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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 more...

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. more...

Published
2020
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2. Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages.

Author

Karen K Klyczek, J Alfred Bonilla, Deborah Jacobs-Sera, Tamarah L Adair, Patricia Afram, Katherine G Allen, Megan L Archambault, Rahat M Aziz, Filippa G Bagnasco, Sarah L Ball, Natalie A Barrett, Robert C Benjamin, Christopher J Blasi, Katherine Borst, Mary A Braun, Haley Broomell, Conner B Brown, Zachary S Brynell, Ashley B Bue, Sydney O Burke, William Casazza, Julia A Cautela, Kevin Chen, Nitish S Chimalakonda, Dylan Chudoff, Jade A Connor, Trevor S Cross, Kyra N Curtis, Jessica A Dahlke, Bethany M Deaton, Sarah J Degroote, Danielle M DeNigris, Katherine C DeRuff, Milan Dolan, David Dunbar, Marisa S Egan, Daniel R Evans, Abby K Fahnestock, Amal Farooq, Garrett Finn, Christopher R Fratus, Bobby L Gaffney, Rebecca A Garlena, Kelly E Garrigan, Bryan C Gibbon, Michael A Goedde, Carlos A Guerrero Bustamante, Melinda Harrison, Megan C Hartwell, Emily L Heckman, Jennifer Huang, Lee E Hughes, Kathryn M Hyduchak, Aswathi E Jacob, Machika Kaku, Allen W Karstens, Margaret A Kenna, Susheel Khetarpal, Rodney A King, Amanda L Kobokovich, Hannah Kolev, Sai A Konde, Elizabeth Kriese, Morgan E Lamey, Carter N Lantz, Jonathan S Lapin, Temiloluwa O Lawson, In Young Lee, Scott M Lee, Julia Y Lee-Soety, Emily M Lehmann, Shawn C London, A Javier Lopez, Kelly C Lynch, Catherine M Mageeney, Tetyana Martynyuk, Kevin J Mathew, Travis N Mavrich, Christopher M McDaniel, Hannah McDonald, C Joel McManus, Jessica E Medrano, Francis E Mele, Jennifer E Menninger, Sierra N Miller, Josephine E Minick, Courtney T Nabua, Caroline K Napoli, Martha Nkangabwa, Elizabeth A Oates, Cassandra T Ott, Sarah K Pellerino, William J Pinamont, Ross T Pirnie, Marie C Pizzorno, Emilee J Plautz, Welkin H Pope, Katelyn M Pruett, Gabbi Rickstrew, Patrick A Rimple, Claire A Rinehart, Kayla M Robinson, Victoria A Rose, Daniel A Russell, Amelia M Schick, Julia Schlossman, Victoria M Schneider, Chloe A Sells, Jeremy W Sieker, Morgan P Silva, Marissa M Silvi, Stephanie E Simon, Amanda K Staples, Isabelle L Steed, Emily L Stowe, Noah A Stueven, Porter T Swartz, Emma A Sweet, Abigail T Sweetman, Corrina Tender, Katrina Terry, Chrystal Thomas, Daniel S Thomas, Allison R Thompson, Lorianna Vanderveen, Rohan Varma, Hannah L Vaught, Quynh D Vo, Zachary T Vonberg, Vassie C Ware, Yasmene M Warrad, Kaitlyn E Wathen, Jonathan L Weinstein, Jacqueline F Wyper, Jakob R Yankauskas, Christine Zhang, and Graham F Hatfull more...

Subjects
Medicine, Science
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. more...

Published
2017
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3. 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 more...

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. more...

Published
2020

4. Complete Genome Sequences of 44

Author

Karen K, Klyczek, Deborah, Jacobs-Sera, Tamarah L, Adair, Sandra D, Adams, Sarah L, Ball, Robert C, Benjamin, J Alfred, Bonilla, Caroline A, Breitenberger, Charles J, Daniels, Bobby L, Gaffney, Melinda, Harrison, Lee E, Hughes, Rodney A, King, Gregory P, Krukonis, A Javier, Lopez, Kirsten, Monsen-Collar, Marie C, Pizzorno, Claire A, Rinehart, Amanda K, Staples, Emily L, Stowe, Rebecca A, Garlena, Daniel A, Russell, Steven G, Cresawn, Welkin H, Pope, and Graham F, Hatfull more...

Subjects
Viruses
Abstract

We report here the complete genome sequences of 44 phages infecting Arthrobacter sp. strain ATCC 21022. These phages have double-stranded DNA genomes with sizes ranging from 15,680 to 70,707 bp and G+C contents from 45.1% to 68.5%. All three tail types (belonging to the families Siphoviridae, Myoviridae, and Podoviridae) are represented. more...

