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Xiong W, Liu B, Lu H, Liu X. Two novel bacteriophages isolated from the environment that can help control activated sludge foaming. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01145-4. [PMID: 38363443 DOI: 10.1007/s12223-024-01145-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
Nocardia spp., which belongs to one of the Nocardio-form filamentous bacteria, is usually surface hydrophobic and when overproduced attaches to the surface of bubbles under the action of surfactants, allowing the stable presence of foam on the surface of aeration tanks, leading to the occurrence of sludge-foaming events. Two novel phages, P69 and KYD2, were isolated from the environment, and their hosts were Nocardia transvalensis and Nocardia carnea, respectively. These two phages are Siphophages-like with long tails. An aeration tank pilot plant was constructed in the laboratory to simulate sludge foaming, and these two strains of phage were applied. Compared with the reactor not dosed with phage, the application of phage could reduce the host level in the reactor, resulting in the highest decrease in turbidity by more than 68% and sludge volume index by more than 25%. The time for surface foam disappearance was 9 h earlier than that of the control group (the group with the same concentration of Nocardia carnea but no bacteriophage applied), significantly improving water quality. The phage can effectively inhibit the propagation of Nocardia in the actual sludge-foaming event, control the sludge foaming, and improve the effluent quality. It provides a novel and relatively economical solution for controlling sludge foaming in sewage treatment plants in the future, shows that the phages have potential application value in the prevention and control of Nocardia, and provides another way to control the sludge-foaming event caused by the excessive reproduction of Nocardia in the future.
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Affiliation(s)
- Wenbin Xiong
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Bingxin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Han Lu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China.
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou, Shandong Province, 256606, China.
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2
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Howell AA, Versoza CJ, Pfeifer SP. Computational host range prediction-The good, the bad, and the ugly. Virus Evol 2023; 10:vead083. [PMID: 38361822 PMCID: PMC10868548 DOI: 10.1093/ve/vead083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 02/17/2024] Open
Abstract
The rapid emergence and spread of antimicrobial resistance across the globe have prompted the usage of bacteriophages (i.e. viruses that infect bacteria) in a variety of applications ranging from agriculture to biotechnology and medicine. In order to effectively guide the application of bacteriophages in these multifaceted areas, information about their host ranges-that is the bacterial strains or species that a bacteriophage can successfully infect and kill-is essential. Utilizing sixteen broad-spectrum (polyvalent) bacteriophages with experimentally validated host ranges, we here benchmark the performance of eleven recently developed computational host range prediction tools that provide a promising and highly scalable supplement to traditional, but laborious, experimental procedures. We show that machine- and deep-learning approaches offer the highest levels of accuracy and precision-however, their predominant predictions at the species- or genus-level render them ill-suited for applications outside of an ecosystems metagenomics framework. In contrast, only moderate sensitivity (<80 per cent) could be reached at the strain-level, albeit at low levels of precision (<40 per cent). Taken together, these limitations demonstrate that there remains room for improvement in the active scientific field of in silico host prediction to combat the challenge of guiding experimental designs to identify the most promising bacteriophage candidates for any given application.
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Affiliation(s)
| | - Cyril J Versoza
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Susanne P Pfeifer
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
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3
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Abdelsattar AS, Eita MA, Hammouda ZK, Gouda SM, Hakim TA, Yakoup AY, Safwat A, El-Shibiny A. The Lytic Activity of Bacteriophage ZCSE9 against Salmonella enterica and Its Synergistic Effects with Kanamycin. Viruses 2023; 15:v15040912. [PMID: 37112892 PMCID: PMC10142335 DOI: 10.3390/v15040912] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Salmonella, the causative agent of several diseases in humans and animals, including salmonellosis, septicemia, typhoid fever, and fowl typhoid, poses a serious threat to global public health and food safety. Globally, reports of therapeutic failures are increasing because of the increase in bacterial antibiotic resistance. Thus, this work highlights the combined phage–antibiotic therapy as a promising approach to combating bacterial resistance. In this manner, the phage ZCSE9 was isolated, and the morphology, host infectivity, killing curve, combination with kanamycin, and genome analysis of this phage were all examined. Morphologically, phage ZCSE9 is a siphovirus with a relatively broad host range. In addition, the phage can tolerate high temperatures until 80 °C with one log reduction and a basic environment (pH 11) without a significant decline. Furthermore, the phage prevents bacterial growth in the planktonic state, according to the results of the time-killing curve. Moreover, using the phage at MOI 0.1 with kanamycin against five different Salmonella serotypes reduces the required antibiotics to inhibit the growth of the bacteria. Comparative genomics and phylogenetic analysis suggested that phage ZCSE9, along with its close relatives Salmonella phages vB_SenS_AG11 and wksl3, belongs to the genus Jerseyvirus. In conclusion, phage ZCSE9 and kanamycin form a robust heterologous antibacterial combination that enhances the effectiveness of a phage-only approach for combating Salmonella.
