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 9.3 (current version)
General
@ref: 7215
BacDive-ID: 16887
DSM-Number: 17882
keywords: genome sequence, 16S sequence, Archaea, hyperthermophilic
description: Thermococcus barossii SHCK-94 is a hyperthermophilic 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/bacdive16887.20250331.9.3
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: 125439
- gram stain: negative
- confidence: 94.4
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 |
|---|---|---|---|
| 7215 | positive | growth | 80 |
| 67770 | positive | growth | 82 |
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: anaerobe
- confidence: 100
spore formation
- @ref: 125439
- spore formation: no
- confidence: 94.6
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 | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 7215 | Thermococcus barossii 16S ribosomal RNA gene, partial sequence | U76535 | 1428 | nuccore | 54077 |
| 124043 | Thermococcus barossii strain DSM 9535 16S ribosomal RNA gene, partial sequence. | AY099173 | 1447 | nuccore | 54077 |
| 124043 | Thermococcus barossii strain DSM 9535 16S-23S ribosomal RNA intergenic spacer region, complete sequence | AY099209 | 183 | nuccore | 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
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 70.385 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 87.851 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 84.685 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.58 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | yes | 78.459 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 78.458 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 94.6 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 68.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 94.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 100 |
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/ | ||
| 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 | |
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | ||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |