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

Complete Genome Sequence of Fusobacterium necrophorum subsp. necrophorum ATCC 25286

Ariana Umaña, Justin A. Lemkul, Daniel J. Slade
David A. Baltrus, Editor
Ariana Umaña
aDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ariana Umaña
Justin A. Lemkul
aDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Justin A. Lemkul
Daniel J. Slade
aDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Daniel J. Slade
David A. Baltrus
University of Arizona
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.00025-19
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Fusobacterium necrophorum is a pathogenic Gram-negative, anaerobic bacterium. In this study, we present the first complete genome sequence of Fusobacterium necrophorum subsp. necrophorum ATCC 25286. These data provide a critical advancement in our understanding of virulence factors that could contribute to F. necrophorum pathogenesis in both human and livestock infections.

ANNOUNCEMENT

Fusobacterium is a genus of anaerobic bacteria that cause serious and even fatal infections of cattle, sheep, and humans. Recent research has uncovered that Fusobacterium nucleatum is overrepresented in colonic tumors, and this bacterium can drive the progression and severity of colorectal cancer (1, 2). In humans, Fusobacterium necrophorum can cause the rare and life-threatening Lemierre syndrome, which begins as bacterial pharyngitis and rapidly progresses to septic thrombophlebitis of the jugular vein (3). Lemierre syndrome most frequently manifests in patients age 15 to 30 and can lead to further complications, including pharyngeal and lung abscesses (4). F. necrophorum have been classified into F. necrophorum subsp. necrophorum (biotype A) and F. necrophorum subsp. funduliforme (biotype B) (5). Fusobacterium necrophorum subsp. funduliforme is most commonly the cause of human infection, with Fusobacterium necrophorum subsp. necrophorum being the predominant animal pathogen. In cattle and sheep, biotype A is primarily responsible for liver abscesses and footrot (necrotic pododermatitis), for which antibiotics are an effective treatment (6).

In this study, we present the first complete genome sequence of Fusobacterium necrophorum subsp. necrophorum ATCC 25286 (5). The genome consists of one 2,678,415-bp circular chromosome (G+C content of 34%) and no plasmids. Annotation detected 2,343 protein open reading frames, 18 rRNAs, and 51 tRNAs. In addition, a 66-kb prophage region (75 protein-encoding genes; genomic position 477708 to 543489) was discovered, with the greatest similarity to a phage from the genus Clostridium identified. We have identified the lktBAC leukotoxin gene cluster and also report an increase in the number of type 5a-secreted autotransporter virulence factors compared with an annotation from the previous draft genome (87 contigs; NCBI BioProject accession number PRJNA257880).

F. necrophorum subsp. necrophorum ATCC 25286 was purchased through the ATCC. Bacteria from a single colony were grown in Columbia Broth, supplemented with hemin (5 µg/mL) and menadione (0.5 µg/mL) (CBHK) to stationary phase at 37°C in an anaerobic chamber (90% N2, 5% CO2, and 5% H2). Genomic DNA was isolated in deionized water (diH2O) using a Wizard isolation kit (Promega) and was quantitated using a Qubit fluorimeter (Life Technologies, Inc.). Long-read sequences were acquired by preparing 500 ng of DNA with a rapid sequencing kit (catalog number SQK-RAD004; Oxford Nanopore Technologies) and sequencing using a SpotON flow cell (R9.4) and a MinION sequencer (Oxford Nanopore Technologies). MinKnow 3.1.8 software was used to acquire raw data and basecall DNA sequences. Sequencing adapters from Oxford Nanopore reads were removed with Porechop (7), and a total of 71,386 reads (mean read length, 1,731 bp; maximum read length, 91,983 bp) were used for genome assembly. The same DNA preparation used for MinION sequencing was used for short-read DNA sequencing on a MiSeq nano instrument at the Genomic Sequence Center at the Virginia Tech Biocomplexity Institute. Briefly, 150 ng of genomic DNA was fragmented to 400 bp using a Covaris M220 focused ultrasonicator. The ends were repaired, and an A base was added to the 3′ end for ligation to the adapters, which have a single T base overhang at their 3′ end. Following ligation, the libraries were amplified by 7 cycles of PCR and barcoded. The library generated was validated by the use of an Agilent TapeStation and quantitated using a Quant-iT double-stranded (dsDNA) high sensitivity (HS) kit (Invitrogen) and quantitative PCR (qPCR). The libraries were then pooled and sequenced using a MiSeq nano instrument. In summary, 999,276 reads at 150 bp each (150 mb total; 56× genome coverage) were used for genome assembly. The F. necrophorum ATCC 25286 genome was assembled using the open-source software package Unicycler under default parameters, version 0.4.3 (8), using our previously described pipeline (9). For Illumina and MinION data, the mean depth of coverage for the genome was 56× and 53×, respectively. Prokka 1.13 under default parameters was used to annotate genes (10). Potential integrated phage were detected using PHASTER (11). Annotation in GenBank was carried out by the NCBI Prokaryotic Genome Annotation Pipeline (12).

