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Riber L, Carstens AB, Dougherty PE, Roy C, Willenbücher K, Hille F, Franz CMAP, Hansen LH. Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus. Microorganisms 2023; 11:1831. [PMID: 37513003 PMCID: PMC10385605 DOI: 10.3390/microorganisms11071831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Bacteriophages are viral agents that infect and replicate within bacterial cells. Despite the increasing importance of phage ecology, environmental phages-particularly those targeting phyllosphere-associated bacteria-remain underexplored, and current genomic databases lack high-quality phage genome sequences linked to specific environmentally important bacteria, such as the ubiquitous sphingomonads. Here, we isolated three novel phages from a Danish wastewater treatment facility. Notably, these phages are among the first discovered to target and regulate a Sphingomonas genus within the wheat phyllosphere microbiome. Two of the phages displayed a non-prolate Siphovirus morphotype and demonstrated a narrow host range when tested against additional Sphingomonas strains. Intergenomic studies revealed limited nucleotide sequence similarity within the isolated phage genomes and to publicly available metagenome data of their closest relatives. Particularly intriguing was the limited homology observed between the DNA polymerase encoding genes of the isolated phages and their closest relatives. Based on these findings, we propose three newly identified genera of viruses: Longusvirus carli, Vexovirus birtae, and Molestusvirus kimi, following the latest ICTV binomial nomenclature for virus species. These results contribute to our current understanding of phage genetic diversity in natural environments and hold promising implications for phage applications in phyllosphere microbiome manipulation strategies.
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Affiliation(s)
- Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Alexander Byth Carstens
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Peter Erdmann Dougherty
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Chayan Roy
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Katharina Willenbücher
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Frank Hille
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
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2
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Four novel Curtobacterium phages isolated from environmental samples. Arch Virol 2023; 168:89. [PMID: 36786922 DOI: 10.1007/s00705-023-05706-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/20/2022] [Indexed: 02/15/2023]
Abstract
Despite Curtobacterium spp. often being associated with the plant phyllosphere, i.e., the areal region of different plant species, only one phage targeting a member of the genus Curtobacterium has been isolated so far. In this study, we isolated four novel plaque-forming Curtobacterium phages, Reje, Penoan, Parvaparticeps, and Pize, with two novel Curtobacterium strains as propagation hosts. Based on the low nucleotide intergenomic similarity (<32.4%) between these four phages and any phage with a genome sequence in the NCBI database, we propose the establishment of the four genera, "Rejevirus", "Pizevirus", "Penoanvirus", and "Parvaparticepsvirus", all in the class of Caudoviricetes.
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3
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Alanin KWS, Olsen NS, Djurhuus AM, Carstens AB, Nielsen TK, Wagner N, Lametsch R, Bak F, Hennessy RC, Nicolaisen MH, Kot W, Hansen LH. Three novel Erwinia billingiae phages isolated from organic waste represent three new genera. Arch Virol 2023; 168:71. [PMID: 36658443 DOI: 10.1007/s00705-023-05700-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/19/2022] [Indexed: 01/21/2023]
Abstract
Despite the ecological significance of viral communities, phages remain insufficiently studied. Current genomic databases lack high-quality phage genome sequences linked to specific bacteria. Bacteria of the genus Erwinia are known to colonize the phyllosphere of plants, both as commensals and as pathogens. We isolated three Erwinia billingiae phages-Zoomie, Pecta, and Snitter-from organic household waste. Based on sequence similarity to their closest relatives, we propose that they represent three new genera: "Pectavirus" within the family Zobellviridae, "Snittervirus" in the subfamily Tempevirinae, family Drexlerviridae, and "Zoomievirus" within the family Autographiviridae, which, together with the genus Limelightvirus, may constitute a new subfamily.
