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Tadeu AD, Duarte J, Trindade D, Costa P, Venâncio C, Lopes I, Oliveira V, Gomes NCM, Almeida A, Pereira C. Bacteriophages to control Vibrio alginolyticus in live feeds prior to their administration in larviculture. J Appl Microbiol 2024; 135:lxae115. [PMID: 38710582 DOI: 10.1093/jambio/lxae115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/16/2024] [Accepted: 05/04/2024] [Indexed: 05/08/2024]
Abstract
AIMS This study aimed to evaluate the efficiency of two phages [VB_VaC_TDDLMA (phage TDD) and VB_VaC_SRILMA (phage SRI)] alone and in a cocktail to control Vibrio alginolyticus in brine shrimp before their administration in larviculture. METHODS AND RESULTS Phages were isolated from seawater samples and characterized by host spectrum, growth parameters, adsorption rate, genomic analysis, and inactivation efficiency. Both phages belong to the Caudoviricetes class and lack known virulence or antibiotic-resistance genes. They exhibit specificity, infecting only their host, V. alginolyticus CECT 521. Preliminary experiments in a culture medium showed that phage TDD (reduction of 5.8 log CFU ml-1 after 10 h) outperformed phage SRI (reduction of 4.6 log CFU ml-1 after 6 h) and the cocktail TDD/SRI (reduction of 5.2 log CFU ml-1 after 8 h). In artificial marine water experiments with Artemia franciscana, both single phage suspensions and the phage cocktail, effectively inactivated V. alginolyticus in culture water (reduction of 4.3, 2.1, and 1.9 log CFU ml-1 for phages TDD, SRI, and the phage cocktail, respectively, after 12 h) and in A. franciscana (reduction of 51.6%, 87.3%, and 85.3% for phages TDD, SRI, and the phage cocktail, respectively, after 24 h). The two phages and the phage cocktail did not affect A. franciscana natural microbiota or other Vibrio species in the brine shrimp. CONCLUSIONS The results suggest that phages can safely and effectively control V. alginolyticus in A. franciscana prior to its administration in larviculture.
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Affiliation(s)
- Amanda Dias Tadeu
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - João Duarte
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - David Trindade
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Pedro Costa
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Cátia Venâncio
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Isabel Lopes
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Vanessa Oliveira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carla Pereira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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Ranveer SA, Dasriya V, Ahmad MF, Dhillon HS, Samtiya M, Shama E, Anand T, Dhewa T, Chaudhary V, Chaudhary P, Behare P, Ram C, Puniya DV, Khedkar GD, Raposo A, Han H, Puniya AK. Positive and negative aspects of bacteriophages and their immense role in the food chain. NPJ Sci Food 2024; 8:1. [PMID: 38172179 PMCID: PMC10764738 DOI: 10.1038/s41538-023-00245-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Bacteriophages infect and replicate inside a bacterial host as well as serve as natural bio-control agents. Phages were once viewed as nuisances that caused fermentation failures with cheese-making and other industrial processes, which lead to economic losses, but phages are now increasingly being observed as being promising antimicrobials that can fight against spoilage and pathogenic bacteria. Pathogen-free meals that fulfil industry requirements without synthetic additives are always in demand in the food sector. This study introduces the readers to the history, sources, and biology of bacteriophages, which include their host ranges, absorption mechanisms, lytic profiles, lysogenic profiles, and the influence of external factors on the growth of phages. Phages and their derivatives have emerged as antimicrobial agents, biodetectors, and biofilm controllers, which have been comprehensively discussed in addition to their potential applications in the food and gastrointestinal tract, and they are a feasible and safe option for preventing, treating, and/or eradicating contaminants in various foods and food processing environments. Furthermore, phages and phage-derived lytic proteins can be considered potential antimicrobials in the traditional farm-to-fork context, which include phage-based mixtures and commercially available phage products. This paper concludes with some potential safety concerns that need to be addressed to enable bacteriophage use efficiently.
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Affiliation(s)
- Soniya Ashok Ranveer
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Vaishali Dasriya
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Md Faruque Ahmad
- Department of Clinical Nutrition, College of Applied Medical Science, Jazan University, Jazan, 45142, Saudi Arabia
| | - Harmeet Singh Dhillon
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Mrinal Samtiya
- Department of Nutrition Biology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, 123031, India
| | - Eman Shama
- Department of Clinical Nutrition, College of Applied Medical Science, Jazan University, Jazan, 45142, Saudi Arabia
| | - Taruna Anand
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar, 125001, India
| | - Tejpal Dhewa
- Department of Nutrition Biology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, 123031, India
| | - Vishu Chaudhary
- University Institute of Biotechnology, Chandigarh University, Sahibzada Ajit Singh Nagar, 140413, India
| | - Priya Chaudhary
- Microbiology Department, VCSG Government Institute of Medical Science and Research, Ganganali Srikot, Srinagar Pauri Garhwal, 246174, India
| | - Pradip Behare
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Chand Ram
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, 132001, India
| | - Dharun Vijay Puniya
- Centre of One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - Gulab D Khedkar
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - António Raposo
- CBIOS (Research Center for Biosciences and Health Technologies), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande, 376, 1749-024 Lisboa, Portugal.
| | - Heesup Han
- College of Hospitality and Tourism Management, Sejong University, 98 Gunja-Dong, Gwanjin-gu, Seoul, 143-747, Republic of Korea.
| | - Anil Kumar Puniya
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, 132001, India.
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3
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Li H, Gao J, Ma S, Xiao R, Zhou X, Feng W, Zhao S, Luo J, Zhang D. Isolation and genome sequencing of a novel lytic Pseudoalteromonas phage SL20. Mar Genomics 2023; 71:101048. [PMID: 37620054 DOI: 10.1016/j.margen.2023.101048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/13/2023] [Accepted: 06/12/2023] [Indexed: 08/26/2023]
Abstract
Phage SL20, a novel lytic Pseudoalteromonas phage, was isolated from the coastal waters of the Yellow Sea, China. The microbiological characterization demonstrated that phage SL20 was relatively stable from 35 to 55 °C and the optimal pH was approximately 6.0. A latent period of approximately 24 min was indicated by a one-step growth curve. The burst size was approximately 12 ± 3 PFU/cell. The genome had a length of 120,295 bp with a G + C content of 35.84%, and predicted 95 ORFs. The phylogenetic tree based on DNA helicase showed that Pseudoalteromonas phage SL20 was related to the Pseudoalteromonas phage H101 and was a member of the family Shandongvirus. The isolation and genomic analysis of SL20 has improved our understanding of host-phage interactions and the ecology of the marine bacteria Pseudoalteromonas.
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Affiliation(s)
- Huifang Li
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, PR China; College of Marine Life Sciences, Ocean University of China, Qingdao, PR China; MNR Key Laboratory of Coastal Salt Marsh Ecosystems and Resources, Jiangsu Ocean University, Lianyungang 222005, PR China
| | - Jie Gao
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, PR China
| | - Shiyun Ma
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, PR China
| | - Rongda Xiao
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, PR China
| | - Xing Zhou
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, PR China
| | - Wanting Feng
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, PR China
| | - Siyu Zhao
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, PR China
| | - Jiaqi Luo
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, PR China
| | - Di Zhang
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, PR China; Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, PR China.
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4
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Marantos A, Mitarai N, Sneppen K. From kill the winner to eliminate the winner in open phage-bacteria systems. PLoS Comput Biol 2022; 18:e1010400. [PMID: 35939510 PMCID: PMC9387927 DOI: 10.1371/journal.pcbi.1010400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/18/2022] [Accepted: 07/17/2022] [Indexed: 11/23/2022] Open
Abstract
Phages and bacteria manage to coexist and sustain ecosystems with a high diversity of strains, despite limited resources and heavy predation. This diversity can be explained by the “kill the winner” model where virulent phages predominantly prey on fast-growing bacteria and thereby suppress the competitive exclusion of slower-growing bacteria. Here we computationally investigate the robustness of these systems against invasions, where new phages or bacteria may interact with more than one of the resident strains. The resulting interaction networks were found to self-organize into a network with strongly interacting specialized predator-prey pairs, resembling that of the “kill the winner” model. Furthermore, the “kill the winner” dynamics is enforced with the occasional elimination of even the fastest-growing bacteria strains due to a phage infecting the fast and slow growers. The frequency of slower-growing strains was increased with the introduction of even a few non-diagonal interactions. Hence, phages capable of infecting multiple hosts play significant roles both in the evolution of the ecosystem by eliminating the winner and in supporting diversity by allowing slow growers to coexist with faster growers. We demonstrate that in an open system of phages and bacteria with very limited resources, a bacterial strain that has a high growth rate can still be outcompeted by a slower-growing strain if they have a common phage. The impact of this on ecosystem structure is significant as soon as there is a small probability to have a common phage among bacterial strains. Furthermore, by analysing the structure of the interaction network we show that it self-organizes into a network with strongly interacting specialized predator-prey pairs, in order to reduce phages competition. Nevertheless, the presence of the remaining links is very important for the network dynamics since even a few of them significantly enhance the frequency of slower-growing strains.
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Affiliation(s)
- Anastasios Marantos
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Namiko Mitarai
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kim Sneppen
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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5
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Jang HB, Chittick L, Li YF, Zablocki O, Sanderson CM, Carrillo A, van den Engh G, Sullivan MB. Viral tag and grow: a scalable approach to capture and characterize infectious virus-host pairs. ISME COMMUNICATIONS 2022; 2:12. [PMID: 37938680 PMCID: PMC9723727 DOI: 10.1038/s43705-022-00093-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/06/2022] [Accepted: 01/13/2022] [Indexed: 04/27/2023]
Abstract
Viral metagenomics (viromics) has reshaped our understanding of DNA viral diversity, ecology, and evolution across Earth's ecosystems. However, viromics now needs approaches to link newly discovered viruses to their host cells and characterize them at scale. This study adapts one such method, sequencing-enabled viral tagging (VT), to establish "Viral Tag and Grow" (VT + Grow) to rapidly capture and characterize viruses that infect a cultivated target bacterium, Pseudoalteromonas. First, baseline cytometric and microscopy data improved understanding of how infection conditions and host physiology impact populations in VT flow cytograms. Next, we extensively evaluated "and grow" capability to assess where VT signals reflect adsorption alone or wholly successful infections that lead to lysis. Third, we applied VT + Grow to a clonal virus stock, which, coupled to traditional plaque assays, revealed significant variability in burst size-findings that hint at a viral "individuality" parallel to the microbial phenotypic heterogeneity literature. Finally, we established a live protocol for public comment and improvement via protocols.io to maximally empower the research community. Together these efforts provide a robust foundation for VT researchers, and establish VT + Grow as a promising scalable technology to capture and characterize viruses from mixed community source samples that infect cultivable bacteria.
