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Steczkiewicz K, Prestel E, Bidnenko E, Szczepankowska AK. Expanding Diversity of Firmicutes Single-Strand Annealing Proteins: A Putative Role of Bacteriophage-Host Arms Race. Front Microbiol 2021; 12:644622. [PMID: 33959107 PMCID: PMC8093625 DOI: 10.3389/fmicb.2021.644622] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/25/2021] [Indexed: 01/21/2023] Open
Abstract
Bacteriophage-encoded single strand annealing proteins (SSAPs) are recombinases which can substitute the classical, bacterial RecA and manage the DNA metabolism at different steps of phage propagation. SSAPs have been shown to efficiently promote recombination between short and rather divergent DNA sequences and were exploited for in vivo genetic engineering mainly in Gram-negative bacteria. In opposition to the conserved and almost universal bacterial RecA protein, SSAPs display great sequence diversity. The importance for SSAPs in phage biology and phage-bacteria evolution is underlined by their role as key players in events of horizontal gene transfer (HGT). All of the above provoke a constant interest for the identification and study of new phage recombinase proteins in vivo, in vitro as well as in silico. Despite this, a huge body of putative ssap genes escapes conventional classification, as they are not properly annotated. In this work, we performed a wide-scale identification, classification and analysis of SSAPs encoded by the Firmicutes bacteria and their phages. By using sequence similarity network and gene context analyses, we created a new high quality dataset of phage-related SSAPs, substantially increasing the number of annotated SSAPs. We classified the identified SSAPs into seven distinct families, namely RecA, Gp2.5, RecT/Redβ, Erf, Rad52/22, Sak3, and Sak4, organized into three superfamilies. Analysis of the relationships between the revealed protein clusters led us to recognize Sak3-like proteins as a new distinct SSAP family. Our analysis showed an irregular phylogenetic distribution of ssap genes among different bacterial phyla and specific phages, which can be explained by the high rates of ssap HGT. We propose that the evolution of phage recombinases could be tightly linked to the dissemination of bacterial phage-resistance mechanisms (e.g., abortive infection and CRISPR/Cas systems) targeting ssap genes and be a part of the constant phage-bacteria arms race.
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Affiliation(s)
| | - Eric Prestel
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Elena Bidnenko
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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2
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Piligrimova EG, Kazantseva OA, Kazantsev AN, Nikulin NA, Skorynina AV, Koposova ON, Shadrin AM. Putative plasmid prophages of Bacillus cereus sensu lato may hold the key to undiscovered phage diversity. Sci Rep 2021; 11:7611. [PMID: 33828147 PMCID: PMC8026635 DOI: 10.1038/s41598-021-87111-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/22/2021] [Indexed: 11/26/2022] Open
Abstract
Bacteriophages are bacterial viruses and the most abundant biological entities on Earth. Temperate bacteriophages can form prophages stably maintained in the host population: they either integrate into the host genome or replicate as plasmids in the host cytoplasm. As shown, tailed temperate bacteriophages may form circular plasmid prophages in many bacterial species of the taxa Firmicutes, Gammaproteobacteria and Spirochaetes. The actual number of such prophages is thought to be underestimated for two main reasons: first, in bacterial whole genome-sequencing assemblies, they are difficult to distinguish from actual plasmids; second, there is an absence of experimental studies which are vital to confirm their existence. In Firmicutes, such prophages appear to be especially numerous. In the present study, we identified 23 genomes from species of the Bacillus cereus group that were deposited in GenBank as plasmids and may belong to plasmid prophages with little or no homology to known viruses. We consider these putative prophages worth experimental assays since it will broaden our knowledge of phage diversity and suggest that more attention be paid to such molecules in all bacterial sequencing projects as this will help in identifying previously unknown phages.
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Affiliation(s)
- Emma G Piligrimova
- 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.
| | - 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
| | - Andrey N Kazantsev
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Pushchino Radio Astronomy Observatory, Pushchino, 142290, Russia
| | - Nikita A Nikulin
- 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
| | - Anna V Skorynina
- 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
| | - Olga N Koposova
- 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
| | - 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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3
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Abstract
Members of the family Herelleviridae are bacterial viruses infecting members of the phylum Firmicutes. The virions have myovirus morphology and virus genomes comprise a linear dsDNA of 125-170 kb. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Herelleviridae, which is available at ictv.global/report/herelleviridae.
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Affiliation(s)
- Jakub Barylski
- Department of Molecular Virology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Collegium Biologicum - Umultowska 89, 61-614 Poznan, Poland
| | - Andrew M Kropinski
- Department of Pathobiology, University of Guelph, 50 Stone Road E, Guelph, Ontario N1G 2W1, Canada
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4
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Barylski J, Enault F, Dutilh BE, Schuller MB, Edwards RA, Gillis A, Klumpp J, Knezevic P, Krupovic M, Kuhn JH, Lavigne R, Oksanen HM, Sullivan MB, Jang HB, Simmonds P, Aiewsakun P, Wittmann J, Tolstoy I, Brister JR, Kropinski AM, Adriaenssens EM. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages. Syst Biol 2020; 69:110-123. [PMID: 31127947 PMCID: PMC7409376 DOI: 10.1093/sysbio/syz036] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/17/2019] [Indexed: 01/01/2023] Open
Abstract
Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order—Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods—including comparative genomics, core genome analysis, and marker gene phylogenetics—to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae—a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.