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Affiliation(s)
- Katrine Wacenius Skov Alanin
- Department for Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark.,Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Nikoline S Olsen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Amaru Miranda Djurhuus
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Alexander Byth Carstens
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Natalia Wagner
- Institute for Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
| | - René Lametsch
- Department of Food Science, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Frederik Bak
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Rosanna Catherine Hennessy
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Mette Haubjerg Nicolaisen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Witold Kot
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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4
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Bumunang EW, McAllister TA, Polo RO, Ateba CN, Stanford K, Schlechte J, Walker M, MacLean K, Niu YD. Genomic Profiling of Non-O157 Shiga Toxigenic Escherichia coli-Infecting Bacteriophages from South Africa. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:221-230. [PMID: 36793886 PMCID: PMC9917312 DOI: 10.1089/phage.2022.0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Background Non-O157 Shiga toxigenic Escherichia coli (STEC) are one of the most important food and waterborne pathogens worldwide. Although bacteriophages (phages) have been used for the biocontrol of these pathogens, a comprehensive understanding of the genetic characteristics and lifestyle of potentially effective candidate phages is lacking. Materials and Methods In this study, 10 non-O157-infecting phages previously isolated from feedlot cattle and dairy farms in the North-West province of South Africa were sequenced, and their genomes were analyzed. Results Comparative genomics and proteomics revealed that the phages were closely related to other E. coli-infecting Tunaviruses, Seuratviruses, Carltongylesviruses, Tequatroviruses, and Mosigviruses from the National Center for Biotechnology Information GenBank database. Phages lacked integrases associated with a lysogenic cycle and genes associated with antibiotic resistance and Shiga toxins. Conclusions Comparative genomic analysis identified a diversity of unique non-O157-infecting phages, which could be used to mitigate the abundance of various non-O157 STEC serogroups without safety concerns.
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Affiliation(s)
- Emmanuel W. Bumunang
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
| | - Rodrigo Ortega Polo
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Canada
| | - Collins N. Ateba
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Kim Stanford
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Canada
| | - Jared Schlechte
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Matthew Walker
- Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada, Winnipeg, Canada
| | - Kellie MacLean
- Cumming School of Medicine, Faculty of Science, University of Calgary, Calgary, Canada
| | - Yan D. Niu
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
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5
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Sprotte S, Rasmussen TS, Cho GS, Brinks E, Lametsch R, Neve H, Vogensen FK, Nielsen DS, Franz CMAP. Morphological and Genetic Characterization of Eggerthella lenta Bacteriophage PMBT5. Viruses 2022; 14:v14081598. [PMID: 35893664 PMCID: PMC9394477 DOI: 10.3390/v14081598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
Eggerthella lenta is a common member of the human gut microbiome. We here describe the isolation and characterization of a putative virulent bacteriophage having E. lenta as host. The double-layer agar method for isolating phages was adapted to anaerobic conditions for isolating bacteriophage PMBT5 from sewage on a strictly anaerobic E. lenta strain of intestinal origin. For this, anaerobically grown E. lenta cells were concentrated by centrifugation and used for a 24 h phage enrichment step. Subsequently, this suspension was added to anaerobically prepared top (soft) agar in Hungate tubes and further used in the double-layer agar method. Based on morphological characteristics observed by transmission electron microscopy, phage PMBT5 could be assigned to the Siphoviridae phage family. It showed an isometric head with a flexible, noncontractile tail and a distinct single 45 nm tail fiber under the baseplate. Genome sequencing and assembly resulted in one contig of 30,930 bp and a mol% GC content of 51.3, consisting of 44 predicted protein-encoding genes. Phage-related proteins could be largely identified based on their amino acid sequence, and a comparison with metagenomes in the human virome database showed that the phage genome exhibits similarity to two distantly related phages.
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Affiliation(s)
- Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
- Correspondence:
| | - Torben S. Rasmussen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - René Lametsch
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
| | - Finn K. Vogensen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Dennis S. Nielsen
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958 Frederiksberg, Denmark; (T.S.R.); (R.L.); (F.K.V.); (D.S.N.)
| | - Charles M. A. P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; (G.-S.C.); (E.B.); (H.N.); (C.M.A.P.F.)
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6
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Olsen NS, Lametsch R, Wagner N, Hansen LH, Kot W. Salmonella phage akira, infecting selected Salmonella enterica Enteritidis and Typhimurium strains, represents a new lineage of bacteriophages. Arch Virol 2022; 167:2049-2056. [PMID: 35764845 DOI: 10.1007/s00705-022-05477-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 04/08/2022] [Indexed: 11/02/2022]
Abstract
Some serovars of Salmonella can cause life-threatening diarrhoeal diseases and bacteriemia. The emergence of multidrug-resistant strains has led to a need for alternative treatments such as phage therapy, which requires available, well-described, diverse, and suitable phages. Phage akira was found to lyse 19 out of 32 Salmonella enterica serovars and farm isolates tested, although plaque formation was observed with only two S. Enteritidis and one S. Typhimurium strain. Phage akira encodes anti-defence genes against type 1 R-M systems, is distinct (<65% nucleotide sequence identity) from related phages and has siphovirus morphology. We propose that akira represents a new genus in the class Caudoviricetes.
