Complete genome sequences of seven Microbacterium foliorum phages Albedo, Kenzers, Swervy, Cranjis, JaimeB, Fullmetal, and Stormbreaker
Keyshla Valentin Caban, Elizabeth Kalesnik, Kaitlyn A. Green, Christopher J. Negro, Ulises Nunez Rodriguez, Milan C. Peele, Casandra T. Nguyen, Sydney Cahill, Keara Dougherty, Melissa Logue, Star Hargraves, Hannah Radziak, Luke Willette, Esther Ogunyinka, Davia C. Campbell

TL;DR
This paper reports the complete genome sequences of seven new bacteriophages isolated from soil using a specific bacterial host.
Contribution
The study provides new insights into the genetic diversity of Microbacterium foliorum phages.
Findings
The seven phages have between 25 and 91 predicted genes.
The phages belong to actinobacteriophage clusters EB, EC, EE, and EK.
Abstract
Seven bacteriophages were isolated from soil in Pennsylvania and Wisconsin using the host Microbacterium foliorum. These bacteriophages range in the number of predicted genes encoded, from 25 to 91, and are distributed across actinobacteriophage clusters EB, EC, EE, and EK.
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
| Phage name | Soil sample collection site | Isolation method | Plaque morphology | Plaque Size | Approx. shotgun coverage (fold) | No. of 150-bp single-end reads | Genome length (bp) | Genome end characteristic | G + C content (%) | No. of ORFs | No. of tRNAs | Cluster |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Albedo | Hudson, WI, 44.984533 N, 92.7545 W | Enriched | Clear with halo | 0.1–1 | 83 | 862,002 | 41,813 | 3′ single-stranded overhang 5′- | 66.6 | 71 | 1 (Gln) | EB |
| Kenzers | Greenville, PA, 41.4124 N, | Enriched | Clear | 1 | 3,293 | 960,944 | 41,261 | 3′ single-stranded overhang 5′- | 66.8 | 70 | 1 (Gln) | EB |
| Swervy | Aston, PA, 39.8657 N, 75.4279 W | Direct | Turbid | 0.5–1 | 325 | 93,814 | 41,510 | 3′ single-stranded overhang 5′- | 66.7 | 71 | 1 (Asn) | EB |
| Cranjis | Upper Chichester, PA, 39.856232 N, 75.443149 W | Direct | Turbid | 3.5–4 | 99 | 40,843 | 53,222 | Circularly permutated | 68.9 | 91 | 0 | EC |
| JaimeB | Aston, PA, | Direct | Clear | 3–4 | 14,635 | 1.8 million | 17,445 | 3′ single-stranded overhang 5′- | 68.7 | 25 | 0 | EE |
| Stormbreaker | Aston, PA, 39.5215 N, 75.260806 W | Direct | Clear | 1 | 1,073 | 74,440 | 54,050 | Circularly permutated | 60 | 54 | 0 | EK |
| Fullmetal | Aston, PA, 39.876667 N, 75.441667 W | Direct | Clear | 1–1.5 | 197 | 410,171 | 54,438 | Circularly permutated | 59.8 | 55 | 0 | EK |
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Taxonomy
TopicsBacteriophages and microbial interactions · Genomics and Phylogenetic Studies · Plant Virus Research Studies
ANNOUNCEMENT
Bacteriophages are incredibly abundant and genetically diverse. To expand our knowledge of bacteriophage evolution and diversity, we report here the characteristics of seven bacteriophages newly isolated using Microbacterium foliorum NRRL B-24224 (1, 2).
All seven bacteriophages were isolated from soil in Pennsylvania and Wisconsin using standard methods as previously described (Table 1) (3, 4). These soil samples were incubated in peptone-yeast extract-calcium (PYCa) liquid medium for 2 hours at 30°C with shaking to suspend phage particles. The suspension was then filtered through a 0.22-µm filter. The filtrate was either directly plated in PYCa soft agar containing M. foliorum or “enriched” by inoculation with M. foliorum and incubation at 30°C for 2–3 days before being filtered and plated (Table 1), yielding phages Albedo, Kenzers, Swervy, Cranjis, JaimeB, Fullmetal, and Stormbreaker. All phages were purified through three rounds of plating. All plates were incubated at 30°C for 24–48 hours.
The Wizard DNA Cleanup Kit (Promega) was used to extract genomic DNA from phage lysates, as previously described (4). Some lysates were concentrated using ZnCl_2_ precipitation prior to genomic DNA extraction (6). The genomic DNA libraries were prepared using a NEBNext Ultra II FS Kit (New England BioLabs) followed by sequencing using Illumina MiSeq (v3 reagents), yielding at least 40,000 150-base single-end reads (Table 1). Raw reads were assembled and then checked for completeness using Newbler v2.9 (7) and Consed v29 (8), respectively (9). Sequencing results and genome characteristics of each bacteriophage are listed in Table 1.
The genomes were autoannotated using DNA Master v5.23.6 (http://cobamide2.bio.pitt.edu), Glimmer v3.02b (10), GeneMark v4.28 (11) and were refined using PECAAN v20221109 (https://pecaan.kbrinsgd.org/index.html), Starterator v462 (https://github.com/SEA-PHAGES/starterator), and Phamerator v539 (12). Transmembrane helices were predicted using SOSUI v1.11 (13), TOPCONS v2.0 (14), TMHMM v2.0 (15), and DeepTMHMM v1.0.24 (16). tRNAs were predicted using ARAGORN v1.2.41 (17) and tRNAscanSE v2.0 (18). Putative functions for other predicted genes were made using HHPRED v3.2 (against the PDB_mmCIF70, NCBI_Conserved_Domains, Pfam-A, and UniProt-SwissProt databases) (19) and BlastP v2.10.0 (against the PhagesDB and NCBI nonredundant databases) (20). All annotations were performed with default parameters.
Phages were assigned to clusters based on gene content similarity (GCS) of at least 35% to sequenced genomes in the Acinobacteriophage database (https://phagesdb.org/) using the GCS tool at phagesDB (5, 21). All seven phages reported here are consistent with features previously described for their respective clusters; the EB cluster phages, Albedo, Kenzers, and Swervy encode for <3 tRNAs; the EC cluster phage Cranjis has all its genes transcribed rightward; the EE cluster phage JaimeB shares all 25 predicted genes including a capsid maturation and protease fusion protein with the other EE cluster members; the EK cluster phages Stormbreaker and Fullmetal have the first ~30 predicted genes transcribed leftward and all the remaining genes transcribed rightward, and they also encode for the largest actinobacteriophage gene product, over 4,400 amino acids (1, 22).
The reference list from the paper itself. Each links out to its DOI / PubMed record.
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