ABSTRACT
This announcement contains the whole genome sequences of five Ackermannviridae that infect members of the Enterobacteriaceae family of bacteria. Four of the five phages were isolated using Salmonella enterica serovar Typhimurium as a bacterial host: AR2819, Sajous1, SilasIsHot, and FrontPhageNews. ChubbyThor was isolated using Shigella boydii.
KEYWORDS: Enterbacteriaceae, bacteriophages, ViO1, Sajous1, FrontPhageNews, ChubbyThor, AR2819, SilasIsHot, Salmonella, Shigella
ANNOUNCEMENT
The Enterobacteriaceae bacterial family is composed of Gram-negative facultative anaerobes and includes common pathogens such as Salmonella enterica serovar Typhimurium, Klebsiella aerogenes, Escherichia coli, and many others. Bacteriophages (phages) are an essential driver of bacterial evolution, including pathogenic traits, due to their prevalence, propensity to transfer genetic elements between strains, ability to persist as prophages within bacterial genomes, and lytic activity (1). This announcement contains the whole genome sequences of five related bacteriophages that infect members of the Enterobacteriaceae.
All five phages (Table 1) were isolated from effluent sewage collected from water treatment plants in the western United States. Four of the five phages were isolated using Salmonella enterica serovar Typhimurium LT2 as a bacterial host: AR2819, Sajous1, SilasIsHot, and FrontPhageNews. The final phage, ChubbyThor, was isolated using Shigella boydi Ewing (ATCC 9207). Briefly, effluent sewage was incubated with bacterial culture and LB nutrient broth at 37°C for 2 days prior to pelleting bacterial debris (8,000 rpm for 20 min) and plating in LB top agar. Single plaques were then picked and replated alongside bacteria in top agar. This plaque purification was repeated three times wherein all five phages appear to be lytic due to high concentration of clear plaques. DNA was purified from lysates containing at least 108 PFU/mL using the Phage DNA Isolation Kit (Norgen Biotek, Canada) and prepared for Illumina iSeq 150 bp paired-end sequencing using the NEBNext Ultra II FS kit (New England Biolabs). Resulting reads were assembled de novo with automatic trimming using Geneious version R11 (2) at default settings. The phage genomes circularized upon assembly, and each genome was annotated using both DNAmaster (3) and GeneMark (4) and was deposited in NCBI GenBank (see Table 1). NCBI Genbank nucleotide database BLASTN analysis (5) as of 6 October 2023 revealed that all five phages display similarity in genome size and nucleotide identity to previously characterized Enterobacteriaceae phage cluster ViO1 (6), which has been classified in the Ackermannviridae family by the International Committee on Taxonomy of Viruses (7). Phages Sajous1 and AR2819 are most like Salmonella phage Guerrero (accession no. OP610151) by BLASTN, sharing a 98.6% and 99.7% nucleotide identity, respectively, over 98% of the genome. FrontPhageNews is most like Sajous1 by BLASTN, with 86.66% identity over 95% of the genome. SilasIsHot is most like Salmonella phage vB_SenM_UTK0004 (OQ359883) with a 98.35% identity over 94% of the genome, while ChubbyThor is most like Shigella phage MK-13 (NC_049455.1) with a percent identity of 96.56% over 88% of the genome. The increased GC content of ChubbyThor, which sits at 50.1% as compared to the other phages that range between 44.61% and 45.13% GC content, may reflect host preference. Further characterization of these phages is currently underway and may help increase our understanding of Enterobacteriaceae evolution.
TABLE 1.