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Affiliation(s)
- Nikoline S Olsen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark.
| | - René Lametsch
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg, Denmark
| | - Natalia Wagner
- Institute for Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Str. 1, 24103, Kiel, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark.
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7
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A New Enterobacter cloacae Bacteriophage EC151 Encodes the Deazaguanine DNA Modification Pathway and Represents a New Genus within the Siphoviridae Family. Viruses 2021; 13:v13071372. [PMID: 34372577 PMCID: PMC8310023 DOI: 10.3390/v13071372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 02/06/2023] Open
Abstract
A novel Enterobacter cloacae phage, EC151, was isolated and characterized. Electron microscopy revealed that EC151 has a siphovirus-like virion morphology. The EC151 nucleotide sequence shows limited similarity to other phage genomes deposited in the NCBI GenBank database. The size of the EC151 genome is 60,753 bp and contains 58 putative genes. Thirty-nine of them encode proteins of predicted function, 18 are defined as hypothetical proteins, and one ORF identifies as the tRNA-Ser-GCT-encoding gene. Six ORFs were predicted to be members of the deazaguanine DNA modification pathway, including the preQ0 transporter. Comparative proteomic phylogenetic analysis revealed that phage EC151 represents a distinct branch within a group of sequences containing clades formed by members of the Seuratvirus, Nonagvirus, and Vidquintavirus genera. In addition, the EC151 genome showed gene synteny typical of the Seuratvirus, Nonagvirus, and Nipunavirus phages. The average genetic distances of EC151/Seuratvirus, EC151/Nonagvirus, and EC151/Vidquintavirus are approximately equal to those between the Seuratvirus, Nonagvirus, and Vidquintavirus genera (~0.7 substitutions per site). Therefore, EC151 may represent a novel genus within the Siphoviridae family. The origin of the deazaguanine DNA modification pathway in the EC151 genome can be traced to Escherichia phages from the Seuratvirus genus.
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8
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Djurhuus AM, Carstens AB, Neve H, Kot W, Hansen LH. Two New Dickeya dadantii Phages with Odd Growth Patterns Expand the Diversity of Phages Infecting Soft Rot Pectobacteriaceae. ACTA ACUST UNITED AC 2020; 1:251-259. [DOI: 10.1089/phage.2020.0039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Amaru Miranda Djurhuus
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Alexander Byth Carstens
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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9
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Pedersen JS, Carstens AB, Djurhuus AM, Kot W, Neve H, Hansen LH. Pectobacterium Phage Jarilo Displays Broad Host Range and Represents a Novel Genus of Bacteriophages Within the Family Autographiviridae. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:237-244. [PMID: 36147289 DOI: 10.1089/phage.2020.0037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background: Soft rot Pectobacteriaceae includes the genera Pectobacterium and Dickeya, which are important plant pathogens being responsible for diseases in a wide range of plant species, with potatoes as the main group. Both genera cause pre- and postharvest losses of potatoes, resulting in huge economic losses linked with the soft rot diseases. Materials and Methods: Organic waste was used to isolate phages, with Pectobacterium carotovorum subsp. carotovorum DSM 30170 as host. Complete genome sequencing, comparative genomics, and electron microscopy were used to characterize the phage. An adsorption assay was used to estimate adsorption rate. Twenty-three strains from the genera Pectobacterium and Dickeya were used to examine the host range of the phage. Results: Pectobacterium phage Jarilo represents a novel genus of bacteriophages within the family Autographiviridae, order Caudovirales. Jarilo possesses a double-stranded DNA genome of 40557 bp with a G+C% content of 50.08% and 50 predicted open reading frames. Gene synteny and products seem to be partly conserved between Pectobacterium phage Jarilo and Enterobacteria phage T7, but limited nucleotide similarity is found between Jarilo and other phages within the family Autographiviridae. The adsorption rate of phage Jarilo increased continuously for 1 h upon infection. Phage Jarilo was not able to infect any strains of P. carotovorum and Dickeya tested with the exception of the P. carotovorum strain used for isolation. However, phage Jarilo infected 10 of 16 Pectobacterium atrosepticum strains tested. Conclusion: We propose Pectobacterium phage Jarilo as the first member of a new genus of bacteriophages within the family Autographiviridae, order Caudovirales, displaying a broad host range within the genera of Pectobacterium.
