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 Actinomyces odontolyticus subsp. actinosynbacter Strain XH001, the Basibiont of an Oral TM7 Epibiont

Jeffrey S. McLean, Quanhui Liu, Batbileg Bor, Joseph K. Bedree, Lujia Cen, Michael Watling, Thao T. To, Roger E. Bumgarner, Xuesong He, Wenyuan Shi
Jeffrey S. McLean
aDepartment of Periodontics, University of Washington, Seattle, Washington, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Quanhui Liu
aDepartment of Periodontics, University of Washington, Seattle, Washington, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Batbileg Bor
bSchool of Dentistry, University of California Los Angeles, Los Angeles, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Joseph K. Bedree
bSchool of Dentistry, University of California Los Angeles, Los Angeles, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lujia Cen
bSchool of Dentistry, University of California Los Angeles, Los Angeles, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michael Watling
cDepartment of Microbiology, University of Washington, Seattle, Washington, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Thao T. To
aDepartment of Periodontics, University of Washington, Seattle, Washington, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Thao T. To
Roger E. Bumgarner
cDepartment of Microbiology, University of Washington, Seattle, Washington, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Xuesong He
bSchool of Dentistry, University of California Los Angeles, Los Angeles, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wenyuan Shi
bSchool of Dentistry, University of California Los Angeles, Los Angeles, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/genomeA.01685-15
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Here, we present the draft genome sequence of Actinomyces odontolyticus subsp. actinosynbacter strain XH001, isolated from the human oral cavity. Uniquely, it was discovered as a host bacterium to the ultrasmall epibiont TM7x, which is the first cultivated member of “Candidatus Saccharibacteria” (formerly candidate phylum TM7).

GENOME ANNOUNCEMENT

Although Actinomyces odontolyticus is a commensal oral species, it is an opportunistic pathogen that has been linked to many diseases, most notably its association with actinomycosis, the formation of painful abscesses in the mouth, lungs, or gastrointestinal tract (1). Furthermore, oral Actinomyces spp. have been linked to childhood caries, periodontitis, and human oral carcinomas (2–4). A newly reported interaction between an obligate ultrasmall epibiont, TM7x (a recently cultivated member of “Candidatus Saccharibacteria,” formerly candidate phylum TM7), and its basibiont A. odontolyticus subsp. actinosynbacter strain XH001 (5) provides a great system to study parasitic epibiont symbiosis in the bacterial kingdom. The genome presented here from the isolated strain derived from human saliva (6, 7) will enable further research into this unique interaction.

A. odontolyticus subsp. actinosynbacter strain XH001 was cultured in brain heart infusion (BHI) medium and incubated at 37°C under microaerobic conditions until exponential phase was reached. Genomic DNA was extracted using the Epicentre MasterPure DNA purification kit. The complete genome sequence was determined via Illumina sequencing using paired-end 300-bp reads. All quality-trimmed reads were de novo assembled using SPAdes version 3.61 (8, 9).

The draft genome is 2,336,127 bp and assembled into 5 contigs, with an overall G+C content of 65.9%. Gene annotation using the Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) provided by National Center for Biotechnology Information (NCBI) identified a total of 1,998 genes, consisting of 1,936 coding sequences, 49 tRNAs, and 6 rRNAs. A set of 49 single-copy genes was extracted and aligned to 100 sequenced genomes using the Department of Energy Systems Biology Knowledgebase (KBase; http://kbase.us). The resulting likelihood-based tree was built from the 49 concatenated genes and indicated relatedness to the sequenced species A. odontolyticus and Actinomyces sp. ICM39; however, the closest sequenced genome, A. odontolyticus F0309, produced an average nucleotide identity of only 93.7% (10). Using an additional method described for the delineation of species using 40 universal marker genes (11), XH001 was just above the cutoff for the A. odontolyticus species. These results support that this strain conservatively represents a subspecies of A. odontolyticus, and the name “A. odontolyticus subsp. actinosynbacter strain XH001” is proposed. The report by Bor et al. (5) presents further physiological characteristics of this strain.

Nucleotide sequence accession numbers.This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LLVT00000000. The version described in this paper is version LLVT00000000.1.

ACKNOWLEDGMENTS

We declare no conflicts of interest.

