Strain identifier
BacDive ID: 16887
Type strain: 
Species: Thermococcus barossii
Strain Designation: SHCK-94
Strain history: E. V. Pikuta SHCK-94 <-- R. M. Kelly.
NCBI tax ID(s): 54077 (species)
version 8.1 (current version)
General
@ref: 7215
BacDive-ID: 16887
DSM-Number: 17882
keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic, Gram-negative
description: Thermococcus barossii SHCK-94 is an anaerobe, hyperthermophilic, Gram-negative archaeon that was isolated from Rock fragments of a hydrothermal vent flange formation.
NCBI tax id
- NCBI tax id: 54077
- Matching level: species
strain history
| @ref | history |
|---|---|
| 7215 | <- E. V. Pikuta, NASA/NSSTC, Huntsville, USA; SHCK-94 <- R. M. Kelly |
| 67770 | E. V. Pikuta SHCK-94 <-- R. M. Kelly. |
doi: 10.13145/bacdive16887.20230509.8.1
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 barossii
- full scientific name: Thermococcus barossii Duffaud et al. 2005
@ref: 7215
domain: Archaea
phylum: Euryarchaeota
class: Thermococci
order: Thermococcales
family: Thermococcaceae
genus: Thermococcus
species: Thermococcus barossii
full scientific name: Thermococcus barossii Duffaud et al. 2005
strain designation: SHCK-94
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.856
Culture and growth conditions
culture medium
- @ref: 7215
- name: MARINE THERMOCOCCUS MEDIUM (DSMZ Medium 760)
- growth: yes
- link: https://mediadive.dsmz.de/medium/760
- composition: 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
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 7215 | positive | growth | 80 | hyperthermophilic | |
| 67770 | positive | growth | 82 | hyperthermophilic | |
| 69480 | thermophilic | 100 |
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: anaerobe
- confidence: 99.678
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 94 |
| 69480 | no | 97.42 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location |
|---|---|---|
| 7215 | Rock fragments of a hydrothermal vent flange formation | northeast Pacific Ocean, East Pacific Rise of the Juan de Fuca Ridge |
| 67770 | Rock fragments of a hydrothermal vent flange formation, located along the East Pacific Rise of the Juan de Fuca Ridge |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Terrestrial | #Geologic |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 7215
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7215
- description: Thermococcus barossii 16S ribosomal RNA gene, partial sequence
- accession: U76535
- length: 1428
- database: ena
- NCBI tax ID: 54077
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermococcus barossii SHCK-94 | GCA_002214465 | complete | ncbi | 54077 |
| 66792 | Thermococcus barossii SHCK-94 | 2758568026 | complete | img | 54077 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 7215 | 60.0 | high performance liquid chromatography (HPLC) |
| 67770 | 60 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 94 | no |
| flagellated | no | 96.283 | no |
| gram-positive | no | 97.026 | no |
| anaerobic | yes | 99.01 | no |
| aerobic | no | 97.561 | no |
| halophile | no | 76.171 | no |
| spore-forming | no | 97.426 | no |
| glucose-util | yes | 79.953 | no |
| thermophile | yes | 100 | yes |
| motile | no | 82.276 | no |
| glucose-ferment | no | 56.059 | no |
External links
@ref: 7215
culture collection no.: DSM 17882, ATCC BAA 1085, JCM 12858, DSM 9535
straininfo link
- @ref: 85893
- straininfo: 131953
literature
- topic: Phylogeny
- Pubmed-ID: 27638197
- title: Thermococcus piezophilus sp. nov., a novel hyperthermophilic and piezophilic archaeon with a broad pressure range for growth, isolated from a deepest hydrothermal vent at the Mid-Cayman Rise.
- authors: Dalmasso C, Oger P, Selva G, Courtine D, L'Haridon S, Garlaschelli A, Roussel E, Miyazaki J, Reveillaud J, Jebbar M, Takai K, Maignien L, Alain K
- journal: Syst Appl Microbiol
- DOI: 10.1016/j.syapm.2016.08.003
- year: 2016
- mesh: Base Composition/genetics, Base Sequence, DNA, Archaeal/genetics, Genome, Bacterial/genetics, Hot Temperature, Hydrothermal Vents/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Sulfur Compounds/*metabolism, Thermococcus/genetics/*growth & development/isolation & purification/*metabolism, Thermotolerance/*physiology, West Indies
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 7215 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17882) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17882 | |
| 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/ | ||
| 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 | |
| 85893 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID131953.1 | StrainInfo: A central database for resolving microbial strain identifiers |