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Title: Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio

Abstract

Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of its morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883T, the type strain of T. acidaminovorans, stain Z-9701T is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Authors:
 [1];  [2];  [3];  [1];  [4];  [1];  [1];  [1];  [3];  [3];  [3];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [5];  [6] more »;  [7];  [2];  [3];  [2];  [1];  [8];  [5];  [9];  [1];  [2];  [1] « less
+ Show Author Affiliations
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Leibniz Inst. DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  4. St. Petersburg State Univ. (Russian Federation); St. Petersburg Academic Univ. (Russian Federation)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. Helmholtz Centre for Infection Research, Braunschweig (Germany)
  7. CSIR-Inst. of Microbial Technology, Chandigarh (India)
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California Davis Genome Center, CA (United States)
  9. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Queensland, Brisbane, QLD (Australia)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); German Research Foundation (DFG); Russian Ministry of Science
OSTI Identifier:
1407205
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC02-06NA25396; AC05-00OR22725; INST 599/1-2; 11.G34.31.0068
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; obligate anaerobic; motile; curved rods; organotrophic; S0-reduction; cyanobacterial mat; Synergistaceae; Synergistetes; GEBA

Citation Formats

Palaniappan, Krishna, Meier-Kolthoff, Jan P., Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Rohde, Manfred, Mayilraj, Shanmugam, Spring, Stefan, Detter, John C., Göker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, and Woyke, Tanja. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio. United States: N. p., 2013. Web. doi:10.4056/sigs.4237901.
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Palaniappan, Krishna, Meier-Kolthoff, Jan P., Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Rohde, Manfred, Mayilraj, Shanmugam, Spring, Stefan, Detter, John C., Göker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, & Woyke, Tanja. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio. United States. https://doi.org/10.4056/sigs.4237901
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Palaniappan, Krishna, Meier-Kolthoff, Jan P., Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Rohde, Manfred, Mayilraj, Shanmugam, Spring, Stefan, Detter, John C., Göker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter, and Woyke, Tanja. Wed . "Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio". United States. https://doi.org/10.4056/sigs.4237901. https://www.osti.gov/servlets/purl/1407205.
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@article{osti_1407205,
title = {Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio},
author = {Palaniappan, Krishna and Meier-Kolthoff, Jan P. and Teshima, Hazuki and Nolan, Matt and Lapidus, Alla and Tice, Hope and Del Rio, Tijana Glavina and Cheng, Jan-Fang and Han, Cliff and Tapia, Roxanne and Goodwin, Lynne A. and Pitluck, Sam and Liolios, Konstantinos and Mavromatis, Konstantinos and Pagani, Ioanna and Ivanova, Natalia and Mikhailova, Natalia and Pati, Amrita and Chen, Amy and Rohde, Manfred and Mayilraj, Shanmugam and Spring, Stefan and Detter, John C. and Göker, Markus and Bristow, James and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Kyrpides, Nikos C. and Klenk, Hans-Peter and Woyke, Tanja},
abstractNote = {Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of its morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883T, the type strain of T. acidaminovorans, stain Z-9701T is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.4237901},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 9,
place = {United States},
year = {Wed Oct 16 00:00:00 EDT 2013},
month = {Wed Oct 16 00:00:00 EDT 2013}
}
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https://doi.org/10.4056/sigs.4237901
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Dietary palmitic acid promotes a prometastatic memory via Schwann cells
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The DNA Bank Network: The Start from a German Initiative
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IMG ER: a system for microbial genome annotation expert review and curation
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journal, April 2000

Thermanaerovibrio velox sp. nov., a new anaerobic, thermophilic, organotrophic bacterium that reduces elemental sulfur, and emended description of the genus Thermanaerovibrio
journal, May 2000

  • Zavarzina, D. G.; Zhilina, T. N.; Tourova, T. P.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 3
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Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010

Genome sequence-based species delimitation with confidence intervals and improved distance functions
journal, January 2013

  • Meier-Kolthoff, Jan P.; Auch, Alexander F.; Klenk, Hans-Peter
  • BMC Bioinformatics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2105-14-60

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012

Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T)
journal, August 2010

  • LaButti, Kurt; Mayilraj, Shanmugam; Clum, Alicia
  • Standards in Genomic Sciences, Vol. 3, Issue 1
  • DOI: 10.4056/sigs.1092865

Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3T)
journal, January 2010

  • Pitluck, Sam; Yasawong, Montri; Held, Brittany
  • Standards in Genomic Sciences, Vol. 3, Issue 3
  • DOI: 10.4056/sigs.1253298

Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314T)
journal, May 2012

  • Göker, Markus; Saunders, Elisabeth; Lapidus, Alla
  • Standards in Genomic Sciences, Vol. 6, Issue 2
  • DOI: 10.4056/sigs.2726028

Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T)
journal, November 2009

  • Chovatia, Mansi; Sikorski, Johannes; Schröder, Maren
  • Standards in Genomic Sciences, Vol. 1, Issue 3
  • DOI: 10.4056/sigs.40645

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
journal, January 2010

  • Auch, Alexander F.; von Jan, Mathias; Klenk, Hans-Peter
  • Standards in Genomic Sciences, Vol. 2, Issue 1
  • DOI: 10.4056/sigs.531120

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
journal, January 2010

  • Auch, Alexander F.; Klenk, Hans-Peter; Göker, Markus
  • Standards in Genomic Sciences, Vol. 2, Issue 1
  • DOI: 10.4056/sigs.541628

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
journal, July 2009

  • Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.
  • Standards in Genomic Sciences, Vol. 1, Issue 1
  • DOI: 10.4056/sigs.632

Complete genome sequence of Aminobacterium colombiense type strain (ALA-1T)
journal, June 2010

  • Chertkov, Olga; Sikorski, Johannes; Brambilla, Evelyne
  • Standards in Genomic Sciences, Vol. 2, Issue 3
  • DOI: 10.4056/sigs.902116
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    Works referencing / citing this record:

    Motile curved bacteria are Pareto-optimal
    journal, July 2019

    • Schuech, Rudi; Hoehfurtner, Tatjana; Smith, David J.
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 29
    • DOI: 10.1073/pnas.1818997116

    Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age
    journal, February 2014

    • Klenk, Hans-Peter; Meier-Kolthoff, Jan P.; Göker, Markus
    • International Journal of Systematic and Evolutionary Microbiology, Vol. 64, Issue 2
    • DOI: 10.1099/ijs.0.056994-0

    Motile curved bacteria are Pareto-optimal
    journal, January 2018

    • Schuech, Rudi; Hoehfurtner, Tatjana; Smith, David
    • Proceedings of the National Academy of Sciences
    • DOI: 10.1101/441139

    Exemplar Abstract for Thermanaerovibrio velox Zavarzina et al. 2000 emend. Palaniappan et al. 2013.
    dataset, January 2013

    • Parker, Charles Thomas; Taylor, Dorothea; Garrity, George M.
    • NamesforLife
    • DOI: 10.1601/ex.4504

    Nomenclature Abstract for Thermanaerovibrio acidaminovorans (Guangsheng et al. 1997) Baena et al. 1999 emend. Palaniappan et al. 2013.
    dataset, January 2013

    • Parker, Charles Thomas; Mannor, Kara; Garrity, George M.
    • NamesforLife
    • DOI: 10.1601/nm.4503
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