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Affiliation(s)
- Julie Stenberg Pedersen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Alexander Byth Carstens
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Amaru Miranda Djurhuus
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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10
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Pedersen JS, Kot W, Plöger M, Lametsh R, Neve H, Franz CM, Hansen LH. A Rare, Virulent Clostridium perfringens Bacteriophage Susfortuna Is the First Isolated Bacteriophage in a New Viral Genus. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:230-236. [PMID: 36147286 PMCID: PMC9041476 DOI: 10.1089/phage.2020.0038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background: Clostridium perfringens is a well known swine pathogen. C. perfringens type A is considered the causative agent of enteric diseases in neonatal and weaned piglets. Phage therapy using C. perfringens phages in vivo has previously proved effective. Materials and Methods: Pig fecal samples were used to isolate phages, with Clostridium perfringens type A as host. Complete genome sequencing, comparative genomics, a proteome analysis and electron microscopy were used to characterize the phage. Results: Clostridium phage Susfortuna has a double-stranded DNA genome of 19,046 bp with a G+C% content of 29.2, inverted terminal repeats and 28 predicted coding sequences (CDSs). Putative functions could not be assigned to most of the CDSs (64.3%). Transmission electron microscopy of phage Susfortuna revealed an isometric head and a short protruding tail stub resembling the structure of the Podoviridae family. A proteome analysis of phage Susfortuna identified seven structural proteins, but only one could be assigned with a putative function. Conclusions: Based on the morphology, the inverted terminal repeats and the small genome size, phage Susfortuna belongs to subfamily Picovirinae within the Podoviridae family in the order Caudovirales. Together with C. perfringens bacteriophage CPD7, phage Susfortuna represent a new genus of bacteriophages with very limited DNA sequence similarity to other known C. perfringens phages. Despite the limited DNA sequence similarity, the gene synteny among putative structural genes of phage Susfortuna is conserved among several C. perfringens bacteriophages belonging to the Podoviridae family indicating a common ancestor.
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Affiliation(s)
- Julie Stenberg Pedersen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Maja Plöger
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Réne Lametsh
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Charles M.A.P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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11
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Kot W, Olsen NS, Nielsen TK, Hutinet G, de Crécy-Lagard V, Cui L, Dedon PC, Carstens AB, Moineau S, Swairjo MA, Hansen LH. Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs. Nucleic Acids Res 2020; 48:10383-10396. [PMID: 32941607 PMCID: PMC7544227 DOI: 10.1093/nar/gkaa735] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/22/2022] Open
Abstract
In the constant evolutionary battle against mobile genetic elements (MGEs), bacteria have developed several defense mechanisms, some of which target the incoming, foreign nucleic acids e.g. restriction-modification (R-M) or CRISPR-Cas systems. Some of these MGEs, including bacteriophages, have in turn evolved different strategies to evade these hurdles. It was recently shown that the siphophage CAjan and 180 other viruses use 7-deazaguanine modifications in their DNA to evade bacterial R-M systems. Among others, phage CAjan genome contains a gene coding for a DNA-modifying homolog of a tRNA-deazapurine modification enzyme, together with four 7-cyano-7-deazaguanine synthesis genes. Using the CRISPR-Cas9 genome editing tool combined with the Nanopore Sequencing (ONT) we showed that the 7-deazaguanine modification in the CAjan genome is dependent on phage-encoded genes. The modification is also site-specific and is found mainly in two separate DNA sequence contexts: GA and GGC. Homology modeling of the modifying enzyme DpdA provides insight into its probable DNA binding surface and general mode of DNA recognition.
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Affiliation(s)
- Witold Kot
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
| | - Nikoline S Olsen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Tue K Nielsen
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL USA.,Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Liang Cui
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexander B Carstens
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec City, PQ, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, PQ, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, PQ, Canada
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA, USA
| | - Lars H Hansen
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
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12
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Hylling O, Carstens AB, Kot W, Hansen M, Neve H, Franz CMAP, Johansen A, Ellegaard-Jensen L, Hansen LH. Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology. Sci Rep 2020; 10:11879. [PMID: 32681144 PMCID: PMC7368026 DOI: 10.1038/s41598-020-68389-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 06/12/2020] [Indexed: 11/09/2022] Open
Abstract
Although bacteriophages are central entities in bacterial ecology and population dynamics, there is currently no literature on the genomes of bacteriophages isolated from groundwater. Using a collection of bacterial isolates from an aquifer as hosts, this study isolated, sequenced and characterised two bacteriophages native to the groundwater reservoir. Host phylogenetic analyses revealed that the phages targeted B. mycoides and a novel Pseudomonas species. These results suggest that both bacteriophages represent new genera, highlighting that groundwater reservoirs, and probably other subsurface environments as well, are underexplored biotopes in terms of the presence and ecology of bacteriophages.
