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
Prokaryotes

Draft Genome Sequence of Acinetobacter sp. Strain VT-511 Isolated from the Stomach of a Patient with Gastric Cancer

George Tetz, Victor Tetz
George Tetz
aInstitute of Human Microbiology, New York, New York, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Victor Tetz
bFirst State I. P. Pavlov Medical University, Saint Petersburg, Russia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/genomeA.01202-15
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

We report the draft genome sequence of Acinetobacter sp. strain VT-511, which was obtained from the stomach of a patient with gastric cancer. The genome of Acinetobacter sp. VT-511 is composed of approximately 3,416,321 bp and includes 3,214 predicted protein-coding genes.

GENOME ANNOUNCEMENT

The genus Acinetobacter includes aerobic, nonmotile, Gram-negative coccobacilli. Species of this genus are widely distributed in nature and have been isolated from soil and water (1). Acinetobacter spp. are associated with nosocomial infections, including pneumonia, meningitis, and sepsis (2-4). In this study, we sequenced and analyzed the genome of clinically isolated Acinetobacter sp. strain VT-511 that was isolated from the stomach of a patient with gastric cancer.

Comparative 16S rRNA analysis revealed 99% sequence identity with Acinetobacter schindleri NIPH 900, a bacterium found on human conjunctiva and not associated with gut microbiota (5).

Acinetobacter sp. VT-511 was then characterized using biochemical analysis and matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry that revealed differences with other A. schindleri strains.

Whole-genome sequencing was performed using the Illumina MiSeq HiSeq 2500 according to the manufacturer's instructions (Illumina, Inc., CA). The generated reads were trimmed and assembled de novo with SPAdes genome assembler software, version 3.5.0 (6). A total of 121 contigs with an average coverage of 125× were generated. The draft genome of Acinetobacter sp. VT-511 consisted of 3,416,321 bp and had a G+C content of 42.7%.

Sequence annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline and by using RAST (7, 8). The genome of Acinetobacter sp. VT-511 was composed of 3,214 predicted protein-coding sequences and 96 predicted RNA genes, including 14 rRNAs, 81 tRNAs, and 1 noncoding RNA. The analysis revealed that the predicted gene sequences for multidrug resistance transporters of ABC, MATE, and RND families and macrolide-specific efflux proteins were also present. In addition, genes encoding resistance to ethidium bromide, fluoroquinolones, macrolides, fosmidomycin, and bacteriocin were identified. The genome also harbored genes encoding virulence factors such as adhesins, polysaccharides, peptidases, and proteases (9, 10).

The genome size of Acinetobacter sp. VT-511 (3,416,321 bp) was larger than that of A. schindleri NIPH 900 (3,404,540 bp), which is the phylogenetically closest organism. However, the number of protein-coding genes harbored by Acinetobacter sp. VT-511 (3,214 genes) was lower than the number harbored by A. schindleri NIPH 900 (3,232 genes). The G+C contents of Acinetobacter sp. VT-511 and A. schindleri NIPH 900 were 42.7% and 42.2%, respectively.

Digital DNA-DNA hybridization (DDH) was performed using Acinetobacter sp. VT-511 and A. schindleri NIPH 900 and assessed with GGDC 2.0. The obtained DDH value of 75.6% was below the threshold value of 79% set for genomes belonging to the same subspecies (11, 12). Acinetobacter sp. VT-511 harbored genes involved in the following processes: metabolism of aromatic compounds, capsular and extracellular polysaccharide expression, antibiotic resistance, and the YefM-YoeB toxin antitoxin system. These genes were not present in A. schindleri NIPH 900. The regions encoding genes involved in biotin synthesis, transcriptional regulators, oxidative stress response, and recycling of peptidoglycan had sequence similarities lower than 50% between the two strains.

In conclusion, the draft genome sequence of Acinetobacter sp. VT-511 was determined. The findings of this study may be useful for identification of Acinetobacter species in microbiota of patients with gastrointestinal tract malignancies.

Nucleotide sequence accession number.This genome sequencing project has been deposited in GenBank under the accession no. LFRE00000000.

ACKNOWLEDGMENTS

This work was supported by the Institute of Human Microbiology, LLC.

We thank Albert Tai for performing sequencing at the Genomics Core Facility of Tufts University.

FOOTNOTES

    • Received 1 September 2015.
    • Accepted 3 September 2015.
    • Published 15 October 2015.
  • Copyright © 2015 Tetz and Tetz.

