identical to phage T4. The phage receptors were identified by whole genome sequencing of spontaneous phage-resistant mutants. The phage-resistant strains had mutations in the ompF, galU, hldD, or hldE genes. OmpF is a porin, and the other genes encode lipopolysaccharide (LPS) biosynthetic enzymes. The ompF, galU, and hldE mutants were successfully complemented in trans with respective wild-type genes. The host recognition was assigned to long tail fiber tip protein Gp38, analogous to that of T-even phages such as Salmonella phage S16, specifically to the distal β-helices connecting loops.
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Affiliation(s)
- Mabruka Salem
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (M.S.); (M.I.P.)
- Department of Microbiology, Faculty of Medicine, University of Benghazi, Benghazi 16063, Libya
| | - Maria I. Pajunen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (M.S.); (M.I.P.)
| | - Jin Woo Jun
- Department of Aquaculture, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea;
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (M.S.); (M.I.P.)
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00290 Helsinki, Finland
- Correspondence: ; Tel.: +358-50-336-0981
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45
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Petrzik K, Lukavský J, Koloniuk I. Novel Virus on Filamentous Arthronema africanum Cyanobacterium. Microb Ecol 2021; 81:454-459. [PMID: 32901386 DOI: 10.1007/s00248-020-01599-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Widely distributed in water environments and in soil, cyanobacteria are hosts of lysogenic or lytic bacterioviruses. A novel, probably lysogenic virus (phage) for which the name Arthronema africanum virus TR020 (Aa-TR020) is proposed, has been isolated from filamentous freshwater cyanobacterium Arthronema africanum. The virus formed turbid plaques on plate culture of A. africanum strain 1980/01 but not on other Arthronema strain and other bacterial species. The genome of Aa-TR020 is linear molecule of dsDNA, 44,805 bp in length with 216 bp long terminal repeats and with G + C content of 46%. Fifty-five genes organized on plus and minus strands were predicted there. The genome size, gene arrangement, and selected protein sequences showed relatedness to Phormidium virus Pf-WMP3 and other viruses known to infect cyanobacteria and classified in the family Podoviridae.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic.
| | - Jaromír Lukavský
- Centre for Phycology, Institute of Botany, Czech Academy of Sciences, Dukelská 135, Třeboň, Czech Republic
| | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic
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46
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Drobysheva AV, Panafidina SA, Kolesnik MV, Klimuk EI, Minakhin L, Yakunina MV, Borukhov S, Nilsson E, Holmfeldt K, Yutin N, Makarova KS, Koonin EV, Severinov KV, Leiman PG, Sokolova ML. Structure and function of virion RNA polymerase of a crAss-like phage. Nature 2021; 589:306-309. [PMID: 33208949 DOI: 10.1038/s41586-020-2921-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/08/2020] [Indexed: 01/29/2023]
Abstract
CrAss-like phages are a recently described expansive group of viruses that includes the most abundant virus in the human gut1-3. The genomes of all crAss-like phages encode a large virion-packaged protein2,4 that contains a DFDxD sequence motif, which forms the catalytic site in cellular multisubunit RNA polymerases (RNAPs)5. Here, using Cellulophaga baltica crAss-like phage phi14:2 as a model system, we show that this protein is a DNA-dependent RNAP that is translocated into the host cell along with the phage DNA and transcribes early phage genes. We determined the crystal structure of this 2,180-residue enzyme in a self-inhibited state, which probably occurs before virion packaging. This conformation is attained with the help of a cleft-blocking domain that interacts with the active site and occupies the cavity in which the RNA-DNA hybrid binds. Structurally, phi14:2 RNAP is most similar to eukaryotic RNAPs that are involved in RNA interference6,7, although most of the phi14:2 RNAP structure (nearly 1,600 residues) maps to a new region of the protein fold space. Considering this structural similarity, we propose that eukaryal RNA interference polymerases have their origins in phage, which parallels the emergence of the mitochondrial transcription apparatus8.