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Affiliation(s)
- Abdallah S. Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Mohamed Atef Eita
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Zainab K. Hammouda
- Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 11787, Egypt
| | - Shrouk Mohamed Gouda
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Toka A. Hakim
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Aghapy Yermans Yakoup
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Anan Safwat
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt
- Faculty of Environmental Agricultural Sciences, Arish University, Arish 45511, Egypt
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4
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Shivaram KB, Bhatt P, Applegate B, Simsek H. Bacteriophage-based biocontrol technology to enhance the efficiency of wastewater treatment and reduce targeted bacterial biofilms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160723. [PMID: 36496019 DOI: 10.1016/j.scitotenv.2022.160723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/13/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Wastewater treatment is an essential process for public health and a sustainable ecosystem. Inadequate wastewater treatment can lead to the release of organic and inorganic pollutants and pathogenic bacteria into the receiving waters which could be further utilized for recreation purposes. The interaction between bacteriophage and bacteria in a wastewater treatment plant plays a major role in maintaining the treatment process. Phage therapy has been proposed as an alternative to conventional treatment methods as bacteriophages can be used on specific targets and leave useful bacteria unharmed. The bacterial species, which are responsible for bulking, foaming, and biofilm formation in a wastewater treatment plant (WWTP) have been identified and their respective phages are isolated to control their growth. Phages with lytic life cycles are preferred to lysogenic. Lytic phages can kill the specific target as they lyse the cell, infect most of the hosts, and have an immediate effect on controlling problems caused by bacteria in a WWTP. The bacteriophages such as T7, SPI1, GTE7, PhaxI, MAG1, MAG2, ϕPh_Se01, ϕPh_Se02, and Bxb1 have been investigated for the removal of bacterial biofilms from wastewater. Novel experimental setups have improved the efficiency of phage therapy in small-scale and pilot-scale experiments. Much more in-depth knowledge of the microbial community and their interaction would help promote the usage of phage therapy in large-scale wastewater treatments. This paper has covered the recent advancements in phage therapy as an effective biocontrol of pathogenic bacteria in the wastewater treatment process and has looked at certain shortcomings that have to be improved.
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Affiliation(s)
- Karthik Basthi Shivaram
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Pankaj Bhatt
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Bruce Applegate
- Department of Food Science, Purdue University, West Lafayette, IN 47906, USA
| | - Halis Simsek
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA.
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5
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Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions. Microorganisms 2023; 11:microorganisms11010170. [PMID: 36677462 PMCID: PMC9863963 DOI: 10.3390/microorganisms11010170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Bacteriophages are being widely harnessed as an alternative to antibiotics due to the global emergence of drug-resistant pathogens. To guide the usage of these bactericidal agents, characterization of their host specificity is vital-however, host range information remains limited for many bacteriophages. This is particularly the case for bacteriophages infecting the Microbacterium genus, despite their importance in agriculture, biomedicine, and biotechnology. Here, we elucidate the phylogenomic relationships between 125 Microbacterium cluster EA bacteriophages-including members from 11 sub-clusters (EA1 to EA11)-and infer their putative host ranges using insights from codon usage bias patterns as well as predictions from both exploratory and confirmatory computational methods. Our computational analyses suggest that cluster EA bacteriophages have a shared infection history across the Microbacterium clade. Interestingly, bacteriophages of all sub-clusters exhibit codon usage preference patterns that resemble those of bacterial strains different from ones used for isolation, suggesting that they might be able to infect additional hosts. Furthermore, host range predictions indicate that certain sub-clusters may be better suited in prospective biotechnological and medical applications such as phage therapy.
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6
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Genome Sequences of Gordonia Phages GrootJr and NovumRegina. Microbiol Resour Announc 2022; 11:e0070322. [DOI: 10.1128/mra.00703-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Two
Gordonia
bacteriophages, GrootJr and NovumRegina, were discovered, sequenced, and annotated. These phages were isolated from distinct soil and water samples, respectively, on
Gordonia terrae
3612. These phages belong to the CR2 subcluster and are similar in genome size and gene content.
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Genome Sequence of a Cluster CR2 Gordonia terrae Phage, StarStruck. Microbiol Resour Announc 2022; 11:e0069422. [PMID: 36040147 PMCID: PMC9583778 DOI: 10.1128/mra.00694-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Bacteriophage StarStruck is a lytic Siphoviridae phage that infects Gordonia terrae 3612. The 68,128-bp genome of StarStruck has a GC content of 65.4% and contains 92 protein-coding genes, including the gene for a HicA-like toxin. StarStruck was assigned to subcluster CR2 based on >35% shared gene content with other cluster CR genomes in the Actinobacteriophage Database.
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8
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Minimizing Foaming and Bulking in Activated Sludge with Bacteriophage Treatment: A Review of Mathematical Modeling. Processes (Basel) 2022. [DOI: 10.3390/pr10081600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The interest in the ability of phages to control bacterial populations has extended from medical applications into the fields of agriculture, aquaculture, and the food industry. In particular, several authors have proposed using bacteriophages as an alternative method to control foaming and bulking in wastewater treatment. This strategy has shown successful results at the laboratory scale. However, this technology is still in development, and there are several challenges to overcome before bacteriophages can be widely used to control foaming and bulking in pilot or larger-scale treatment plants. Several models of the infection mechanisms in individual bacteria–phage pairs have been reported, i.e., for controlled systems with only one bacterium species in the presence of one phage species. However, activated sludge treatment systems largely differ from this situation, which opens a large horizon for future research. Mathematical models will play a key role in this development process, and this review offers an overview of the proposed models: their applications, potential, and challenges. A particular focus is placed on the model properties, such as parameter identifiability and states’ observability, which are essential for process prediction, monitoring, or dynamic optimization.
