Strain identifier
BacDive ID: 24652
Type strain: 
Species: Thermococcus cleftensis
Strain Designation: CL1
Strain history: <- J. Holden, UMASS; CL1
NCBI tax ID(s): 163003 (species)
version 9.1 (current version)
General
@ref: 21061
BacDive-ID: 24652
DSM-Number: 27260
keywords: genome sequence, 16S sequence, Archaea, anaerobe, Gram-negative
description: Thermococcus cleftensis CL1 is an anaerobe, Gram-negative archaeon that was isolated from polychaete worm of the genus Paralvinella in a fragment of a black smoker.
NCBI tax id
- NCBI tax id: 163003
- Matching level: species
strain history
- @ref: 21061
- history: <- J. Holden, UMASS; CL1
doi: 10.13145/bacdive24652.20240916.9.1
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 cleftensis
- full scientific name: Thermococcus cleftensis Hensley et al. 2014
@ref: 21061
domain: Archaea
phylum: Euryarchaeota
class: Thermococci
order: Thermococcales
family: Thermococcaceae
genus: Thermococcus
species: Thermococcus cleftensis
full scientific name: Thermococcus cleftensis Hensley et al. 2014
strain designation: CL1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 21061
- 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: 21061
- growth: positive
- type: growth
- temperature: 80
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 91.302
Isolation, sampling and environmental information
isolation
- @ref: 21061
- sample type: polychaete worm of the genus Paralvinella in a fragment of a black smoker
- host species: Paralvinella
- geographic location: north-eastern Pacific Ocean, Cleft Segment of the Juan de Fuca Ridge at a depth of 2350 m (44° 30' 00'' N 130° 30' 00'' W)
- latitude: 44.5
- longitude: -130.5
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Host | #Invertebrates (Other) | #Annelida |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 21061
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21061
- description: Thermococcus cleftensis strain CL1 16S ribosomal RNA gene, partial sequence
- accession: AF350369
- length: 1367
- database: nuccore
- NCBI tax ID: 163003
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermococcus cleftensis CL1 | GCA_000265525 | complete | ncbi | 163003 |
| 66792 | Thermococcus cleftensis CL1 | 2518645553 | complete | img | 163003 |
GC content
- @ref: 21061
- GC-content: 55.8
- method: sequence analysis
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 80 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 70.002 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 86.973 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 88.094 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 91.302 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | yes | 80.71 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 82.458 | no |
External links
@ref: 21061
culture collection no.: DSM 27260, KACC 17922
straininfo link
- @ref: 88492
- straininfo: 402342
literature
- topic: Phylogeny
- Pubmed-ID: 25082851
- title: Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents.
- authors: Hensley SA, Jung JH, Park CS, Holden JF
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.066100-0
- year: 2014
- mesh: Animals, DNA, Archaeal/genetics, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Pacific Ocean, *Phylogeny, Polychaeta/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thermococcus/*classification/genetics/isolation & purification
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 21061 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27260 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27260) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 88492 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID402342.1 |