Strain identifier

BacDive ID: 16868

Type strain: Yes

Species: Thermococcus peptonophilus

Strain Designation: OG-1

Strain history: C. Kato; JAMSTEC, Japan; OG1.

NCBI tax ID(s): 523851 (strain), 53952 (species)

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General

@ref: 3913

BacDive-ID: 16868

DSM-Number: 10343

keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic, Gram-negative

description: Thermococcus peptonophilus OG-1 is an anaerobe, hyperthermophilic, Gram-negative archaeon that was isolated from deep-sea hydrothermal vent.

NCBI tax id

NCBI tax idMatching level
53952species
523851strain

strain history

@refhistory
3913<- JCM
67770C. Kato; JAMSTEC, Japan; OG1.

doi: 10.13145/bacdive16868.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Thermococci
  • order: Thermococcales
  • family: Thermococcaceae
  • genus: Thermococcus
  • species: Thermococcus peptonophilus
  • full scientific name: Thermococcus peptonophilus González et al. 1996

@ref: 3913

domain: Archaea

phylum: Euryarchaeota

class: Thermococci

order: Thermococcales

family: Thermococcaceae

genus: Thermococcus

species: Thermococcus peptonophilus

full scientific name: Thermococcus peptonophilus González et al. 1996

strain designation: OG-1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.912

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3913MARINE THERMOCOCCUS MEDIUM (DSMZ Medium 760)yeshttps://mediadive.dsmz.de/medium/760Name: MARINE THERMOCOCCUS MEDIUM (DSMZ Medium 760) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
3913THERMOCOCCUS PROFUNDUS MEDIUM (DSMZ Medium 673)yeshttps://mediadive.dsmz.de/medium/673Name: THERMOCOCCUS PROFUNDUS MEDIUM (DSMZ Medium 673) Composition: NaCl 25.0 g/l Peptone 5.0 g/l Sulfur 5.0 g/l (NH4)2SO4 1.3 g/l Yeast extract 1.0 g/l KH2PO4 0.28 g/l MgSO4 x 7 H2O 0.25 g/l CaCl2 x 2 H2O 0.07 g/l FeCl3 x 6 H2O 0.02 g/l Na2B4O7 x 10 H2O 0.0045 g/l MnCl2 x 4 H2O 0.0018 g/l Resazurin 0.001 g/l ZnSO4 x 7 H2O 0.00022 g/l CuCl2 x 2 H2O 5e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l VOSO4 x 2 H2O 3e-05 g/l CoSO4 x 7 H2O 1e-05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
3913positivegrowth85hyperthermophilic
67770positivegrowth85hyperthermophilic
69480thermophilic100

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
3913anaerobe
69480anaerobe99.429

spore formation

@refspore formationconfidence
69481no98
69480no99.605

Isolation, sampling and environmental information

isolation

@refsample type
3913deep-sea hydrothermal vent
67770Deep-sea hydrothermal vent in the western Pacific Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Hydrothermal vent
#Environmental#Aquatic#Marine
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

  • @ref: 3913
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Thermococcus peptonophilus gene for 16S rRNA, partial sequenceAB033625788ena523851
20218Thermococcus peptonophilus gene for 16S rRNA, partial sequence, strain:JCM 9653AB0551251423ena523851
20218Thermococcus peptonophilus 16S rRNA gene, strain DSM 10343 TypeAJ2918101320ena523851
20218Thermococcus peptonophilus strain DSM 10343 16S ribosomal RNA gene, partial sequenceAY0991831445ena523851
20218Thermococcus peptonophilus strain DSM 10343 16S-23S ribosomal RNA intergenic spacer region, complete sequenceAY099219182ena523851
3913Thermococcus peptonophilus partial 16S rRNA gene, strain DSM 10343AJ2988711320ena523851
67770Thermococcus peptonophilus gene for 16S ribosomal RNA, partial sequenceD37982924ena523851

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermococcus peptonophilus OG-1GCA_001592435completencbi53952
66792Thermococcus peptonophilus OG-1 = JCM 9653GCA_001315905contigncbi523851
66792Thermococcus peptonophilus JCM 96532681813028draftimg523851
66792Thermococcus peptonophilus OG-12687453162completeimg53952
66792Thermococcus peptonophilus JCM 9653523851.4wgspatric523851

GC content

  • @ref: 67770
  • GC-content: 52
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
flagellatedno95.813no
gram-positiveno95.462no
anaerobicyes99.357yes
aerobicno98.494yes
halophileno82.364no
spore-formingno96.464no
glucose-utilyes76.419no
motileno76.725no
thermophileyes100no
glucose-fermentno53.234no

External links

@ref: 3913

culture collection no.: DSM 10343, JCM 9653, ATCC 700098, CIP 104782

straininfo link

  • @ref: 85876
  • straininfo: 43770

literature

  • topic: Phylogeny
  • Pubmed-ID: 7545383
  • title: Thermococcus peptonophilus sp. nov., a fast-growing, extremely thermophilic archaebacterium isolated from deep-sea hydrothermal vents.
  • authors: Gonzalez JM, Kato C, Horikoshi K
  • journal: Arch Microbiol
  • year: 1995
  • mesh: Archaea/*classification/cytology/*isolation & purification/physiology, Base Composition, Base Sequence, Culture Media, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Hot Temperature, Hydrogen-Ion Concentration, Molecular Sequence Data, Pacific Ocean, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Homology, Nucleic Acid, Sodium Chloride/pharmacology, *Water Microbiology
  • topic2: Cultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3913Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10343)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10343
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
85876Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43770.1StrainInfo: A central database for resolving microbial strain identifiers