This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

REFERENCES

  1. 1.↵
    1. Warskow AL,
    2. Juni E
    . 1972. Nutritional requirements of Acinetobacter strains isolated from soil, water, and sewage. J Bacteriol 112:1014–1016.
    OpenUrlAbstract/FREE Full Text
  2. 2.↵
    1. Horrevorts A,
    2. Bergman K,
    3. Kollee L,
    4. Breuker I,
    5. Tjernberg I,
    6. Dijkshoorn L
    . 1995. Clinical and epidemiological investigations of Acinetobacter genomospecies 3 in a neonatal intensive care unit. J Clin Microbiol 6:1567–1572.
    OpenUrl
  3. 3.↵
    1. Jiménez-Mejías ME,
    2. Pachón J,
    3. Becerril B,
    4. Palomino-Nicás J,
    5. Rodríguez-Cobacho A,
    6. Revuelta M
    . 1997. Treatment of multidrug-resistant Acinetobacter baumannii meningitis with ampicillin/sulbactam. Clin Infect Dis 24:932–935. doi:10.1093/clinids/24.5.932.
    OpenUrlCrossRefPubMedWeb of Science
  4. 4.↵
    1. Nakwan N,
    2. Chokephaibulkit K
    . 2013. Carbapenem-resistant Acinetobacter baumannii bacteremia in neonates. Pediatr Infect Dis J 32:197. doi:10.1097/INF.0b013e31827c97ba.
    OpenUrlCrossRefPubMed
  5. 5.↵
    1. Nemec A,
    2. De Baere T,
    3. Tjernberg I,
    4. Vaneechoutte M,
    5. Van Der Reijden TJ,
    6. Dijkshoorn L
    . 2001. Acinetobacter ursingii sp. nov. and Acinetobacter schindleri sp. nov., isolated from human clinical specimens. Int J Syst Evol Microbiol 51(PT 5):1891–1899. doi:10.1099/00207713-51-5-1891.
    OpenUrlCrossRefPubMedWeb of Science
  6. 6.↵
    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
  7. 7.↵
    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
  8. 8.↵
    1. Tatusova T,
    2. DiCuccio M,
    3. Badretdin A,
    4. Chetvernin V,
    5. Ciufo S,
    6. Li W
    . 2013. Prokaryotic genome annotation pipeline. In Beck J, Benson D, Coleman J, Hoeppner M, Johnson M, Maglott D, Mizrachi I, Morris R, Ostell J, Pruitt K, Rubinstein W, Sayers E, Sirotkin K, Tatusova T (ed), The NCBI handbook, 2nd ed. National Center for Biotechnology Information, Bethesda, MD.
  9. 9.↵
    1. Tetz GV,
    2. Artemenko NK,
    3. Tetz VV
    . 2009. Effect of DNase and antibiotics on biofilm characteristics. Antimicrob Agents Chemother 53:1204–1209. doi:10.1128/AAC.00471-08.
    OpenUrlAbstract/FREE Full Text
  10. 10.↵
    1. Braun G
    . 2008. Virulence mechanisms of Acinetobacter, p 145–154. In Bendinelli M, Friedman H, Bergogne-Berezin E (ed), Acinetobacter biology and pathogenesis. Springer Verlag, New York, NY.
  11. 11.↵
    1. Auch AF,
    2. von Jan M,
    3. Klenk H-P,
    4. Göker M
    . 2010. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134. doi:10.4056/sigs.531120.
    OpenUrlCrossRefPubMedWeb of Science
  12. 12.↵
    1. Chun J,
    2. Rainey FA
    . 2014. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 64:316–324. doi:10.1099/ijs.0.054171-0.
    OpenUrlCrossRefPubMed
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Genome Sequence of Acinetobacter sp. Strain VT-511 Isolated from the Stomach of a Patient with Gastric Cancer
George Tetz, Victor Tetz
Genome Announcements Oct 2015, 3 (5) e01202-15; DOI: 10.1128/genomeA.01202-15

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 Acinetobacter sp. Strain VT-511 Isolated from the Stomach of a Patient with Gastric Cancer
(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 Acinetobacter sp. Strain VT-511 Isolated from the Stomach of a Patient with Gastric Cancer
George Tetz, Victor Tetz
Genome Announcements Oct 2015, 3 (5) e01202-15; DOI: 10.1128/genomeA.01202-15
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • GENOME 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