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1. Genomic diversity of bacteriophages infecting Microbacterium spp.

Author

Deborah Jacobs-Sera, Lawrence A Abad, Richard M Alvey, Kirk R Anders, Haley G Aull, Suparna S Bhalla, Lawrence S Blumer, David W Bollivar, J Alfred Bonilla, Kristen A Butela, Roy J Coomans, Steven G Cresawn, Tom D'Elia, Arturo Diaz, Ashley M Divens, Nicholas P Edgington, Gregory D Frederick, Maria D Gainey, Rebecca A Garlena, Kenneth W Grant, Susan M R Gurney, Heather L Hendrickson, Lee E Hughes, Margaret A Kenna, Karen K Klyczek, Hari Kotturi, Travis N Mavrich, Angela L McKinney, Evan C Merkhofer, Jordan Moberg Parker, Sally D Molloy, Denise L Monti, Dana A Pape-Zambito, Richard S Pollenz, Welkin H Pope, Nathan S Reyna, Claire A Rinehart, Daniel A Russell, Christopher D Shaffer, Viknesh Sivanathan, Ty H Stoner, Joseph Stukey, C Nicole Sunnen, Sara S Tolsma, Philippos K Tsourkas, Jamie R Wallen, Vassie C Ware, Marcie H Warner, Jacqueline M Washington, Kristi M Westover, JoAnn L Whitefleet-Smith, Helen I Wiersma-Koch, Daniel C Williams, Kira M Zack, and Graham F Hatfull

Subjects
Medicine, Science
Abstract

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.

Published
2020
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2. Genomic diversity of bacteriophages infecting Microbacterium spp

Author

Arturo Diaz, Kirk R. Anders, Travis N. Mavrich, Claire A. Rinehart, Haley G. Aull, Ty H. Stoner, Lawrence Abad, Ashley M. Divens, Deborah Jacobs-Sera, Heather Hendrickson, Susan M. R. Gurney, Richard S. Pollenz, Lee E. Hughes, Lawrence S. Blumer, Viknesh Sivanathan, Hari Kotturi, Vassie C. Ware, Evan C. Merkhofer, Tom D’Elia, Jordan Moberg Parker, Dana A. Pape-Zambito, Jamie R. Wallen, Suparna S. Bhalla, Karen K. Klyczek, David Bollivar, J. Alfred Bonilla, Kenneth W. Grant, Roy J. Coomans, JoAnn L. Whitefleet-Smith, Nicholas P. Edgington, Sally D. Molloy, Nathan S. Reyna, Denise L Monti, Richard M Alvey, Kristi M. Westover, Daniel C Williams, Gregory D. Frederick, Helen Wiersma-Koch, Steven G. Cresawn, Sara S. Tolsma, Kristen Butela, Jacqueline Washington, Angela L. McKinney, Marcie H. Warner, Margaret A. Kenna, Joseph Stukey, Philippos K. Tsourkas, Welkin H. Pope, Christopher D. Shaffer, Daniel A. Russell, C. Nicole Sunnen, Maria D. Gainey, Graham F. Hatfull, Kira M. Zack, and Rebecca A. Garlena

Subjects
Genes, Viral, viruses, Genome, Recombineering, Virions, Bacteriophage, Database and Informatics Methods, Capsids, Caudovirales, Bacteriophages, Phylogeny, Genetics, 0303 health sciences, education.field_of_study, Base Composition, Viral Genomics, Multidisciplinary, biology, Genomics, Actinobacteria, Viruses, Medicine, Sequence Analysis, Research Article, Bioinformatics, Science, Microbacterium, Population, Genome, Viral, Microbial Genomics, Viral Structure, Research and Analysis Methods, Microbiology, 03 medical and health sciences, Sequence Motif Analysis, Virology, education, Gene Prediction, Gene, 030304 developmental biology, 030306 microbiology, Organisms, Genetic Variation, Biology and Life Sciences, Computational Biology, Comparative Genomics, biology.organism_classification, Genome Analysis, DNA, Viral, Viral Fusion Proteins
Abstract

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.