Sequencing summary and properties of five Ackermannviridae that infect Enterobacteriaceae
| Phage name | Original bacterial host | Sewage sampling location coordinates | Sample acquisition date | GenBank accession no. | SRA accession no. | Total no. of reads | Fold coverage range (mean) | Length (bp) | GC %a |
|---|---|---|---|---|---|---|---|---|---|
| AR2819 | Salmonella Typhimurium | 40.2729°N, 111.7382°W | 10 September 2019 | MW021753 | SRR22024852 | 437,180 | 89–699 (284.6) | 156,899 | 44.97 |
| SilasIsHot | Salmonella Typhimurium | 40.9012°N, 111.9302°W | 10 September 2019 | MW021760 | SRR22024849 | 114,525 | 1–373 (235.9) | 160,559 | 45.13 |
| Sajous1 | Salmonella Typhimurium | 42.2134°N, 111.6500°W | 10 September 2019 | MW021757 | SRR22024851 | 37,3801 | 35–250 (214.6) | 157,255 | 44.86 |
| FrontPhageNews | Salmonella Typhimurium | 40.7418°N, 73.9883°W | 13 May 2020 | MW021754 | SRR22024850 | 60,142 | 24–97 (55.7) | 157,832 | 44.61 |
| ChubbyThor | Shigella boydii | 33.4152°N, 111.8315°W | 1 September 2018 | OL615013 | SRR11575116 | 827,950 | 931 (737.9) | 159,319 | 50.1 |
GC content was calculated using the GC-profile tool (8) with a halting parameter of 50 and 1,000 minimum segment length per recommendations provided with the tool.
ACKNOWLEDGMENTS
The authors acknowledge the generous phage analysis training and support of Howard Hughes Medical Institute Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES). We would like to thank Chandler Bagely, Travis Komm, Kayla Maas, Joe Salmons, and Jacob Ward for their work toward phage annotation in this project.
This study was funded by the Department of Microbiology and Molecular Biology and the College of Life Sciences at Brigham Young University (J.H.G.).
Contributor Information
Julianne H. Grose, Email: julianne_grose@byu.edu.
Kenneth M. Stedman, Portland State University, Portland, Oregon, USA
DATA AVAILABILITY
This whole genome sequencing project has been deposited in GenBank under two accession numbers, accession no. PRJNA891723 for phages AR2819 (MW021753), SilasisHot (MW021760), Sajous1 (MW021757), and FrontPhageNews (MW021754) and accession no. PRJNA626377 for phage ChubbyThor (OL615013). The versions described in this paper are the first versions, PRJNA891723 and PRJNA626377. See Table 1 for SRA accession numbers.
REFERENCES
- 1. Klimenko AI, Matushkin YG, Kolchanov NA, Lashin SA. 2016. Bacteriophages affect evolution of bacterial communities in spacially distributed habitats: a simulation study. BMC Microbiol 16:67. doi: 10.1186/s12866-016-0677-8 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. doi: 10.1093/bioinformatics/bts199 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Lawrence J. 2007. DNA Master. Available from: http://cobamide2.bio.pitt.edu/
- 4. Besemer J, Lomsadze A, Borodovsky M. 2001. Genemarks: a self-training method for prediction of gene starts in microbial genomes. implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618. doi: 10.1093/nar/29.12.2607 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410. doi: 10.1016/S0022-2836(05)80360-2 [DOI] [PubMed] [Google Scholar]
- 6. Grose JH, Casjens SR. 2014. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Virology 468–470:421–443. doi: 10.1016/j.virol.2014.08.024 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Lefkowitz EJ, Dempsey DM, Hendrickson RC, Orton RJ, Siddell SG, Smith DB. 2018. Virus Taxonomy: The database of the International Committee on 84 Taxonomy of viruses (ICTV. Nucleic Acids Res 46:D708–D717. doi: 10.1093/nar/gkx932 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Gao F, Zhang C-T. 2006. GC-profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res 34:W686–91. doi: 10.1093/nar/gkl040 [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
This whole genome sequencing project has been deposited in GenBank under two accession numbers, accession no. PRJNA891723 for phages AR2819 (MW021753), SilasisHot (MW021760), Sajous1 (MW021757), and FrontPhageNews (MW021754) and accession no. PRJNA626377 for phage ChubbyThor (OL615013). The versions described in this paper are the first versions, PRJNA891723 and PRJNA626377. See Table 1 for SRA accession numbers.