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

Draft Genome Sequence of Lactobacillus crispatus UMB1163, Isolated from the Female Urinary Tract

Fabeiha Khan, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
Steven R. Gill, Editor
Fabeiha Khan
aDepartment of Biology, Loyola University Chicago, Chicago, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Taylor Miller-Ensminger
bBioinformatics 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
Adelina Voukadinova
bBioinformatics 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
Alan J. Wolfe
cDepartment of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Catherine Putonti
aDepartment of Biology, Loyola University Chicago, Chicago, Illinois, USA
bBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
cDepartment of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
dDepartment of Computer Science, Loyola University Chicago, Chicago, 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
Steven R. Gill
University of Rochester School of Medicine and Dentistry
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.00404-20
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Lactobacillus crispatus is a Gram-positive bacterium shown to protect against urinary and vaginal infections. Here, we report the draft genome sequence of L. crispatus UMB1163, isolated from the female urinary tract.

ANNOUNCEMENT

Lactobacillus crispatus is a nonpathogenic bacterium native to the healthy female urogenital tract (1, 2). L. crispatus is critical in preventing common bacterial infections (3–5), such as bacterial vaginosis and vulvovaginal atrophy (VVA), by preserving low pH and producing hydrogen peroxide (4). L. crispatus creates a biofilm in the vaginal epithelium, providing protection against pathogens that cause sexually transmitted diseases and urinary tract infections. Due to its ability to limit pathogens in the urogenital system, L. crispatus strains are being explored for use as a probiotic to prevent urinary tract infections (UTI) in women (6). Here, we present the draft genome sequence of L. crispatus UMB1163, isolated from the bladder of a female with a UTI.

The urine specimen was collected via a transurethral catheter from a woman seeking clinical care at Loyola University Medical Center’s Female Pelvic Medicine and Reconstructive Surgery Center (Maywood, IL, USA) as part of a prior institutional review board (IRB)-approved study (Loyola University Chicago, IRB approval no. 206469) (7). L. crispatus was isolated from this urine specimen using the expanded quantitative urinary culture (EQUC) method (8). The genus and species of the bacterium were determined using matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (8) prior to storage at −80°C. L. crispatus UMB1163 was streaked onto a Columbia nalidixic acid (CNA) agar plate and incubated for 24 h at 35°C with 5% CO2. A single colony was selected and incubated in De Man, Rogosa, and Sharpe (MRS) liquid medium supplemented with newborn calf serum (50 ml/liter) and incubated for 24 h at 35°C with 5% CO2. DNA was extracted using the Qiagen DNeasy blood and tissue kit with a Gram-positive protocol modified as follows: 230 μl of lysis buffer (180 μl of 20 mM Tris-Cl, 2 mM sodium EDTA, and 1.2% Triton X-100) and 50 μl of lysozyme were used in step 2, and the incubation time in step 5 was reduced to 10 min. The DNA was quantified using a Qubit fluorometer. Sequencing was done at the University of Pittsburgh Microbial Genomic Sequencing Center (MiGS) on the Illumina NextSeq 550 platform. MiGS created the libraries using the Illumina Nextera kit. Sequencing produced 1,781,766 pairs of 150-bp reads. Sickle v1.33 (https://github.com/najoshi/sickle) was used to trim the raw reads, which were then assembled using SPAdes v3.13.0 with the “only-assemble” option for k values of 55, 77, 99, and 127 (9). Genome coverage was calculated using BBMap v38.4 (https://sourceforge.net/projects/bbmap/). We used PATRIC v3.6.3 to annotate the genome (10). The publicly available genome was annotated with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v4.11 (11). Unless otherwise stated, default parameters were used for each software tool.

The L. crispatus UMB1163 draft genome sequence is 2,384,113 bp long assembled into 151 contigs with an N50 score of 26,484 bp, genome coverage of 177×, and GC content of 36.6%. The L. crispatus assembly has 66 tRNAs and 5 complete rRNAs (3 5S, 1 16S, and 1 23S). PGAP identified 2,353 protein-coding genes. PATRIC identified 1 CRISPR array, with 7 spacer sequences. While numerous genomes of L. crispatus strains from the vaginal microbiome are available, a greater representation of the genetic diversity of this species within the urinary tract is needed. Sequencing isolates from the urinary tract will provide insight into the role that L. crispatus plays in the female urinary tract.

Data availability.This whole-genome shotgun project has been deposited in GenBank under the accession no. JAAUWJ000000000. The raw sequence reads were deposited in the SRA under the accession no. SRR11441017.