Published
2020

3. Genome Sequences of Four Cluster P Mycobacteriophages

Author

Deborah M. Tobiason, Graham F. Hatfull, Rebecca A. Garlena, Hannah Carlstedt, Erin L. Doyle, Deanna Byrnes, Ty H. Stoner, Nathan S. Reyna, Jackie Lewis, Meredyth D. Wenta, Nancy Guild, Paul J. Bisesi, Jonathan L. Askins, Lucinda R. Krenzke, Reid G. Rogers, Noah Nalley, Tristan R. Grams, Christy Fillman, Tyler Z. Yates, Cali McEntee, Deborah Jacobs-Sera, Kyla J. Foster, Daniel A. Russell, Kinnon S. Dodson, Sarah K. Vickers, Megan J. Fallert, Kelsey Snyder, Justin C. McGee, Chas F. Young, Ashlynn C. Baker, Daniel E. Westholm, Brittany P. Backus, Kali Uhrich, Chelsey D. Vermillion, Cassidy R. Kepler, J.B. Schipper, Steven G. Cresawn, Daniel N. Games, Autumn Hurd, Ruth Plymale, Kelly Luekens, Welkin H. Pope, Nicholas Iwata, Harrison S. Ballard, Logan Bond, and Jade Prochaska

Subjects
0301 basic medicine, Genetics, Mycobacteriophages, biology, viruses, Mycobacterium smegmatis, biology.organism_classification, Disease cluster, Genome, 03 medical and health sciences, 030104 developmental biology, Viruses, Molecular Biology
Abstract

Four bacteriophages infecting Mycobacterium smegmatis mc 2 155 (three belonging to subcluster P1 and one belonging to subcluster P2) were isolated from soil and sequenced. All four phages are similar in the left arm of their genomes, but the P2 phage differs in the right arm. All four genomes contain features of temperate phages.

Published
2018
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4. Genome Sequences of Mycobacteriophages Amgine, Amohnition, Bella96, Cain, DarthP, Hammy, Krueger, LastHope, Peanam, PhelpsODU, Phrank, SirPhilip, Slimphazie, and Unicorn

Author

William Buchser, Mark H. Forsyth, Tristan Tobias, Michael R. Rubin, Kirk R. Anders, Aaron A. Best, William A. D’Angelo, Hui-Min Chung, Natalia Y. Maldonado-Vazquez, Gregory D. Frederick, Greta J. Held, Nana Yaa A. Amoh, Frederick N. Baliraine, Sea-Phages, Claudia H. Moonsammy, Steven G. Cresawn, Gabriella M. Reyes, Kara F. Gallo, Anna G. Fortier, Peace Namboote, Deborah Jacobs-Sera, Christian T. Farris, Thomas P. Cast, Daniel A. Russell, Margaret S. Saha, Carmen E. Chamberlain, Haley D. Fischman, Joseph Stukey, Sudip Paudel, Mariceli Fernandez-Martinez, Miguel A. Lomas, Welkin H. Pope, Ty H. Stoner, Nazir Barekzi, Graham F. Hatfull, Rebecca A. Garlena, Sarah-Elizabeth M. Polley, Edwin Vazquez, and Dmitri V. Mavrodi

Subjects
0301 basic medicine, Genetics, Mycobacteriophages, biology, Mycobacterium smegmatis, Integrases, biology.organism_classification, Genome, 03 medical and health sciences, 030104 developmental biology, Viruses, Molecular Biology, Sequence (medicine)
Abstract

We report the genome sequences of 14 cluster K mycobacteriophages isolated using Mycobacterium smegmatis mc²155 as host. Four are closely related to subcluster K1 phages, and 10 are members of subcluster K6. The phage genomes span considerable sequence diversity, including multiple types of integrases and integration sites.