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Affiliation(s)
- Arina V Drobysheva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sofia A Panafidina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Matvei V Kolesnik
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evgeny I Klimuk
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Leonid Minakhin
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Maria V Yakunina
- Peter the Great St Petersburg Polytechnic University, St Petersburg, Russia
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ, USA
| | - Emelie Nilsson
- Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Karin Holmfeldt
- Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Konstantin V Severinov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
| | - Maria L Sokolova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.
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47
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Coughlan S, Das A, O’Herlihy E, Shanahan F, O’Toole P, Jeffery I. The gut virome in Irritable Bowel Syndrome differs from that of controls. Gut Microbes 2021; 13:1-15. [PMID: 33602058 PMCID: PMC7899630 DOI: 10.1080/19490976.2021.1887719] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/28/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
Irritable Bowel Syndrome (IBS), the most common gastrointestinal disorder, is diagnosed solely on symptoms. Potentially diagnostic alterations in the bacterial component of the gut microbiome (the bacteriome) are associated with IBS, but despite the known role of the virome (particularly bacteriophages), in shaping the gut bacteriome, few studies have investigated the virome in IBS. We performed metagenomic sequencing of fecal Virus-Like Particles (VLPs) from 55 patients with IBS and 51 control individuals. We detected significantly lower alpha diversity of viral clusters comprising both known and novel viruses (viral 'dark matter') in IBS and a significant difference in beta diversity compared to controls, but not between IBS symptom subtypes. The three most abundant bacteriophage clusters belonged to the Siphoviridae, Myoviridae, and Podoviridae families (Order Caudovirales). A core virome (defined as a cluster present in at least 50% of samples) of 5 and 12 viral clusters was identified in IBS and control subjects, respectively. We also identified a subset of viral clusters that showed differential abundance between IBS and controls. The virome did not co-vary significantly with the bacteriome, with IBS clinical subtype, or with Bile Acid Malabsorption status. However, differences in the virome could be related back to the bacteriome as analysis of CRISPR spacers indicated that the virome alterations were at least partially related to the alterations in the bacteriome. We found no evidence for a shift from lytic to lysogenic replication of core viral clusters, a phenomenon reported for the gut virome of patients with Inflammatory Bowel Disease. Collectively, our data show alterations in the virome of patients with IBS, regardless of clinical subtype, which may facilitate development of new microbiome-based therapeutics.
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Affiliation(s)
- S. Coughlan
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - A. Das
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - E. O’Herlihy
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - F. Shanahan
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
| | - P.W. O’Toole
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
| | - I.B. Jeffery
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
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48
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Auslander N, Gussow AB, Benler S, Wolf YI, Koonin EV. Seeker: alignment-free identification of bacteriophage genomes by deep learning. Nucleic Acids Res 2020; 48:e121. [PMID: 33045744 PMCID: PMC7708075 DOI: 10.1093/nar/gkaa856] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Recent advances in metagenomic sequencing have enabled discovery of diverse, distinct microbes and viruses. Bacteriophages, the most abundant biological entity on Earth, evolve rapidly, and therefore, detection of unknown bacteriophages in sequence datasets is a challenge. Most of the existing detection methods rely on sequence similarity to known bacteriophage sequences, impeding the identification and characterization of distinct, highly divergent bacteriophage families. Here we present Seeker, a deep-learning tool for alignment-free identification of phage sequences. Seeker allows rapid detection of phages in sequence datasets and differentiation of phage sequences from bacterial ones, even when those phages exhibit little sequence similarity to established phage families. We comprehensively validate Seeker's ability to identify previously unidentified phages, and employ this method to detect unknown phages, some of which are highly divergent from the known phage families. We provide a web portal (seeker.pythonanywhere.com) and a user-friendly Python package (github.com/gussow/seeker) allowing researchers to easily apply Seeker in metagenomic studies, for the detection of diverse unknown bacteriophages.