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9
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Versoza CJ, Howell AA, Aftab T, Blanco M, Brar A, Chaffee E, Howell N, Leach W, Lobatos J, Luca M, Maddineni M, Mirji R, Mitra C, Strasser M, Munig S, Patel Z, So M, Sy M, Weiss S, Pfeifer SP. Comparative Genomics of Closely-Related Gordonia Cluster DR Bacteriophages. Viruses 2022; 14:v14081647. [PMID: 36016269 PMCID: PMC9413003 DOI: 10.3390/v14081647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/16/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
Bacteriophages infecting bacteria of the genus Gordonia have increasingly gained interest in the scientific community for their diverse applications in agriculture, biotechnology, and medicine, ranging from biocontrol agents in wastewater management to the treatment of opportunistic pathogens in pulmonary disease patients. However, due to the time and costs associated with experimental isolation and cultivation, host ranges for many bacteriophages remain poorly characterized, hindering a more efficient usage of bacteriophages in these areas. Here, we perform a series of computational genomic inferences to predict the putative host ranges of all Gordonia cluster DR bacteriophages known to date. Our analyses suggest that BiggityBass (as well as several of its close relatives) is likely able to infect host bacteria from a wide range of genera—from Gordonia to Nocardia to Rhodococcus, making it a suitable candidate for future phage therapy and wastewater treatment strategies.
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Affiliation(s)
- Cyril J. Versoza
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Abigail A. Howell
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Tanya Aftab
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Madison Blanco
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Akarshi Brar
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Elaine Chaffee
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Nicholas Howell
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Willow Leach
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Jackelyn Lobatos
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Michael Luca
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Meghna Maddineni
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Ruchira Mirji
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Corinne Mitra
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Maria Strasser
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Saige Munig
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Zeel Patel
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Minerva So
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Makena Sy
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Sarah Weiss
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (T.A.); (M.B.); (A.B.); (E.C.); (N.H.); (J.L.); (M.L.); (R.M.); (C.M.); (M.S.); (S.M.); (Z.P.); (M.S.); (M.S.); (S.W.)
| | - Susanne P. Pfeifer
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
- Correspondence:
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10
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Abstract
Mycobacteriophages-bacteriophages infecting Mycobacterium hosts-contribute substantially to our understanding of viral diversity and evolution, provide resources for advancing Mycobacterium genetics, are the basis of high-impact science education programs, and show considerable therapeutic potential. Over 10,000 individual mycobacteriophages have been isolated by high school and undergraduate students using the model organism Mycobacterium smegmatis mc2155 and 2,100 have been completely sequenced, giving a high-resolution view of the phages that infect a single common host strain. The phage genomes are revealed to be highly diverse and architecturally mosaic and are replete with genes of unknown function. Mycobacteriophages have provided many widely used tools for Mycobacterium genetics including integration-proficient vectors and recombineering systems, as well as systems for efficient delivery of reporter genes, transposons, and allelic exchange substrates. The genomic insights and engineering tools have facilitated exploration of phages for treatment of Mycobacterium infections, although their full therapeutic potential has yet to be realized.
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11
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Petrovski S, Batinovic S, Rose JJ, Seviour RJ. Biological control of problem bacterial populations causing foaming in activated sludge wastewater treatment plants - phage therapy and beyond. Lett Appl Microbiol 2022; 75:776-784. [PMID: 35598184 DOI: 10.1111/lam.13742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
The production of a stable foam on the surfaces of reactors is a global operating problem in activated sludge plants. In many cases these foams are stabilized by hydrophobic members of the Mycolata, a group of Actinobacteria whose outer membranes contains long chain hydroxylated mycolic acids. There is currently no single strategy which works for all foams. One attractive approach is to use lytic bacteriophages specific for the foam stabilizing Mycolata population. Such phages are present in activated sludge mixed liquor, and can be recovered readily from it. However, no phage has been recovered which lyses Gordonia amarae and Gordonia pseudoamarae, probably the most common foaming Mycolata members. Whole genome sequencing revealed that both G. amarae and G. pseudoamarae from plants around the world are particularly well endowed with genes encoding anti-viral defence mechanisms. However, both these populations were lysed rapidly by a parasitic nanobacterium isolated from a plant in Australia. This organism, a member of the Saccharibacteria was also effective against many other Mycolata, thus providing a potential agent for control of foams stabilized by them.
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Affiliation(s)
- Steve Petrovski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Steven Batinovic
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Jayson Ja Rose
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
| | - Robert J Seviour
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, 3086, Victoria, Australia
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12
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Abstract
Actinobacteriophages are viruses that infect bacterial hosts in the phylum Actinobacteria. More than 17,000 actinobacteriophages have been described and over 3,000 complete genome sequences reported, resulting from large-scale, high-impact, integrated research-education initiatives such as the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) program. Their genomic diversity is enormous; actinobacteriophages comprise many architecturally mosaic genomes with distinct DNA sequences. Their genome diversity is driven by the highly dynamic interactions between phages and their hosts, and prophages can confer a variety of systems that defend against attack by genetically distinct phages; phages can neutralize these defense systems by coding for counter-defense proteins. These phages not only provide insights into diverse and dynamic phage populations but also have provided numerous tools for mycobacterial genetics. A case study using a three-phage cocktail to treat a patient with a drug-resistant Mycobacterium abscessus suggests that phages may have considerable potential for the therapeutic treatment of mycobacterial infections.
