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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

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