Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Genome Sequences

Genome Sequence of Pseudomonas Phage UMP151, Isolated from the Female Bladder Microbiota

Genevieve Johnson, Catherine Putonti
Simon Roux, Editor
Genevieve Johnson
aBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Catherine Putonti
aBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
bDepartment of Biology, Loyola University Chicago, Chicago, Illinois, USA
cDepartment of Computer Science, Loyola University Chicago, Chicago, Illinois, USA
dDepartment of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Catherine Putonti
Simon Roux
DOE Joint Genome Institute
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.00853-19
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

A temperate bacteriophage, designated UMP151, was isolated from a Pseudomonas aeruginosa strain from a catheterized urine sample of a woman with overactive bladder (OAB) symptoms. The 41,303-bp genome sequence of Pseudomonas phage UMP151 exhibits sequence similarity to prophage and lytic phage sequences isolated from other areas of the human body.

ANNOUNCEMENT

Prior studies of the female urinary microbiota have identified associations between bladder bacteria and urinary symptoms (1–6). Recent surveys have found that viruses, particularly bacteriophages (phages), far outnumber bacteria in the urinary tract (7) and that the majority of these bacterial members are lysogens, some harboring upwards of 10 intact prophages (8). In our ongoing effort to characterize the phage population of the urinary tract microbiota, we describe here the genome sequence of a new isolate, Pseudomonas phage UMP151, a temperate phage induced from a Pseudomonas aeruginosa strain isolated from the urine collected via transurethral catheterization from a woman with overactive bladder (OAB) symptoms. P. aeruginosa is not frequently found within the bladder microbiota of healthy women (9); rather, it is an opportunistic pathogen of the urinary tract typically associated with nosocomial urinary tract infections (10). Furthermore, no association between P. aeruginosa and OAB has been identified (9). Pseudomonas phage UMP151 is the fourth Pseudomonas phage isolated from the urinary tract to be described in the literature (11–13) and the first genome of a Pseudomonas phage from the bladder microbiota.

P. aeruginosa strain UMB0151 was isolated via culture from a prior study (1, 2, 6, 9) and stored at −80°C. We streaked this bacterial strain on an LB agar plate and grew it overnight at 37°C. A single colony was selected to inoculate liquid LB medium and was grown overnight with shaking at 37°C. The overnight culture was centrifuged for 8 min at 13,000 × g and filtered through a 0.2-μm cellulose acetate syringe filter, and then the filtrate was spotted (10 μl) onto a lawn of P. aeruginosa ATCC 15692. The plate was incubated overnight at 37°C. Plaques were found where the filtrate was spotted. Spots were harvested, suspended in LB medium, and filtered using a 0.2-μm cellulose acetate syringe filter. A sample of 300 μl was pipetted and treated with 5 U of Optizyme DNase I (Fisher BioReagents) prior to DNA extraction using the Quick-DNA kit (Zymo) following the manufacturer’s instructions. The Nextera XT DNA library preparation kit was used, and the library was sequenced on an Illumina MiSeq sequencer using the MiSeq reagent kit v2 (500 cycles), producing 278,404 paired-end 250-bp reads. Raw reads were first trimmed for quality using sickle (https://github.com/najoshi/sickle) and then assembled by SPAdes (v3.11.1) (14) using the “only assembler” option for k value of 55, 77, 99, and 127. In total, 4,828 assembled contigs were produced, ranging in size from 128 to 41,303 bp. Coverage was calculated using BBmap v38.47 (http://sourceforge.net/projects/bbmap). The largest contig, representative of the complete genome sequence of UMP151, had a significantly greater coverage (768×) than the other contigs assembled (∼1×). The genome termini were determined using PhageTerm v1.0.12 (15) via Galaxy (16), and the genome was annotated via RAST using the Classic RAST pipeline (17).

The complete genome for Pseudomonas phage UMP151 is 41,303 bp with a GC content of 63.2%. The genome encodes 56 genes. The complete genome sequence was queried against the NCBI nr/nt database via MegaBLAST, identifying 100% sequence identity and coverage with P. aeruginosa strain MRSN12280 (GenBank accession number CP028162), which was isolated from the sacrum of an individual. The best hit to an isolated phage was to the siphovirus Pseudomonas phage CF5 (GenBank accession number MK511057; query coverage, 77%; sequence identity, 97.48%), which was isolated from the lung of a cystic fibrosis patient (18).

Data availability.The draft whole-genome project for Pseudomonas phage UMP151 has been deposited at DDBJ/EMBL/GenBank under accession number MK934841. Raw sequence reads are deposited at DDBJ/EMBL/GenBank under accession number SRR9072121, which is part of BioProject number PRJNA494532.

ACKNOWLEDGMENTS

We thank Alan J. Wolfe for the bacterial isolate and Roberto Limeira for whole-genome sequencing of the isolate at Loyola’s Genomics Facility (Maywood, IL).

G.J.’s research was supported through the Loyola University Mulcahy Research Fellowship.