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Affiliation(s)
- Jakub Barylski
- Department of Molecular Virology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Collegium Biologicum - Umultowska 89, 61-614 Poznań, Poland
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Margo Bp Schuller
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Robert A Edwards
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA.,Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, Croix du Sud 2-L7.05.12, 1348 Louvain-la-Neuve, Belgium
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, 25 rue du Dr. Roux, 75015 Paris, France
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 - box 2462, 3001 Leuven, Belgium
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56 (Viikinkaari 9B), 00014 Helsinki, Finland
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, 496 W 12thAvenue, Columbus, OH 43210, USA.,Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, 496 W 12thAvenue, Columbus, OH 43210, USA
| | - Ho Bin Jang
- Department of Microbiology, The Ohio State University, 496 W 12thAvenue, Columbus, OH 43210, USA.,Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, 496 W 12thAvenue, Columbus, OH 43210, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford OX1 3SY, UK
| | - Pakorn Aiewsakun
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford OX1 3SY, UK.,Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Johannes Wittmann
- Leibniz-Institut DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124 Braunschweig, Germany
| | - Igor Tolstoy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda MD 20894, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda MD 20894, USA
| | - Andrew M Kropinski
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada.,Department of Pathobiology, University of Guelph, 50 Stone Road E, Guelph, Ontario N1G 2W1, Canada
| | - Evelien M Adriaenssens
- Department of Functional & Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK.,Gut Microbes & Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, James Watson Road, Norwich NR4 7UQ Norwich, UK
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5
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Łubowska N, Grygorcewicz B, Kosznik-Kwaśnicka K, Zauszkiewicz-Pawlak A, Węgrzyn A, Dołęgowska B, Piechowicz L. Characterization of the Three New Kayviruses and Their Lytic Activity Against Multidrug-Resistant Staphylococcus aureus. Microorganisms 2019; 7:E471. [PMID: 31635437 DOI: 10.3390/microorganisms7100471] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 11/17/2022] Open
Abstract
The development of antimicrobial resistance has become a global concern. One approach to overcome the problem of drug resistance is the application of bacteriophages. This study aimed at characterizing three phages isolated from sewage, which show lytic activity against clinical isolates of multidrug-resistant Staphylococcus aureus. Morphology, genetics and biological properties, including host range, adsorption rate, latent time, phage burst size and lysis profiles, were studied in all three phages. As analyzed by transmission electron microscopy (TEM), phages vB_SauM-A, vB_SauM-C, vB_SauM-D have a myovirion morphology. One of the tested phages, vB_SauM-A, has relatively rapid adsorption (86% in 17.5 min), short latent period (25 min) and extremely large burst size (~500 plaque-forming units (PFU) per infected cell). The genomic analysis revealed that vB_SauM-A, vB_SauM-C, vB_SauM-D possess large genomes (vB_SauM-A 139,031 bp, vB_SauM-C 140,086 bp, vB_SauM-D 139,088 bp) with low G+C content (~30.4%) and are very closely related to the phage K (95-97% similarity). The isolated bacteriophages demonstrate broad host range against MDR S. aureus strains, high lytic activity corresponding to strictly virulent life cycle, suggesting their potential to treat S. aureus infections.