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Affiliation(s)
- Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Lauren Chittick
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Yueh-Fen Li
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Olivier Zablocki
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Alfonso Carrillo
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
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6
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Bartlau N, Wichels A, Krohne G, Adriaenssens EM, Heins A, Fuchs BM, Amann R, Moraru C. Highly diverse flavobacterial phages isolated from North Sea spring blooms. THE ISME JOURNAL 2022; 16:555-568. [PMID: 34475519 PMCID: PMC8776804 DOI: 10.1038/s41396-021-01097-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/17/2021] [Indexed: 11/24/2022]
Abstract
It is generally recognized that phages are a mortality factor for their bacterial hosts. This could be particularly true in spring phytoplankton blooms, which are known to be closely followed by a highly specialized bacterial community. We hypothesized that phages modulate these dense heterotrophic bacteria successions following phytoplankton blooms. In this study, we focused on Flavobacteriia, because they are main responders during these blooms and have an important role in the degradation of polysaccharides. A cultivation-based approach was used, obtaining 44 lytic flavobacterial phages (flavophages), representing twelve new species from two viral realms. Taxonomic analysis allowed us to delineate ten new phage genera and ten new families, from which nine and four, respectively, had no previously cultivated representatives. Genomic analysis predicted various life styles and genomic replication strategies. A likely eukaryote-associated host habitat was reflected in the gene content of some of the flavophages. Detection in cellular metagenomes and by direct-plating showed that part of these phages were actively replicating in the environment during the 2018 spring bloom. Furthermore, CRISPR/Cas spacers and re-isolation during two consecutive years suggested that, at least part of the new flavophages are stable components of the microbial community in the North Sea. Together, our results indicate that these diverse flavophages have the potential to modulate their respective host populations.
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Affiliation(s)
- Nina Bartlau
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antje Wichels
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Biologische Anstalt Helgoland, Heligoland, Germany
| | - Georg Krohne
- Imaging Core Facility, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Anneke Heins
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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7
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Bacteriophages in the Control of Aeromonas sp. in Aquaculture Systems: An Integrative View. Antibiotics (Basel) 2022; 11:antibiotics11020163. [PMID: 35203766 PMCID: PMC8868336 DOI: 10.3390/antibiotics11020163] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022] Open
Abstract
Aeromonas species often cause disease in farmed fish and are responsible for causing significant economic losses worldwide. Although vaccination is the ideal method to prevent infectious diseases, there are still very few vaccines commercially available in the aquaculture field. Currently, aquaculture production relies heavily on antibiotics, contributing to the global issue of the emergence of antimicrobial-resistant bacteria and resistance genes. Therefore, it is essential to develop effective alternatives to antibiotics to reduce their use in aquaculture systems. Bacteriophage (or phage) therapy is a promising approach to control pathogenic bacteria in farmed fish that requires a heavy understanding of certain factors such as the selection of phages, the multiplicity of infection that produces the best bacterial inactivation, bacterial resistance, safety, the host’s immune response, administration route, phage stability and influence. This review focuses on the need to advance phage therapy research in aquaculture, its efficiency as an antimicrobial strategy and the critical aspects to successfully apply this therapy to control Aeromonas infection in fish.
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8
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Hammerl JA, Barac A, Bienert A, Demir A, Drüke N, Jäckel C, Matthies N, Jun JW, Skurnik M, Ulrich J, Hertwig S. Birds Kept in the German Zoo "Tierpark Berlin" Are a Common Source for Polyvalent Yersinia pseudotuberculosis Phages. Front Microbiol 2022; 12:634289. [PMID: 35046908 PMCID: PMC8762354 DOI: 10.3389/fmicb.2021.634289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 11/30/2021] [Indexed: 11/15/2022] Open
Abstract
Yersinia pseudotuberculosis is an important animal pathogen, particularly for birds, rodents, and monkeys, which is also able to infect humans. Indeed, an increasing number of reports have been published on zoo animals that were killed by this species. One option to treat diseased animals is the application of strictly lytic (virulent) phages. However, thus far relatively few phages infecting Y. pseudotuberculosis have been isolated and characterized. To determine the prevalence of Y. pseudotuberculosis phages in zoo animals, fecal samples of birds and some primates, maras, and peccaries kept in the Tierpark Berlin were analyzed. Seventeen out of 74 samples taken in 2013 and 2017 contained virulent phages. The isolated phages were analyzed in detail and could be allocated to three groups. The first group is composed of 10 T4-like phages (PYps2T taxon group: Myoviridae; Tevenvirinae; Tequatrovirus), the second group (PYps23T taxon group: Chaseviridae; Carltongylesvirus; Escherichia virus ST32) consists of five phages encoding a podovirus-like RNA polymerase that is related to an uncommon genus of myoviruses (e.g., Escherichia coli phage phiEcoM-GJ1), while the third group is comprised of two podoviruses (PYps50T taxon group: Autographiviridae; Studiervirinae; Berlinvirus) which are closely related to T7. The host range of the isolated phages differed significantly. Between 5.5 and 86.7% of 128 Y. pseudotuberculosis strains belonging to 20 serotypes were lysed by each phage. All phages were additionally able to lyse Y. enterocolitica B4/O:3 strains, when incubated at 37°C. Some phages also infected Y. pestis strains and even strains belonging to other genera of Enterobacteriaceae. A cocktail containing two of these phages would be able to lyse almost 93% of the tested Y. pseudotuberculosis strains. The study indicates that Y. pseudotuberculosis phages exhibiting a broad-host range can be isolated quite easily from zoo animals, particularly birds.
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Affiliation(s)
- Jens Andre Hammerl
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Andrea Barac
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Anja Bienert
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Aslihan Demir
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Niklas Drüke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Claudia Jäckel
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Nina Matthies
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jin Woo Jun
- Department of Aquaculture, Korea National College of Agriculture and Fisheries, Jeonju, South Korea
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Juliane Ulrich
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Stefan Hertwig
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Sedghi LM, Bacino M, Kapila YL. Periodontal Disease: The Good, The Bad, and The Unknown. Front Cell Infect Microbiol 2021; 11:766944. [PMID: 34950607 PMCID: PMC8688827 DOI: 10.3389/fcimb.2021.766944] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/11/2021] [Indexed: 01/08/2023] Open
Abstract
Periodontal disease is classically characterized by progressive destruction of the soft and hard tissues of the periodontal complex, mediated by an interplay between dysbiotic microbial communities and aberrant immune responses within gingival and periodontal tissues. Putative periodontal pathogens are enriched as the resident oral microbiota becomes dysbiotic and inflammatory responses evoke tissue destruction, thus inducing an unremitting positive feedback loop of proteolysis, inflammation, and enrichment for periodontal pathogens. Keystone microbial pathogens and sustained gingival inflammation are critical to periodontal disease progression. However, recent studies have revealed the importance of previously unidentified microbes involved in disease progression, including various viruses, phages and bacterial species. Moreover, newly identified immunological and genetic mechanisms, as well as environmental host factors, including diet and lifestyle, have been discerned in recent years as further contributory factors in periodontitis. These factors have collectively expanded the established narrative of periodontal disease progression. In line with this, new ideologies related to maintaining periodontal health and treating existing disease have been explored, such as the application of oral probiotics, to limit and attenuate disease progression. The role of systemic host pathologies, such as autoimmune disorders and diabetes, in periodontal disease pathogenesis has been well noted. Recent studies have additionally identified the reciprocated importance of periodontal disease in potentiating systemic disease states at distal sites, such as in Alzheimer's disease, inflammatory bowel diseases, and oral cancer, further highlighting the importance of the oral cavity in systemic health. Here we review long-standing knowledge of periodontal disease progression while integrating novel research concepts that have broadened our understanding of periodontal health and disease. Further, we delve into innovative hypotheses that may evolve to address significant gaps in the foundational knowledge of periodontal disease.
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Affiliation(s)
- Lea M. Sedghi
- School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
| | - Margot Bacino
- School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
| | - Yvonne Lorraine Kapila
- School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
- Department of Periodontology, School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
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10
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Kumar P, Meghvansi MK, Kamboj DV. Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage. Sci Rep 2021; 11:22197. [PMID: 34772986 PMCID: PMC8590004 DOI: 10.1038/s41598-021-01419-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Shigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controlling Shigella infections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity against Shigella dysenteriae, Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticus and Enterococcus faecium. The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genus Hanrivervirus of subfamily Tempevirinae under the family Drexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members of Drexlerviridae taking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genus Hanrivervirus. The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.
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Affiliation(s)
- Prince Kumar
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- Regional Ayurveda Research Institute, Gwalior, Madhya Pradesh, 474009, India
| | - Mukesh K Meghvansi
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- Bioprocess Technology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - D V Kamboj
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India.
- Defence Research Laboratory, Tezpur, Assam, 784001, India.
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11
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Hammerl JA, Barac A, Erben P, Fuhrmann J, Gadicherla A, Kumsteller F, Lauckner A, Müller F, Hertwig S. Properties of Two Broad Host Range Phages of Yersinia enterocolitica Isolated from Wild Animals. Int J Mol Sci 2021; 22:11381. [PMID: 34768812 PMCID: PMC8583763 DOI: 10.3390/ijms222111381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/11/2021] [Accepted: 10/19/2021] [Indexed: 12/18/2022] Open
Abstract
Yersinia (Y.) enterocolitica and Y. pseudotuberculosis are important zoonotic agents which can infect both humans and animals. To combat these pathogens, the application of strictly lytic phages may be a promising tool. Since only few Yersinia phages have been described yet, some of which demonstrated a high specificity for certain serotypes, we isolated two phages from game animals and characterized them in terms of their morphology, host specificity, lytic activity on two bio-/serotypes and genome composition. The T7-related podovirus vB_YenP_Rambo and the myovirus vB_YenM_P281, which is very similar to a previously described phage PY100, showed a broad host range. Together, they lysed all the 62 tested pathogenic Y. enterocolitica strains belonging to the most important bio-/serotypes in Europe. A cocktail containing these two phages strongly reduced cultures of a bio-/serotype B4/O:3 and a B2/O:9 strain, even at very low MOIs (multiplicity of infection) and different temperatures, though, lysis of bio-/serotype B2/O:9 by vB_YenM_P281 and also by the related phage PY100 only occurred at 37 °C. Both phages were additionally able to lyse various Y. pseudotuberculosis strains at 28 °C and 37 °C, but only when the growth medium was supplemented with calcium and magnesium cations.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Stefan Hertwig
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn Str. 8-10, D-10589 Berlin, Germany; (J.A.H.); (A.B.); (P.E.); (J.F.); (A.G.); (F.K.); (A.L.); (F.M.)
