Strain identifier

BacDive ID: 17056

Type strain: Yes

Species: Thermosipho japonicus

Strain Designation: IHB1

Strain history: K. Takai IHB1.

NCBI tax ID(s): 90323 (species)

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General

@ref: 5058

BacDive-ID: 17056

DSM-Number: 13481

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative

description: Thermosipho japonicus IHB1 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from deep-sea hydrothermal vent chimney, 972 m depth.

NCBI tax id

  • NCBI tax id: 90323
  • Matching level: species

strain history

@refhistory
5058<- JCM <- K. Takai, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Yokosuka; IHB1
67770K. Takai IHB1.

doi: 10.13145/bacdive17056.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/thermotogota
  • domain: Bacteria
  • phylum: Thermotogota
  • class: Thermotogae
  • order: Thermotogales
  • family: Fervidobacteriaceae
  • genus: Thermosipho
  • species: Thermosipho japonicus
  • full scientific name: Thermosipho japonicus Takai and Horikoshi 2000

@ref: 5058

domain: Bacteria

phylum: Thermotogae

class: Thermotogae

order: Thermotogales

family: Fervidobacteriaceae

genus: Thermosipho

species: Thermosipho japonicus

full scientific name: Thermosipho japonicus Takai and Horikoshi 2000

strain designation: IHB1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.807

Culture and growth conditions

culture medium

  • @ref: 5058
  • name: PYROCOCCUS MEDIUM (DSMZ Medium 377)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/377
  • composition: Name: PYROCOCCUS MEDIUM (DSMZ Medium 377) Composition: Sulfur 30.0 g/l Peptone 5.0 g/l MgCl2 x 6 H2O 2.75 g/l Yeast extract 1.0 g/l KH2PO4 0.5 g/l Na2S x 9 H2O 0.5 g/l KCl 0.33 g/l NaBr 0.05 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l (NH4)2SO4 0.01 g/l SrCl2 x 6 H2O 0.007 g/l Citric acid 0.005 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l CaCl2 x 2 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l CuSO4 x 5 H2O 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l KI 5e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
5058positivegrowth70thermophilic
67770positivegrowth70thermophilic
69480thermophilic100

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5058anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481no98
69480no99.989

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5058deep-sea hydrothermal vent chimney, 972 m depthOkinawa area, Ilheya Basin hydrothermal fieldJapanJPNAsia
67770Deep-sea hydrothermal vent chimneyIheya Basin in the Okinawa areaJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_84847.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_93;96_347;97_387;98_444;99_84847&stattab=map
  • Last taxonomy: Thermosipho
  • 16S sequence: AB024932
  • Sequence Identity:
  • Total samples: 6
  • soil counts: 1
  • aquatic counts: 5

Safety information

risk assessment

  • @ref: 5058
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5058
  • description: Thermosipho japonicus gene for 16S rRNA, partial sequence
  • accession: AB024932
  • length: 1503
  • database: ena
  • NCBI tax ID: 90323

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermosipho japonicus DSM 13481GCA_014201655scaffoldncbi90323
66792Thermosipho japonicus strain DSM 1348190323.3wgspatric90323
66792Thermosipho japonicus DSM 134812861242185draftimg90323

GC content

  • @ref: 5058
  • GC-content: 31.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
flagellatedno90.384no
gram-positiveno94.522no
anaerobicyes99.392yes
aerobicno98.892yes
halophileno92.389no
spore-formingno87.461no
glucose-utilyes87.299no
thermophileyes100no
motileyes88.868no
glucose-fermentno53.825no

External links

@ref: 5058

culture collection no.: DSM 13481, JCM 10495

straininfo link

  • @ref: 86056
  • straininfo: 49474

literature

  • topic: Phylogeny
  • Pubmed-ID: 10741832
  • title: Thermosipho japonicus sp. nov., an extremely thermophilic bacterium isolated from a deep-sea hydrothermal vent in Japan.
  • authors: Takai K, Horikoshi K
  • journal: Extremophiles
  • DOI: 10.1007/s007920050002
  • year: 2000
  • mesh: Anti-Bacterial Agents/pharmacology, Archaea/classification/drug effects/*physiology, DNA, Archaeal/chemistry, DNA, Ribosomal/chemistry, Electron Transport, Hydrogen-Ion Concentration, Japan, Lipids/analysis, Microscopy, Electron, Microscopy, Phase-Contrast, Muramidase/pharmacology, Nucleic Acid Hybridization, Phylogeny, Temperature, *Water Microbiology
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitle
5058Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13481)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13481
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
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
86056Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49474.1StrainInfo: A central database for resolving microbial strain identifiers