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6
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Hock L, Leprince A, Tournay M, Gillis A, Mahillon J. Biocontrol potential of phage Deep-Blue against psychrotolerant Bacillus weihenstephanensis. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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da Silva Duarte V, Giaretta S, Campanaro S, Treu L, Armani A, Tarrah A, Oliveira de Paula S, Giacomini A, Corich V. A Cryptic Non-Inducible Prophage Confers Phage-Immunity on the Streptococcus thermophilus M17PTZA496. Viruses 2018; 11:v11010007. [PMID: 30583530 PMCID: PMC6356513 DOI: 10.3390/v11010007] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/14/2018] [Accepted: 12/19/2018] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus is considered one of the most important species for the dairy industry. Due to their diffusion in dairy environments, bacteriophages can represent a threat to this widely used bacterial species. Despite the presence of a CRISPR-Cas system in the S. thermophilus genome, some lysogenic strains harbor cryptic prophages that can increase the phage-host resistance defense. This characteristic was identified in the dairy strain S. thermophilus M17PTZA496, which contains two integrated prophages 51.8 and 28.3 Kb long, respectively. In the present study, defense mechanisms, such as a lipoprotein-encoding gene and Siphovirus Gp157, the last associated to the presence of a noncoding viral DNA element, were identified in the prophage M17PTZA496 genome. The ability to overexpress genes involved in these defense mechanisms under specific stressful conditions, such as phage attack, has been demonstrated. Despite the addition of increasing amounts of Mitomycin C, M17PTZA496 was found to be non-inducible. However, the transcriptional activity of the phage terminase large subunit was detected in the presence of the antagonist phage vB_SthS-VA460 and of Mitomycin C. The discovery of an additional immune mechanism, associated with bacteriophage-insensitive strains, is of utmost importance, for technological applications and industrial processes. To our knowledge, this is the first study reporting the capability of a prophage integrated into the S. thermophilus genome expressing different phage defense mechanisms. Bacteriophages are widespread entities that constantly threaten starter cultures in the dairy industry. In cheese and yogurt manufacturing, the lysis of Streptococcus thermophilus cultures by viral attacks can lead to huge economic losses. Nowadays S. thermophilus is considered a well-stablished model organism for the study of natural adaptive immunity (CRISPR-Cas) against phage and plasmids, however, the identification of novel bacteriophage-resistance mechanisms, in this species, is strongly desirable. Here, we demonstrated that the presence of a non-inducible prophage confers phage-immunity to an S. thermophilus strain, by the presence of ltp and a viral noncoding region. S. thermophilus M17PTZA496 arises as an unconventional model to study phage resistance and potentially represents an alternative starter strain for dairy productions.
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Affiliation(s)
- Vinícius da Silva Duarte
- Department of Microbiology, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, Viçosa-MG 36570-900, Brazil.
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | - Sabrina Giaretta
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | | | - Laura Treu
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
- Department of Biology, University of Padova, 35121 Padova, Italy.
| | - Andrea Armani
- Venetian Institute of Molecular Medicine, 35129 Padova, Italy.
| | - Armin Tarrah
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | | | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | - Viviana Corich
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
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8
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Ghosh K, Kim KP. Complete nucleotide sequence analysis of a novel Bacillus subtilis-infecting phage, BSP38, possibly belonging to a new genus in the subfamily Spounavirinae. Arch Virol 2018; 164:875-878. [PMID: 30506469 DOI: 10.1007/s00705-018-4110-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/11/2018] [Indexed: 02/07/2023]
Abstract
Bacillus subtilis-infecting phage BSP38 was isolated from a sewage sample. Morphologically, BSP38 was found to be similar to members of the subfamily Spounavirinae, family Myoviridae. Its genome is 153,268 bp long with 41.8% G+C content and 254 putative open reading frames (ORFs) as well as six tRNAs. A distinguishing feature for this phage among the reported B. subtilis-infecting phages is the presence of an encoding ORF, putative tRNAHis guanylyltransferase-like protein. Genomic comparisons with the other reported phages strongly suggest that BSP38 should be considered a member of a new genus in the subfamily Spounavirinae.
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Affiliation(s)
- Kuntal Ghosh
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
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9
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Ghosh K, Kang HS, Hyun WB, Kim KP. High prevalence of Bacillus subtilis-infecting bacteriophages in soybean-based fermented foods and its detrimental effects on the process and quality of Cheonggukjang. Food Microbiol 2018; 76:196-203. [PMID: 30166141 DOI: 10.1016/j.fm.2018.05.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/20/2018] [Indexed: 01/12/2023]
Abstract
While the detrimental effect of bacteriophages on lactic acid bacterial fermentation is well documented, the importance of Bacillus subtilis phages in soybean-based fermented foods is not. In this study, we show for the first time that 100% of Korean soybean-based fermented foods (Doenjang, Gochujang, and Cheonggukjang) and 70% of raw materials (Meju and rice straw) were contaminated with B. subtilis-infecting phages (as high as 3.7 × 104 PFU g-1). Among 15 isolated B. subtilis-infecting phages, BSP18 was selected for further studies due to its specificity to and relatively broad host infectivity (34%) against B. subtilis. This Myoviridae family phage, BSP18 could infect all of the tested wild-type and commercially-used strains for soybean-based fermented food preparation. Furthermore, artificial contamination of as low as 102 PFU g-1 of BSP18 significantly inhibited B. subtilis growth during Cheonggukjang fermentation. Moreover, phage-treated samples contained considerably more degraded γ-PGA which could negatively affect the functional property of Cheonggukjang. We also present the data, strongly suggesting BSP18-encoded, not bacterial, γ-PGA hydrolase was responsible for γ-PGA degradation. In conclusion, B. subtilis phages are widespread in Korean soybean-based fermented foods and it should be of great concern as phages may hamper the bacterial growth during fermentation and yield poor quality products.
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Affiliation(s)
- Kuntal Ghosh
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, South Korea
| | - Hai Seong Kang
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, South Korea
| | - Woo Bin Hyun
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, South Korea
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do 561-756, South Korea.