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12
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Makalatia K, Kakabadze E, Bakuradze N, Grdzelishvili N, Stamp B, Herman E, Tapinos A, Coffey A, Lee D, Papadopoulos NG, Robertson DL, Chanishvili N, Megremis S. Investigation of Salmonella Phage-Bacteria Infection Profiles: Network Structure Reveals a Gradient of Target-Range from Generalist to Specialist Phage Clones in Nested Subsets. Viruses 2021; 13:1261. [PMID: 34203492 PMCID: PMC8310288 DOI: 10.3390/v13071261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/16/2021] [Accepted: 06/23/2021] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages that lyse Salmonella enterica are potential tools to target and control Salmonella infections. Investigating the host range of Salmonella phages is a key to understand their impact on bacterial ecology, coevolution and inform their use in intervention strategies. Virus-host infection networks have been used to characterize the "predator-prey" interactions between phages and bacteria and provide insights into host range and specificity. Here, we characterize the target-range and infection profiles of 13 Salmonella phage clones against a diverse set of 141 Salmonella strains. The environmental source and taxonomy contributed to the observed infection profiles, and genetically proximal phages shared similar infection profiles. Using in vitro infection data, we analyzed the structure of the Salmonella phage-bacteria infection network. The network has a non-random nested organization and weak modularity suggesting a gradient of target-range from generalist to specialist species with nested subsets, which are also observed within and across the different phage infection profile groups. Our results have implications for our understanding of the coevolutionary mechanisms shaping the ecological interactions between Salmonella phages and their bacterial hosts and can inform strategies for targeting Salmonella enterica with specific phage preparations.
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Affiliation(s)
- Khatuna Makalatia
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0162, Georgia; (K.M.); (E.K.); (N.B.); (N.G.)
- Faculty of Medicine, Teaching University Geomedi, Tbilisi 0114, Georgia
| | - Elene Kakabadze
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0162, Georgia; (K.M.); (E.K.); (N.B.); (N.G.)
| | - Nata Bakuradze
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0162, Georgia; (K.M.); (E.K.); (N.B.); (N.G.)
| | - Nino Grdzelishvili
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0162, Georgia; (K.M.); (E.K.); (N.B.); (N.G.)
| | - Ben Stamp
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; (B.S.); (D.L.R.)
| | - Ezra Herman
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK;
| | - Avraam Tapinos
- Division of Evolution and Genomic Sciences, The University of Manchester, Manchester M13 9GB, UK;
| | - Aidan Coffey
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (A.C.); (D.L.)
| | - David Lee
- Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland; (A.C.); (D.L.)
| | - Nikolaos G. Papadopoulos
- Division of Infection, Immunity and Respiratory Medicine, The University of Manchester, Manchester M13 9PL, UK;
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK; (B.S.); (D.L.R.)
| | - Nina Chanishvili
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi 0162, Georgia; (K.M.); (E.K.); (N.B.); (N.G.)
| | - Spyridon Megremis
- Division of Evolution and Genomic Sciences, The University of Manchester, Manchester M13 9GB, UK;
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13
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Duarte J, Pereira C, Costa P, Almeida A. Bacteriophages with Potential to Inactivate Aeromonas hydrophila in Cockles: In Vitro and In Vivo Preliminary Studies. Antibiotics (Basel) 2021; 10:antibiotics10060710. [PMID: 34204770 PMCID: PMC8231581 DOI: 10.3390/antibiotics10060710] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/05/2021] [Accepted: 06/09/2021] [Indexed: 01/13/2023] Open
Abstract
The recurrent emergence of infection outbreaks associated with shellfish consumption is of extreme importance for public health. The present study investigated the potential application of phages AH-1, AH-4, and AH-5 to inactivate Aeromonas hydrophila, a causative agent of infections in humans associated with bivalve shellfish consumption. The inactivation of A. hydrophila was assessed in vitro, using a liquid culture medium, and in vivo, using artificially contaminated cockles with A. hydrophila ATCC 7966. In the in vitro experiments, all phages were effective against A. hydrophila, but phage AH-1 (with a maximum reduction of 7.7 log colonies forming units CFU/mL) was more effective than phages AH-4 and AH-5 (with reductions of 4.9 and 4.5 log CFU/mL, respectively). The cocktails AH-1/AH-4, AH-1/AH-5, AH-4/AH-5, and AH-1/AH-4/AH-5 were slightly more effective than the single phage suspensions. The phages presented a low emergence rate of phage-resistant mutants. When artificially contaminated cockles were treated in static seawater with phage AH-1, around 44% of the added A. hydrophila (1.0 log CFU/g) was inactivated. The results of this study suggest that phage therapy can be an effective alternative to control human pathogenic bacteria during depuration.
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14
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Tao C, Yi Z, Zhang Y, Wang Y, Zhu H, Afayibo DJA, Li T, Tian M, Qi J, Ding C, Gao S, Wang S, Yu S. Characterization of a Broad-Host-Range Lytic Phage SHWT1 Against Multidrug-Resistant Salmonella and Evaluation of Its Therapeutic Efficacy in vitro and in vivo. Front Vet Sci 2021; 8:683853. [PMID: 34179174 PMCID: PMC8222671 DOI: 10.3389/fvets.2021.683853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/14/2021] [Indexed: 12/27/2022] Open
Abstract
Inappropriate use of antibiotics has accelerated to the emergence of multidrug-resistant bacteria, becoming a major health threat. Moreover, bacterial biofilms contribute to antibiotic resistance and prolonged infections. Bacteriophage (phage) therapy may provide an alternative strategy for controlling multidrug-resistant bacterial infections. In this study, a broad-host-range phage, SHWT1, with lytic activity against multidrug-resistant Salmonella was isolated, characterized and evaluated for the therapeutic efficacy in vitro and in vivo. Phage SHWT1 exhibited specific lytic activity against the prevalent Salmonella serovars, such as Salmonella Pullorum, Salmonella Gallinarum, Salmonella Enteritidis, and Salmonella Typhimurium. Morphological analysis showed that phage SHWT1 was a member of the family Siphoviridae and the order Caudovirales. Phage SHWT1 had a latent period of 5 min and burst size of ~150 plaque-forming units (PFUs)/cell. The phage was stable from pH 3-12 and 4–65°C. Phage SHWT1 also showed capacity to lyse Salmonella planktonic cells and inhibit the biofilm formation at optimal multiplicity of infection (MOI) of 0.001, 0.01, 0.1, and 100, respectively. In addition, phage SHWT1 was able to lyse intracellular Salmonella within macrophages. Genome sequencing and phylogenetic analyses revealed that SHWT1 was a lytic phage without toxin genes, virulence genes, antibiotic resistance genes, or significant genomic rearrangements. We found that phage SHWT1 could successfully protect mice against S. enteritidis and S. typhimurium infection. Elucidation of the characteristics and genome sequence of phage SHWT1 demonstrates that this phage is a potential therapeutic agent against the salmonellosis caused by multidrug-resistant Salmonella.
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Affiliation(s)
- Chenglin Tao
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhengfei Yi
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yaodong Zhang
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yao Wang
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hong Zhu
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Dossêh Jean Apôtre Afayibo
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Tao Li
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Mingxing Tian
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Jingjing Qi
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
| | - Song Gao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Shaohui Wang
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Shengqing Yu
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, China
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15
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Gabashvili E, Kobakhidze S, Koulouris S, Robinson T, Kotetishvili M. Bi- and Multi-directional Gene Transfer in the Natural Populations of Polyvalent Bacteriophages, and Their Host Species Spectrum Representing Foodborne Versus Other Human and/or Animal Pathogens. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:179-202. [PMID: 33484405 DOI: 10.1007/s12560-021-09460-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Unraveling the trends of phage-host versus phage-phage coevolution is critical for avoiding possible undesirable outcomes from the use of phage preparations intended for therapeutic, food safety or environmental safety purposes. We aimed to investigate a phenomenon of intergeneric recombination and its trajectories across the natural populations of phages predominantly linked to foodborne pathogens. The results from the recombination analyses, using a large array of the recombination detection algorithms imbedded in SplitsTree, RDP4, and Simplot software packages, provided strong evidence (fit: 100; P ≤ 0.014) for both bi- and multi-directional intergeneric recombination of the genetic loci involved collectively in phage morphogenesis, host specificity, virulence, replication, and persistence. Intergeneric recombination was determined to occur not only among conspecifics of the virulent versus temperate phages but also between the phages with these different lifestyles. The recombining polyvalent phages were suggested to interact with fairly large host species networks, including sometimes genetically very distinct species, such as e.g., Salmonella enterica and/or Escherichia coli versus Staphylococcus aureus or Yersinia pestis. Further studies are needed to understand whether phage-driven intergeneric recombination can lead to undesirable changes of intestinal and other microbiota in humans and animals.
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Affiliation(s)
- Ekaterine Gabashvili
- School of Natural Sciences and Medicine, Ilia State University, 1 Giorgi Tsereteli exit, 0162, Tbilisi, Georgia
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia
| | - Saba Kobakhidze
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia
| | - Stylianos Koulouris
- Engagement and Cooperation Unit, European Food Safety Authority, Via Carlo Magno 1A, 43126, Parma, Italy
| | - Tobin Robinson
- Scientific Committee, and Emerging Risks Unit, European Food Safety Authority, Via Carlo Magno 1A, 43126, Parma, Italy
| | - Mamuka Kotetishvili
- Division of Risk Assessment, Scientific-Research Center of Agriculture, 6 Marshal Gelovani ave., 0159, Tbilisi, Georgia.
- Hygiene and Medical Ecology, G. Natadze Scientific-Research Institute of Sanitation, 78 D. Uznadze St., 0102, Tbilisi, Georgia.