Data availability.The complete sequence and all raw data for the Fusobacterium necrophorum subsp. necrophorum ATCC 25286 genome have been deposited in NCBI under the accession numbers CP034842 (GenBank), PRJNA513186 (BioProject), SAMN10697414 (BioSample), and SRR8400822 and SRR8400823 (SRA raw sequencing reads). In addition, all data for this genome and additional bioinformatic analysis will be freely available on the FusoPortal (13) data repository of Fusobacterium genomes (http://fusoportal.org) and our Open Science Framework site (https://osf.io/2c8pv/). The deposited data are the first version of this genome.

ACKNOWLEDGMENTS

This work was supported by funding from the Commonwealth Health Research Board of Virginia and the USDA National Institute of Food and Agriculture to D.J.S. We thank the Open Access Subvention Fund of Virginia Tech for publication funding.

We thank Austin Compton (Virginia Tech) for MinION sequencing optimization.

FOOTNOTES

    • Received 11 January 2019.
    • Accepted 25 January 2019.
    • Published 21 February 2019.
  • Copyright © 2019 Umaña 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. Brennan CA,
    2. Garrett WS
    . 2018. Fusobacterium nucleatum—symbiont, opportunist and oncobacterium. Nat Rev Microbiol. doi:10.1038/s41579-018-0129-6.
    OpenUrlCrossRef
  2. 2.↵
    1. Han YW
    . 2015. Fusobacterium nucleatum: a commensal-turned pathogen. Curr Opin Microbiol 23:141–147. doi:10.1016/j.mib.2014.11.013.
    OpenUrlCrossRefPubMed
  3. 3.↵
    1. Riordan T
    . 2007. Human infection with Fusobacterium necrophorum (Necrobacillosis), with a focus on Lemierre’s syndrome. Clin Microbiol Rev 20:622–659. doi:10.1128/CMR.00011-07.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    1. Faraone A,
    2. Fortini A,
    3. Nenci G,
    4. Boccadori C,
    5. Mangani V,
    6. Oggioni R
    . 2016. Fusobacterium necrophorum pharyngitis complicated by Lemierre’s syndrome. Case Rep Med 2016:3608346. doi:10.1155/2016/3608346.
    OpenUrlCrossRef
  5. 5.↵
    1. Shinjo T,
    2. Fujisawa T,
    3. Mitsuoka T
    . 1991. Proposal of two subspecies of Fusobacterium necrophorum (Flügge) Moore and Holdeman: Fusobacterium necrophorum subsp. necrophorum subsp. nov., nom. rev. (ex Flügge 1886), and Fusobacterium necrophorum subsp. funduliforme subsp. nov., nom. rev. (ex Hallé 1898). Int J Syst Bacteriol 41:395–397. doi:10.1099/00207713-41-3-395.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Zhou H,
    2. Bennett G,
    3. Hickford JGH
    . 2009. Variation in Fusobacterium necrophorum strains present on the hooves of footrot infected sheep, goats and cattle. Vet Microbiol 135:363–367. doi:10.1016/j.vetmic.2008.09.084.
    OpenUrlCrossRefPubMed
  7. 7.↵
    1. Wick RR
    . 2018. PoreChop. GitHub repository. https://github.com/rrwick/Porechop.
  8. 8.↵
    1. Wick RR,
    2. Judd LM,
    3. Gorrie CL,
    4. Holt KE
    . 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:e1005595. doi:10.1371/journal.pcbi.1005595.
    OpenUrlCrossRef
  9. 9.↵
    1. Todd SM,
    2. Settlage RE,
    3. Lahmers KK,
    4. Slade DJ
    . 2018. Fusobacterium genomics using MinION and Illumina sequencing enables genome completion and correction. mSphere 3:e00269-18. doi:10.1128/mSphere.00269-18.
    OpenUrlAbstract/FREE Full Text
  10. 10.↵
    1. Seemann T
    . 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi:10.1093/bioinformatics/btu153.
    OpenUrlCrossRefPubMedWeb of Science
  11. 11.↵
    1. Arndt D,
    2. Grant JR,
    3. Marcu A,
    4. Sajed T,
    5. Pon A,
    6. Liang Y,
    7. Wishart DS
    . 2016. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44:W16–W21. doi:10.1093/nar/gkw387.
    OpenUrlCrossRefPubMed
  12. 12.↵
    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
  13. 13.↵
    1. Sanders BE,
    2. Umaña A,
    3. Lemkul JA,
    4. Slade DJ
    . 2018. FusoPortal: an interactive repository of hybrid MinION-sequenced Fusobacterium genomes improves gene identification and characterization. mSphere 3:e00228-18. doi:10.1128/mSphere.00228-18.
    OpenUrlAbstract/FREE Full Text
PreviousNext
Back to top
Download PDF
Citation Tools
Complete Genome Sequence of Fusobacterium necrophorum subsp. necrophorum ATCC 25286
Ariana Umaña, Justin A. Lemkul, Daniel J. Slade
Microbiology Resource Announcements Feb 2019, 8 (8) e00025-19; DOI: 10.1128/MRA.00025-19

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.
Complete Genome Sequence of Fusobacterium necrophorum subsp. necrophorum ATCC 25286
(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
Complete Genome Sequence of Fusobacterium necrophorum subsp. necrophorum ATCC 25286
Ariana Umaña, Justin A. Lemkul, Daniel J. Slade
Microbiology Resource Announcements Feb 2019, 8 (8) e00025-19; DOI: 10.1128/MRA.00025-19
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