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10
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Badran S, Morales N, Schick P, Jacoby B, Villella W, Lorenz T. Complete Genome Sequence of the Bacillus pumilus Phage Leo2. Genome Announc 2018; 6:e00066-18. [PMID: 29449395 DOI: 10.1128/genomeA.00066-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacillus spp. are ubiquitous Gram-positive microbes with many ecological and symbiotic interactions and can be pathogens. Phage Leo2 was found to infect a Bacillus pumilus strain isolated from soil. The sequence of phage Leo2 revealed 74 genes; 31% of the genes have associated functions, and 67% of coding regions are unidentified open reading frames.
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11
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Ma L, Green SI, Trautner BW, Ramig RF, Maresso AW. Metals Enhance the Killing of Bacteria by Bacteriophage in Human Blood. Sci Rep 2018; 8:2326. [PMID: 29396496 PMCID: PMC5797145 DOI: 10.1038/s41598-018-20698-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
Multidrug-resistant bacterial pathogens are a major medical concern. E. coli, particularly the pathotype extraintestinal pathogenic E. coli (ExPEC), is a leading cause of bloodstream infections. As natural parasites of bacteria, bacteriophages are considered a possible solution to treat patients infected with antibiotic resistant strains of bacteria. However, the development of phage as an anti-infective therapeutic is hampered by limited knowledge of the physiologic factors that influence their properties in complex mammalian environments such as blood. To address this barrier, we tested the ability of phage to kill ExPEC in human blood. Phages are effective at killing ExPEC in conventional media but are substantially restricted in this ability in blood. This phage killing effect is dependent on the levels of free metals and is inhibited by the anticoagulant EDTA. The EDTA-dependent inhibition of ExPEC killing is overcome by exogenous iron, magnesium, and calcium. Metal-enhanced killing of ExPEC by phage was observed for several strains of ExPEC, suggesting a common mechanism. The addition of metals to a murine host infected with ExPEC stimulated a phage-dependent reduction in ExPEC levels. This work defines a role for circulating metals as a major factor that is essential for the phage-based killing of bacteria in blood.
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Affiliation(s)
- Li Ma
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX, USA
| | - Sabrina I Green
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX, USA
| | - Barbara W Trautner
- Michael E. Debakey Veterans Affairs Medical Center, Houston, TX, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Robert F Ramig
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX, USA
| | - Anthony W Maresso
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX, USA.
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12
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Nowicki G, Walkowiak-Nowicka K, Zemleduch-Barylska A, Mleczko A, Frąckowiak P, Nowaczyk N, Kozdrowska E, Barylski J. Complete genome sequences of two novel autographiviruses infecting a bacterium from the Pseudomonas fluorescens group. Arch Virol 2017; 162:2907-2911. [PMID: 28551853 PMCID: PMC5563517 DOI: 10.1007/s00705-017-3419-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 03/28/2017] [Accepted: 05/15/2017] [Indexed: 01/11/2023]
Abstract
In this paper, we describe two independent isolates of a new member of the subfamily Autographivirinae, Pseudomonas phage KNP. The type strain (KNP) has a linear, 40,491-bp-long genome with GC content of 57.3%, and 50 coding DNA sequences (CDSs). The genome of the second strain (WRT) contains one CDS less, encodes a significantly different tail fiber protein and is shorter (40,214 bp; GC content, 57.4%). Phylogenetic analysis indicates that both KNP and WRT belong to the genus T7virus. Together with genetically similar Pseudomonas phages (gh-1, phiPSA2, phiPsa17, PPPL-1, shl2, phi15, PPpW-4, UNO-SLW4, phiIBB-PF7A, Pf-10, and Phi-S1), they form a divergent yet coherent group that stands apart from the T7-like viruses (sensu lato). Analysis of the diversity of this group and its relatedness to other members of the subfamily Autographivirinae led us to the conclusion that this group might be considered as a candidate for a new genus.
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Affiliation(s)
- Grzegorz Nowicki
- Department of Molecular Virology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznań, Poland
| | - Karolina Walkowiak-Nowicka
- Department of Animal Physiology and Development, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznań, Poland
| | - Agata Zemleduch-Barylska
- Department of Molecular Virology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznań, Poland
| | - Anna Mleczko
- Department of Molecular Virology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznań, Poland
| | - Patryk Frąckowiak
- Department of Molecular Virology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznań, Poland
| | - Natalia Nowaczyk
- Department of Molecular Virology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznań, Poland
| | - Emilia Kozdrowska
- Department of Molecular Virology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznań, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznań, Poland.