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16
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Pereira C, Costa P, Duarte J, Balcão VM, Almeida A. Phage therapy as a potential approach in the biocontrol of pathogenic bacteria associated with shellfish consumption. Int J Food Microbiol 2020; 338:108995. [PMID: 33316593 DOI: 10.1016/j.ijfoodmicro.2020.108995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022]
Abstract
Infectious human diseases acquired from bivalve shellfish consumption constitute a public health threat. These health threats are largely related to the filter-feeding phenomenon, by which bivalve organisms retain and concentrate pathogenic bacteria from their surrounding waters. Even after depuration, bivalve shellfish are still involved in outbreaks caused by pathogenic bacteria, which increases the demand for new and efficient strategies to control transmission of shellfish infection. Bacteriophage (or phage) therapy represents a promising, tailor-made approach to control human pathogens in bivalves, but its success depends on a deep understanding of several factors that include the bacterial communities present in the harvesting waters, the appropriate selection of phage particles, the multiplicity of infection that produces the best bacterial inactivation, chemical and physical factors, the emergence of phage-resistant bacterial mutants and the life cycle of bivalves. This review discusses the need to advance phage therapy research for bivalve decontamination, highlighting their efficiency as an antimicrobial strategy and identifying critical aspects to successfully apply this therapy to control human pathogens associated with bivalve consumption.
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Affiliation(s)
- Carla Pereira
- Department of Biology & CESAM, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
| | - Pedro Costa
- Department of Biology & CESAM, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - João Duarte
- Department of Biology & CESAM, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Victor M Balcão
- Department of Biology & CESAM, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal; PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, 18023-000 Sorocaba, São Paulo, Brazil
| | - Adelaide Almeida
- Department of Biology & CESAM, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
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17
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Edwards KF, Steward GF, Schvarcz CR. Making sense of virus size and the tradeoffs shaping viral fitness. Ecol Lett 2020; 24:363-373. [PMID: 33146939 DOI: 10.1111/ele.13630] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/26/2020] [Accepted: 09/27/2020] [Indexed: 12/18/2022]
Abstract
Viruses span an impressive size range, with genome length varying a thousandfold and virion volume nearly a millionfold. For cellular organisms the scaling of traits with size is a pervasive influence on ecological processes, but whether size plays a central role in viral ecology is unknown. Here, we focus on viruses of aquatic unicellular organisms, which exhibit the greatest known range of virus size. We outline hypotheses within a quantitative framework, and analyse data where available, to consider how size affects the primary components of viral fitness. We argue that larger viruses have fewer offspring per infection and slower contact rates with host cells, but a larger genome tends to increase infection efficiency, broaden host range, and potentially increase attachment success and decrease decay rate. These countervailing selective pressures may explain why a breadth of sizes exist and even coexist when infecting the same host populations. Oligotrophic ecosystems may be enriched in "giant" viruses, because environments with resource-limited phagotrophs at low concentrations may select for broader host range, better control of host metabolism, lower decay rate and a physical size that mimics bacterial prey. Finally, we describe where further research is needed to understand the ecology and evolution of viral size diversity.
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Affiliation(s)
- Kyle F Edwards
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Grieg F Steward
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
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18
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Wang W, Ren J, Tang K, Dart E, Ignacio-Espinoza JC, Fuhrman JA, Braun J, Sun F, Ahlgren NA. A network-based integrated framework for predicting virus-prokaryote interactions. NAR Genom Bioinform 2020; 2:lqaa044. [PMID: 32626849 PMCID: PMC7324143 DOI: 10.1093/nargab/lqaa044] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 03/12/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences; however, it remains challenging to identify the host(s) of these new viruses. We developed VirHostMatcher-Net, a flexible, network-based, Markov random field framework for predicting virus–prokaryote interactions using multiple, integrated features: CRISPR sequences and alignment-free similarity measures (\documentclass[12pt]{minimal}
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}{}$s_2^*$\end{document} and WIsH). Evaluation of this method on a benchmark set of 1462 known virus–prokaryote pairs yielded host prediction accuracy of 59% and 86% at the genus and phylum levels, representing 16–27% and 6–10% improvement, respectively, over previous single-feature prediction approaches. We applied our host prediction tool to crAssphage, a human gut phage, and two metagenomic virus datasets: marine viruses and viral contigs recovered from globally distributed, diverse habitats. Host predictions were frequently consistent with those of previous studies, but more importantly, this new tool made many more confident predictions than previous tools, up to nearly 3-fold more (n > 27 000), greatly expanding the diversity of known virus–host interactions.
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Affiliation(s)
- Weili Wang
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Jie Ren
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Kujin Tang
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Emily Dart
- Biology Department, Clark University, Worcester, MA 01610, USA
| | | | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jonathan Braun
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Fengzhu Sun
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
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19
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Schulfer A, Santiago-Rodriguez TM, Ly M, Borin JM, Chopyk J, Blaser MJ, Pride DT. Fecal Viral Community Responses to High-Fat Diet in Mice. mSphere 2020; 5:e00833-19. [PMID: 32102942 PMCID: PMC7045389 DOI: 10.1128/msphere.00833-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
Alterations in diet can have significant impact on the host, with high-fat diet (HFD) leading to obesity, diabetes, and inflammation of the gut. Although membership and abundances in gut bacterial communities are strongly influenced by diet, substantially less is known about how viral communities respond to dietary changes. Examining fecal contents of mice as the mice were transitioned from normal chow to HFD, we found significant changes in the relative abundances and the diversity in the gut of bacteria and their viruses. Alpha diversity of the bacterial community was significantly diminished in response to the diet change but did not change significantly in the viral community. However, the diet shift significantly impacted the beta diversity in both the bacterial and viral communities. There was a significant shift away from the relatively abundant Siphoviridae accompanied by increases in bacteriophages from the Microviridae family. The proportion of identified bacteriophage structural genes significantly decreased after the transition to HFD, with a conserved loss of integrase genes in all four experimental groups. In total, this study provides evidence for substantial changes in the intestinal virome disproportionate to bacterial changes, and with alterations in putative viral lifestyles related to chromosomal integration as a result of shift to HFD.IMPORTANCE Prior studies have shown that high-fat diet (HFD) can have profound effects on the gastrointestinal (GI) tract microbiome and also demonstrate that bacteria in the GI tract can affect metabolism and lean/obese phenotypes. We investigated whether the composition of viral communities that also inhabit the GI tract are affected by shifts from normal to HFD. We found significant and reproducible shifts in the content of GI tract viromes after the transition to HFD. The differences observed in virome community membership and their associated gene content suggest that these altered viral communities are populated by viruses that are more virulent toward their host bacteria. Because HFD also are associated with significant shifts in GI tract bacterial communities, we believe that the shifts in the viral community may serve to drive the changes that occur in associated bacterial communities.
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Affiliation(s)
| | | | - Melissa Ly
- Department of Pathology, University of California, San Diego, California, USA
| | - Joshua M Borin
- Division of Biological Sciences, University of California, San Diego, California, USA
| | - Jessica Chopyk
- Department of Pathology, University of California, San Diego, California, USA
| | - Martin J Blaser
- New York University, New York, New York, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - David T Pride
- Department of Pathology, University of California, San Diego, California, USA
- Department of Medicine, University of California, San Diego, California, USA
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20
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Kallies R, Kiesel B, Schmidt M, Ghanem N, Zopfi J, Hackermüller J, Harms H, Wick LY, Chatzinotas A. Complete genome sequence of Pseudoalteromonas virus vB_PspP-H6/1 that infects Pseudoalteromonas sp. strain H6. Mar Genomics 2019. [DOI: 10.1016/j.margen.2019.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Fong K, Tremblay DM, Delaquis P, Goodridge L, Levesque RC, Moineau S, Suttle CA, Wang S. Diversity and Host Specificity Revealed by Biological Characterization and Whole Genome Sequencing of Bacteriophages Infecting Salmonella enterica. Viruses 2019; 11:v11090854. [PMID: 31540091 PMCID: PMC6783827 DOI: 10.3390/v11090854] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 12/12/2022] Open
Abstract
Phages infecting members of the opportunistic human pathogen, Salmonella enterica, are widespread in natural environments and offer a potential source of agents that could be used for controlling populations of this bacterium; yet, relatively little is known about these phages. Here we describe the isolation and characterization of 45 phages of Salmonella enterica from disparate geographic locations within British Columbia, Canada. Host-range profiling revealed host-specific patterns of susceptibility and resistance, with several phages identified that have a broad-host range (i.e., able to lyse >40% of bacterial hosts tested). One phage in particular, SE13, is able to lyse 51 out of the 61 Salmonella strains tested. Comparative genomic analyses also revealed an abundance of sequence diversity in the sequenced phages. Alignment of the genomes grouped the phages into 12 clusters with three singletons. Phages within certain clusters exhibited extraordinarily high genome homology (>98% nucleotide identity), yet between clusters, genomes exhibited a span of diversity (<50% nucleotide identity). Alignment of the major capsid protein also supported the clustering pattern observed with alignment of the whole genomes. We further observed associations between genomic relatedness and the site of isolation, as well as genetic elements related to DNA metabolism and host virulence. Our data support the knowledge framework for phage diversity and phage-host interactions that are required for developing phage-based applications for various sectors, including biocontrol, detection and typing.
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Affiliation(s)
- Karen Fong
- Food, Nutrition and Health, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Denise M Tremblay
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC G1V 0A6, Canada.
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC G1V 0A6, Canada.
| | - Pascal Delaquis
- Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada.
| | - Lawrence Goodridge
- Food Science Department, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada.
| | - Sylvain Moineau
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC G1V 0A6, Canada.
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC G1V 0A6, Canada.
