Strain identifier
BacDive ID: 16865
Type strain: 
Species: Thermococcus profundus
Strain Designation: DT5432
Strain history: T. Kobayashi DT5432.
NCBI tax ID(s): 49899 (species)
version 8.1 (current version)
General
@ref: 3616
BacDive-ID: 16865
DSM-Number: 9503
keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic
description: Thermococcus profundus DT5432 is an anaerobe, hyperthermophilic archaeon that was isolated from deep sea hydrothermal vent, depth 1.395 m in the Middle Okinawa Trench .
NCBI tax id
- NCBI tax id: 49899
- Matching level: species
strain history
| @ref | history |
|---|---|
| 3616 | <- JCM <- K. Kobayashi, DT5432 |
| 67770 | T. Kobayashi DT5432. |
doi: 10.13145/bacdive16865.20230509.8.1
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 profundus
- full scientific name: Thermococcus profundus corrig. Kobayashi and Horikoshi 1995
synonyms
- @ref: 20215
- synonym: Thermus profundus
@ref: 3616
domain: Archaea
phylum: Euryarchaeota
class: Thermococci
order: Thermococcales
family: Thermococcaceae
genus: Thermococcus
species: Thermococcus profundus
full scientific name: Thermococcus profundus Kobayashi and Horikoshi 1995
strain designation: DT5432
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 3616 | MARINE THERMOCOCCUS MEDIUM (DSMZ Medium 760) | yes | https://mediadive.dsmz.de/medium/760 | Name: 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 |
| 3616 | THERMOCOCCUS PROFUNDUS MEDIUM (DSMZ Medium 673) | yes | https://mediadive.dsmz.de/medium/673 | Name: 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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 3616 | positive | growth | 80 | hyperthermophilic |
| 67770 | positive | growth | 80 | hyperthermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 3616
- oxygen tolerance: anaerobe
compound production
- @ref: 67770
- compound: Extracellular amylase
- excreted: yes
Isolation, sampling and environmental information
isolation
| @ref | sample type |
|---|---|
| 3616 | deep sea hydrothermal vent, depth 1.395 m in the Middle Okinawa Trench (27°33'N, 126°58'E) |
| 67770 | Hydrothermal vent at the Mid-Okinawa Trough |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_187292.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17827;96_68785;97_89427;98_121709;99_187292&stattab=map
- Last taxonomy: Thermococcus
- 16S sequence: Z75233
- Sequence Identity:
- Total samples: 9
- aquatic counts: 9
Safety information
risk assessment
- @ref: 3616
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Thermococcus profundus strain DSM 9503 16S ribosomal RNA gene, partial sequence | AY099184 | 1447 | ena | 49899 |
| 20218 | Thermococcus profundus strain DSM 9503 16S-23S ribosomal RNA intergenic spacer region, complete sequence | AY099220 | 181 | ena | 49899 |
| 20218 | T.profundus 16S rRNA and 23S rRNA genes | Z75233 | 1906 | ena | 49899 |
Genome sequences
- @ref: 67770
- description: Thermococcus profundus DT 5432
- accession: GCA_002214585
- assembly level: complete
- database: ncbi
- NCBI tax ID: 49899
GC content
- @ref: 67770
- GC-content: 52.5
- method: high performance liquid chromatography (HPLC)
External links
@ref: 3616
culture collection no.: DSM 9503, ATCC 51592, JCM 9378, CIP 105121
straininfo link
- @ref: 85873
- straininfo: 43067
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 11282592 | Purification, characterization, and application of a novel dye-linked L-proline dehydrogenase from a hyperthermophilic archaeon, Thermococcus profundus. | Sakuraba H, Takamatsu Y, Satomura T, Kawakami R, Ohshima T | Appl Environ Microbiol | 10.1128/AEM.67.4.1470-1475.2001 | 2001 | 2,6-Dichloroindophenol/metabolism, Amino Acid Sequence, Coloring Agents/chemistry, Molecular Sequence Data, Proline/metabolism, Proline Oxidase/chemistry/*isolation & purification/*metabolism, Substrate Specificity, Thermococcus/*enzymology/growth & development | Metabolism |
| Enzymology | 16534999 | Purification and Properties of Extracellular Amylase from the Hyperthermophilic Archaeon Thermococcus profundus DT5432. | Chung YC, Kobayashi T, Kanai H, Akiba T, Kudo T | Appl Environ Microbiol | 10.1128/aem.61.4.1502-1506.1995 | 1995 | ||
| Enzymology | 22752365 | Comparative analysis of the catalytic components in the archaeal dye-linked L-proline dehydrogenase complexes. | Kawakami R, Noguchi C, Higashi M, Sakuraba H, Ohshima T | Appl Microbiol Biotechnol | 10.1007/s00253-012-4201-2 | 2012 | 2,6-Dichloroindophenol/metabolism, Chromatography, Affinity, Cloning, Molecular, Enzyme Stability, Escherichia coli/genetics/metabolism, Ferricyanides/metabolism, Gene Expression, Hot Temperature, Kinetics, Proline/*metabolism, Proline Oxidase/genetics/*metabolism, Protein Stability, Pyrococcus/*enzymology/genetics, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Thermococcus/*enzymology/genetics, Time Factors | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3616 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9503) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-9503 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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 | |||
| 85873 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43067.1 | StrainInfo: A central database for resolving microbial strain identifiers |