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13
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Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Peña MJ, Martínez JM, Anton J, Gasol JM, Rosselli R, Rodriguez-Valera F, Sullivan MB, Acinas SG, Martinez-Garcia M. Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nat Commun 2017; 8:15892. [PMID: 28643787 PMCID: PMC5490008 DOI: 10.1038/ncomms15892] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [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: 12/19/2016] [Accepted: 05/10/2017] [Indexed: 12/22/2022] Open
Abstract
Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates. This indicates that vSAGs likely best represent the dsDNA viral populations dominating the oceans. Species-specific recruitment patterns and virome simulation data suggest that vSAGs are highly microdiverse and that microdiversity hinders the metagenomic assembly, which could explain why their genomes have not been identified before. Altogether, SVGs enable the discovery of some of the likely most abundant and ecologically relevant marine viral species, such as vSAG 37-F6, which were overlooked by other methodologies.
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Affiliation(s)
- Francisco Martinez-Hernandez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Oscar Fornas
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Carrer del Doctor Aiguader, 88, PRBB Building, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Doctor Aiguader, 88, PRBB Building, Barcelona 08003, Spain
| | - Monica Lluesma Gomez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, 105 Biological Sciences Building, 484 West 12th Avenue Columbus, Ohio 43210, USA
| | - Maria Jose de la Cruz Peña
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Joaquín Martínez Martínez
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, PO Box 380, East Boothbay, Maine 04544, USA
| | - Josefa Anton
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
| | - Josep M. Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Passeig Marítim, 47, Barcelona 08003, Spain
| | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, 105 Biological Sciences Building, 484 West 12th Avenue Columbus, Ohio 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, The Ohio State University, 105 Biological Sciences Building, 484 West 12th Avenue Columbus, Ohio 43210, USA
| | - Silvia G. Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Passeig Marítim, 47, Barcelona 08003, Spain
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante 03690, Spain
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14
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Willms IM, Hoppert M, Hertel R. Characterization of Bacillus Subtilis Viruses vB_BsuM-Goe2 and vB_BsuM-Goe3. Viruses 2017; 9:E146. [PMID: 28604650 PMCID: PMC5490822 DOI: 10.3390/v9060146] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 03/27/2017] [Revised: 06/01/2017] [Accepted: 06/01/2017] [Indexed: 12/25/2022] Open
Abstract
The Spounavirinae viruses are ubiquitous in nature and have an obligatory virulent lifestyle. They infect Firmicutes, a bacterial phylum containing an array of environmental non-pathogenic and pathogenic organisms. To expand the knowledge of this viral subfamily, new strains were isolated and investigated in this study. Here we present two new viruses, vB_BsuM-Goe2 and vB_BsuM-Goe3, isolated from raw sewage and infecting Bacillus species. Both were morphologically classified via transmission electron microscopy (TEM) as members of the Spounavirinae subfamily belonging to the Myoviridae family. Genomic sequencing and analyses allowed further affiliation of vB_BsuM-Goe2 to the SPO1-like virus group and vB_BsuM-Goe3 to the Bastille-like virus group. Experimentally determined adsorption constant, latency period, burst size and host range for both viruses revealed different survival strategies. Thus vB_BsuM-Goe2 seemed to rely on fewer host species compared to vB_BsuM-Goe3, but efficiently recruits those. Stability tests pointed out that both viruses are best preserved in LB-medium or TMK-buffer at 4 or 21 °C, whereas cryopreservation strongly reduced viability.
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Affiliation(s)
- Inka M Willms
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany.
| | - Michael Hoppert
- Department of General Microbiology, Institute of Microbiology and Genetics, University of Goettingen, 37077 Goettingen, Germany.
| | - Robert Hertel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, 37077, Goettingen, Germany.
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15
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Adriaenssens EM, Krupovic M, Knezevic P, Ackermann HW, Barylski J, Brister JR, Clokie MRC, Duffy S, Dutilh BE, Edwards RA, Enault F, Jang HB, Klumpp J, Kropinski AM, Lavigne R, Poranen MM, Prangishvili D, Rumnieks J, Sullivan MB, Wittmann J, Oksanen HM, Gillis A, Kuhn JH. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee. Arch Virol 2016; 162:1153-1157. [PMID: 28040838 DOI: 10.1007/s00705-016-3173-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/27/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Evelien M Adriaenssens
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom.,Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Mart Krupovic
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015, Paris, France
| | - Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Hans-Wolfgang Ackermann
- L'Institut de biologie intégrative et des systems, Université Laval, Pavillon Charles-Eugène-Marchand, Quebec, QC, G1V 0A6, Canada
| | - Jakub Barylski
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznan, Poland
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Martha R C Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, LE1 9HN, UK
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Robert A Edwards
- Departments of Computer Science and Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Francois Enault
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France.,CNRS UMR 6023, LMGE, Aubière, France
| | - Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
| | - Andrew M Kropinski
- Departments of Food Science, Molecular and Cellular Biologyand PathobiologyUniversity of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada.
