---
id: "edwards-2022-fizzles"
title: "Complete Genome Sequence of Bacteriophage Fizzles, Isolated from Microbacterium foliorum"
authors:
  - "Skyler Adams"
  - "Gabrielle Spotz"
  - "Riley Babcock"
  - "Chloe Butler"
  - "Samantha Conger"
  - "Madison Crew"
  - "Stephanie Garcia"
  - "Joanna Gonzalez"
  - "Jocelyn Hodges"
  - "Alondra Martinez"
  - "Samuel Munoz"
  - "Chloe O’Grady"
  - "Abigail Quirl"
  - "Kristin Sefcik"
  - "Tanner Taylor"
  - "Gustavo Vazquez"
  - "Faith Cox"
  - "Dustin Edwards"
venue: "Microbiology Resource Announcements"
year: 2022
date: "2022-01-20"
doi: "10.1128/MRA.01077-21"
url: "/research/publications/10-1128-mra-01077-21/"
pdf: "/research/publications/10-1128-mra-01077-21/dustin-edwards-10-1128-mra-01077-21.pdf"
pmc: "https://pmc.ncbi.nlm.nih.gov/articles/PMC8759393/"
openAccess: true
license: "cc-by"
accessions:
  - "genbank:MW924638"
  - "sra:SRX11067172"
citedBy: 1
citedBySource: "OpenAlex, read 2026-09-12"
---
# Complete Genome Sequence of Bacteriophage Fizzles, Isolated from Microbacterium foliorum

Genome of phage Fizzles, isolated from an ant hill in Stephenville; 62,078 bp, 104 genes, only 84 percent similar to its nearest relatives.

## Abstract

Microbacteriophage Fizzles has a 62,078-bp linear double-stranded DNA genome sequence, predicted to contain 104 protein-coding genes. Fizzles is a Siphoviridae actinobacteriophage isolated from an ant hill soil sample collected in Stephenville, TX. Microbacteriophage Fizzles has >83.6% nucleotide identity with microbacteriophages Squash and Nike.

## Full text

Machine-extracted from the PDF linked above. It carries the artifacts that come with reading a typeset two-column page: running heads, figure captions in the flow of the prose, and words broken across line ends. The abstract above is the registry's deposit and is the authoritative text.