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC G1V 0A6, Canada.
| | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany, and the Institute for Oceans and Fisheries, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Siyun Wang
- Food, Nutrition and Health, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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22
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Ghose C, Ly M, Schwanemann LK, Shin JH, Atab K, Barr JJ, Little M, Schooley RT, Chopyk J, Pride DT. The Virome of Cerebrospinal Fluid: Viruses Where We Once Thought There Were None. Front Microbiol 2019; 10:2061. [PMID: 31555247 PMCID: PMC6742758 DOI: 10.3389/fmicb.2019.02061] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/21/2019] [Indexed: 01/21/2023] Open
Abstract
Traditionally, medicine has held that some human body sites are sterile and that the introduction of microbes to these sites results in infections. This paradigm shifted significantly with the discovery of the human microbiome and acceptance of these commensal microbes living across the body. However, the central nervous system (CNS) is still believed by many to be sterile in healthy people. Using culture-independent methods, we examined the virome of cerebrospinal fluid (CSF) from a cohort of mostly healthy human subjects. We identified a community of DNA viruses, most of which were identified as bacteriophages. Compared to other human specimen types, CSF viromes were not ecologically distinct. There was a high alpha diversity cluster that included feces, saliva, and urine, and a low alpha diversity cluster that included CSF, body fluids, plasma, and breast milk. The high diversity cluster included specimens known to have many bacteria, while other specimens traditionally assumed to be sterile formed the low diversity cluster. There was an abundance of viruses shared among CSF, breast milk, plasma, and body fluids, while each generally shared less with urine, feces, and saliva. These shared viruses ranged across different virus families, indicating that similarities between these viromes represent more than just a single shared virus family. By identifying a virome in the CSF of mostly healthy individuals, it is now less likely that any human body site is devoid of microbes, which further highlights the need to decipher the role that viral communities may play in human health.
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Affiliation(s)
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Leila K Schwanemann
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Ji Hyun Shin
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Katayoon Atab
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Mark Little
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Robert T Schooley
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Jessica Chopyk
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - David T Pride
- Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
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23
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Shahin K, Bao H, Komijani M, Barazandeh M, Bouzari M, Hedayatkhah A, Zhang L, Zhao H, He T, Pang M, Wang R. Isolation, characterization, and PCR-based molecular identification of a siphoviridae phage infecting Shigella dysenteriae. Microb Pathog 2019; 131:175-180. [DOI: 10.1016/j.micpath.2019.03.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 10/27/2022]
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24
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Mizuno CM, Prajapati B, Lucas‐Staat S, Sime‐Ngando T, Forterre P, Bamford DH, Prangishvili D, Krupovic M, Oksanen HM. Novel haloarchaeal viruses from Lake Retba infecting
Haloferax
and
Halorubrum
species. Environ Microbiol 2019; 21:2129-2147. [DOI: 10.1111/1462-2920.14604] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/15/2019] [Accepted: 03/21/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Carolina M. Mizuno
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Bina Prajapati
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
| | - Soizick Lucas‐Staat
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Telesphore Sime‐Ngando
- CNRS UMR 6023, Université Clermont‐AuvergneLaboratoire "Microorganismes: Génome et Environnement" (LMGE) F‐63000, Clermont‐Ferrand France
| | - Patrick Forterre
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Dennis H. Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
| | - David Prangishvili
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
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25
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Gencay YE, Gambino M, Prüssing TF, Brøndsted L. The genera of bacteriophages and their receptors are the major determinants of host range. Environ Microbiol 2019; 21:2095-2111. [PMID: 30888719 DOI: 10.1111/1462-2920.14597] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 01/21/2023]
Abstract
The host range of phages is a key to understand their impact on bacterial ecology and evolution. Because of the complexity of phage-host interactions, the variables that determine the breadth of a phage host range remain poorly understood. Here, we propose a novel holistic approach to identify the host range determinants of a new collection of phages infecting Salmonella, isolated from animal, environmental and wastewater samples that were able to infect 58 of the 71 Salmonella strains in our collection. By using a set of statistic approaches (non-metric dimensional scaling, Bray-Curtis distance, PERMANOVA), we analysed phenotypic (host range on wild-type and receptor mutants) and genetic data (taxonomic assignment and receptor binding proteins) to evaluate the impact of isolation strain and niche, phage receptor and genus on the host range. Statistical analysis revealed that two phage characteristics influence the host range by explaining the most variance: the receptor by 45% and the genus by 51%. Interestingly, phage genus and receptor in combination explained 79% of the variance, establishing these characteristics as the major determinants of the host range. This study demonstrates the power and the novelty of applying statistical approaches to phenotypic and genetic data to investigate the ecology of phage-host interactions.
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Affiliation(s)
- Yilmaz Emre Gencay
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Tessa From Prüssing
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
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26
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A novel phage from periodontal pockets associated with chronic periodontitis. Virus Genes 2019; 55:381-393. [PMID: 30927185 DOI: 10.1007/s11262-019-01658-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/19/2019] [Indexed: 12/19/2022]
Abstract
Bacteriophages often constitute the majority of periodontal viral communities, but phages that infect oral bacteria remain uncharacterized. Here, we present the genetic analysis of the genome of a novel siphovirus, named Siphoviridae_29632, which was isolated from a patient with periodontitis using a viral metagenomics-based approach. Among 43 predicted open reading frames (ORFs) in the genome, the viral genes encoding structural proteins were distinct from the counterparts of other viruses, although a distant homology is shared among viral morphogenesis proteins. A total of 28 predicted coding sequences had significant homology to other known phage ORF sequences. In addition, the prevalence of Siphoviridae_29632 in a cohort of patients with chronic periodontitis was 41.67%, which was significantly higher than that in the healthy group (4.55%, P < 0.001), suggesting that this virus as well as its hosts may contribute to the ecological environment favored for chronic periodontitis.
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27
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Drucker VV, Belykh OI, Gorshkova AS, Bondar AA, Sykilinda NN. Autochthonous Bacteriophages in the Microbial Loop Structure of Different Biotopes of Lake Baikal. CONTEMP PROBL ECOL+ 2019. [DOI: 10.1134/s1995425519020045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Mäntynen S, Sundberg LR, Oksanen HM, Poranen MM. Half a Century of Research on Membrane-Containing Bacteriophages: Bringing New Concepts to Modern Virology. Viruses 2019; 11:E76. [PMID: 30669250 PMCID: PMC6356626 DOI: 10.3390/v11010076] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/14/2022] Open
Abstract
Half a century of research on membrane-containing phages has had a major impact on virology, providing new insights into virus diversity, evolution and ecological importance. The recent revolutionary technical advances in imaging, sequencing and lipid analysis have significantly boosted the depth and volume of knowledge on these viruses. This has resulted in new concepts of virus assembly, understanding of virion stability and dynamics, and the description of novel processes for viral genome packaging and membrane-driven genome delivery to the host. The detailed analyses of such processes have given novel insights into DNA transport across the protein-rich lipid bilayer and the transformation of spherical membrane structures into tubular nanotubes, resulting in the description of unexpectedly dynamic functions of the membrane structures. Membrane-containing phages have provided a framework for understanding virus evolution. The original observation on membrane-containing bacteriophage PRD1 and human pathogenic adenovirus has been fundamental in delineating the concept of "viral lineages", postulating that the fold of the major capsid protein can be used as an evolutionary fingerprint to trace long-distance evolutionary relationships that are unrecognizable from the primary sequences. This has brought the early evolutionary paths of certain eukaryotic, bacterial, and archaeal viruses together, and potentially enables the reorganization of the nearly immeasurable virus population (~1 × 1031) on Earth into a reasonably low number of groups representing different architectural principles. In addition, the research on membrane-containing phages can support the development of novel tools and strategies for human therapy and crop protection.
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Affiliation(s)
- Sari Mäntynen
- Center of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
| | - Lotta-Riina Sundberg
- Center of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
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29
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Garin-Fernandez A, Pereira-Flores E, Glöckner FO, Wichels A. The North Sea goes viral: Occurrence and distribution of North Sea bacteriophages. Mar Genomics 2018; 41:31-41. [PMID: 29866485 DOI: 10.1016/j.margen.2018.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/19/2018] [Accepted: 05/19/2018] [Indexed: 01/17/2023]
Abstract
Marine viruses are dominated by phages and have an enormous influence on microbial population dynamics, due to lysis and horizontal gene transfer. The aim of this study is to analyze the occurrence and diversity of phages in the North Sea, considering the virus-host interactions and biogeographic factors. The virus community of four sampling stations were described using virus metagenomics (viromes). The results show that the virus community was not evenly distributed throughout the North Sea. The dominant phage members were identified as unclassified phage group, followed by Caudovirales order. Myoviridae was the dominant phage family in the North Sea, which occurrence decreased from the coast to the open sea. In contrast, the occurrence of Podoviridae increased and the occurrence of Siphoviridae was low throughout the North Sea. The occurrence of other groups such as Phycodnaviridae decreased from the coast to the open sea. The coastal virus community was genetically more diverse than the open sea community. The influence of riverine inflow and currents, for instance the English Channel flow affects the genetic virus diversity with the community carrying genes from a variety of metabolic pathways and other functions. The present study offers the first insights in the virus community in the North Sea using viromes and shows the variation in virus diversity and the genetic information moved from coastal to open sea areas.
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30
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Poduval PB, Noronha JM, Bansal SK, Ghadi SC. Characterization of a new virulent phage ϕMC1 specific to Microbulbifer strain CMC-5. Virus Res 2018; 257:7-13. [DOI: 10.1016/j.virusres.2018.08.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 06/11/2018] [Accepted: 08/28/2018] [Indexed: 11/29/2022]
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31
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Jun JW, Park SC, Wicklund A, Skurnik M. Bacteriophages reduce Yersinia enterocolitica contamination of food and kitchenware. Int J Food Microbiol 2018; 271:33-47. [DOI: 10.1016/j.ijfoodmicro.2018.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/01/2018] [Accepted: 02/05/2018] [Indexed: 01/12/2023]
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32
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Jasna V, Pradeep Ram AS, Parvathi A, Sime-Ngando T. Differential impact of lytic viruses on prokaryotic morphopopulations in a tropical estuarine system (Cochin estuary, India). PLoS One 2018; 13:e0194020. [PMID: 29534102 PMCID: PMC5849291 DOI: 10.1371/journal.pone.0194020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/22/2018] [Indexed: 11/19/2022] Open
Abstract
Our understanding on the importance of viral lysis in the functioning of tropical estuarine ecosystem is limited. This study examines viral infection of prokaryotes and subsequent lysis of cells belonging to different morphotypes across a salinity gradient in monsoon driven estuarine ecosystem (Cochin estuary, India). High standing stock of viruses and prokaryotes accompanied by lytic infection rates in the euryhaline/mesohaline region of the estuary suggests salinity to have an influential role in driving interactions between prokaryotes and viruses. High prokaryotic mortality rates, up to 42% of prokaryote population in the pre-monsoon season is further substantiated by a high virus to prokaryote ratio (VPR), suggesting that maintenance of a high number of viruses is dependent on the most active fraction of bacterioplankton. Although myoviruses were the dominant viral morphotype (mean = 43%) throughout the study period, there was significant variation among prokaryotic morphotypes susceptible to viral infection. Among them, the viral infected short rod prokaryote morphotype with lower burst estimates (mean = 18 viruses prokaryote-1) was dominant (35%) in the dry seasons whereas a substantial increase in cocci forms (30%) infected by viruses with high burst size (mean = 31 viruses prokaryote-1) was evident during the monsoon season. Such preferential infections of prokaryotic morphopopulations with respect to seasons can have a strong and variable impact on the carbon and energy flow in this tropical ecosystem.