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001, Leuven, Belgium
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - David Prangishvili
- Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015, Paris, France
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Center, Riga, LV-1067, Latvia
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Johannes Wittmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124, Braunschweig, Germany
| | - Hanna M Oksanen
- Department of Biosciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA
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16
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van Zyl LJ, Nemavhulani S, Cass J, Cowan DA, Trindade M. Three novel bacteriophages isolated from the East African Rift Valley soda lakes. Virol J 2016; 13:204. [PMID: 27912769 PMCID: PMC5135824 DOI: 10.1186/s12985-016-0656-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/21/2016] [Indexed: 12/21/2022] Open
Abstract
Background Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and consequently few bacteriophages that infect bacteria from haloalkaline environments have been described. Methods Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on two different Bacillus species and one Paracoccus species using agar overlays. The growth characteristics of each phage in its host was investigated and the genome sequences determined and analysed by comparison with known phages. Results Phage Shbh1 belongs to the family Myoviridae while Mgbh1 and Shpa belong to the Siphoviridae family. Tetranucleotide usage frequencies and G + C content suggests that Shbh1 and Mgbh1 do not regularly infect, and have therefore not evolved with, the hosts they were isolated on here. Shbh1 was shown capable of infecting two different Bacillus species from the two different lakes demonstrating its potential broad-host range. Comparative analysis of their genome sequence with known phages revealed that, although novel, Shbh1 does share substantial amino acid similarity with previously described Bacillus infecting phages (Grass, phiNIT1 and phiAGATE) and belongs to the Bastille group, while Mgbh1 and Shpa are highly novel. Conclusion The addition of these phages to current databases should help with metagenome/metavirome annotation efforts. We describe a highly novel Paracoccus infecting virus (Shpa) which together with NgoΦ6 and vB_PmaS_IMEP1 is one of only three phages known to infect Paracoccus species but does not show similarity to these phages. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0656-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa.
| | - Shonisani Nemavhulani
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa
| | - James Cass
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa
| | - Donald Arthur Cowan
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa.,Department of Genetics, University of Pretoria, Pretoria, 0002, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa
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17
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Ozaki T, Abe N, Kimura K, Suzuki A, Kaneko J. Genomic analysis of Bacillus subtilis lytic bacteriophage ϕNIT1 capable of obstructing natto fermentation carrying genes for the capsule-lytic soluble enzymes poly-γ-glutamate hydrolase and levanase. Biosci Biotechnol Biochem 2016; 81:135-146. [PMID: 27885938 DOI: 10.1080/09168451.2016.1232153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacillus subtilis strains including the fermented soybean (natto) starter produce capsular polymers consisting of poly-γ-glutamate and levan. Capsular polymers may protect the cells from phage infection. However, bacteriophage ϕNIT1 carries a γ-PGA hydrolase gene (pghP) that help it to counteract the host cell's protection strategy. ϕNIT had a linear double stranded DNA genome of 155,631-bp with a terminal redundancy of 5,103-bp, containing a gene encoding an active levan hydrolase. These capsule-lytic enzyme genes were located in the possible foreign gene cluster regions between central core and terminal redundant regions, and were expressed at the late phase of the phage lytic cycle. All tested natto origin Spounavirinae phages carried both genes for capsule degrading enzymes similar to ϕNIT1. A comparative genomic analysis revealed the diversity among ϕNIT1 and Bacillus phages carrying pghP-like and levan-hydrolase genes, and provides novel understanding on the acquisition mechanism of these enzymatic genes.
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Affiliation(s)
- Tatsuro Ozaki
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| | - Naoki Abe
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| | - Keitarou Kimura
- b Laboratory of Applied Microbiology , Food Research Institute-National Agriculture and Food Research Organization (NFRI-NARO) , Tsukuba , Japan
| | - Atsuto Suzuki
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| | - Jun Kaneko
- a Department of Microbial Biotechnology, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
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18
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Hock L, Gillis A, Mahillon J. Complete Genome Sequence of Bacteriophage Deep-Blue Infecting Emetic Bacillus cereus. Genome Announc 2016; 4:e00115-16. [PMID: 27313285 PMCID: PMC4911464 DOI: 10.1128/genomea.00115-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/04/2016] [Indexed: 01/20/2023]
Abstract
The Bacillus cereus emetic pathotype is responsible for important food-borne intoxications. Here, we describe the complete genome sequence of bacteriophage Deep-Blue, which is able to infect emetic strains of B. cereus Deep-Blue is a 159-kb myophage of the Bastille-like group within the Spounavirinae.
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Affiliation(s)
- Louise Hock
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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19
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Asare PT, Jeong TY, Ryu S, Klumpp J, Loessner MJ, Merrill BD, Kim KP. Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel Bastille-like group of phages in the subfamily Spounavirinae. BMC Genomics 2015; 16:582. [PMID: 26250905 PMCID: PMC4528723 DOI: 10.1186/s12864-015-1757-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/07/2015] [Indexed: 12/12/2022] Open
Abstract
Background Spounavirinae viruses have received an increasing interest as tools for the control of harmful bacteria due to their relatively broad host range and strictly virulent phenotype. Results In this study, we collected and analyzed the complete genome sequences of 61 published phages, either ICTV-classified or candidate members of the Spounavirinae subfamily of the Myoviridae. A set of comparative analyses identified a distinct, recently proposed Bastille-like phage group within the Spounavirinae. More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers. We also show that the members of this group encode beta-lactamase and/or sporulation-related SpoIIIE homologs, possibly questioning their suitability as biocontrol agents. Conclusions We confirm the creation of a new genus—the “Bastille-like group”—in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group. In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1757-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul Tetteh Asare
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
| | - Tae-Yong Jeong
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Korea. .,Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, Seoul National University, Seoul, Korea. .,Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Bryan D Merrill
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA.