ACKNOWLEDGMENTS

This work was conducted as part of Loyola University Chicago’s Department of Biology Bacterial Genomics course. For prior patient recruitment, we acknowledge the Loyola Urinary Education and Research Collaborative (LUEREC) and the patients who provided the samples for this study.

FOOTNOTES

    • Received 13 April 2020.
    • Accepted 18 May 2020.
    • Published 4 June 2020.
  • Copyright © 2020 Khan et al.

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

REFERENCES

  1. 1.↵
    1. Lepargneur J-P
    . 2016. Lactobacillus crispatus as biomarker of the healthy vaginal tract. Ann Biol Clin (Paris) 74:421–427. (In French.) doi:10.1684/abc.2016.1169.
    OpenUrlCrossRef
  2. 2.↵
    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
  3. 3.↵
    1. Brotman RM,
    2. Shardell MD,
    3. Gajer P,
    4. Fadrosh D,
    5. Chang K,
    6. Silver MI,
    7. Viscidi RP,
    8. Burke AE,
    9. Ravel J,
    10. Gravitt PE
    . 2018. Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy. Menopause 25:1321–1330. doi:10.1097/GME.0000000000001236.
    OpenUrlCrossRef
  4. 4.↵
    1. Mitchell C,
    2. Manhart LE,
    3. Thomas K,
    4. Fiedler T,
    5. Fredricks DN,
    6. Marrazzo J
    . 2012. Behavioral predictors of colonization with Lactobacillus crispatus or Lactobacillus jensenii after treatment for bacterial vaginosis: a cohort study. Infect Dis Obstet Gynecol 2012:706540. doi:10.1155/2012/706540.
    OpenUrlCrossRefPubMed
  5. 5.↵
    1. Aroutcheva A,
    2. Gariti D,
    3. Simon M,
    4. Shott S,
    5. Faro J,
    6. Simoes JA,
    7. Gurguis A,
    8. Faro S
    . 2001. Defense factors of vaginal lactobacilli. Am J Obstet Gynecol 185:375–379. doi:10.1067/mob.2001.115867.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Li T,
    2. Liu Z,
    3. Zhang X,
    4. Chen X,
    5. Wang S
    . 2019. Local probiotic Lactobacillus crispatus and Lactobacillus delbrueckii exhibit strong antifungal effects against vulvovaginal candidiasis in a rat model. Front Microbiol 10:1033. doi:10.3389/fmicb.2019.01033.
    OpenUrlCrossRef
  7. 7.↵
    1. Price TK,
    2. Dune T,
    3. Hilt EE,
    4. Thomas-White KJ,
    5. Kliethermes S,
    6. Brincat C,
    7. Brubaker L,
    8. Wolfe AJ,
    9. Mueller ER,
    10. Schreckenberger PC
    . 2016. The clinical urine culture: enhanced techniques improve detection of clinically relevant microorganisms. J Clin Microbiol 54:1216–1222. doi:10.1128/JCM.00044-16.
    OpenUrlAbstract/FREE Full Text
  8. 8.↵
    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
  9. 9.↵
    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
  10. 10.↵
    1. Brettin T,
    2. Davis JJ,
    3. Disz T,
    4. Edwards RA,
    5. Gerdes S,
    6. Olsen GJ,
    7. Olson R,
    8. Overbeek R,
    9. Parrello B,
    10. Pusch GD,
    11. Shukla M,
    12. Thomason JA,
    13. Stevens R,
    14. Vonstein V,
    15. Wattam AR,
    16. Xia F
    . 2015. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365. doi:10.1038/srep08365.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Tatusova T,
    2. DiCuccio M,
    3. Badretdin A,
    4. Chetvernin V,
    5. Nawrocki EP,
    6. Zaslavsky L,
    7. Lomsadze A,
    8. Pruitt KD,
    9. Borodovsky M,
    10. Ostell J
    . 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi:10.1093/nar/gkw569.
    OpenUrlCrossRefPubMed
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Genome Sequence of Lactobacillus crispatus UMB1163, Isolated from the Female Urinary Tract
Fabeiha Khan, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
Microbiology Resource Announcements Jun 2020, 9 (23) e00404-20; DOI: 10.1128/MRA.00404-20

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.
Draft Genome Sequence of Lactobacillus crispatus UMB1163, Isolated from the Female Urinary Tract
(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
Draft Genome Sequence of Lactobacillus crispatus UMB1163, Isolated from the Female Urinary Tract
Fabeiha Khan, Taylor Miller-Ensminger, Adelina Voukadinova, Alan J. Wolfe, Catherine Putonti
Microbiology Resource Announcements Jun 2020, 9 (23) e00404-20; DOI: 10.1128/MRA.00404-20
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