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Affiliation(s)
- Ole Hylling
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Alexander B Carstens
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark.,Department of Plant- and Environmental Sciences, Section for Microbial Ecology and Biotechnology, University of Copenhagen, Copenhagen, Denmark
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark.,Department of Plant- and Environmental Sciences, Section for Microbial Ecology and Biotechnology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, 24103, Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, 24103, Kiel, Germany
| | - Anders Johansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark. .,Department of Plant- and Environmental Sciences, Section for Microbial Ecology and Biotechnology, University of Copenhagen, Copenhagen, Denmark.
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13
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Carstens AB, Djurhuus AM, Kot W, Hansen LH. A novel six-phage cocktail reduces Pectobacterium atrosepticum soft rot infection in potato tubers under simulated storage conditions. FEMS Microbiol Lett 2020; 366:5490331. [PMID: 31095303 DOI: 10.1093/femsle/fnz101] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/14/2019] [Indexed: 01/18/2023] Open
Abstract
Pectobacterium atrosepticum is a species of plant pathogenic bacteria responsible for significant losses in potato production worldwide. Pectobacterium atrosepticum can cause blackleg disease on potato stems as well as the tuber disease termed potato soft rot. Methods for the effective control of these diseases are limited and are primarily based on good agricultural practices. Bacteriophages, viruses of bacteria, could be used as an alternative, environmentally friendly, control measure. Here, we describe the isolation and characterization of 29 phages virulent to P. atrosepticum. The phages belong to 12 different species based on a 95% sequence identity cut-off. Furthermore, based on sequence diversity and propagation results, we selected six of these phages to form a phage cocktail. The phages in the cocktail was tested on a number of P. atrosepticum strains in order to determine their host range. The phages was found to lyse 93% of the tested strains. The cocktail was subsequently tested for its effectiveness in combatting potato soft rot under simulated storage conditions. Use of the phage cocktail reduced both disease incidence and disease severity by 61% and 64%, respectively, strongly indicating that phage biocontrol has the potential to reduce the economic impact of soft rot in potato production.
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Affiliation(s)
- Alexander Byth Carstens
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, DK 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK 1871, Denmark
| | - Amaru Miranda Djurhuus
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, DK 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK 1871, Denmark
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, DK 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK 1871, Denmark
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, DK 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK 1871, Denmark
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14
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Kyrkou I, Carstens AB, Ellegaard-Jensen L, Kot W, Zervas A, Djurhuus AM, Neve H, Franz CMAP, Hansen M, Hansen LH. Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, "Silenusvirus". Sci Rep 2020; 10:8763. [PMID: 32472049 PMCID: PMC7260188 DOI: 10.1038/s41598-020-65366-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 05/04/2020] [Indexed: 11/10/2022] Open
Abstract
Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database, but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus "Silenusvirus".
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Affiliation(s)
- Ifigeneia Kyrkou
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, 2100, Denmark
| | - Alexander Byth Carstens
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
| | - Amaru Miranda Djurhuus
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, Kiel, 24103, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, Kiel, 24103, Germany
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, Roskilde, 4000, Denmark.
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark.
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15
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Hutinet G, Kot W, Cui L, Hillebrand R, Balamkundu S, Gnanakalai S, Neelakandan R, Carstens AB, Fa Lui C, Tremblay D, Jacobs-Sera D, Sassanfar M, Lee YJ, Weigele P, Moineau S, Hatfull GF, Dedon PC, Hansen LH, de Crécy-Lagard V. 7-Deazaguanine modifications protect phage DNA from host restriction systems. Nat Commun 2019; 10:5442. [PMID: 31784519 PMCID: PMC6884629 DOI: 10.1038/s41467-019-13384-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
Abstract
Genome modifications are central components of the continuous arms race between viruses and their hosts. The archaeosine base (G+), which was thought to be found only in archaeal tRNAs, was recently detected in genomic DNA of Enterobacteria phage 9g and was proposed to protect phage DNA from a wide variety of restriction enzymes. In this study, we identify three additional 2'-deoxy-7-deazaguanine modifications, which are all intermediates of the same pathway, in viruses: 2'-deoxy-7-amido-7-deazaguanine (dADG), 2'-deoxy-7-cyano-7-deazaguanine (dPreQ0) and 2'-deoxy-7- aminomethyl-7-deazaguanine (dPreQ1). We identify 180 phages or archaeal viruses that encode at least one of the enzymes of this pathway with an overrepresentation (60%) of viruses potentially infecting pathogenic microbial hosts. Genetic studies with the Escherichia phage CAjan show that DpdA is essential to insert the 7-deazaguanine base in phage genomic DNA and that 2'-deoxy-7-deazaguanine modifications protect phage DNA from host restriction enzymes.