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
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20
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Asare PT, Bandara N, Jeong TY, Ryu S, Klumpp J, Kim KP. Complete genome sequence analysis and identification of putative metallo-beta-lactamase and SpoIIIE homologs in Bacillus cereus group phage BCP8-2, a new member of the proposed Bastille-like group. Arch Virol 2015; 160:2647-50. [PMID: 26234184 DOI: 10.1007/s00705-015-2548-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 07/20/2015] [Indexed: 11/25/2022]
Abstract
Bacillus cereus group-specific bacteriophage BCP8-2 exhibits a broad lysis spectrum among food and human isolates (330/364) of B. cereus while not infecting B. subtilis (50) or B. licheniformis (12) strains. Its genome is 159,071 bp long with 220 open reading frames, including genes for putative methyltransferases, metallo-beta-lactamase, and a sporulation-related SpoIIIE homolog, as wells as 18 tRNAs. Comparative genome analysis showed that BCP8-2 is related to the recently proposed Bastille-like phages, but not with either SPO1-like or Twort-like phages of the subfamily Spounavirinae.
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Affiliation(s)
- Paul Tetteh Asare
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea
| | - Nadeeka Bandara
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea
| | - Tae-Yong Jeong
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Center for Agricultural Biomaterials, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea.,Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Kwang-Pyo Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
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21
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Makart L, Gillis A, Mahillon J. pXO16 from Bacillus thuringiensis serovar israelensis: Almost 350 kb of terra incognita. Plasmid 2015; 80:8-15. [PMID: 25770691 DOI: 10.1016/j.plasmid.2015.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 01/08/2015] [Revised: 02/21/2015] [Accepted: 03/03/2015] [Indexed: 11/20/2022]
Abstract
Bacillus thuringiensis strains usually harbor large sets of plasmids, some of which carrying the entomopathogenic δ-endotoxins. B. thuringiensis serovar israelensis, active on Dipteran larvae, carries the very large conjugative plasmid pXO16 (350 kb). pXO16 displays a macroscopic aggregation phenotype when liquid cultures of conjugative partners are mixed. Its conjugative apparatus is able of transferring itself and other non-conjugative and non-mobilizable plasmids in a fast and very efficient manner. Even though its conjugative kinetics and capabilities have been extensively studied, the genetic bases for this unique transfer system remain largely unknown. In this work, the sequence of pXO16 has been identified in the existing sequenced genome of B. thuringiensis sv. israelensis HD-789 as corresponding to the p01 plasmid. Despite pXO16 sequence being highly coding, few CDS possess homologs in the databases. However, potential regions responsible for the aggregation phenotype and the plasmid replication have been highlighted. The common orientation of all CDS and the presence of a high number of potential paralogs suggested a phage-like nature. Concerning conjugative functions, no significant type IV secretion system homologs have been found, indicating that pXO16 encodes an unforeseen conjugative system.
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Affiliation(s)
- Lionel Makart
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium.