FOOTNOTES

    • Received 17 July 2019.
    • Accepted 24 July 2019.
    • Published 15 August 2019.
  • Copyright © 2019 Johnson and Putonti.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Pearce MM,
    2. Hilt EE,
    3. Rosenfeld AB,
    4. Zilliox MJ,
    5. Thomas-White K,
    6. Fok C,
    7. Kliethermes S,
    8. Schreckenberger PC,
    9. Brubaker L,
    10. Gai X,
    11. Wolfe AJ
    . 2014. The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. mBio 5:e01283-14. doi:10.1128/mBio.01283-14.
    OpenUrlAbstract/FREE Full Text
  2. 2.↵
    1. Pearce MM,
    2. Zilliox MJ,
    3. Rosenfeld AB,
    4. Thomas-White KJ,
    5. Richter HE,
    6. Nager CW,
    7. Visco AG,
    8. Nygaard IE,
    9. Barber MD,
    10. Schaffer J,
    11. Moalli P,
    12. Sung VW,
    13. Smith AL,
    14. Rogers R,
    15. Nolen TL,
    16. Wallace D,
    17. Meikle SF,
    18. Gai X,
    19. Wolfe AJ,
    20. Brubaker L
    . 2015. The female urinary microbiome in urgency urinary incontinence. Am J Obstet Gynecol 213:347.e1–347.e11. doi:10.1016/j.ajog.2015.07.009.
    OpenUrlCrossRef
  3. 3.↵
    1. Fok CS,
    2. McKinley K,
    3. Mueller ER,
    4. Kenton K,
    5. Schreckenberger P,
    6. Wolfe A,
    7. Brubaker L
    . 2013. Day of surgery urine cultures identify urogynecologic patients at increased risk for postoperative urinary tract infection. J Urol 189:1721–1724. doi:10.1016/j.juro.2012.11.167.
    OpenUrlCrossRef
  4. 4.↵
    1. Karstens L,
    2. Asquith M,
    3. Davin S,
    4. Stauffer P,
    5. Fair D,
    6. Gregory WT,
    7. Rosenbaum JT,
    8. McWeeney SK,
    9. Nardos R
    . 2016. Does the urinary microbiome play a role in urgency urinary incontinence and its severity? Front Cell Infect Microbiol 6:78. doi:10.3389/fcimb.2016.00078.
    OpenUrlCrossRef
  5. 5.↵
    1. Nienhouse V,
    2. Gao X,
    3. Dong Q,
    4. Nelson DE,
    5. Toh E,
    6. McKinley K,
    7. Schreckenberger P,
    8. Shibata N,
    9. Fok CS,
    10. Mueller ER,
    11. Brubaker L,
    12. Wolfe AJ,
    13. Radek KA
    . 2014. Interplay between bladder microbiota and urinary antimicrobial peptides: mechanisms for human urinary tract infection risk and symptom severity. PLoS One 9:e114185. doi:10.1371/journal.pone.0114185.
    OpenUrlCrossRef
  6. 6.↵
    1. Thomas-White KJ,
    2. Hilt EE,
    3. Fok C,
    4. Pearce MM,
    5. Mueller ER,
    6. Kliethermes S,
    7. Jacobs K,
    8. Zilliox MJ,
    9. Brincat C,
    10. Price TK,
    11. Kuffel G,
    12. Schreckenberger P,
    13. Gai X,
    14. Brubaker L,
    15. Wolfe AJ
    . 2016. Incontinence medication response relates to the female urinary microbiota. Int Urogynecol J 27:723–733. doi:10.1007/s00192-015-2847-x.
    OpenUrlCrossRef
  7. 7.↵
    1. Garretto A,
    2. Miller-Ensminger T,
    3. Wolfe AJ,
    4. Putonti C
    . 2019. Bacteriophages of the lower urinary tract. Nat Rev Urol 16:422–432. doi:10.1038/s41585-019-0192-4.
    OpenUrlCrossRef
  8. 8.↵
    1. Miller-Ensminger T,
    2. Garretto A,
    3. Brenner J,
    4. Thomas-White K,
    5. Zambom A,
    6. Wolfe AJ,
    7. Putonti C
    . 2018. Bacteriophages of the urinary microbiome. J Bacteriol 200:e00738-17. doi:10.1128/JB.00738-17.
    OpenUrlAbstract/FREE Full Text
  9. 9.↵
    1. Hilt EE,
    2. McKinley K,
    3. Pearce MM,
    4. Rosenfeld AB,
    5. Zilliox MJ,
    6. Mueller ER,
    7. Brubaker L,
    8. Gai X,
    9. Wolfe AJ,
    10. Schreckenberger PC
    . 2014. Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J Clin Microbiol 52:871–876. doi:10.1128/JCM.02876-13.
    OpenUrlAbstract/FREE Full Text
  10. 10.↵
    1. Djordjevic Z,
    2. Folic MM,
    3. Zivic Z,
    4. Markovic V,
    5. Jankovic SM
    . 2013. Nosocomial urinary tract infections caused by Pseudomonas aeruginosa and Acinetobacter species: sensitivity to antibiotics and risk factors. Am J Infect Control 41:1182–1187. doi:10.1016/j.ajic.2013.02.018.
