Strain identifier
BacDive ID: 16862
Type strain: 
Species: Thermococcus litoralis
Strain Designation: NS-C
Strain history: DSM 5473 <-- A. Neuner <-- K. O. Stetter <-- S. Belkin and H. W. Jannasch NS-C.
NCBI tax ID(s): 523849 (strain), 2265 (species)
version 8.1 (current version)
General
@ref: 2175
BacDive-ID: 16862
DSM-Number: 5473
keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic, Gram-negative
description: Thermococcus litoralis NS-C is an anaerobe, hyperthermophilic, Gram-negative archaeon that was isolated from shallow marine thermal spring.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 523849 | strain |
| 2265 | species |
strain history
| @ref | history |
|---|---|
| 2175 | <- A. Neuner <- K.O. Stetter <- S. Belkin and H. W. Jannasch; NS-C |
| 67770 | DSM 5473 <-- A. Neuner <-- K. O. Stetter <-- S. Belkin and H. W. Jannasch NS-C. |
doi: 10.13145/bacdive16862.20230509.8.1
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 litoralis
- full scientific name: Thermococcus litoralis Neuner et al. 2001
@ref: 2175
domain: Archaea
phylum: Euryarchaeota
class: Thermococci
order: Thermococcales
family: Thermococcaceae
genus: Thermococcus
species: Thermococcus litoralis
full scientific name: Thermococcus litoralis Neuner et al. 2001
strain designation: NS-C
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.979
Culture and growth conditions
culture medium
- @ref: 2175
- 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 |
|---|---|---|---|---|---|
| 2175 | positive | growth | 83 | hyperthermophilic | |
| 67770 | positive | growth | 85 | hyperthermophilic | |
| 69480 | thermophilic | 99.999 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 2175 | anaerobe | |
| 69480 | anaerobe | 99.683 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.642
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 2175 | shallow marine thermal spring | Naples, Bay of Lucrino | Italy | ITA | Europe |
| 67770 | Shallow submarine hot spring near Lucrino | Bay of Naples | Italy | ITA | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 2175
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Thermococcus litoralis gene for 16S rRNA, partial sequence | AB033623 | 788 | ena | 523849 |
| 20218 | Thermococcus litoralis partial 16S rRNA gene, type strain DSM 5473T | FR749899 | 1353 | ena | 2265 |
| 67770 | Thermococcus litoralis gene for 16S rRNA, partial sequence, strain: JCM 8560 | AB603515 | 1360 | ena | 523849 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermococcus litoralis DSM 5473 | 2513237398 | complete | img | 523849 |
| 67770 | Thermococcus litoralis DSM 5473 | GCA_000246985 | contig | ncbi | 523849 |
| 66792 | Thermococcus litoralis DSM 5473 | 523849.5 | complete | patric | 523849 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 2175 | 38.0 | |
| 67770 | 38 | |
| 67770 | 39.1 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
- trait: spore-forming
- prediction: yes
- confidence: 56
- training_data: no
External links
@ref: 2175
culture collection no.: DSM 5473, ATCC 51850, JCM 8560
straininfo link
- @ref: 85870
- straininfo: 46920
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 11532010 | A novel hyperthermophilic archaeal glyoxylate reductase from Thermococcus litoralis. Characterization, gene cloning, nucleotide sequence and expression in Escherichia coli. | Ohshima T, Nunoura-Kominato N, Kudome T, Sakuraba H | Eur J Biochem | 10.1046/j.1432-1327.2001.02394.x | 2001 | Alcohol Oxidoreductases/*genetics/isolation & purification/metabolism, Amino Acid Sequence, Base Sequence, Cloning, Molecular, Coenzymes/metabolism, DNA, Archaeal/analysis, Escherichia coli, Genomic Library, Molecular Sequence Data, Recombinant Proteins/metabolism, Sequence Homology, Amino Acid, Substrate Specificity, Thermococcus/*enzymology/genetics | Metabolism |
| Genetics | 22493191 | Genome sequence of the model hyperthermophilic archaeon Thermococcus litoralis NS-C. | Gardner AF, Kumar S, Perler FB | J Bacteriol | 10.1128/JB.00123-12 | 2012 | Chromosomes, Archaeal, Gene Expression Regulation, Archaeal, Genome, Archaeal, Molecular Sequence Data, Thermococcus/*genetics | |
| Enzymology | 25161870 | Ornithine cyclodeaminase/mu-crystallin homolog from the hyperthermophilic archaeon Thermococcus litoralis functions as a novel Delta(1)-pyrroline-2-carboxylate reductase involved in putative trans-3-hydroxy-l-proline metabolism. | Watanabe S, Tozawa Y, Watanabe Y | FEBS Open Bio | 10.1016/j.fob.2014.07.005 | 2014 | Metabolism | |
| Metabolism | 27438592 | Molecular cloning and enzymological characterization of pyridoxal 5'-phosphate independent aspartate racemase from hyperthermophilic archaeon Thermococcus litoralis DSM 5473. | Washio T, Kato S, Oikawa T | Extremophiles | 10.1007/s00792-016-0860-8 | 2016 | Amino Acid Isomerases/chemistry/genetics/*metabolism, Amino Acid Substitution, Archaeal Proteins/chemistry/genetics/*metabolism, Conserved Sequence, Enzyme Stability, *Hot Temperature, Hydrogen-Ion Concentration, Pyridoxal Phosphate/*metabolism, Substrate Specificity, Thermococcus/*enzymology/genetics | Enzymology |
| Enzymology | 29143132 | Thermostable and highly specific L-aspartate oxidase from Thermococcus litoralis DSM 5473: cloning, overexpression, and enzymological properties. | Washio T, Oikawa T | Extremophiles | 10.1007/s00792-017-0977-4 | 2017 | Amino Acid Oxidoreductases/chemistry/genetics/*metabolism, Archaeal Proteins/chemistry/genetics/*metabolism, Aspartic Acid/metabolism, Cloning, Molecular, Enzyme Stability, Protein Denaturation, Substrate Specificity, Thermococcus/*enzymology, *Thermotolerance | Metabolism |
| Enzymology | 32355045 | Structure of Thermococcus litoralis Delta(1)-pyrroline-2-carboxylate reductase in complex with NADH and L-proline. | Ferrario E, Miggiano R, Rizzi M, Ferraris DM | Acta Crystallogr D Struct Biol | 10.1107/S2059798320004866 | 2020 | Archaeal Proteins/chemistry, NAD/*chemistry, Proline/*chemistry, Protein Binding, Protein Conformation, Pyrroles/*chemistry, Pyrroline Carboxylate Reductases/*chemistry, Thermococcus/*enzymology | |
| Metabolism | 33942867 | Characterization of a novel moderate-substrate specificity amino acid racemase from the hyperthermophilic archaeon Thermococcus litoralis. | Kawakami R, Kinoshita C, Kawase T, Sato M, Hayashi J, Sakuraba H, Ohshima T | Biosci Biotechnol Biochem | 10.1093/bbb/zbab078 | 2021 | Amino Acid Isomerases/chemistry/*metabolism, Amino Acid Sequence, Archaeal Proteins/chemistry/*metabolism, Electrophoresis, Polyacrylamide Gel, Genes, Archaeal, Molecular Chaperones/metabolism, Phylogeny, Substrate Specificity, Thermococcus/*enzymology/genetics | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 2175 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5473) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5473 | |||
| 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 | |
| 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) | |||
| 85870 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46920.1 | StrainInfo: A central database for resolving microbial strain identifiers |