Strain identifier
BacDive ID: 17056
Type strain:
Species: Thermosipho japonicus
Strain Designation: IHB1
Strain history: K. Takai IHB1.
NCBI tax ID(s): 90323 (species)
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
@ref | history |
---|---|
5058 | <- JCM <- K. Takai, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Yokosuka; IHB1 |
67770 | K. 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
@ref | growth | type | temperature | range | confidence |
---|---|---|---|---|---|
5058 | positive | growth | 70 | thermophilic | |
67770 | positive | growth | 70 | thermophilic | |
69480 | thermophilic | 100 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
5058 | anaerobe | |
69480 | anaerobe | 99.999 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 98 |
69480 | no | 99.989 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
5058 | deep-sea hydrothermal vent chimney, 972 m depth | Okinawa area, Ilheya Basin hydrothermal field | Japan | JPN | Asia |
67770 | Deep-sea hydrothermal vent chimney | Iheya Basin in the Okinawa area | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Thermosipho japonicus DSM 13481 | GCA_014201655 | scaffold | ncbi | 90323 |
66792 | Thermosipho japonicus strain DSM 13481 | 90323.3 | wgs | patric | 90323 |
66792 | Thermosipho japonicus DSM 13481 | 2861242185 | draft | img | 90323 |
GC content
- @ref: 5058
- GC-content: 31.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 98 | no |
flagellated | no | 90.384 | no |
gram-positive | no | 94.522 | no |
anaerobic | yes | 99.392 | yes |
aerobic | no | 98.892 | yes |
halophile | no | 92.389 | no |
spore-forming | no | 87.461 | no |
glucose-util | yes | 87.299 | no |
thermophile | yes | 100 | no |
motile | yes | 88.868 | no |
glucose-ferment | no | 53.825 | no |
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
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
5058 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13481) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13481 | |
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
69479 | João 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 | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
86056 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49474.1 | StrainInfo: A central database for resolving microbial strain identifiers |