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Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA;
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13
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Batinovic S, Rose JJA, Ratcliffe J, Seviour RJ, Petrovski S. Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams. Nat Microbiol 2021; 6:703-711. [PMID: 33927381 DOI: 10.1038/s41564-021-00892-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 03/22/2021] [Indexed: 02/02/2023]
Abstract
Many wastewater treatment plants around the world suffer from the operational problem of foaming. This is characterized by a persistent stable foam that forms on the aeration basin, which reduces effluent quality. The foam is often stabilized by a highly hydrophobic group of Actinobacteria known as the Mycolata1. Gordonia amarae is one of the most frequently reported foaming members1. With no currently reliable method for treating foams, phage biocontrol has been suggested as an attractive treatment strategy2. Phages isolated from related foaming bacteria can destabilize foams at the laboratory scale3,4; however, no phage has been isolated that lyses G. amarae. Here, we assemble the complete genomes of G. amarae and a previously undescribed species, Gordonia pseudoamarae, to examine mechanisms that encourage stable foam production. We show that both of these species are recalcitrant to phage infection via a number of antiviral mechanisms including restriction, CRISPR-Cas and bacteriophage exclusion. Instead, we isolate and cocultivate an environmental ultrasmall epiparasitic bacterium from the phylum Saccharibacteria that lyses G. amarae and G. pseudoamarae and several other Mycolata commonly associated with wastewater foams. The application of this parasitic bacterium, 'Candidatus Mycosynbacter amalyticus', may represent a promising strategy for the biocontrol of bacteria responsible for stabilizing wastewater foams.
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Affiliation(s)
- Steven Batinovic
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Jayson J A Rose
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Julian Ratcliffe
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Robert J Seviour
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia.
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14
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Genome Sequences of Microviruses Identified in a Sample from a Sewage Treatment Oxidation Pond. Microbiol Resour Announc 2021; 10:10/19/e00373-21. [PMID: 33986100 PMCID: PMC8142586 DOI: 10.1128/mra.00373-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Oxidation ponds are often used in the treatment of sewage as an aeration step prior to discharge. We identified 99 microvirus genomes from a sample from a sewage oxidation pond. This diverse group of microviruses expands our knowledge of bacteriophages associated with sewage oxidation pond ecosystems. Oxidation ponds are often used in the treatment of sewage as an aeration step prior to discharge. We identified 99 microvirus genomes from a sample from a sewage oxidation pond. This diverse group of microviruses expands our knowledge of bacteriophages associated with sewage oxidation pond ecosystems.
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15
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Ferreira R, Amado R, Padrão J, Ferreira V, Dias NM, Melo LDR, Santos SB, Nicolau A. The first sequenced Sphaerotilus natans bacteriophage- characterization and potential to control its filamentous bacterium host. FEMS Microbiol Ecol 2021; 97:6136272. [PMID: 33587121 DOI: 10.1093/femsec/fiab029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 02/12/2021] [Indexed: 01/01/2023] Open
Abstract
Bacteriophages (phages) are ubiquitous entities present in every conceivable habitat as a result of their bacterial parasitism. Their prevalence and impact in the ecology of bacterial communities and their ability to control pathogens make their characterization essential, particularly of new phages, improving knowledge and potential application. The isolation and characterization of a new lytic phage against Sphaerotilus natans strain DSM 6575, named vB_SnaP-R1 (SnaR1), is here described. Besides being the first sequenced genome of a Sphaerotilus natans infecting phage, 99% of its 41507 bp genome lacks homology with any other sequenced phage, revealing its uniqueness and previous lack of knowledge. Moreover, SnaR1 is the first Podoviridae phage described infecting this bacterium. Sphaerotilus natans is an important filamentous bacterium due to its deleterious effect on wastewater treatment plants (WWTP) and thus, phages may play a role as novel biotechnological tools against filamentous overgrowth in WWTP. The lytic spectrum of SnaR1 was restricted to its host strain, infecting only one out of three S. natans strains and infection assays revealed its ability to reduce bacterial loads. Results suggest SnaR1 as the prototype of a new phage genus and demonstrates its potential as a non-chemical alternative to reduce S. natans DSM 6575 cells.
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Affiliation(s)
- Rute Ferreira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Rui Amado
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Jorge Padrão
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Vânia Ferreira
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Nicolina M Dias
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Luís D R Melo
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Sílvio B Santos
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ana Nicolau
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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16
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Characterization of Novel Lytic Bacteriophages of Achromobacter marplantensis Isolated from a Pneumonia Patient. Viruses 2020; 12:v12101138. [PMID: 33049935 PMCID: PMC7600146 DOI: 10.3390/v12101138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 01/21/2023] Open
Abstract
Achromobacter spp. are becoming increasingly associated with lung infections in patients suffering from cystic fibrosis (CF). A. marplatensis, which is closely related to A. xylosoxidans, has been isolated from the lungs of CF patients and other human infections. This article describes the isolation, morphology and characterization of two lytic bacteriophages specific for an A. marplatensis strain isolated from a pneumonia patient. This host strain was the causal agent of hospital acquired pneumonia–the first clinical report of such an occurrence. Full genome sequencing revealed bacteriophage genomes ranging in size from 45901 to 46,328 bp. Transmission electron microscopy revealed that the two bacteriophages AMA1 and AMA2 belonged to the Siphoviridae family. Host range analysis showed that their host range did not extend to A. xylosoxidans. The possibility exists for future testing of such bacteriophages in the control of Achromobacter infections such as those seen in CF and other infections of the lungs. The incidence of antibiotic resistance in this genus highlights the importance of seeking adjuncts and alternatives in CF and other lung infections.