Complete Genome Sequence of Bacteriophage Fizzles, Isolated
from Microbacterium foliorum
Skyler Adams,a Gabrielle Spotz,a Riley Babcock,a Chloe Butler,a Samantha Conger,a Madison Crew,a Stephanie Garcia,a
Joanna Gonzalez,a Jocelyn Hodges,a Alondra Martinez,a Samuel Munoz,a Chloe O’Grady,a Abigail Quirl,a Kristin Sefcik,a
Tanner Taylor,a Gustavo Vazquez,a Faith Cox,a Dustin Edwardsa
aDepartment of Biological Sciences, Tarleton State University, Stephenville, Texas, USA
ABSTRACT Microbacteriophage Fizzles has a 62,078-bp linear double-stranded DNA ge-
nome sequence, predicted to contain 104 protein-coding genes. Fizzles is a Siphoviridae
actinobacteriophage isolated from an ant hill soil sample collected in Stephenville, TX.
Microbacteriophage Fizzles has .83.6% nucleotide identity with microbacteriophages
Squash and Nike.
To further understand bacteriophage genomic diversity as part of the Howard Hughes
Medical Institute Science Education Alliance Phage Hunters Advancing Genomic and
Evolutionary Science program (1), we report the genome sequence of microbacteriophage
Fizzles (2). Fizzles was extracted from dry soil collected from an ant bed in Stephenville, TX,
USA (global positioning system [GPS] coordinates, 32.2197N, 98.1989W). The soil samples
were washed with peptone-yeast extract-calcium (PYCa) liquid medium, and bacteriophages
were extracted through a 0.22-
mm filter. The filtered medium was mixed with soft agar con-
taining Microbacterium foliorum strain SEA B-24224, overlaid on PYCa agar, and incubated at
29°C for 48 h. Bacteriophage replication produced small, lytic plaques. Fizzles was isolated by
two rounds of picking a single, well-separated plaque, followed by diluting the bacteriophage
sample in a 10-fold dilution series and plating with M. foliorum. Negative-staining transmis-
sion electron microscopy showed Siphoviridae morphology, with a tail length of 160 nm and
an isometric capsid 65 nm in diameter (Fig. 1), as measured using ImageJ v1.53m (3).
High-titer lysate was produced by flooding “webbed” plates, as described in the
Phage Discovery Guide (4). Genomic DNA was extracted from high-titer lysate using a
modified zinc chloride precipitation method (4, 5). Genomic sequencing libraries were
prepared using the NEBNext Ultra II kit (New England Biolabs, Ipswich, MA) and
sequenced using an Illumina MiSeq instrument at the Pittsburgh Bacteriophage
Institute (Pittsburgh, PA). Sequencing was performed to 2,719-fold coverage from
1,194,881 total reads of 150-bp read length. Assembly to produce a single-bacterio-
phage contig was performed using Newbler v2.9 with default settings, and Consed
v29.0 was used for assembly of a single bacteriophage contig to ensure performance
for quality control (6, 7). Fizzles has a double-stranded linear DNA genome 62,078 bp
long, with 181-bp direct terminal repeats and a 68.2% G1C content. Whole-genome
nucleotide alignment using BLASTn (https://blast.ncbi.nlm.nih.gov/) (8) showed that
Fizzles has a nucleotide sequence identity of .83.6% with Microbacterium phages
Squash (GenBank accession number MH153813) and Nike (MT114166).
Initial auto-annotation was performed using GLIMMER v3.02 (9) and GeneMark v2.5p
(10, 11), and the annotation was manually refined using Phamerator (http://phamerator
.org/), DNA Master v5.23.2 (http://phagesdb.org/DNAMaster/), and PECAAN. No tRNA
genes were identified using Aragorn v1.2.38 (12) and tRNAscan-SE v2.0 (13). Putative func-
tions for 72 of 104 predicted protein-coding genes were assigned using NCBI BLASTp (8)
and HHpred v3.0beta (14, 15). All tools were run with default parameters. Start codon
Editor John J. Dennehy, Queens College CUNY
Copyright © 2022 Adams et al. This is an
open-access article distributed under the terms
of the Creative Commons Attribution 4.0
International license.
Address correspondence to Dustin Edwards,
dcedwards@tarleton.edu.
The authors declare no conflict of interest.
Received 3 November 2021
Accepted 6 December 2021
Published 6 January 2022
Volume 11 Issue 1 e01077-21 mra.asm.org 1
GENOME SEQUENCES
Downloaded from https://journals.asm.org/journal/mra on 26 July 2026 by 156.146.253.207.

