Strain identifier

BacDive ID: 7003

Type strain: Yes

Species: Methanothermococcus okinawensis

Strain Designation: IH1

Strain history: K. Takai IH1.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 5251

BacDive-ID: 7003

DSM-Number: 14208

keywords: genome sequence, 16S sequence, Archaea, anaerobe, thermophilic

description: Methanothermococcus okinawensis IH1 is an anaerobe, thermophilic archaeon that was isolated from hydrothermal vent chimney, 972 m depth.

NCBI tax id

NCBI tax idMatching level
647113strain
155863species

strain history

@refhistory
5251<- K. Takai, Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC); IH1 <- K. Takai {2000}
67770K. Takai IH1.

doi: 10.13145/bacdive7003.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Methanococci
  • order: Methanococcales
  • family: Methanococcaceae
  • genus: Methanothermococcus
  • species: Methanothermococcus okinawensis
  • full scientific name: Methanothermococcus okinawensis Takai et al. 2002

@ref: 5251

domain: Archaea

phylum: Euryarchaeota

class: Methanococci

order: Methanococcales

family: Methanococcaceae

genus: Methanothermococcus

species: Methanothermococcus okinawensis

full scientific name: Methanothermococcus okinawensis Takai et al. 2002

strain designation: IH1

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 5251
  • name: METHANOCALDOCOCCUS MEDIUM (DSMZ Medium 282)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/282
  • composition: Name: METHANOCALDOCOCCUS MEDIUM (DSMZ Medium 282) Composition: MgCl2 x 6 H2O 4.05138 g/l NaHCO3 0.988142 g/l Na2S x 9 H2O 0.494071 g/l L-Cysteine HCl x H2O 0.494071 g/l KCl 0.326087 g/l NH4Cl 0.247036 g/l K2HPO4 0.13834 g/l MgSO4 x 7 H2O 0.0296443 g/l Nitrilotriacetic acid 0.0148221 g/l NaCl 0.00988142 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.00988142 g/l MnSO4 x H2O 0.00494071 g/l ZnSO4 x 7 H2O 0.00177866 g/l CoSO4 x 7 H2O 0.00177866 g/l CaCl2 x 2 H2O 0.000988142 g/l FeSO4 x 7 H2O 0.000988142 g/l Sodium resazurin 0.000494071 g/l NiCl2 x 6 H2O 0.000296443 g/l AlK(SO4)2 x 12 H2O 0.000197628 g/l Na2MoO4 x 2 H2O 9.88142e-05 g/l CuSO4 x 5 H2O 9.88142e-05 g/l H3BO3 9.88142e-05 g/l Pyridoxine hydrochloride 9.88142e-05 g/l Thiamine HCl 4.94071e-05 g/l (DL)-alpha-Lipoic acid 4.94071e-05 g/l p-Aminobenzoic acid 4.94071e-05 g/l Riboflavin 4.94071e-05 g/l Nicotinic acid 4.94071e-05 g/l Calcium D-(+)-pantothenate 4.94071e-05 g/l Biotin 1.97628e-05 g/l Folic acid 1.97628e-05 g/l Na2WO4 x 2 H2O 3.95257e-06 g/l Na2SeO3 x 5 H2O 2.96443e-06 g/l Vitamin B12 9.88142e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
5251positivegrowth65thermophilic
67770positivegrowth60thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 5251
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
5251hydrothermal vent chimney, 972 m depthOkinawa Trough, Iheya RidgeJapanJPNAsia27.7833126.9
67770Deep-sea hydrothermal vent chimney at the Iheya RidgeOkinawa TroughJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_192212.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17939;96_69644;97_90449;98_125299;99_192212&stattab=map
  • Last taxonomy: Methanothermococcus
  • 16S sequence: AB057722
  • Sequence Identity:
  • Total samples: 8
  • aquatic counts: 8

Safety information

risk assessment

  • @ref: 5251
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5251
  • description: Methanothermococcus okinawensis gene for 16S rRNA, partial sequence
  • accession: AB057722
  • length: 1392
  • database: ena
  • NCBI tax ID: 155863

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methanothermococcus okinawensis IH1GCA_000179575completencbi647113
66792Methanothermococcus okinawensis IH1650716055completeimg647113
66792Methanothermococcus okinawensis IH1647113.14plasmidpatric647113
66792Methanothermococcus okinawensis IH1647113.11completepatric647113

GC content

  • @ref: 5251
  • GC-content: 33.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno85.457no
flagellatedno94.808no
gram-positiveno96.221no
anaerobicyes98.988yes
aerobicno96.209yes
halophileno88.138no
spore-formingno97.038no
thermophileyes98.574no
glucose-utilyes71.508no
glucose-fermentno54.727no

External links

@ref: 5251

culture collection no.: DSM 14208, JCM 11175

straininfo link

  • @ref: 76464
  • straininfo: 100753

literature

  • topic: Phylogeny
  • Pubmed-ID: 12148612
  • title: Methanothermococcus okinawensis sp. nov., a thermophilic, methane-producing archaeon isolated from a Western Pacific deep-sea hydrothermal vent system.
  • authors: Takai K, Inoue A, Horikoshi K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-4-1089
  • year: 2002
  • mesh: DNA, Ribosomal/analysis, Japan, Methane/*metabolism, Methanococcaceae/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
5251Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14208)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14208
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
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/
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
76464Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100753.1StrainInfo: A central database for resolving microbial strain identifiers