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17
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Oliveira SR, Castelhano J, Sereno J, Vieira HLA, Duarte CB, Castelo-Branco M. Response of the cerebral vasculature to systemic carbon monoxide administration-Regional differences and sexual dimorphism. Eur J Neurosci 2020; 52:2771-2780. [PMID: 32168385 DOI: 10.1111/ejn.14725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 02/22/2020] [Accepted: 02/29/2020] [Indexed: 01/18/2023]
Abstract
Previous studies about the modulation of the vasculature by CO were performed exclusively in male or sexually immature animals. Understanding the sex differences regarding systemic drug processing and pharmacodynamics is an important feature for safety assessment of drug dosing and efficacy. In this work, we used CORM-A1 as source of CO to examine the effects of this gasotransmitter on brain perfusion and the sex-dependent differences. Dynamic contrast-enhanced imaging (DCE)-based analysis was used to characterize the properties of CO in the modulation of cerebral vasculature in vivo, in adult C57BL/6 healthy mice. Perfusion of the temporal muscle, maxillary vein and in hippocampus, cortex and striatum was analysed for 108 min following CORM-A1 administration of 3 or 5 mg/kg. Under control conditions, brain perfusion was lower in females when compared with males. Under CO treatment, females showed a surprisingly overall reduced perfusion compared with controls (F = 3.452, p = .0004), while no major alterations (or even the expected increase) were observed in males. Cortical structures were only modulated in females. A striking female-dominated vasoconstriction effect was observed in the hippocampus and striatum following administration of CO, in this mixed-sex cohort. As these two regions are implicated in episodic and procedural memory formation, CO may have a relevant impact in learning and memory.
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Affiliation(s)
- Sara R Oliveira
- CNC-Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal.,CEDOC, Chronic Diseases Research Centre, NOVA Medical School/Faculdade de Ciência Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - João Castelhano
- CIBIT, Coimbra Institute for Biomedical Imaging and Life Sciences, ICNAS, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - José Sereno
- CIBIT, Coimbra Institute for Biomedical Imaging and Life Sciences, ICNAS, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Helena L A Vieira
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School/Faculdade de Ciência Médicas, Universidade Nova de Lisboa, Lisboa, Portugal.,Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,UCIBIO, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Carlos B Duarte
- CNC-Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.,Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Miguel Castelo-Branco
- CIBIT, Coimbra Institute for Biomedical Imaging and Life Sciences, ICNAS, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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18
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Abstract
Mycobacteriophages are viruses that infect mycobacterial hosts. A large number of mycobacteriophages have been isolated and genomically characterized, providing insights into viral diversity and evolution, as well as fueling development of tools for mycobacterial genetics. Mycobacteriophages have intimate relationships with their hosts and provide insights into the genetics and physiology of the mycobacteria and tools for potential clinical applications such as drug development, diagnosis, vaccines, and potentially therapy.
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19
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Pascelli C, Laffy PW, Kupresanin M, Ravasi T, Webster NS. Morphological characterization of virus-like particles in coral reef sponges. PeerJ 2018; 6:e5625. [PMID: 30356950 PMCID: PMC6195793 DOI: 10.7717/peerj.5625] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/22/2018] [Indexed: 12/03/2022] Open
Abstract
Marine sponges host complex microbial consortia that vary in their abundance, diversity and stability amongst host species. While our understanding of sponge-microbe interactions has dramatically increased over the past decade, little is known about how sponges and their microbial symbionts interact with viruses, the most abundant entities in the ocean. In this study, we employed three transmission electron microscopy (TEM) preparation methods to provide the first comprehensive morphological assessment of sponge-associated viruses. The combined approaches revealed 50 different morphologies of viral-like particles (VLPs) represented across the different sponge species. VLPs were visualized within sponge cells, within the sponge extracellular mesohyl matrix, on the sponge ectoderm and within sponge-associated microbes. Non-enveloped, non-tailed icosahedral VLPs were the most commonly observed morphotypes, although tailed bacteriophage, brick-shaped, geminate and filamentous VLPs were also detected. Visualization of sponge-associated viruses using TEM has confirmed that sponges harbor not only diverse communities of microorganisms but also diverse communities of viruses.
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Affiliation(s)
- Cecília Pascelli
- Australian Institute of Marine Science, Townsville, Queensland, Australia.,James Cook University, Townsville, Queensland, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia
| | - Patrick W Laffy
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Marija Kupresanin
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia.,AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Queensland, Australia
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20
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Petrovski S, Seviour R. Activated sludge foaming: can phage therapy provide a control strategy? MICROBIOLOGY AUSTRALIA 2018. [DOI: 10.1071/ma18048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Foaming in activated sludge systems is a global problem leading to environmental, cosmetic and operational problems. Proliferation of filamentous hydrophobic bacteria (including the Mycolata) are responsible for the stabilisation of foams. Currently no reliable methods exist to control these. Reducing the levels of the filamentous bacteria with bacteriophages below the threshold supporting foaming is an attractive approach to control their impact. We have isolated 88 bacteriophages that target members of the foaming Mycolata. These double stranded DNA phages have been characterised and are currently being assessed for their performance as antifoam agents.
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21
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Abstract
The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed and contain double-stranded DNA, but these remain poorly characterized genomically. A collection of over 1,000 phages infecting Mycobacterium smegmatis reveals the diversity of phages of a common bacterial host, but their relationships to phages of phylogenetically proximal hosts are not known. Comparative sequence analysis of 79 phages isolated on Gordonia shows these also to be diverse and that the phages can be grouped into 14 clusters of related genomes, with an additional 14 phages that are “singletons” with no closely related genomes. One group of six phages is closely related to Cluster A mycobacteriophages, but the other Gordonia phages are distant relatives and share only 10% of their genes with the mycobacteriophages. The Gordonia phage genomes vary in genome length (17.1 to 103.4 kb), percentage of GC content (47 to 68.8%), and genome architecture and contain a variety of features not seen in other phage genomes. Like the mycobacteriophages, the highly mosaic Gordonia phages demonstrate a spectrum of genetic relationships. We show this is a general property of bacteriophages and suggest that any barriers to genetic exchange are soft and readily violable. Despite the numerical dominance of bacteriophages in the biosphere, there is a dearth of complete genomic sequences. Current genomic information reveals that phages are highly diverse genomically and have mosaic architectures formed by extensive horizontal genetic exchange. Comparative analysis of 79 phages of Gordonia shows them to not only be highly diverse, but to present a spectrum of relatedness. Most are distantly related to phages of the phylogenetically proximal host Mycobacterium smegmatis, although one group of Gordonia phages is more closely related to mycobacteriophages than to the other Gordonia phages. Phage genome sequence space remains largely unexplored, but further isolation and genomic comparison of phages targeted at related groups of hosts promise to reveal pathways of bacteriophage evolution.