Published
2017

5. Genome Sequences of Chancellor, Mitti, and Wintermute, Three Subcluster K4 Phages Isolated Using

Author

Nicholas P, Edgington, Stephanie M, Voshell, Vassie C, Ware, Francis F, Akoto, Alexa A, Alhout, Gurvina J, Atwal, John B, Balyozian, Zachary A, Cadieux, Brianna M, Chop, Steven G, Cresawn, Netta, Cudkevich, Dylan Z, Faltine-Gonzalez, Rebecca A, Garlena, Blair J, Gilmer, Lee H, Graham, Matthew S, Grapel, Maaz M, Haleem, Deborah, Jacobs-Sera, Margaret A, Kenna, Maryam A, Khan, Taylor N, Klein, Jamie B, Korenberg, Brooke P, Lichak, Catherine M, Mageeney, Lauren N, McKinley, Kourtney R, Mendello, Cameron M, Myers, Alexander T, Nguyen, Bryan A, Pasqualucci, Welkin H, Pope, Lauren M, Pyfer, Wascar A, Ramirez, Julia R, Reisner, Daniel A, Russell, Paulene A, Sapao, Virginia C, Saux, Inderjeet, Singh, Ty H, Stoner, Rachel H, Swope, Matthew J, Thoonkuzhy, Madeleine L, Walters, Lauren A, Vargas, Croldy A, Veliz, Kevin D, Zhang, Caitlin M, Zuilkoski, and Graham F, Hatfull

Subjects
Viruses
Abstract

Mycobacteriophages Chancellor, Mitti, and Wintermute infect Mycobacterium smegmatis mc2155 and are closely related to phages Cheetobro and Fionnbharth in subcluster K4. Genome sizes range from 57,697 bp to 58,046 bp. Phages are predicted to be temperate and to infect the pathogen Mycobacterium tuberculosis.

Published
2017

6. Genome Sequences of Chancellor, Mitti, and Wintermute, Three Subcluster K4 Phages Isolated Using Mycobacterium smegmatis mc 2 155

Author

Kevin D. Zhang, Kourtney R. Mendello, Jamie B. Korenberg, Daniel A. Russell, John B. Balyozian, Nicholas P. Edgington, Gurvina J. Atwal, Graham F. Hatfull, Francis F. Akoto, Stephanie M. Voshell, Croldy A. Veliz, Netta Cudkevich, Brianna M. Chop, Catherine M. Mageeney, Bryan A. Pasqualucci, Inderjeet Singh, Dylan Z. Faltine-Gonzalez, Lauren N. McKinley, Rachel H. Swope, Lauren A. Vargas, Rebecca A. Garlena, Madeleine L. Walters, Alexander T. Nguyen, Brooke P. Lichak, Zachary A. Cadieux, Alexa A. Alhout, Vassie C. Ware, Welkin H. Pope, Julia R. Reisner, Cameron M. Myers, Lee H. Graham, Maryam A. Khan, Matthew S. Grapel, Ty H. Stoner, Deborah Jacobs-Sera, Caitlin M. Zuilkoski, Lauren M. Pyfer, Maaz M. Haleem, Margaret A. Kenna, Wascar A. Ramirez, Blair J. Gilmer, Steven G. Cresawn, Taylor N. Klein, Matthew J. Thoonkuzhy, Paulene Sapao, and Virginia C. Saux

Subjects
0301 basic medicine, Mycobacterium tuberculosis, 03 medical and health sciences, 030104 developmental biology, biology, Mycobacteriophages, Mycobacterium smegmatis, Genetics, biology.organism_classification, Molecular Biology, Genome, Virology, Pathogen
Abstract

Mycobacteriophages Chancellor, Mitti, and Wintermute infect Mycobacterium smegmatis mc 2 155 and are closely related to phages Cheetobro and Fionnbharth in subcluster K4. Genome sizes range from 57,697 bp to 58,046 bp. Phages are predicted to be temperate and to infect the pathogen Mycobacterium tuberculosis .