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22
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KUSMIATUN ANIK, RUSMANA IMAN, BUDIARTI SRI. Characterization of Bacteriophage Specific to Bacillus pumilus from Ciapus River in Bogor, West Java, Indonesia. HAYATI Journal of Biosciences 2015. [DOI: 10.4308/hjb.22.1.27] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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23
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Yuan Y, Peng Q, Wu D, Kou Z, Wu Y, Liu P, Gao M. Effects of actin-like proteins encoded by two Bacillus pumilus phages on unstable lysogeny, revealed by genomic analysis. Appl Environ Microbiol 2015; 81:339-50. [PMID: 25344242 PMCID: PMC4272706 DOI: 10.1128/aem.02889-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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: 09/04/2014] [Accepted: 10/20/2014] [Indexed: 12/16/2022] Open
Abstract
We characterized two newly isolated myoviruses, Bp8p-C and Bp8p-T, infecting the ginger rhizome rot disease pathogen Bacillus pumilus GR8. The plaque of Bp8p-T exhibited a clear center with a turbid rim, suggesting that Bp8p-T could transform into latent phage. Lysogeny assays showed that both the two phages could form latent states, while Bp8p-T could form latent phage at a higher frequency and stability than Bp8p-C. The genomes of Bp8p-C and Bp8p-T were 151,417 and 151,419 bp, respectively; both encoded 212 putative proteins, and only differed by three nucleotides. Moreover, owing to this difference, Bp8p-C encoded a truncated, putative actin-like plasmid segregation protein Gp27-C. Functional analysis of protein Gp27 showed that Gp27-T encoded by Bp8p-T exhibited higher ATPase activity and assembly ability than Gp27-C. The results indicate that the difference in Gp27 affected the phage lysogenic ability. Structural proteome analysis of Bp8p-C virion resulted in the identification of 14 structural proteins, among which a pectin lyase-like protein, a putative poly-gamma-glutamate hydrolase, and three proteins with unknown function, were firstly identified as components of the phage virion. Both phages exhibited specific lytic ability to the host strain GR8. Bp8p-C showed better control effect on the pathogen in ginger rhizome slices than Bp8p-T, suggesting that Bp8p-C has a potential application in bio-control of ginger rhizome rot disease.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Qin Peng
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Dandan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Zheng Kou
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Yan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Pengming Liu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
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Grose JH, Jensen GL, Burnett SH, Breakwell DP. Correction: genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity. BMC Genomics 2014; 15:1184. [PMID: 25547158 PMCID: PMC4464726 DOI: 10.1186/1471-2164-15-1184] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 12/04/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains. RESULTS Whole genome nucleotide and proteome comparison of the 83 extant, fully sequenced Bacillus phages revealed 10 distinct clusters, 24 subclusters and 15 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,442 protein families (phams) of which only 894 (20%) had a predicted function. In addition, 2,583 (58%) of phams were orphams (phams containing a single member). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function. These included several genes that may contribute to the pathogenicity of Bacillus strains. CONCLUSIONS This analysis provides a basis for understanding and characterizing Bacillus and other related phages as well as their contributions to the evolution and pathogenicity of Bacillus cereus group bacteria. The presence of sparsely populated clusters, the high ratio of singletons to clusters, and the large number of uncharacterized, conserved proteins confirms the need for more Bacillus phage isolation in order to understand the full extent of their diversity as well as their impact on host evolution.
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Affiliation(s)
- Julianne H Grose
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT, USA.
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Abstract
The genus Lelliottia was recently created from the group of environmental gammaproteobacteria previously included in the genus Enterobacter. Here, we report the complete genome sequence of phD2B, the first (according to our current knowledge) known phage that infects bacterium from the taxon.
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Grose JH, Jensen GL, Burnett SH, Breakwell DP. Genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity. BMC Genomics 2014; 15:855. [PMID: 25280881 DOI: 10.1186/1471-2164-15-855] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/24/2014] [Indexed: 01/01/2023] Open
Abstract
Background The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains. Results Whole genome nucleotide and proteome comparison of the 93 extant Bacillus phages revealed 12 distinct clusters, 28 subclusters and 14 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member of the group. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,922 protein families (phams) of which only 951 (19%) had a predicted function. In addition, 3,058 (62%) of phams were orphams (phams containing a gene product from a single phage). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function. These included several genes that may contribute to the pathogenicity of Bacillus strains. Conclusions This analysis provides a basis for understanding and characterizing Bacillus phages and other related phages as well as their contributions to the evolution and pathogenicity of Bacillus cereus group bacteria. The presence of sparsely populated clusters, the high ratio of singletons to clusters, and the large number of uncharacterized, conserved proteins confirms the need for more Bacillus phage isolation in order to understand the full extent of their diversity as well as their impact on host evolution.
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Gillis A, Mahillon J. Phages preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: past, present and future. Viruses 2014; 6:2623-72. [PMID: 25010767 PMCID: PMC4113786 DOI: 10.3390/v6072623] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [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: 03/04/2014] [Revised: 05/19/2014] [Accepted: 06/18/2014] [Indexed: 01/18/2023] Open
Abstract
Many bacteriophages (phages) have been widely studied due to their major role in virulence evolution of bacterial pathogens. However, less attention has been paid to phages preying on bacteria from the Bacillus cereus group and their contribution to the bacterial genetic pool has been disregarded. Therefore, this review brings together the main information for the B. cereus group phages, from their discovery to their modern biotechnological applications. A special focus is given to phages infecting Bacillus anthracis, B. cereus and Bacillus thuringiensis. These phages belong to the Myoviridae, Siphoviridae, Podoviridae and Tectiviridae families. For the sake of clarity, several phage categories have been made according to significant characteristics such as lifestyles and lysogenic states. The main categories comprise the transducing phages, phages with a chromosomal or plasmidial prophage state, γ-like phages and jumbo-phages. The current genomic characterization of some of these phages is also addressed throughout this work and some promising applications are discussed here.
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Affiliation(s)
- Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, Croix du Sud 2, L7.05.12, B-1348 Louvain-la-Neuve, Belgium.
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, Croix du Sud 2, L7.05.12, B-1348 Louvain-la-Neuve, Belgium.
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