    OpenUrlCrossRef
  11. 11.↵
    1. Brown-Jaque M,
    2. Muniesa M,
    3. Navarro F
    . 2016. Bacteriophages in clinical samples can interfere with microbiological diagnostic tools. Sci Rep 6:33000. doi:10.1038/srep33000.
    OpenUrlCrossRef
  12. 12.↵
    1. Jalil MB,
    2. Al-Hmudi HA,
    3. Al-Alsaad LA,
    4. Abdul-Hussein ZR
    . 2018. Isolation and characterization of bacterio phagesagainst multiple drug resistant Pseudomonas aeruginosa with using the bacteriophage as a therpy in the mice model. Int J Dev Res 7:11519.
    OpenUrl
  13. 13.↵
    1. Johnson G,
    2. Wolfe AJ,
    3. Putonti C
    . 2019. Characterization of the φCTX-like Pseudomonas aeruginosa phage Dobby isolated from the kidney stone microbiota. Access Microbiol 1. doi:10.1099/acmi.0.000002.
    OpenUrlCrossRef
  14. 14.↵
    1. Bankevich A,
    2. Nurk S,
    3. Antipov D,
    4. Gurevich AA,
    5. Dvorkin M,
    6. Kulikov AS,
    7. Lesin VM,
    8. Nikolenko SI,
    9. Pham S,
    10. Prjibelski AD,
    11. Pyshkin AV,
    12. Sirotkin AV,
    13. Vyahhi N,
    14. Tesler G,
    15. Alekseyev MA,
    16. Pevzner PA
    . 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:10.1089/cmb.2012.0021.
    OpenUrlCrossRefPubMed
  15. 15.↵
    1. Garneau JR,
    2. Depardieu F,
    3. Fortier L-C,
    4. Bikard D,
    5. Monot M
    . 2017. PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data. Sci Rep 7:8292. doi:10.1038/s41598-017-07910-5.
    OpenUrlCrossRef
  16. 16.↵
    1. Afgan E,
    2. Baker D,
    3. Batut B,
    4. van den Beek M,
    5. Bouvier D,
    6. Čech M,
    7. Chilton J,
    8. Clements D,
    9. Coraor N,
    10. Grüning BA,
    11. Guerler A,
    12. Hillman-Jackson J,
    13. Hiltemann S,
    14. Jalili V,
    15. Rasche H,
    16. Soranzo N,
    17. Goecks J,
    18. Taylor J,
    19. Nekrutenko A,
    20. Blankenberg D
    . 2018. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res 46:W537–W544. doi:10.1093/nar/gky379.
    OpenUrlCrossRefPubMed
  17. 17.↵
    1. Aziz RK,
    2. Bartels D,
    3. Best AA,
    4. DeJongh M,
    5. Disz T,
    6. Edwards RA,
    7. Formsma K,
    8. Gerdes S,
    9. Glass EM,
    10. Kubal M,
    11. Meyer F,
    12. Olsen GJ,
    13. Olson R,
    14. Osterman AL,
    15. Overbeek RA,
    16. McNeil LK,
    17. Paarmann D,
    18. Paczian T,
    19. Parrello B,
    20. Pusch GD,
    21. Reich C,
    22. Stevens R,
    23. Vassieva O,
    24. Vonstein V,
    25. Wilke A,
    26. Zagnitko O
    . 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi:10.1186/1471-2164-9-75.
    OpenUrlCrossRefPubMed
  18. 18.↵
    1. Tariq MA,
    2. Everest FLC,
    3. Cowley LA,
    4. Wright R,
    5. Holt GS,
    6. Ingram H,
    7. Duignan LAM,
    8. Nelson A,
    9. Lanyon CV,
    10. Perry A,
    11. Perry JD,
    12. Bourke S,
    13. Brockhurst MA,
    14. Bridge SH,
    15. De Soyza A,
    16. Smith DL
    . 2019. Temperate bacteriophages from chronic Pseudomonas aeruginosa lung infections show disease-specific changes in host range and modulate antimicrobial susceptibility. mSystems 4:e00191-18. doi:10.1128/mSystems.00191-18.
    OpenUrlAbstract/FREE Full Text
PreviousNext
Back to top
Download PDF
Citation Tools
Genome Sequence of Pseudomonas Phage UMP151, Isolated from the Female Bladder Microbiota
Genevieve Johnson, Catherine Putonti
Microbiology Resource Announcements Aug 2019, 8 (33) e00853-19; DOI: 10.1128/MRA.00853-19

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Genome Sequence of Pseudomonas Phage UMP151, Isolated from the Female Bladder Microbiota
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Genome Sequence of Pseudomonas Phage UMP151, Isolated from the Female Bladder Microbiota
Genevieve Johnson, Catherine Putonti
Microbiology Resource Announcements Aug 2019, 8 (33) e00853-19; DOI: 10.1128/MRA.00853-19
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X