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22
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Klyczek KK, Bonilla JA, Jacobs-Sera D, Adair TL, Afram P, Allen KG, Archambault ML, Aziz RM, Bagnasco FG, Ball SL, Barrett NA, Benjamin RC, Blasi CJ, Borst K, Braun MA, Broomell H, Brown CB, Brynell ZS, Bue AB, Burke SO, Casazza W, Cautela JA, Chen K, Chimalakonda NS, Chudoff D, Connor JA, Cross TS, Curtis KN, Dahlke JA, Deaton BM, Degroote SJ, DeNigris DM, DeRuff KC, Dolan M, Dunbar D, Egan MS, Evans DR, Fahnestock AK, Farooq A, Finn G, Fratus CR, Gaffney BL, Garlena RA, Garrigan KE, Gibbon BC, Goedde MA, Guerrero Bustamante CA, Harrison M, Hartwell MC, Heckman EL, Huang J, Hughes LE, Hyduchak KM, Jacob AE, Kaku M, Karstens AW, Kenna MA, Khetarpal S, King RA, Kobokovich AL, Kolev H, Konde SA, Kriese E, Lamey ME, Lantz CN, Lapin JS, Lawson TO, Lee IY, Lee SM, Lee-Soety JY, Lehmann EM, London SC, Lopez AJ, Lynch KC, Mageeney CM, Martynyuk T, Mathew KJ, Mavrich TN, McDaniel CM, McDonald H, McManus CJ, Medrano JE, Mele FE, Menninger JE, Miller SN, Minick JE, Nabua CT, Napoli CK, Nkangabwa M, Oates EA, Ott CT, Pellerino SK, Pinamont WJ, Pirnie RT, Pizzorno MC, Plautz EJ, Pope WH, Pruett KM, Rickstrew G, Rimple PA, Rinehart CA, Robinson KM, Rose VA, Russell DA, Schick AM, Schlossman J, Schneider VM, Sells CA, Sieker JW, Silva MP, Silvi MM, Simon SE, Staples AK, Steed IL, Stowe EL, Stueven NA, Swartz PT, Sweet EA, Sweetman AT, Tender C, Terry K, Thomas C, Thomas DS, Thompson AR, Vanderveen L, Varma R, Vaught HL, Vo QD, Vonberg ZT, Ware VC, Warrad YM, Wathen KE, Weinstein JL, Wyper JF, Yankauskas JR, Zhang C, Hatfull GF. Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages. PLoS One 2017; 12:e0180517. [PMID: 28715480 PMCID: PMC5513430 DOI: 10.1371/journal.pone.0180517] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/17/2017] [Indexed: 11/19/2022] Open
Abstract
The vast bacteriophage population harbors an immense reservoir of genetic information. Almost 2000 phage genomes have been sequenced from phages infecting hosts in the phylum Actinobacteria, and analysis of these genomes reveals substantial diversity, pervasive mosaicism, and novel mechanisms for phage replication and lysogeny. Here, we describe the isolation and genomic characterization of 46 phages from environmental samples at various geographic locations in the U.S. infecting a single Arthrobacter sp. strain. These phages include representatives of all three virion morphologies, and Jasmine is the first sequenced podovirus of an actinobacterial host. The phages also span considerable sequence diversity, and can be grouped into 10 clusters according to their nucleotide diversity, and two singletons each with no close relatives. However, the clusters/singletons appear to be genomically well separated from each other, and relatively few genes are shared between clusters. Genome size varies from among the smallest of siphoviral phages (15,319 bp) to over 70 kbp, and G+C contents range from 45-68%, compared to 63.4% for the host genome. Although temperate phages are common among other actinobacterial hosts, these Arthrobacter phages are primarily lytic, and only the singleton Galaxy is likely temperate.