FOOTNOTES

    • Received 7 December 2015.
    • Accepted 9 December 2015.
    • Published 4 February 2016.
  • Copyright © 2016 McLean 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. Aas JA,
    2. Paster BJ,
    3. Stokes LN,
    4. Olsen I,
    5. Dewhirst FE
    . 2005. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43:5721–5732. doi:10.1128/JCM.43.11.5721-5732.2005.
    OpenUrlAbstract/FREE Full Text
  2. 2.↵
    1. Colombo AV,
    2. Silva CM,
    3. Haffajee A,
    4. Colombo AP
    . 2006. Identification of oral bacteria associated with crevicular epithelial cells from chronic periodontitis lesions. J Med Microbiol 55:609–615. doi:10.1099/jmm.0.46417-0.
    OpenUrlCrossRefPubMedWeb of Science
  3. 3.↵
    1. Becker MR,
    2. Paster BJ,
    3. Leys EJ,
    4. Moeschberger ML,
    5. Kenyon SG,
    6. Galvin JL,
    7. Boches SK,
    8. Dewhirst FE,
    9. Griffen AL
    . 2002. Molecular analysis of bacterial species associated with childhood caries. J Clin Microbiol 40:1001–1009. doi:10.1128/JCM.40.3.1001-1009.2002.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    1. Nagy KN,
    2. Sonkodi I,
    3. Szöke I,
    4. Nagy E,
    5. Newman HN
    . 1998. The microflora associated with human oral carcinomas. Oral Oncol 34:304–308. doi:10.1016/S1368-8375(98)80012-2.
    OpenUrlCrossRefPubMedWeb of Science
  5. 5.↵
    1. Bor B,
    2. Poweleit N,
    3. Bois J,
    4. Cen L,
    5. Bedree J,
    6. Zhou ZH,
    7. Gunsalus R,
    8. Lux R,
    9. McLean J,
    10. He X,
    11. Shi W
    . 2015. Phenotypic and physiological characterization of the epibiotic interaction between TM7x and its basibiont Actinomyces. Microb. Ecol.
  6. 6.↵
    1. Edlund A,
    2. Yang Y,
    3. Hall AP,
    4. Guo L,
    5. Lux R,
    6. He X,
    7. Nelson KE,
    8. Nealson KH,
    9. Yooseph S,
    10. Shi W,
    11. McLean JS
    . 2013. An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome. Microbiome 1:25. doi:10.1186/2049-2618-1-25.
    OpenUrlCrossRefPubMed
  7. 7.↵
    1. He X,
    2. McLean JS,
    3. Edlund A,
    4. Yooseph S,
    5. Hall AP,
    6. Liu SY,
    7. Dorrestein PC,
    8. Esquenazi E,
    9. Hunter RC,
    10. Cheng G,
    11. Nelson KE,
    12. Lux R,
    13. Shi W
    . 2015. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proc Natl Acad Sci USA 112:244–249. doi:10.1073/pnas.1419038112.
    OpenUrlAbstract/FREE Full Text
  8. 8.↵
    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
  9. 9.↵
    1. Nurk S,
    2. Bankevich A,
    3. Antipov D,
    4. Gurevich AA,
    5. Korobeynikov A,
    6. Lapidus A,
    7. Prjibelski AD,
    8. Pyshkin A,
    9. Sirotkin A,
    10. Sirotkin Y,
    11. Stepanauskas R,
    12. Clingenpeel SR,
    13. Woyke T,
    14. McLean JS,
    15. Lasken R,
    16. Tesler G,
    17. Alekseyev MA,
    18. Pevzner PA
    . 2013. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20:714–737. doi:10.1089/cmb.2013.0084.
    OpenUrlCrossRefPubMed
  10. 10.↵
    1. Varghese NJ,
    2. Mukherjee S,
    3. Ivanova N,
    4. Konstantinidis KT,
    5. Mavrommatis K,
    6. Kyrpides NC,
    7. Pati A
    . 2015. Microbial species delineation using whole genome sequences. Nucleic Acids Res 43:6761–6771. doi:10.1093/nar/gkv657.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Mende DR,
    2. Sunagawa S,
    3. Zeller G,
    4. Bork P
    . 2013. Accurate and universal delineation of prokaryotic species. Nat Methods 10:881–884. doi:10.1038/nmeth.2575.
    OpenUrlCrossRefPubMedWeb of Science
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Genome Sequence of Actinomyces odontolyticus subsp. actinosynbacter Strain XH001, the Basibiont of an Oral TM7 Epibiont
Jeffrey S. McLean, Quanhui Liu, Batbileg Bor, Joseph K. Bedree, Lujia Cen, Michael Watling, Thao T. To, Roger E. Bumgarner, Xuesong He, Wenyuan Shi
Genome Announcements Feb 2016, 4 (1) e01685-15; DOI: 10.1128/genomeA.01685-15

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 Actinomyces odontolyticus subsp. actinosynbacter Strain XH001, the Basibiont of an Oral TM7 Epibiont
(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 Actinomyces odontolyticus subsp. actinosynbacter Strain XH001, the Basibiont of an Oral TM7 Epibiont
Jeffrey S. McLean, Quanhui Liu, Batbileg Bor, Joseph K. Bedree, Lujia Cen, Michael Watling, Thao T. To, Roger E. Bumgarner, Xuesong He, Wenyuan Shi
Genome Announcements Feb 2016, 4 (1) e01685-15; DOI: 10.1128/genomeA.01685-15
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