skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring

Abstract

A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T (DSM 21565 T = KCTC 5659 T ) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species Dethiosulfovibrio salsuginis USBA 82T. The genome consisted of 2.68 Mbp with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82T genome six Synergistetes conserved signature indels (CSIs), specific for Jonquetella, Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operon genes couldmore » be related to de novo synthesis of proline to protect the cell in response to high osmolarity. Our bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to identify bacteriocins genes in the genome.« less

Authors:
 [1];  [1];  [2];  [2];  [3];  [3];  [3];  [2]; ORCiD logo [1]
  1. Pontificia Univ. Javeriana, Bogotá (Colombia)
  2. Univ. de los Andes, Bogotá (Colombia)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1544025
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Genetics & Heredity; Microbiology; Dethiosulfovibrio salsuginis; Synergistetes; Halophilic; Anaerobe; Fermentation of amino acids; Saline spring

Citation Formats

Díaz-Cárdenas, Carolina, López, Gina, Alzate-Ocampo, José David, González, Laura N., Shapiro, Nicole, Woyke, Tanja, Kyrpides, Nikos C., Restrepo, Silvia, and Baena, Sandra. Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring. United States: N. p., 2017. Web. doi:10.1186/s40793-017-0303-x.
Díaz-Cárdenas, Carolina, López, Gina, Alzate-Ocampo, José David, González, Laura N., Shapiro, Nicole, Woyke, Tanja, Kyrpides, Nikos C., Restrepo, Silvia, & Baena, Sandra. Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring. United States. doi:10.1186/s40793-017-0303-x.
Díaz-Cárdenas, Carolina, López, Gina, Alzate-Ocampo, José David, González, Laura N., Shapiro, Nicole, Woyke, Tanja, Kyrpides, Nikos C., Restrepo, Silvia, and Baena, Sandra. Wed . "Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring". United States. doi:10.1186/s40793-017-0303-x. https://www.osti.gov/servlets/purl/1544025.
@article{osti_1544025,
title = {Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring},
author = {Díaz-Cárdenas, Carolina and López, Gina and Alzate-Ocampo, José David and González, Laura N. and Shapiro, Nicole and Woyke, Tanja and Kyrpides, Nikos C. and Restrepo, Silvia and Baena, Sandra},
abstractNote = {A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T (DSM 21565 T = KCTC 5659 T ) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species Dethiosulfovibrio salsuginis USBA 82T. The genome consisted of 2.68 Mbp with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82T genome six Synergistetes conserved signature indels (CSIs), specific for Jonquetella, Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operon genes could be related to de novo synthesis of proline to protect the cell in response to high osmolarity. Our bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to identify bacteriocins genes in the genome.},
doi = {10.1186/s40793-017-0303-x},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United States},
year = {2017},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Anaerobaculum thermoterrenum gen. nov., sp. nov., a Novel, Thermophilic Bacterium Which Ferments Citrate
journal, January 1997

  • Rees, G. N.; Patel, B. K. C.; Grassia, G. S.
  • International Journal of Systematic Bacteriology, Vol. 47, Issue 1
  • DOI: 10.1099/00207713-47-1-150

Cultivation of a Synergistetes strain representing a previously uncultivated lineage: Cultivation of previously uncultivated Synergistetes
journal, January 2010


The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
journal, October 2015

  • Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/s40793-015-0077-y

Dethiosulfovibrio salsuginis sp. nov., an anaerobic, slightly halophilic bacterium isolated from a saline spring
journal, August 2009

  • Diaz-Cardenas, C.; Lopez, G.; Patel, B. K. C.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 4
  • DOI: 10.1099/ijs.0.010835-0

Rarity associated with specific ecological niches in the bacterial world: the 'Synergistes' example
journal, February 2005


Focus: Synergistetes
journal, June 2009


BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides
journal, May 2013

  • van Heel, Auke J.; de Jong, Anne; Montalbán-López, Manuel
  • Nucleic Acids Research, Vol. 41, Issue W1
  • DOI: 10.1093/nar/gkt391

High-quality draft assemblies of mammalian genomes from massively parallel sequence data
journal, December 2010

  • Gnerre, S.; MacCallum, I.; Przybylski, D.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
  • DOI: 10.1073/pnas.1017351108

Jonquetella anthropi gen. nov., sp. nov., the first member of the candidate phylum 'Synergistetes' isolated from man
journal, December 2007

  • Jumas-Bilak, E.; Carlier, J. -P.; Jean-Pierre, H.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 12
  • DOI: 10.1099/ijs.0.65213-0

Solexa Ltd
journal, June 2004


The phylum Synergistetes in gingivitis and necrotizing ulcerative gingivitis
journal, August 2012

  • Baumgartner, A.; Thurnheer, T.; Luthi-Schaller, H.
  • Journal of Medical Microbiology, Vol. 61, Issue Pt_11
  • DOI: 10.1099/jmm.0.047456-0

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
journal, June 1990

  • Woese, C. R.; Kandler, O.; Wheelis, M. L.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 12
  • DOI: 10.1073/pnas.87.12.4576

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010


Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains
journal, August 2014


Molecular Phylogenetic Diversity of the Bacterial Community in the Gut of the Termite Coptotermes formosanus
journal, January 2005

  • Shinzato, Naoya; Muramatsu, Mizuho; Matsui, Toru
  • Bioscience, Biotechnology, and Biochemistry, Vol. 69, Issue 6
  • DOI: 10.1271/bbb.69.1145

Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates
journal, November 2015

  • Jumas-Bilak, Estelle; Bouvet, Philippe; Allen-Vercoe, Emma
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 11
  • DOI: 10.1099/ijsem.0.000520

Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field
journal, April 2013

  • Honda, T.; Fujita, T.; Tonouchi, A.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 10
  • DOI: 10.1099/ijs.0.052225-0

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


Osmotically Controlled Synthesis of the Compatible Solute Proline Is Critical for Cellular Defense of Bacillus subtilis against High Osmolarity
journal, July 2011

  • Brill, J.; Hoffmann, T.; Bleisteiner, M.
  • Journal of Bacteriology, Vol. 193, Issue 19
  • DOI: 10.1128/JB.05490-11

Aminomonas paucivorans gen. nov., sp. nov., a mesophilic, anaerobic, amino-acid-utilizing bacterium
journal, July 1999

  • Baena, S.; Fardeau, M. -L.; Ollivier, B.
  • International Journal of Systematic Bacteriology, Vol. 49, Issue 3
  • DOI: 10.1099/00207713-49-3-975

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
  • DOI: 10.1099/00207713-50-3-1287

Isolation and characterization of a nicotinic acid-degrading sulfate-reducing bacterium, Desulfococcus niacini sp. nov.
journal, January 1983

  • Imhoff-Stuckle, Dorothee; Pfennig, Norbert
  • Archives of Microbiology, Vol. 136, Issue 3
  • DOI: 10.1007/BF00409843

Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'
journal, April 2009

  • Jumas-Bilak, E.; Roudiere, L.; Marchandin, H.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 5
  • DOI: 10.1099/ijs.0.006718-0

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
journal, June 2010


Anaerobaculum mobile sp. nov., a novel anaerobic, moderately thermophilic, peptide-fermenting bacterium that uses crotonate as an electron acceptor, and emended description of the genus Anaerobaculum.
journal, January 2002

  • Muxí, Lucía; Menes, Rodolfo Javier
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 1
  • DOI: 10.1099/00207713-52-1-157

Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a New Anaerobic, Slightly Halophilic, Thiosulfate-Reducing Bacterium from Corroding Offshore Oil Wells
journal, July 1997

  • Magot, M.; Ravot, G.; Campaignolle, X.
  • International Journal of Systematic Bacteriology, Vol. 47, Issue 3
  • DOI: 10.1099/00207713-47-3-818

Culture-Dependent and Culture-Independent Characterization of Microbial Assemblages Associated with High-Temperature Petroleum Reservoirs
journal, February 2000


Aminiphilus circumscriptus gen. nov., sp. nov., an anaerobic amino-acid-degrading bacterium from an upflow anaerobic sludge reactor
journal, August 2007

  • Diaz, C.; Baena, S.; Fardeau, M. -L.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 57, Issue 8
  • DOI: 10.1099/ijs.0.63614-0

Molecular signatures for the phylum Synergistetes and some of its subclades
journal, June 2012


Lactivibrio alcoholicus gen. nov., sp. nov., an anaerobic, mesophilic, lactate-, alcohol-, carbohydrate- and amino-acid-degrading bacterium in the phylum Synergistetes
journal, March 2014

  • Qiu, Y. -L.; Hanada, S.; Kamagata, Y.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 6
  • DOI: 10.1099/ijs.0.060681-0

Accelerated Profile HMM Searches
journal, October 2011


The minimum information about a genome sequence (MIGS) specification
journal, May 2008

  • Field, Dawn; Garrity, George; Gray, Tanya
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1360

Aminobacterium colombiensegen. nov. sp. nov., an Amino Acid-degrading Anaerobe Isolated from Anaerobic Sludge
journal, October 1998


Thermovirga lienii gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, amino-acid-degrading bacterium isolated from a North Sea oil well
journal, July 2006

  • Dahle, H.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 56, Issue 7
  • DOI: 10.1099/ijs.0.63894-0

Aminobacterium mobile sp. nov., a new anaerobic amino-acid-degrading bacterium
journal, January 2000

  • Baena, S.; Fardeau, M. L.; Labat, M.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 50, Issue 1
  • DOI: 10.1099/00207713-50-1-259

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
journal, May 2015

  • Weber, Tilmann; Blin, Kai; Duddela, Srikanth
  • Nucleic Acids Research, Vol. 43, Issue W1
  • DOI: 10.1093/nar/gkv437

Infernal 1.1: 100-fold faster RNA homology searches
journal, September 2013


The division “Synergistes”
journal, June 2007


Cloacibacillus evryensis gen. nov., sp. nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum 'Synergistetes', isolated from an anaerobic sludge digester
journal, September 2008

  • Ganesan, A.; Chaussonnerie, S.; Tarrade, A.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 9
  • DOI: 10.1099/ijs.0.65645-0

IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009


MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
journal, March 2016

  • Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro
  • Molecular Biology and Evolution, Vol. 33, Issue 7
  • DOI: 10.1093/molbev/msw054

    Works referencing / citing this record:

    Estudio de la Diversidad de Microorganismos de Ambientes Termales y Salinos de la Región Andina Central de Colombia
    dataset, January 2019

    • Baena, Sandra; Cardenas, Carolina Diaz; Ramirez, Gina López
    • Pontificia Universidad Javeriana
    • DOI: 10.15472/lefufh