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Affiliation(s)
- Karen K. Klyczek
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - J. Alfred Bonilla
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Tamarah L. Adair
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Patricia Afram
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Katherine G. Allen
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Megan L. Archambault
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Rahat M. Aziz
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Filippa G. Bagnasco
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Sarah L. Ball
- Center for Life Sciences Education, The Ohio State University, Columbus, Ohio, United States of America
| | - Natalie A. Barrett
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Robert C. Benjamin
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Christopher J. Blasi
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Katherine Borst
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Mary A. Braun
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Haley Broomell
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Conner B. Brown
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Zachary S. Brynell
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Ashley B. Bue
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Sydney O. Burke
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - William Casazza
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Julia A. Cautela
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Kevin Chen
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | | | - Dylan Chudoff
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Jade A. Connor
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Trevor S. Cross
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Kyra N. Curtis
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jessica A. Dahlke
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Bethany M. Deaton
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Sarah J. Degroote
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Danielle M. DeNigris
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Katherine C. DeRuff
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Milan Dolan
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - David Dunbar
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Marisa S. Egan
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Daniel R. Evans
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Abby K. Fahnestock
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Amal Farooq
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Garrett Finn
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | | | - Bobby L. Gaffney
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Rebecca A. Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kelly E. Garrigan
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Bryan C. Gibbon
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Michael A. Goedde
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | | | - Melinda Harrison
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Megan C. Hartwell
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Emily L. Heckman
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Jennifer Huang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Lee E. Hughes
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Kathryn M. Hyduchak
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Aswathi E. Jacob
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Machika Kaku
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Allen W. Karstens
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Margaret A. Kenna
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Susheel Khetarpal
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rodney A. King
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Amanda L. Kobokovich
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Hannah Kolev
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Sai A. Konde
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Elizabeth Kriese
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Morgan E. Lamey
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Carter N. Lantz
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jonathan S. Lapin
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Temiloluwa O. Lawson
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - In Young Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Scott M. Lee
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Julia Y. Lee-Soety
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Emily M. Lehmann
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Shawn C. London
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - A. Javier Lopez
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Kelly C. Lynch
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Catherine M. Mageeney
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Tetyana Martynyuk
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Kevin J. Mathew
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Travis N. Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christopher M. McDaniel
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Hannah McDonald
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - C. Joel McManus
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jessica E. Medrano
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Francis E. Mele
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Jennifer E. Menninger
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Sierra N. Miller
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Josephine E. Minick
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Courtney T. Nabua
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Caroline K. Napoli
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Martha Nkangabwa
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Elizabeth A. Oates
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Cassandra T. Ott
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sarah K. Pellerino
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - William J. Pinamont
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Ross T. Pirnie
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Marie C. Pizzorno
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Emilee J. Plautz
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Katelyn M. Pruett
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Gabbi Rickstrew
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Patrick A. Rimple
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Claire A. Rinehart
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Kayla M. Robinson
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Victoria A. Rose
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Amelia M. Schick
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Julia Schlossman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Victoria M. Schneider
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chloe A. Sells
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jeremy W. Sieker
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Morgan P. Silva
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Marissa M. Silvi
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Stephanie E. Simon
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Amanda K. Staples
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Isabelle L. Steed
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Emily L. Stowe
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Noah A. Stueven
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Porter T. Swartz
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Emma A. Sweet
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Abigail T. Sweetman
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Corrina Tender
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Katrina Terry
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Chrystal Thomas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Daniel S. Thomas
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Allison R. Thompson
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Lorianna Vanderveen
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rohan Varma
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Hannah L. Vaught
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Quynh D. Vo
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Zachary T. Vonberg
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Vassie C. Ware
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Yasmene M. Warrad
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Kaitlyn E. Wathen
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Jonathan L. Weinstein
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Jacqueline F. Wyper
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jakob R. Yankauskas
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Christine Zhang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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23
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Kaliniene L, Šimoliūnas E, Truncaitė L, Zajančkauskaitė A, Nainys J, Kaupinis A, Valius M, Meškys R. Molecular Analysis of Arthrobacter Myovirus vB_ArtM-ArV1: We Blame It on the Tail. J Virol 2017; 91:e00023-17. [PMID: 28122988 PMCID: PMC5375659 DOI: 10.1128/jvi.00023-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/23/2017] [Indexed: 11/20/2022] Open
Abstract
This is the first report on a myophage that infects Arthrobacter A novel virus, vB_ArtM-ArV1 (ArV1), was isolated from soil using Arthrobacter sp. strain 68b for phage propagation. Transmission electron microscopy showed its resemblance to members of the family Myoviridae: ArV1 has an isometric head (∼74 nm in diameter) and a contractile, nonflexible tail (∼192 nm). Phylogenetic and comparative sequence analyses, however, revealed that ArV1 has more genes in common with phages from the family Siphoviridae than it does with any myovirus characterized to date. The genome of ArV1 is a linear, circularly permuted, double-stranded DNA molecule (71,200 bp) with a GC content of 61.6%. The genome includes 101 open reading frames (ORFs) yet contains no tRNA genes. More than 50% of ArV1 genes encode unique proteins that either have no reliable identity to database entries or have homologues only in Arthrobacter phages, both sipho- and myoviruses. Using bioinformatics approaches, 13 ArV1 structural genes were identified, including those coding for head, tail, tail fiber, and baseplate proteins. A further 6 ArV1 ORFs were annotated as encoding putative structural proteins based on the results of proteomic analysis. Phylogenetic analysis based on the alignment of four conserved virion proteins revealed that Arthrobacter myophages form a discrete clade that seems to occupy a position somewhat intermediate between myo- and siphoviruses. Thus, the data presented here will help to advance our understanding of genetic diversity and evolution of phages that constitute the order CaudoviralesIMPORTANCE Bacteriophages, which likely originated in the early Precambrian Era, represent the most numerous population on the planet. Approximately 95% of known phages are tailed viruses that comprise three families: Podoviridae (with short tails), Siphoviridae (with long noncontractile tails), and Myoviridae (with contractile tails). Based on the current hypothesis, myophages, which may have evolved from siphophages, are thought to have first emerged among Gram-negative bacteria, whereas they emerged only later among Gram-positive bacteria. The results of the molecular characterization of myophage vB_ArtM-ArV1 presented here conform to the aforementioned hypothesis, since, at a glance, bacteriophage vB_ArtM-ArV1 appears to be a siphovirus that possesses a seemingly functional contractile tail. Our work demonstrates that such "chimeric" myophages are of cosmopolitan nature and are likely characteristic of the ecologically important soil bacterial genus Arthrobacter.
