Department
Biology
Document Type
Article
Publication Date
6-1-2020
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.
Publication Title
PLoS ONE
Publisher Statement
Copyright © the Authors
DOI
10.1371/journal.pone.0234636
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Recommended Citation
Jacobs-Sera D, Reyna NS, et al. "Genomic diversity of bacteriophages infecting Microbacterium spp," PLoS One. (June 2020) 15(6):e0234636. doi: 10.1371/journal.pone.0234636.
S1 Table: Average nucleotide identities of Microbacterium phage genomes
pone.0234636.s002.xlsx (43 kB)
S2 Table: Gene content similarity of Microbacterium phage genomes
pone.0234636.s003.tif (1207 kB)
S1 Figure: Genome organization of Microbacterium subcluster EA2 phage Eleri
pone.0234636.s004.tif (1313 kB)
S2 Figure: Genome organization of Microbacterium subcluster EA3 phage casey
pone.0234636.s005.tif (809 kB)
S3 Figure: Genome organization of Microbacterium subcluster EA4 golden
pone.0234636.s006.tif (805 kB)
S4 Figure: Genome organization of Microbacterium subcluster EA5 neferthena
pone.0234636.s007.tif (810 kB)
S5 Figure: Genome organization of Microbacterium subcluster EA6 chepli
pone.0234636.s008.tif (753 kB)
S6 Figure: Genome organization of Microbacterium subcluster EA7 theresita
pone.0234636.s009.tif (830 kB)
S7 Figure: Genome organization of Microbacterium subcluster EA8 schubert
pone.0234636.s010.tif (2403 kB)
S8 Figure: Genome organization of Microbacterium cluster EB phages
pone.0234636.s011.tif (1651 kB)
S9 Figure: Genome organization of Microbacterium cluster EC phages
pone.0234636.s012.tif (2089 kB)
S10 Figure: Repeated sequence motifs in Microbacterium phages
pone.0234636.s013.tif (1753 kB)
S11 Figure: Genome organization of Microbacterium cluster ED phages
pone.0234636.s014.tif (1471 kB)
S12 Figure: Genome organization of Microbacterium cluster EE phages
pone.0234636.s015.tif (1591 kB)
S13 Figure: Genome organizations of Microbacterium cluster EG phages
pone.0234636.s016.tif (966 kB)
S14 Figure: Genome organization of Microbacterium cluster EH phages
pone.0234636.s017.tif (936 kB)
S15 Figure: Genome organization of Microbacterium cluster EI phages
pone.0234636.s018.tif (732 kB)
S16 Figure: Genome organization of Microbacterium cluster EJ phages
pone.0234636.s019.tif (1022 kB)
S17 Figure: Relationships between phage genomes of different Actinobacterium hosts
pone.0234636.s020.tif (990 kB)
S18 Figure: Inter-cluster relationships among Microbacterium phages
pone.0234636.s021.tif (152 kB)
S19 Figure: Raw image of Figure 16