Published
2018

5. Complete Genome Sequences of 44 Arthrobacter Phages

Author

Tamarah L. Adair, Charles J. Daniels, Lee E. Hughes, Phire Program, Emily L. Stowe, Bobby L. Gaffney, Kirsten Monsen-Collar, Melinda Harrison, A. Javier Lopez, Robert C. Benjamin, Sandra D. Adams, Sarah Ball, Graham F. Hatfull, Daniel A. Russell, Amanda K. Staples, Rebecca A. Garlena, Gregory P. Krukonis, Steven G. Cresawn, J. Alfred Bonilla, Sea-Phages Program, Karen K. Klyczek, Deborah Jacobs-Sera, Welkin H. Pope, Caroline A. Breitenberger, Marie C. Pizzorno, Rodney A. King, and Claire A. Rinehart more...

Subjects
0301 basic medicine, Whole genome sequencing, Genetics, biology, Arthrobacter sp, Myoviridae, biology.organism_classification, Genome, Siphoviridae, 03 medical and health sciences, Podoviridae, chemistry.chemical_compound, 030104 developmental biology, chemistry, Arthrobacter, Molecular Biology, DNA
Abstract

We report here the complete genome sequences of 44 phages infecting Arthrobacter sp. strain ATCC 21022. These phages have double-stranded DNA genomes with sizes ranging from 15,680 to 70,707 bp and G+C contents from 45.1% to 68.5%. All three tail types (belonging to the families Siphoviridae , Myoviridae , and Podoviridae ) are represented. more...

Published
2018
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6. Genome Sequences of 19

Author

J Alfred, Bonilla, Sharon, Isern, Ann M, Findley, Karen K, Klyczek, Scott F, Michael, Margaret S, Saha, William J, Buchser, Mark H, Forsyth, Sudip, Paudel, Christopher R, Gissendanner, Allison M D, Wiedemeier, Fernanda L, Alonzo, Rebecca A, Garlena, Daniel A, Russell, Welkin H, Pope, Steven G, Cresawn, Deborah, Jacobs-Sera, and Graham F, Hatfull more...

Subjects
Viruses
Abstract

We report the complete genome sequences of 19 cluster CA bacteriophages isolated from environmental samples using Rhodococcus erythropolis as a host. All of the phages are Siphoviridae, have similar genome lengths (46,314 to 46,985 bp) and G+C contents (58.5 to 58.8%), and share nucleotide sequence similarity. more...

Published
2017

7. Complete Genome Sequences of Arthrobacter Phages Beans, Franzy, Jordan, Piccoletto, Shade, and Timinator

Author

Germán Rosas-Acosta, Charles A. Bowman, Julia Y. Lee-Soety, Daniel A. Russell, Deborah Jacobs-Sera, Graham F. Hatfull, Karen K. Klyczek, Welkin H. Pope, Melinda Harrison, Steven G. Cresawn, Rebecca A. Garlena, Tamarah L. Adair, and J. Alfred Bonilla more...

Subjects
0301 basic medicine, Genetics, biology, Arthrobacter sp, biology.organism_classification, Genome, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, chemistry, Arthrobacter, Viruses, Botany, Molecular Biology, DNA
Abstract

We report here the genome sequences of six newly isolated bacteriophages infecting Arthrobacter sp. ATCC 21022. All six have myoviral morphologies and have double-stranded DNA genomes with circularly permuted ends. The six phages are closely related with average nucleotide identities of 73.4 to 93.0% across genomes lengths of 49,797 to 51,347 bp. more...

Published
2017
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8. Complete Genome Sequences of 38 Gordonia sp. Bacteriophages

Author

Karen K. Klyczek, Randall J. DeJong, John T. Wertz, Matthew T. Montgomery, Deborah Jacobs-Sera, Carlos A. Guerrero Bustamante, Daniel A. Russell, J. Alfred Bonilla, Graham F. Hatfull, Rebecca A. Garlena, and Welkin H. Pope more...

Subjects
0301 basic medicine, Genetics, Gordonia terrae, Nucleic acid sequence, Biology, medicine.disease_cause, Genome, Gordonia neofelifaecis, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, chemistry, Viruses, medicine, Molecular Biology, Gordonia sp, DNA
Abstract

We report here the genome sequences of 38 newly isolated bacteriophages using Gordonia terrae 3612 (ATCC 25594) and Gordonia neofelifaecis NRRL59395 as bacterial hosts. All of the phages are double-stranded DNA (dsDNA) tail phages with siphoviral morphologies, with genome sizes ranging from 17,118 bp to 93,843 bp and spanning considerable nucleotide sequence diversity. more...