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Affiliation(s)
- Vijayan Jasna
- CSIR-National Institute of Oceanography, Regional Centre (CSIR), Kochi, India
| | - Angia Sriram Pradeep Ram
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont Auvergne, 1 Impasse Amélie Murat, Aubière, France
| | - Ammini Parvathi
- CSIR-National Institute of Oceanography, Regional Centre (CSIR), Kochi, India
| | - Telesphore Sime-Ngando
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont Auvergne, 1 Impasse Amélie Murat, Aubière, France
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33
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Shahin K, Bouzari M, Wang R. Isolation, characterization and genomic analysis of a novel lytic bacteriophage vB_SsoS-ISF002 infecting Shigella sonnei and Shigella flexneri. J Med Microbiol 2018; 67:376-386. [PMID: 29458535 DOI: 10.1099/jmm.0.000683] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Khashayar Shahin
- Department of Biology, Faculty of Sciences, University of Isfahan, Hezar Jereeb Street, 81746-73441, Isfahan, Iran
- State Key Laboratory Cultivation Base of MOST, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China
| | - Majid Bouzari
- Department of Biology, Faculty of Sciences, University of Isfahan, Hezar Jereeb Street, 81746-73441, Isfahan, Iran
| | - Ran Wang
- State Key Laboratory Cultivation Base of MOST, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China
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34
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Liu Z, Li H, Wang M, Jiang Y, Yang Q, Zhou X, Gong Z, Liu Q, Shao H. Isolation, characterization and genome sequencing of the novel phage SL25 from the Yellow Sea, China. Mar Genomics 2017; 37:31-34. [PMID: 33250123 DOI: 10.1016/j.margen.2017.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 09/27/2017] [Accepted: 09/27/2017] [Indexed: 10/18/2022]
Abstract
Outnumbering all other biological entities on earth, bacteriophages play critical roles in structuring microbial communities. However, only a small number of phages have so far been reported. In this study, a novel Pseudoalteromonas phage, SL25, was isolated from the yellow sea, China. Transmission electron microscope observations showed that phage has an icosahedral head, 100±1nm in diameter, and a tail with a length of 150±1nm, and should be grouped into the Siphoviridae family. To better understand the genetic diversity of this phage, the complete genome was characterized. It consists 29,130-bp-length double-stranded DNA with a GC content of 41.04% and is predicted to have 61 open reading frames (ORFs) with an average length of 504 nucleotides. This study adds a new Siphoviridae phage to the marine bacteriophage dataset that could potentially infect Pseudoalteromonas. It also provides useful data for further molecular research on the interaction mechanism between bacteriophages and their hosts.
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Affiliation(s)
- Zhaoyang Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Huifang Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Qingwei Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xinhao Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zheng Gong
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Qian Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
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35
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Duhaime MB, Solonenko N, Roux S, Verberkmoes NC, Wichels A, Sullivan MB. Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept. Front Microbiol 2017; 8:1241. [PMID: 28729861 PMCID: PMC5498523 DOI: 10.3389/fmicb.2017.01241] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/20/2017] [Indexed: 11/25/2022] Open
Abstract
Viruses influence the ecology and evolutionary trajectory of microbial communities. Yet our understanding of their roles in ecosystems is limited by the paucity of model systems available for hypothesis generation and testing. Further, virology is limited by the lack of a broadly accepted conceptual framework to classify viral diversity into evolutionary and ecologically cohesive units. Here, we introduce genomes, structural proteomes, and quantitative host range data for eight Pseudoalteromonas phages isolated from Helgoland (North Sea, Germany) and use these data to advance a genome-based viral operational taxonomic unit (OTU) definition. These viruses represent five new genera and inform 498 unaffiliated or unannotated protein clusters (PCs) from global virus metagenomes. In a comparison of previously sequenced Pseudoalteromonas phage isolates (n = 7) and predicted prophages (n = 31), the eight phages are unique. They share a genus with only one other isolate, Pseudoalteromonas podophage RIO-1 (East Sea, South Korea) and two Pseudoalteromonas prophages. Mass-spectrometry of purified viral particles identified 12–20 structural proteins per phage. When combined with 3-D structural predictions, these data led to the functional characterization of five previously unidentified major capsid proteins. Protein functional predictions revealed mechanisms for hijacking host metabolism and resources. Further, they uncovered a hybrid sipho-myovirus that encodes genes for Mu-like infection rarely described in ocean systems. Finally, we used these data to evaluate a recently introduced definition for virus populations that requires members of the same population to have >95% average nucleotide identity across at least 80% of their genes. Using physiological traits and genomics, we proposed a conceptual model for a viral OTU definition that captures evolutionarily cohesive and ecologically distinct units. In this trait-based framework, sensitive hosts are considered viral niches, while host ranges and infection efficiencies are tracked as viral traits. Quantitative host range assays revealed conserved traits within virus OTUs that break down between OTUs, suggesting the defined units capture niche and fitness differentiation. Together these analyses provide a foundation for model system-based hypothesis testing that will improve our understanding of marine copiotrophs, as well as phage–host interactions on the ocean particles and aggregates where Pseudoalteromonas thrive.
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Affiliation(s)
- Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann ArborMI, United States
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, ColumbusOH, United States
| | - Simon Roux
- Department of Microbiology, The Ohio State University, ColumbusOH, United States
| | - Nathan C Verberkmoes
- Department of Biological Sciences, Border Biomedical Research Center, University of Texas at El Paso, El PasoTX, United States
| | - Antje Wichels
- Biologische Anstalt Helgoland, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine ResearchHelgoland, Germany
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, ColumbusOH, United States.,Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, ColumbusOH, United States
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36
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Jäckel C, Hertwig S, Scholz HC, Nöckler K, Reetz J, Hammerl JA. Prevalence, Host Range, and Comparative Genomic Analysis of Temperate Ochrobactrum Phages. Front Microbiol 2017; 8:1207. [PMID: 28713341 PMCID: PMC5492332 DOI: 10.3389/fmicb.2017.01207] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/14/2017] [Indexed: 11/13/2022] Open
Abstract
Ochrobactrum and Brucella are closely related bacteria that populate different habitats and differ in their pathogenic properties. Only little is known about mobile genetic elements in these genera which might be important for survival and virulence. Previous studies on Brucella lysogeny indicated that active phages are rare in this genus. To gain insight into the presence and nature of prophages in Ochrobactrum, temperate phages were isolated from various species and characterized in detail. In silico analyses disclosed numerous prophages in published Ochrobactrum genomes. Induction experiments showed that Ochrobactrum prophages can be induced by various stress factors and that some strains released phage particles even under non-induced conditions. Sixty percent of lysates prepared from 125 strains revealed lytic activity. The host range and DNA similarities of 19 phages belonging to the families Myoviridae, Siphoviridae, or Podoviridae were determined suggesting that they are highly diverse. Some phages showed relationship to the temperate Brucella inopinata phage BiPB01. The genomic sequences of the myovirus POA1180 (41,655 bp) and podovirus POI1126 (60,065 bp) were analyzed. Phage POA1180 is very similar to a prophage recently identified in a Brucella strain isolated from an exotic frog. The POA1180 genome contains genes which may confer resistance to chromate and the ability to take up sulfate. Phage POI1126 is related to podoviruses of Sinorhizobium meliloti (PCB5), Erwinia pyrifoliae (Pep14), and Burkholderia cenocepacia (BcepIL02) and almost identical to an unnamed plasmid of the Ochrobactrum intermedium strain LMG 3301. Further experiments revealed that the POI1126 prophage indeed replicates as an extrachromosomal element. The data demonstrate for the first time that active prophages are common in Ochrobactrum and suggest that atypical brucellae also may be a reservoir for temperate phages.
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Affiliation(s)
- Claudia Jäckel
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Stefan Hertwig
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Holger C Scholz
- German Center for Infection Research, Bundeswehr Institute of MicrobiologyMunich, Germany
| | - Karsten Nöckler
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Jochen Reetz
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Jens A Hammerl
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
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37
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Gong Z, Wang M, Yang Q, Li Z, Xia J, Gao Y, Jiang Y, Meng X, Liu Z, Yang D, Zhang F, Shao H, Wang D. Isolation and Complete Genome Sequence of a Novel Pseudoalteromonas Phage PH357 from the Yangtze River Estuary. Curr Microbiol 2017; 74:832-839. [DOI: 10.1007/s00284-017-1244-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/01/2017] [Indexed: 10/19/2022]
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38
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Motlagh AM, Bhattacharjee AS, Coutinho FH, Dutilh BE, Casjens SR, Goel RK. Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses. Front Microbiol 2017; 8:352. [PMID: 28316597 PMCID: PMC5334351 DOI: 10.3389/fmicb.2017.00352] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/20/2017] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages, as the most abundant biological entities on Earth, place significant predation pressure on their hosts. This pressure plays a critical role in the evolution, diversity, and abundance of bacteria. In addition, phages modulate the genetic diversity of prokaryotic communities through the transfer of auxiliary metabolic genes. Various studies have been conducted in diverse ecosystems to understand phage-host interactions and their effects on prokaryote metabolism and community composition. However, hypersaline environments remain among the least studied ecosystems and the interaction between the phages and prokaryotes in these habitats is poorly understood. This study begins to fill this knowledge gap by analyzing bacteriophage-host interactions in the Great Salt Lake, the largest prehistoric hypersaline lake in the Western Hemisphere. Our metagenomics analyses allowed us to comprehensively identify the bacterial and phage communities with Proteobacteria, Firmicutes, and Bacteroidetes as the most dominant bacterial species and Siphoviridae, Myoviridae, and Podoviridae as the most dominant viral families found in the metagenomic sequences. We also characterized interactions between the phage and prokaryotic communities of Great Salt Lake and determined how these interactions possibly influence the community diversity, structure, and biogeochemical cycles. In addition, presence of prophages and their interaction with the prokaryotic host was studied and showed the possibility of prophage induction and subsequent infection of prokaryotic community present in the Great Salt Lake environment under different environmental stress factors. We found that carbon cycle was the most susceptible nutrient cycling pathways to prophage induction in the presence of environmental stresses. This study gives an enhanced snapshot of phage and prokaryote abundance and diversity as well as their interactions in a hypersaline complex ecosystem, which can pave the way for further research studies.