Published
2017
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7. Complete Genome Sequences of Mycobacteriophages Clautastrophe, Kingsolomon, Krypton555, and Nicholas

Author

Mah Noor Zahra, Tom D’Elia, Ty H. Stoner, Sierra Hobbs, Daniel A. Russell, Michelle Lapak, Lauren Thornton, May Zaw, Sarah C. Bertrand, Kelsey M. Green, Claude F. Albritton, Grace Worley, Noah Thrift, Julia M. Dane, Huyen M. Duong, Lydia P. Bricker, Michael L. Do, Camilla Do, Joseph F. Ross, Dalia H. El-Desoky, Deborah Jacobs-Sera, Molly-Catherine Brantley, Amara Ejikemeuwa, Hui-Min Chung, Donald P. Vaughan, Nicholas Ludergnani, Samuel M. Alvarado, Carson Crist, Brett W. Farran, Courtney R. Butler, Allison McMullen, Shanzay Chaudhry, Conner Lovell, Welkin H. Pope, Vzair A. Cheema, Steven G. Cresawn, James M. Vu, Rhea N. Lee, Graham F. Hatfull, Sohail A. Mirza, and Rebecca A. Garlena

Subjects
0301 basic medicine, Genetics, Mycobacteriophages, Mycobacteriophage, Mycobacterium smegmatis, Nucleic acid sequence, Biology, biology.organism_classification, Genome, 03 medical and health sciences, 030104 developmental biology, Viruses, Gene duplication, Insertion, Molecular Biology, Comparative genomic hybridization
Abstract

We report here the complete genome sequences of four subcluster L3 mycobacteriophages newly isolated from soil samples, using Mycobacterium smegmatis mc 2 155 as the host. Comparative genomic analyses with four previously described subcluster L3 phages reveal strong nucleotide similarity and gene conservation, with several large insertions/deletions near their right genome ends.

Published
2017
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8. Genome Sequences of Mycobacteriophages Findley, Hurricane, and TBond007

Author

Thinh V. Pham, Jacqueline R. Ramos, Steven G. Cresawn, Sanghamitra Saha, Maria Ilyas, Aissa Mendez, Guanqiao Feng, Jacqueline Washington, Joshua Kaiser, W. Brad Barbazuk, Wenbo Yan, Stephen J. Monroe, Welkin H. Pope, Rebecca A. Garlena, Rachna Sadana, Daniel A. Russell, Ty H. Stoner, Graham F. Hatfull, William B. Davis, Deborah Jacobs-Sera, Miranda Edmonds, and Rosa H. Medellin

Subjects
0301 basic medicine, Genetics, 03 medical and health sciences, 030104 developmental biology, Mycobacteriophages, Mycobacterium smegmatis, viruses, Viruses, Biology, biology.organism_classification, Molecular Biology, Genome
Abstract

We report here the genome sequences of three newly isolated phages that infect Mycobacterium smegmatis mc 2 155. Phages Findley, Hurricane, and TBond007 were discovered in geographically distinct locations and are related to cluster K mycobacteriophages, with Findley being similar to subcluster K2 phages and Hurricane and TBond007 being similar to subcluster K3 phages.

Published
2017

9. Genome Sequences of Gordonia Phages Bowser and Schwabeltier

Author

Aleksandra Basina, Graham F. Hatfull, Sarah R. Grubb, Ty H. Stoner, Rebecca A. Garlena, Matthew T. Montgomery, Marcie H. Warner, Welkin H. Pope, Deborah Jacobs-Sera, Johnathon G. Schiebel, Emily C. Furbee, Zachary M. Arnold, Ankitha M. Iyer, Naomi S. Kasturiarachi, Catherine A. Pressimone, and Daniel A. Russell

Subjects
0301 basic medicine, Genetics, Gordonia terrae, food.ingredient, viruses, 030106 microbiology, Integrases, Biology, Gordonia, Genome, 03 medical and health sciences, 030104 developmental biology, food, Viruses, Bowser, Molecular Biology, Gene
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.

Published
2016

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