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Affiliation(s)
- Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Liang Cui
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Roman Hillebrand
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Nitto Denko Avecia, 125 Fortune Boulevard, Milford, MA, 01757, USA
| | - Seetharamsingh Balamkundu
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Shanmugavel Gnanakalai
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | - Ramesh Neelakandan
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
| | | | - Chuan Fa Lui
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Denise Tremblay
- Département de Biochimie, Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Deborah Jacobs-Sera
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Mandana Sassanfar
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Peter Weigele
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Sylvain Moineau
- Département de Biochimie, Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Graham F Hatfull
- Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore, 138602, Singapore
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
- University of Florida, Genetics Institute, Gainesville, Florida, 32610, USA.
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16
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Alves DR, Nzakizwanayo J, Dedi C, Olympiou C, Hanin A, Kot W, Hansen L, Lametsch R, Gahan CGM, Schellenberger P, Ogilvie LA, Jones BV. Genomic and Ecogenomic Characterization of Proteus mirabilis Bacteriophages. Front Microbiol 2019; 10:1783. [PMID: 31447809 PMCID: PMC6691071 DOI: 10.3389/fmicb.2019.01783] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/18/2019] [Indexed: 01/21/2023] Open
Abstract
Proteus mirabilis often complicates the care of catheterized patients through the formation of crystalline biofilms which block urine flow. Bacteriophage therapy has been highlighted as a promising approach to control this problem, but relatively few phages infecting P. mirabilis have been characterized. Here we characterize five phages capable of infecting P. mirabilis, including those shown to reduce biofilm formation, and provide insights regarding the wider ecological and evolutionary relationships of these phages. Transmission electron microscopy (TEM) imaging of phages vB_PmiP_RS1pmA, vB_PmiP_RS1pmB, vB_PmiP_RS3pmA, and vB_PmiP_RS8pmA showed that all share morphologies characteristic of the Podoviridae family. The genome sequences of vB_PmiP_RS1pmA, vB_PmiP_RS1pmB, and vB_PmiP_RS3pmA showed these are species of the same phage differing only by point mutations, and are closely related to vB_PmiP_RS8pmA. Podophages characterized in this study were also found to share similarity in genome architecture and composition to other previously described P. mirabilis podophages (PM16 and PM75). In contrast, vB_PimP_RS51pmB showed morphology characteristic of the Myoviridae family, with no notable similarity to other phage genomes examined. Ecogenomic profiling of all phages revealed no association with human urinary tract viromes, but sequences similar to vB_PimP_RS51pmB were found within human gut, and human oral microbiomes. Investigation of wider host-phage evolutionary relationships through tetranucleotide profiling of phage genomes and bacterial chromosomes, indicated vB_PimP_RS51pmB has a relatively recent association with Morganella morganii and other non-Proteus members of the Morganellaceae family. Subsequent host range assays confirmed vB_PimP_RS51pmB can infect M. morganii.