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Affiliation(s)
- Amir Mohaghegh Motlagh
- Department of Civil and Environmental Engineering, University of Utah Salt Lake, UT, USA
| | - Ananda S Bhattacharjee
- Department of Civil and Environmental Engineering, University of Utah Salt Lake, UT, USA
| | - Felipe H Coutinho
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil; Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics, Radboud University Medical CentreNijmegen, Netherlands
| | - Bas E Dutilh
- Instituto de Biologia, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil; Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics, Radboud University Medical CentreNijmegen, Netherlands; Theoretical Biology and Bioinformatics, Utrecht UniversityUtrecht, Netherlands
| | | | - Ramesh K Goel
- Department of Civil and Environmental Engineering, University of Utah Salt Lake, UT, USA
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Kallies R, Kiesel B, Schmidt M, Kacza J, Ghanem N, Narr A, Zopfi J, Wick LY, Hackermüller J, Harms H, Chatzinotas A. Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies. Stand Genomic Sci 2017; 12:20. [PMID: 28168014 PMCID: PMC5288847 DOI: 10.1186/s40793-017-0235-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 01/22/2017] [Indexed: 11/10/2022] Open
Abstract
Pseudoalteromonas phage vB_PspS-H40/1 is a lytic phage that infects Pseudoalteromonas sp. strain H40. Both, the phage and its host were isolated in the 1970s from seawater samples collected from the North Sea near the island of Helgoland, Germany. The phage particle has an icosahedral capsid with a diameter of ~43 to 45 nm and a long non-contractile tail of ~68 nm in length, a typical morphology for members of the Siphoviridae family. The linear dsDNA genome of Pseudoalteromonas phage vB_PspS-H40/1 has a sequence length of 45,306 bp and a GC content of 40.6%. The genome has a modular structure and contains a high proportion of sequence information for hypothetical proteins, typically seen in phage genome sequences. This is the first report of the complete genome sequence of this lytic phage, which has been frequently used since the 1990s as biological tracer in hydrogeological transport studies.
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Affiliation(s)
- René Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Bärbel Kiesel
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Matthias Schmidt
- Department of Isotope Biogeochemistry, ProVis - Centre for Chemical Microscopy, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Johannes Kacza
- Institute of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Nawras Ghanem
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Anja Narr
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Jakob Zopfi
- Department of Environmental Sciences - Aquatic and Stable Isotope Biogeochemistry, University of Basel, 4056 Basel, Switzerland
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Jörg Hackermüller
- Young Investigators Group Bioinformatics & Transcriptomics, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
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40
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Ghanem N, Kiesel B, Kallies R, Harms H, Chatzinotas A, Wick LY. Marine Phages As Tracers: Effects of Size, Morphology, and Physico-Chemical Surface Properties on Transport in a Porous Medium. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:12816-12824. [PMID: 27715020 DOI: 10.1021/acs.est.6b04236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Although several studies examined the transport of viruses in terrestrial systems only few studies exist on the use of marine phages (i.e., nonterrestrial viruses infecting marine host bacteria) as sensitively detectable microbial tracers for subsurface colloid transport and water flow. Here, we systematically quantified and compared for the first time the effects of size, morphology and physicochemical surface properties of six marine phages and two coliphages (MS2, T4) on transport in sand-filled percolated columns. Phage-sand interactions were described by colloidal filtration theory and the extended Derjaguin-Landau-Verwey-Overbeek approach (XDLVO), respectively. The phages belonged to different families and comprised four phages never used in transport studies (i.e., PSA-HM1, PSA-HP1, PSA-HS2, and H3/49). Phage transport was influenced by size, morphology and hydrophobicity in an approximate order of size > hydrophobicity ≥ morphology. Two phages PSA-HP1, PSA-HS2 (Podoviridae and Siphoviridae) exhibited similar mass recovery as commonly used coliphage MS2 and were 7-fold better transported than known marine phage vB_PSPS-H40/1. Differing properties of the marine phages may be used to trace transport of indigenous viruses, natural colloids or anthropogenic nanomaterials and, hence, contribute to better risk analysis. Our results underpin the potential role of marine phages as microbial tracer for transport of colloidal particles and water flow.
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Affiliation(s)
- Nawras Ghanem
- Helmholtz Centre for Environmental Research - UFZ , Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Bärbel Kiesel
- Helmholtz Centre for Environmental Research - UFZ , Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
| | - René Kallies
- Helmholtz Centre for Environmental Research - UFZ , Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Hauke Harms
- Helmholtz Centre for Environmental Research - UFZ , Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Antonis Chatzinotas
- Helmholtz Centre for Environmental Research - UFZ , Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research - UFZ , Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
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41
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Ahlgren NA, Ren J, Lu YY, Fuhrman JA, Sun F. Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences. Nucleic Acids Res 2016; 45:39-53. [PMID: 27899557 PMCID: PMC5224470 DOI: 10.1093/nar/gkw1002] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/31/2016] [Indexed: 01/17/2023] Open
Abstract
Viruses and their host genomes often share similar oligonucleotide frequency (ONF) patterns, which can be used to predict the host of a given virus by finding the host with the greatest ONF similarity. We comprehensively compared 11 ONF metrics using several k-mer lengths for predicting host taxonomy from among ∼32 000 prokaryotic genomes for 1427 virus isolate genomes whose true hosts are known. The background-subtracting measure [Formula: see text] at k = 6 gave the highest host prediction accuracy (33%, genus level) with reasonable computational times. Requiring a maximum dissimilarity score for making predictions (thresholding) and taking the consensus of the 30 most similar hosts further improved accuracy. Using a previous dataset of 820 bacteriophage and 2699 bacterial genomes, [Formula: see text] host prediction accuracies with thresholding and consensus methods (genus-level: 64%) exceeded previous Euclidian distance ONF (32%) or homology-based (22-62%) methods. When applied to metagenomically-assembled marine SUP05 viruses and the human gut virus crAssphage, [Formula: see text]-based predictions overlapped (i.e. some same, some different) with the previously inferred hosts of these viruses. The extent of overlap improved when only using host genomes or metagenomic contigs from the same habitat or samples as the query viruses. The [Formula: see text] ONF method will greatly improve the characterization of novel, metagenomic viruses.
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Affiliation(s)
- Nathan A Ahlgren
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy Los, Angeles, CA 90089, USA
| | - Jie Ren
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA
| | - Yang Young Lu
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy Los, Angeles, CA 90089, USA
| | - Fengzhu Sun
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy Los, Angeles, CA 90089, USA.,Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA.,Center for Computational Systems Biology, Fudan University, Shanghai 200433, China
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42
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Holmfeldt K, Solonenko N, Howard-Varona C, Moreno M, Malmstrom RR, Blow MJ, Sullivan MB. Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environ Microbiol 2016; 18:3949-3961. [PMID: 27235779 DOI: 10.1111/1462-2920.13392] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/21/2015] [Indexed: 01/21/2023]
Abstract
Microbes drive ecosystem functioning and their viruses modulate these impacts through mortality, gene transfer and metabolic reprogramming. Despite the importance of virus-host interactions and likely variable infection efficiencies of individual phages across hosts, such variability is seldom quantified. Here, we quantify infection efficiencies of 38 phages against 19 host strains in aquatic Cellulophaga (Bacteroidetes) phage-host model systems. Binary data revealed that some phages infected only one strain while others infected 17, whereas quantitative data revealed that efficiency of infection could vary 10 orders of magnitude, even among phages within one population. This provides a baseline for understanding and modeling intrapopulation host range variation. Genera specific host ranges were also informative. For example, the Cellulophaga Microviridae, showed a markedly broader intra-species host range than previously observed in Escherichia coli systems. Further, one phage genus, Cba41, was examined to investigate nonheritable changes in plating efficiency and burst size that depended on which host strain it most recently infected. While consistent with host modification of phage DNA, no differences in nucleotide sequence or DNA modifications were detected, leaving the observation repeatable, but the mechanism unresolved. Overall, this study highlights the importance of quantitatively considering replication variations in studies of phage-host interactions.
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Affiliation(s)
- Karin Holmfeldt
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.,Department of Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Natalie Solonenko
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | - Mario Moreno
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | | | - Matthew B Sullivan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
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43
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Perez Sepulveda B, Redgwell T, Rihtman B, Pitt F, Scanlan DJ, Millard A. Marine phage genomics: the tip of the iceberg. FEMS Microbiol Lett 2016; 363:fnw158. [PMID: 27338950 PMCID: PMC4928673 DOI: 10.1093/femsle/fnw158] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 01/07/2023] Open
Abstract
Marine viruses are the most abundant biological entity in the oceans, the majority of which infect bacteria and are known as bacteriophages. Yet, the bulk of bacteriophages form part of the vast uncultured dark matter of the microbial biosphere. In spite of the paucity of cultured marine bacteriophages, it is known that marine bacteriophages have major impacts on microbial population structure and the biogeochemical cycling of key elements. Despite the ecological relevance of marine bacteriophages, there are relatively few isolates with complete genome sequences. This minireview focuses on knowledge gathered from these genomes put in the context of viral metagenomic data and highlights key advances in the field, particularly focusing on genome structure and auxiliary metabolic genes. Only a tiny fraction of marine phages have been discovered, yet are known to have important roles in the ocean.
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Affiliation(s)
| | - Tamsin Redgwell
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Branko Rihtman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Frances Pitt
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Andrew Millard
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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44
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Rihtman B, Meaden S, Clokie MRJ, Koskella B, Millard AD. Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes. PeerJ 2016; 4:e2055. [PMID: 27280068 PMCID: PMC4893331 DOI: 10.7717/peerj.2055] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 04/29/2016] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages are the most abundant biological entities on the planet, playing crucial roles in the shaping of bacterial populations. Phages have smaller genomes than their bacterial hosts, yet there are currently fewer fully sequenced phage than bacterial genomes. We assessed the suitability of Illumina technology for high-throughput sequencing and subsequent assembly of phage genomes. In silico datasets reveal that 30× coverage is sufficient to correctly assemble the complete genome of ~98.5% of known phages, with experimental data confirming that the majority of phage genomes can be assembled at 30× coverage. Furthermore, in silico data demonstrate it is possible to co-sequence multiple phages from different hosts, without introducing assembly errors.