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Affiliation(s)
- Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Aurelija Zajančkauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Juozas Nainys
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
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24
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Abstract
Hotorobo, Woes, and Monty are newly isolated bacteriophages of Gordonia terrae 3612. The three phages are related, and their genomes are similarly sized (76,972 bp, 73,752 bp, and 75,680 bp for Hotorobo, Woes, and Monty, respectively) and organized. They have extremely long tails and among the longest tape measure protein genes described to date.
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Abstract
Gordonia bacteriophage Yvonnetastic was isolated from soil in Pittsburgh, PA, using Gordonia terrae 3612 as a host. Yvonnetastic has siphoviral morphology and a genome of 98,136 bp, with 198 predicted protein-coding genes and five tRNA genes. Yvonnetastic does not share substantial sequence similarity with other sequenced bacteriophage genomes.
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26
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Abstract
Emalyn is a newly isolated bacteriophage of Gordonia terrae 3612 and has a double-stranded DNA genome 43,982 bp long with 67 predicted protein-encoding genes, 32 of which we can assign putative functions. Emalyn has a prolate capsid and has extensive nucleotide similarity with several previously sequenced phages.
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27
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Abstract
BetterKatz is a bacteriophage isolated from a soil sample collected in Pittsburgh, Pennsylvania using the host Gordonia terrae 3612. BetterKatz’s genome is 50,636 bp long and contains 75 predicted protein-coding genes, 35 of which have been assigned putative functions. BetterKatz is not closely related to other sequenced Gordonia phages.
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28
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Genome Sequences of
Gordonia terrae
Bacteriophages Phinally and Vivi2. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00599-16. [PMID: 27540050 PMCID: PMC4991695 DOI: 10.1128/genomea.00599-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacteriophages Phinally and Vivi2 were isolated from soil from Pittsburgh, Pennsylvania, USA, using host Gordonia terrae 3612. The Phinally and Vivi2 genomes are 59,265 bp and 59,337 bp, respectively, and share sequence similarity with each other and with GTE6. Fewer than 25% of the 87 to 89 putative genes have predictable functions.
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29
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Abstract
Gordonia phages Bowser and Schwabeltier are newly isolated phages infecting Gordonia terrae 3612. Bowser and Schwabeltier have similar siphoviral morphologies and their genomes are related to each other, but not to other phages. Their lysis cassettes are atypically situated among virion tail genes, and Bowser encodes two tyrosine integrases.
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30
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Locating and Activating Molecular 'Time Bombs': Induction of Mycolata Prophages. PLoS One 2016; 11:e0159957. [PMID: 27487243 PMCID: PMC4972346 DOI: 10.1371/journal.pone.0159957] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 07/11/2016] [Indexed: 11/23/2022] Open
Abstract
Little is known about the prevalence, functionality and ecological roles of temperate phages for members of the mycolic acid producing bacteria, the Mycolata. While many lytic phages infective for these organisms have been isolated, and assessed for their suitability for use as biological control agents of activated sludge foaming, no studies have investigated how temperate phages might be induced for this purpose. Bioinformatic analysis using the PHAge Search Tool (PHAST) on Mycolata whole genome sequence data in GenBank for members of the genera Gordonia, Mycobacterium, Nocardia, Rhodococcus, and Tsukamurella revealed 83% contained putative prophage DNA sequences. Subsequent prophage inductions using mitomycin C were conducted on 17 Mycolata strains. This led to the isolation and genome characterization of three novel Caudovirales temperate phages, namely GAL1, GMA1, and TPA4, induced from Gordonia alkanivorans, Gordonia malaquae, and Tsukamurella paurometabola, respectively. All possessed highly distinctive dsDNA genome sequences.
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31
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Genome Sequences of Gordonia terrae Phages Benczkowski14 and Katyusha. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00578-16. [PMID: 27340062 PMCID: PMC4919401 DOI: 10.1128/genomea.00578-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacteriophages Katyusha and Benczkowski14 are newly isolated phages that infect Gordonia terrae 3612. Both have siphoviral morphologies with isometric heads and long tails (500 nm). The genomes are 75,380 bp long and closely related, and the tape measure genes (9 kbp) are among the largest to be identified.
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32
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Genome Sequences of Gordonia Bacteriophages Obliviate, UmaThurman, and Guacamole. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00595-16. [PMID: 27365348 PMCID: PMC4929511 DOI: 10.1128/genomea.00595-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We describe three newly isolated phages—Obliviate, UmaThurman, and Guacamole—that infect Gordonia terrae 3612. The three genomes are related to one another but are not closely related to other previously sequenced phages or prophages. The three phages are predicted to use integration-dependent immunity systems as described in several mycobacteriophages.
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33
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Abstract
Attis and SoilAssassin are two closely related bacteriophages isolated on Gordonia terrae 3612 from separate soil samples in Pittsburgh, PA. The Attis and SoilAssassin genomes are 47,881 bp and 47,880 bp, respectively, and have 74 predicted protein-coding genes, including toxin-antitoxin systems, but no tRNAs.
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34
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Genome Sequences of Pseudomonas oryzihabitans Phage POR1 and Pseudomonas aeruginosa Phage PAE1. GENOME ANNOUNCEMENTS 2016; 4:4/3/e01515-15. [PMID: 27313312 PMCID: PMC4911491 DOI: 10.1128/genomea.01515-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the genome sequences of two double-stranded DNA siphoviruses, POR1 infective for Pseudomonas oryzihabitans and PAE1 infective for Pseudomonas aeruginosa. The phage POR1 genome showed no nucleotide sequence homology to any other DNA phage sequence in the GenBank database, while phage PAE1 displayed synteny to P. aeruginosa phages M6, MP1412, and YuA.
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