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Affiliation(s)
- Diana R. Alves
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
- Blond McIndoe Research Foundation, Queen Victoria Hospital, East Grinstead, United Kingdom
- Queen Victoria Hospital NHS Foundation Trust, East Grinstead, United Kingdom
| | - Jonathan Nzakizwanayo
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Cinzia Dedi
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Chara Olympiou
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
- School of Pharmacy, Queen’s University, Belfast, United Kingdom
| | - Aurélie Hanin
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rene Lametsch
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Cormac G. M. Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Pharmacy, University College Cork, Cork, Ireland
| | | | - Lesley A. Ogilvie
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Brian V. Jones
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
- Queen Victoria Hospital NHS Foundation Trust, East Grinstead, United Kingdom
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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17
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Expanding the Diversity of Myoviridae Phages Infecting Lactobacillus plantarum-A Novel Lineage of Lactobacillus Phages Comprising Five New Members. Viruses 2019; 11:v11070611. [PMID: 31277436 PMCID: PMC6669764 DOI: 10.3390/v11070611] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/07/2019] [Accepted: 07/02/2019] [Indexed: 01/01/2023] Open
Abstract
Lactobacillus plantarum is a bacterium with probiotic properties and promising applications in the food industry and agriculture. So far, bacteriophages of this bacterium have been moderately addressed. We examined the diversity of five new L. plantarum phages via whole genome shotgun sequencing and in silico protein predictions. Moreover, we looked into their phylogeny and their potential genomic similarities to other complete phage genome records through extensive nucleotide and protein comparisons. These analyses revealed a high degree of similarity among the five phages, which extended to the vast majority of predicted virion-associated proteins. Based on these, we selected one of the phages as a representative and performed transmission electron microscopy and structural protein sequencing tests. Overall, the results suggested that the five phages belong to the family Myoviridae, they have a long genome of 137,973-141,344 bp, a G/C content of 36.3-36.6% that is quite distinct from their host's, and surprisingly, 7 to 15 tRNAs. Only an average 41/174 of their predicted genes were assigned a function. The comparative analyses unraveled considerable genetic diversity for the five L. plantarum phages in this study. Hence, the new genus "Semelevirus" was proposed, comprising exclusively of the five phages. This novel lineage of Lactobacillus phages provides further insight into the genetic heterogeneity of phages infecting Lactobacillus sp. The five new Lactobacillus phages have potential value for the development of more robust starters through, for example, the selection of mutants insensitive to phage infections. The five phages could also form part of phage cocktails, which producers would apply in different stages of L. plantarum fermentations in order to create a range of organoleptic outputs.
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18
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Complete Genome Sequence of Vibrio anguillarum Nontailed Bacteriophage NO16. Microbiol Resour Announc 2019; 8:8/15/e00020-19. [PMID: 30975794 PMCID: PMC6460017 DOI: 10.1128/mra.00020-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A rare nontailed virus designated NO16 was isolated against Vibrio anguillarum, a major aquaculture pathogen for both fish and shellfish. Here, we announce the 10,594-bp genome sequence of Vibrio phage NO16 with a 23-gene content. A rare nontailed virus designated NO16 was isolated against Vibrio anguillarum, a major aquaculture pathogen for both fish and shellfish. Here, we announce the 10,594-bp genome sequence of Vibrio phage NO16 with a 23-gene content.
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19
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Complete Genome Sequence of Escherichia coli Siphophage BRET. Microbiol Resour Announc 2019; 8:MRA01644-18. [PMID: 30714038 PMCID: PMC6357644 DOI: 10.1128/mra.01644-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 01/07/2019] [Indexed: 01/29/2023] Open
Abstract
The lytic Escherichia coli siphophage BRET was isolated from a chicken obtained at a local market in Abidjan, Côte d'Ivoire. Its linear genome sequence consists of 59,550 bp (43.4% GC content) and contains 88 predicted genes, including 4 involved in archaeosine biosynthesis. Phage BRET is related (95% nucleotide identity) to Enterobacteria phage JenK1.
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20
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Sazinas P, Redgwell T, Rihtman B, Grigonyte A, Michniewski S, Scanlan DJ, Hobman J, Millard A. Comparative Genomics of Bacteriophage of the Genus Seuratvirus. Genome Biol Evol 2018; 10:72-76. [PMID: 29272407 PMCID: PMC5758909 DOI: 10.1093/gbe/evx275] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 01/08/2023] Open
Abstract
Despite being more abundant and having smaller genomes than their bacterial host, relatively few bacteriophages have had their genomes sequenced. Here, we isolated 14 bacteriophages from cattle slurry and performed de novo genome sequencing, assembly, and annotation. The commonly used marker genes polB and terL showed these bacteriophages to be closely related to members of the genus Seuratvirus. We performed a core-gene analysis using the 14 new and four closely related genomes. A total of 58 core genes were identified, the majority of which has no known function. These genes were used to construct a core-gene phylogeny, the results of which confirmed the new isolates to be part of the genus Seuratvirus and expanded the number of species within this genus to four. All bacteriophages within the genus contained the genes queCDE encoding enzymes involved in queuosine biosynthesis. We suggest these genes are carried as a mechanism to modify DNA in order to protect these bacteriophages against host endonucleases.