Published
2017

9. Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages

Author

Filippa G. Bagnasco, Melinda Harrison, Garrett Finn, David Dunbar, Machika Kaku, Rahat M. Aziz, Rodney A. King, Marisa Egan, Nitish S. Chimalakonda, Hannah M. Kolev, Daniel R. Evans, Allen W. Karstens, Christopher M. McDaniel, Lee E. Hughes, Megan L. Archambault, Marie C. Pizzorno, Jennifer E. Menninger, Robert C. Benjamin, Emily M. Lehmann, Karen K. Klyczek, Jakob R. Yankauskas, Hannah McDonald, Amelia M. Schick, Josephine E. Minick, Deborah Jacobs-Sera, Jade Connor, Megan C. Hartwell, Kayla M. Robinson, Haley Broomell, Kaitlyn E. Wathen, Kelly C. Lynch, Julia Y. Lee-Soety, Victoria A. Rose, Emily L. Stowe, Vassie C. Ware, Daniel S. Thomas, Bobby L. Gaffney, Shawn C. London, Daniel A. Russell, Kathryn M. Hyduchak, Jonathan L. Weinstein, Yasmene M. Warrad, Christine Zhang, Zachary T. Vonberg, Sarah Ball, Lorianna Vanderveen, Christopher J. Blasi, Corrina Tender, Morgan P. Silva, Katelyn M. Pruett, Claire A. Rinehart, Trevor Cross, Allison R. Thompson, Jeremy W. Sieker, Carter N. Lantz, Carlos A. Guerrero Bustamante, Katherine Borst, Jessica A. Dahlke, William Casazza, Cassandra T. Ott, Sarah K. Pellerino, Kelly E. Garrigan, J. Alfred Bonilla, Zachary S. Brynell, Morgan E. Lamey, Aswathi E. Jacob, Kate Allen, Emma A. Sweet, Francis E. Mele, Sierra N. Miller, Dylan Chudoff, Ashley B. Bue, Julia Schlossman, Graham F. Hatfull, Margaret A. Kenna, Kevin Hong Chen, Conner B. Brown, Christopher R. Fratus, Quynh D. Vo, Martha Nkangabwa, Mary A. Braun, Sydney O. Burke, Natalie Barrett, Bryan C. Gibbon, Courtney T. Nabua, Catherine M. Mageeney, William J. Pinamont, Stephanie E. Simon, Porter T. Swartz, Milan Dolan, Rohan Varma, Temiloluwa O. Lawson, Ross T. Pirnie, Kevin J. Mathew, Caroline K. Napoli, Rebecca A. Garlena, Jessica E. Medrano, Bethany M. Deaton, Welkin H. Pope, Chrystal Thomas, Michael A. Goedde, Amal Farooq, Gabbi Rickstrew, Hannah L. Vaught, A. Javier Lopez, Noah A. Stueven, Amanda L. Kobokovich, Tamarah L. Adair, Elizabeth A. Oates, Jacqueline F. Wyper, Elizabeth Kriese, Victoria M. Schneider, Susheel K. Khetarpal, Emily L. Heckman, Abby K. Fahnestock, Emilee J. Plautz, Travis N. Mavrich, Amanda K. Staples, Jonathan S. Lapin, Danielle M. DeNigris, Katrina Terry, In Young Lee, Sai A. Konde, Chloe A. Sells, Jennifer Huang, Marissa M. Silvi, Tetyana Martynyuk, Katherine C. DeRuff, Isabelle L. Steed, Kyra N. Curtis, Sarah J. Degroote, Scott M. Lee, Patrick A. Rimple, C. Joel McManus, Abigail T. Sweetman, Julia A. Cautela, and Patricia Afram more...

Subjects
0301 basic medicine, viruses, lcsh:Medicine, Astronomical Sciences, Genome, Biochemistry, Nucleotide diversity, Bacteriophage, Database and Informatics Methods, Rhodococcus, Bacteriophages, lcsh:Science, Genetics, education.field_of_study, Viral Genomics, Multidisciplinary, biology, Genomics, Proteases, Genomic Databases, Celestial Objects, Enzymes, Actinobacteria, Viruses, Physical Sciences, Research Article, Population, Genome, Viral, Microbial Genomics, Research and Analysis Methods, Microbiology, 03 medical and health sciences, Lysogenic cycle, Virology, Arthrobacter, education, Genome size, Comparative genomics, Bacteria, lcsh:R, Organisms, Genetic Variation, Biology and Life Sciences, Computational Biology, Proteins, Comparative Genomics, biology.organism_classification, Genome Analysis, Galaxies, 030104 developmental biology, Biological Databases, Enzymology, lcsh:Q
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. more...

Published
2017