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Affiliation(s)
- Noam Auslander
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Ayal B Gussow
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sean Benler
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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49
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Kim SG, Lee SB, Giri SS, Kim HJ, Kim SW, Kwon J, Park J, Roh E, Park SC. Characterization of Novel Erwinia amylovora Jumbo Bacteriophages from Eneladusvirus Genus. Viruses 2020; 12:E1373. [PMID: 33266226 PMCID: PMC7760394 DOI: 10.3390/v12121373] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Jumbo phages, which have a genome size of more than 200 kb, have recently been reported for the first time. However, limited information is available regarding their characteristics because few jumbo phages have been isolated. Therefore, in this study, we aimed to isolate and characterize other jumbo phages. We performed comparative genomic analysis of three Erwinia phages (pEa_SNUABM_12, pEa_SNUABM_47, and pEa_SNUABM_50), each of which had a genome size of approximately 360 kb (32.5% GC content). These phages were predicted to harbor 546, 540, and 540 open reading frames with 32, 34, and 35 tRNAs, respectively. Almost all of the genes in these phages could not be functionally annotated but showed high sequence similarity with genes encoded in Serratia phage BF, a member of Eneladusvirus. The detailed comparative and phylogenetic analyses presented in this study contribute to our understanding of the diversity and evolution of Erwinia phage and the genus Eneladusvirus.
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Affiliation(s)
- Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Hyoun Joong Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Sang Wha Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Jungkum Park
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (J.P.); (E.R.)
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (J.P.); (E.R.)
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
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50
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Kosznik-Kwaśnicka K, Grabowski Ł, Grabski M, Kaszubski M, Górniak M, Jurczak-Kurek A, Węgrzyn G, Węgrzyn A. Bacteriophages vB_Sen-TO17 and vB_Sen-E22, Newly Isolated Viruses from Chicken Feces, Specific for Several Salmonella enterica Strains. Int J Mol Sci 2020; 21:ijms21228821. [PMID: 33233449 PMCID: PMC7700153 DOI: 10.3390/ijms21228821] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 11/16/2022] Open
Abstract
Two newly discovered bacteriophages, isolated from chicken feces and infecting Salmonella enterica strains, are described in this report. These phages have been named vB_Sen-TO17 and vB_Sen-E22, and we present their molecular and functional characterization. Both studied viruses are able to infect several S. enterica strains and develop lytically, but their specific host ranges differ significantly. Electron microscopic analyses of virions have been performed, and full genome sequences were determined and characterized, along with molecular phylogenetic studies. Genomes of vB_Sen-TO17 (ds DNA of 41,658 bp) and vB_Sen-E22 (dsDNA of 108,987 bp) are devoid of homologs of any known or putative gene coding for toxins or any other proteins potentially deleterious for eukaryotic cells. Both phages adsorbed efficiently (>95% adsorbed virions) within 10 min at 42 °C (resembling chicken body temperature) on cells of most tested host strains. Kinetics of lytic development of vB_Sen-TO17 and vB_Sen-E22, determined in one-step growth experiments, indicated that development is complete within 30-40 min at 42 °C, whereas burst sizes vary from 9 to 79 progeny phages per cell for vB_Sen-TO17 and from 18 to 64 for vB_Sen-E22, depending on the host strain. Virions of both phages were relatively stable (from several percent to almost 100% survivability) under various conditions, including acidic and alkaline pH values (from 3 to 12), temperatures from -80 °C to 60 °C, 70% ethanol, chloroform, and 10% DMSO. These characteristics of vB_Sen-TO17 and vB_Sen-E22 indicate that these phages might be considered in further studies on phage therapy, particularly in attempts to eliminate S. enterica from chicken intestine.
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Affiliation(s)
- Katarzyna Kosznik-Kwaśnicka
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (K.K.-K.); (Ł.G.)
| | - Łukasz Grabowski
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (K.K.-K.); (Ł.G.)
| | - Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (M.K.); (G.W.)
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Mateusz Kaszubski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (M.K.); (G.W.)
| | - Marcin Górniak
- Department of Molecular Evolution, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (A.J.-K.)
| | - Agata Jurczak-Kurek
- Department of Molecular Evolution, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (A.J.-K.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (M.K.); (G.W.)
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (K.K.-K.); (Ł.G.)
- Correspondence: ; Tel.: +48-58-523-6024
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