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Affiliation(s)
- Branko Rihtman
- School of Life Sciences, University of Warwick , Coventry , United Kingdom
| | - Sean Meaden
- College of Life and Environmental Sciences, University of Exeter , United Kingdom
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester
| | - Britt Koskella
- College of Life and Environmental Sciences, University of Exeter, United Kingdom; Department of Integrative Biology, University of California, Berkeley, California, United States
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45
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Daniel ADC, Pedrós-Alió C, Pearce DA, Alcamí A. Composition and Interactions among Bacterial, Microeukaryotic, and T4-like Viral Assemblages in Lakes from Both Polar Zones. Front Microbiol 2016; 7:337. [PMID: 27047459 PMCID: PMC4796948 DOI: 10.3389/fmicb.2016.00337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/03/2016] [Indexed: 02/01/2023] Open
Abstract
In this study we assess global biogeography and correlation patterns among three components of microbial life: bacteria, microeukaryotes, and T4-like myoviruses. In addition to environmental and biogeographical considerations, we have focused our study on samples from high-latitude pristine lakes from both poles, since these simple island-like ecosystems represent ideal ecological models to probe the relationships among microbial components and with the environment. Bacterial assemblages were dominated by members of the same groups found to dominate freshwater ecosystems elsewhere, and microeukaryotic assemblages were dominated by photosynthetic microalgae. Despite inter-lake variations in community composition, the overall percentages of OTUs shared among sites was remarkable, indicating that many microeukaryotic, bacterial, and viral OTUs are globally-distributed. We observed an intriguing negative correlation between bacterial and microeukaryotic diversity values. Notably, our analyses show significant global correlations between bacterial and microeukaryotic community structures, and between the phylogenetic compositions of bacterial and T4-like virus assemblages. Overall, environmental filtering emerged as the main factor driving community structures.
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Affiliation(s)
- Aguirre de Cárcer Daniel
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid Madrid, Spain
| | | | - David A Pearce
- British Antarctic Survey, Natural Environment Research CouncilCambridge, UK; Faculty of Health and Life Sciences, University of NorthumbriaNewcastle Upon Tyne, UK; University Center in SvalbardLonyearbyen, Norway
| | - Antonio Alcamí
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid Madrid, Spain
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46
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Six Pseudoalteromonas Strains Isolated from Surface Waters of Kabeltonne, Offshore Helgoland, North Sea. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01697-15. [PMID: 26868390 PMCID: PMC4751314 DOI: 10.1128/genomea.01697-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Draft genomes are presented for 6 Pseudoalteromonas sp. strains isolated from surface waters at Kabeltonne, Helgoland, a long-term ecological research station in the North Sea. These strains contribute knowledge of the genomic underpinnings of a developing model system to study phage-host dynamics of a particle-associated ocean copiotroph.
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47
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Edlund A, Santiago-Rodriguez TM, Boehm TK, Pride DT. Bacteriophage and their potential roles in the human oral cavity. J Oral Microbiol 2015; 7:27423. [PMID: 25861745 PMCID: PMC4393417 DOI: 10.3402/jom.v7.27423] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/11/2015] [Accepted: 03/13/2015] [Indexed: 12/26/2022] Open
Abstract
The human oral cavity provides the perfect portal of entry for viruses and bacteria in the environment to access new hosts. Hence, the oral cavity is one of the most densely populated habitats of the human body containing some 6 billion bacteria and potentially 35 times that many viruses. The role of these viral communities remains unclear; however, many are bacteriophage that may have active roles in shaping the ecology of oral bacterial communities. Other implications for the presence of such vast oral phage communities include accelerating the molecular diversity of their bacterial hosts as both host and phage mutate to gain evolutionary advantages. Additional roles include the acquisitions of new gene functions through lysogenic conversions that may provide selective advantages to host bacteria in response to antibiotics or other types of disturbances, and protection of the human host from invading pathogens by binding to and preventing pathogens from crossing oral mucosal barriers. Recent evidence suggests that phage may be more involved in periodontal diseases than were previously thought, as their compositions in the subgingival crevice in moderate to severe periodontitis are known to be significantly altered. However, it is unclear to what extent they contribute to dysbiosis or the transition of the microbial community into a state promoting oral disease. Bacteriophage communities are distinct in saliva compared to sub- and supragingival areas, suggesting that different oral biogeographic niches have unique phage ecology shaping their bacterial biota. In this review, we summarize what is known about phage communities in the oral cavity, the possible contributions of phage in shaping oral bacterial ecology, and the risks to public health oral phage may pose through their potential to spread antibiotic resistance gene functions to close contacts.
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Affiliation(s)
- Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA.,School of Dentistry, University of California, Los Angeles, CA, USA
| | | | - Tobias K Boehm
- Western University College of Dental Medicine, Pomona, CA, USA
| | - David T Pride
- Department of Pathology, University of California, San Diego, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA;
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48
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Yu ZC, Chen XL, Shen QT, Zhao DL, Tang BL, Su HN, Wu ZY, Qin QL, Xie BB, Zhang XY, Yu Y, Zhou BC, Chen B, Zhang YZ. Filamentous phages prevalent in Pseudoalteromonas spp. confer properties advantageous to host survival in Arctic sea ice. ISME JOURNAL 2015; 9:871-81. [PMID: 25303713 PMCID: PMC4817708 DOI: 10.1038/ismej.2014.185] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 12/30/2022]
Abstract
Sea ice is one of the most frigid environments for marine microbes. In contrast to other ocean ecosystems, microbes in permanent sea ice are space confined and subject to many extreme conditions, which change on a seasonal basis. How these microbial communities are regulated to survive the extreme sea ice environment is largely unknown. Here, we show that filamentous phages regulate the host bacterial community to improve survival of the host in permanent Arctic sea ice. We isolated a filamentous phage, f327, from an Arctic sea ice Pseudoalteromonas strain, and we demonstrated that this type of phage is widely distributed in Arctic sea ice. Growth experiments and transcriptome analysis indicated that this phage decreases the host growth rate, cell density and tolerance to NaCl and H2O2, but enhances its motility and chemotaxis. Our results suggest that the presence of the filamentous phage may be beneficial for survival of the host community in sea ice in winter, which is characterized by polar night, nutrient deficiency and high salinity, and that the filamentous phage may help avoid over blooming of the host in sea ice in summer, which is characterized by polar day, rich nutrient availability, intense radiation and high concentration of H2O2. Thus, while they cannot kill the host cells by lysing them, filamentous phages confer properties advantageous to host survival in the Arctic sea ice environment. Our study provides a foremost insight into the ecological role of filamentous phages in the Arctic sea ice ecosystem.
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Affiliation(s)
- Zi-Chao Yu
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan, China [2] Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Xiu-Lan Chen
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan, China [2] Marine Biotechnology Research Center, Shandong University, Jinan, China [3] Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China
| | - Qing-Tao Shen
- Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Dian-Li Zhao
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan, China [2] Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Bai-Lu Tang
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan, China [2] Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Hai-Nan Su
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan, China [2] Marine Biotechnology Research Center, Shandong University, Jinan, China [3] Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China
| | - Zhao-Yu Wu
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan, China [2] Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Qi-Long Qin
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan, China [2] Marine Biotechnology Research Center, Shandong University, Jinan, China [3] Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China
| | - Bin-Bin Xie
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan, China [2] Marine Biotechnology Research Center, Shandong University, Jinan, China [3] Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China
| | - Xi-Ying Zhang
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan, China [2] Marine Biotechnology Research Center, Shandong University, Jinan, China [3] Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Yu-Zhong Zhang
- 1] State Key Laboratory of Microbial Technology, Shandong University, Jinan, China [2] Marine Biotechnology Research Center, Shandong University, Jinan, China [3] Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China
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Lara E, Holmfeldt K, Solonenko N, Sà EL, Ignacio-Espinoza JC, Cornejo-Castillo FM, Verberkmoes NC, Vaqué D, Sullivan MB, Acinas SG. Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the northwestern Mediterranean Sea. PLoS One 2015; 10:e0114829. [PMID: 25587991 PMCID: PMC4294664 DOI: 10.1371/journal.pone.0114829] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 11/14/2014] [Indexed: 11/18/2022] Open
Abstract
Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new ‘rare virosphere’ phage–host model system.
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Affiliation(s)
- Elena Lara
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Karin Holmfeldt
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Natalie Solonenko
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Elisabet Laia Sà
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - J. Cesar Ignacio-Espinoza
- University of Arizona, Department of Molecular and Cellular Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Francisco M. Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Nathan C. Verberkmoes
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Matthew B. Sullivan
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
- University of Arizona, Department of Molecular and Cellular Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Silvia G. Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
- * E-mail:
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Richards GP. Bacteriophage remediation of bacterial pathogens in aquaculture: a review of the technology. BACTERIOPHAGE 2014; 4:e975540. [PMID: 26713223 PMCID: PMC4590005 DOI: 10.4161/21597081.2014.975540] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/03/2014] [Accepted: 10/07/2014] [Indexed: 11/19/2022]
Abstract
Bacteriophages have been proposed as an alternative to antibiotic usage and several studies on their application in aquaculture have been reported. This review highlights progress to date on phage therapies for the following fish and shellfish diseases and associated pathogens: hemorrhagic septicemia (Aeromonas hydrophila) in loaches, furunculosis (Aeromonas salmonicida) in trout and salmon, edwardsiellosis (Edwardsiella tarda) in eel, columnaris disease (Flavobacterium columnare) in catfish, rainbow trout fry syndrome or cold water disease (Flavobacterium psychrophilum) in trout and salmon, lactococcosis (Lactococcus spp.) in yellowtail, ulcerative skin lesions (Pseudomonas aeruginosa) in freshwater catfish, bacterial hemorrhagic ascites disease (Pseudomonas plecoglossicida) in ayu fish, streptococcosis (Streptococcus iniae) in flounder, and luminescent vibriosis (Vibrio harveyi) in shrimp. Information is reviewed on phage specificity, host resistance, routes of administration, and dosing of fish and shellfish. Limitations in phage research are described and recommended guidelines are provided for conducting future phage studies involving fish and shellfish.
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Affiliation(s)
- Gary P Richards
- United States Department of Agriculture; Agricultural Research Service; Delaware State University ; Dover, DE USA
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