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Affiliation(s)
- Pavelas Sazinas
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Tamsin Redgwell
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Branko Rihtman
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | | | | | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jon Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, United Kingdom
| | - Andrew Millard
- Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom
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21
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Nielsen TK, Carstens AB, Browne P, Lametsch R, Neve H, Kot W, Hansen LH. The first characterized phage against a member of the ecologically important sphingomonads reveals high dissimilarity against all other known phages. Sci Rep 2017; 7:13566. [PMID: 29051555 PMCID: PMC5648845 DOI: 10.1038/s41598-017-13911-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/29/2017] [Indexed: 01/26/2023] Open
Abstract
This study describes the first molecular characterization of a bacteriophage infecting a member of the environmentally important Sphingomonadaceae family. Both bacteriophage Lacusarx and its host Sphingobium sp. IP1 were isolated from activated sludge from a wastewater treatment plant. Genome sequencing revealed that the phage genes display little similarity to other known phages, despite a remarkable conservation of the synteny in which the functional genes occur among distantly related phages. Phylogenetic analyses confirmed that Lacusarx represents a hitherto undescribed genus of phages. A classical lysis cassette could not be identified in Lacusarx, suggesting that the genes encoding endolysin, holin, and spanin are host-specific and not found in phages infecting other bacteria. The virus harbors 24 tRNA genes corresponding to 18 different amino acids and furthermore has a significantly different codon usage than its host. Proteomic analysis of Lacusarx revealed the protein components of the phage particle. A lysogeny test indicated that Lacusarx is not a temperate phage.
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Affiliation(s)
- Tue Kjærgaard Nielsen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, 4000, Roskilde, Denmark
| | - Alexander Byth Carstens
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, 4000, Roskilde, Denmark
| | - Patrick Browne
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, 4000, Roskilde, Denmark
| | - René Lametsch
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, 24103, Kiel, Germany
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, 4000, Roskilde, Denmark
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399C, 4000, Roskilde, Denmark.
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22
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Complete Genome Sequence of Streptococcus pneumoniae Virulent Phage MS1. GENOME ANNOUNCEMENTS 2017; 5:5/28/e00333-17. [PMID: 28705957 PMCID: PMC5511896 DOI: 10.1128/genomea.00333-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The lytic Streptococcus pneumoniae phage MS1 was isolated from a throat swab of a patient with symptoms of upper respiratory tract infection. The genome of this siphophage has 56,075 bp, 42.3% G+C content, and 77 open reading frames, including queuosine biosynthesis genes. Phage MS1 is related to pneumococcal phage Dp-1.
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23
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Flores V, Sepúlveda-Robles O, Cazares A, Kameyama L, Guarneros G. Comparative genomic analysis of Pseudomonas aeruginosa phage PaMx25 reveals a novel siphovirus group related to phages infecting hosts of different taxonomic classes. Arch Virol 2017; 162:2345-2355. [PMID: 28462462 DOI: 10.1007/s00705-017-3366-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/12/2017] [Indexed: 12/20/2022]
Abstract
Bacteriophages (phages) are estimated to be the most abundant and diverse entities in the biosphere harboring vast amounts of novel genetic information. Despite the genetic diversity observed, many phages share common features, such as virion morphology, genome size and organization, and can readily be associated with clearly defined phage groups. However, other phages display unique genomes or, alternatively, mosaic genomes composed of regions that share homology with those of phages of diverse origins; thus, their relationships cannot be easily assessed. In this work, we present a functional and comparative genomic analysis of Pseudomonas aeruginosa phage PaMx25, a virulent member of the Siphoviridae family. The genomes of PaMx25 and a highly homologous phage NP1, bore sequence homology and synteny with the genomes of phages that infect hosts different than Pseudomonas. In order to understand the relationship of the PaMx25 genome with that of other phages, we employed several computational approaches. We found that PaMx25 and NP1 effectively bridged several phage groups. It is expected that as more phage genomes become available, more gaps will be filled, blurring the boundaries that currently separate phage groups.
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Affiliation(s)
- Víctor Flores
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Omar Sepúlveda-Robles
- Catedrático CONACyT - Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social (IMSS), Centro Médico Nacional Siglo XXI, Mexico City, Mexico
| | - Adrián Cazares
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Luis Kameyama
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Gabriel Guarneros
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico.
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