usage was 77.7% for AUG, 21.4% for GUG, and 0.97% for UUG. Genes were transcribed
rightward (48.1% of genome) and leftward (51.9% of genome) and encode structural pro-
teins, histidine triad nucleotide-binding protein, hydrolase, MazG-like nucleotide pyrophos-
phohydrolase, HNH endonuclease, RuvC-like resolvase, DNA primase/helicase, RecA-like
DNA recombinase, nucleotide pyrophosphohydrolase, and DnaJ-like chaperonin.
Data availability. The genome sequence for microbacteriophage Fizzles is avail-
able at GenBank under accession number MW924638. The raw reads are available
under SRA accession number SRX11067172.
ACKNOWLEDGMENTS
Support for this research was provided by Tarleton State University College of
Science and Technology and by the Howard Hughes Medical Institute Science
Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-
PHAGES) research and education program.
We thank Graham Hatfull, Welkin Pope, Deborah Jacobs-Sera, Daniel Russell,
Rebecca Garlena, Sally Malloy, and Phoebe Doss for their technical support during the
imaging of the virion and the isolation, sequencing, and annotation of this genome.
REFERENCES
1. Jordan TC, Burnett SH, Carson S, Caruso SM, Clase K, DeJong RJ, Dennehy
JJ, Denver DR, Dunbar D, Elgin SCR, Findley AM, Gissendanner CR,
Golebiewska UP, Guild N, Hartzog GA, Grillo WH, Hollowell GP, Hughes LE,
Johnson A, King RA, Lewis LO, Li W, Rosenzweig F, Rubin MR, Saha MS,
Sandoz J, Shaffer CD, Taylor B, Temple L, Vazquez E, Ware VC, Barker LP,
Bradley KW, Jacobs-Sera D, Pope WH, Russell DA, Cresawn SG, Lopatto D,
Bailey CP, Hatfull GF. 2014. A broadly implementable research course in
phage discovery and genomics for first-year undergraduate students.
mBio 5:e01051-13. https://doi.org/10.1128/mBio.01051-13.
2. Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database.
Bioinformatics 33:784–786. https://doi.org/10.1093/bioinformatics/btw711.
3. Schneider CA, Rasband WS, Eliceiri KW. 2012. NIH Image to ImageJ: 25 years of
image analysis. Nat Methods 9:671–675. https://doi.org/10.1038/nmeth.2089.
4. Poxleitner M, Pope W, Jacobs-Sera D, Sivanathan V, Hatfull G. 2018.
Phage discovery guide. Howard Hughes Medical Institute, Chevy Chase,
MD.
5. Santos MA. 1991. An improved method for the small scale prepara-
tion of bacteriophage DNA based on phage precipitation by zinc
chloride. Nucleic Acids Res 19:5442. https://doi.org/10.1093/nar/19
.19.5442.
6. Russell DA. 2018. Sequencing, assembling, and finishing complete bacte-
riophage genomes. Methods Mol Biol 1681:109–125. https://doi.org/10
.1007/978-1-4939-7343-9_9.
7. Gordon D, Green P. 2013. Consed: a graphical editor for next-generation
sequencing. Bioinformatics 29:2936–2937. https://doi.org/10.1093/bioinformatics/
btt515.
FIG 1 Transmission electron microscopy (TEM) of microbacteriophage Fizzles. High-titer lysate was
placed on a carbon type-B 300-mesh grid, stained with 1% uranyl acetate, and imaged using an FEI
Tecnai G2 Spirit BioTwin instrument (NL1.160G). TEM micrographs of negatively stained Fizzles
particles show a tail length of 160 nm and an icosahedral capsid 65 nm in diameter.
Adams et al.
Volume 11 Issue 1 e01077-21 mra.asm.org 2
Downloaded from https://journals.asm.org/journal/mra on 26 July 2026 by 156.146.253.207.

8. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local align-
ment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022
-2836(05)80360-2.
9. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved micro-
bial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641.
https://doi.org/10.1093/nar/27.23.4636.
10. Borodovsky M, Mills R, Besemer J, Lomsadze A. 2003. Prokaryotic
gene prediction using GeneMark and GeneMark.hmm. Curr Protoc
Bioinformatics 1:4.5.1–4.5.16. https://doi.org/10.1002/0471250953
.bi0405s01.
11. Besemer J, Borodovsky M. 2005. GeneMark: Web software for gene finding
in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33:W451–W454.
https://doi.org/10.1093/nar/gki487.
12. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes
and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16.
https://doi.org/10.1093/nar/gkh152.
13. Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and con-
text for analysis of transfer RNA genes. Nucleic Acids Res 44:W54–W57.
https://doi.org/10.1093/nar/gkw413.
14. Söding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for
protein homology detection and structure prediction. Nucleic Acids Res
33:W244–W248. https://doi.org/10.1093/nar/gki408.
15. Zimmermann L, Stephens A, Nam S-Z, Rau D, Kübler J, Lozajic M, Gabler F,
Söding J, Lupas AN, Alva V. 2018. A completely reimplemented MPI Bioin-
formatics Toolkit with a new HHpred server at its core. J Mol Biol 430:
2237–2243. https://doi.org/10.1016/j.jmb.2017.12.007.
Microbiology Resource Announcement
Volume 11 Issue 1 e01077-21 mra.asm.org 3
Downloaded from https://journals.asm.org/journal/mra on 26 July 2026 by 156.146.253.207.