Strain identifier
BacDive ID: 16874
Type strain:
Species: Thermococcus aggregans
Strain Designation: TY
Strain history: F. Canganella TY.
NCBI tax ID(s): 110163 (species)
General
@ref: 4834
BacDive-ID: 16874
DSM-Number: 12819
keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic
description: Thermococcus aggregans TY is an anaerobe, hyperthermophilic archaeon that was isolated from hydrothermal vent site .
NCBI tax id
- NCBI tax id: 110163
- Matching level: species
strain history
@ref | history |
---|---|
4834 | <- JCM <- F. Canganella |
67770 | F. Canganella TY. |
doi: 10.13145/bacdive16874.20230509.8.1
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 aggregans
- full scientific name: Thermococcus aggregans Canganella et al. 1998
@ref: 4834
domain: Archaea
phylum: Euryarchaeota
class: Thermococci
order: Thermococcales
family: Thermococcaceae
genus: Thermococcus
species: Thermococcus aggregans
full scientific name: Thermococcus aggregans Canganella et al. 1998
strain designation: TY
type strain: yes
Culture and growth conditions
culture medium
- @ref: 4834
- 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 |
---|---|---|---|---|
4834 | positive | growth | 85 | hyperthermophilic |
67770 | positive | growth | 85 | hyperthermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 4834
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
4834 | hydrothermal vent site (2000 m) | Gulf of California, Guaymas Basin | USA | USA | North America |
67770 | Guaymas Basin hydrothermal vent | Gulf of California | Pacific Ocean |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Hydrothermal vent |
#Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_188570.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17916;96_69485;97_90251;98_122785;99_188570&stattab=map
- Last taxonomy: Thermococcus
- 16S sequence: Y08384
- Sequence Identity:
- Total samples: 2
- aquatic counts: 2
Safety information
risk assessment
- @ref: 4834
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 4834
- description: Thermococcus aggregans 16S rRNA gene, strain DSM 10597
- accession: Y08384
- length: 1301
- database: ena
- NCBI tax ID: 110163
Genome sequences
- @ref: 66792
- description: Thermococcus aggregans TY
- accession: GCA_024022995
- assembly level: chromosome
- database: ncbi
- NCBI tax ID: 110163
GC content
@ref | GC-content | method |
---|---|---|
4834 | 42 | thermal denaturation, midpoint method (Tm) |
67770 | 42 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 94.933 | no |
gram-positive | no | 95.345 | no |
anaerobic | yes | 99.175 | yes |
aerobic | no | 96.924 | yes |
halophile | no | 70.353 | no |
spore-forming | no | 97.448 | no |
motile | no | 75.322 | no |
glucose-ferment | no | 53.726 | no |
thermophile | yes | 100 | no |
glucose-util | yes | 84.786 | no |
External links
@ref: 4834
culture collection no.: DSM 12819, DSM 10597, JCM 10137
straininfo link
- @ref: 85882
- straininfo: 49367
literature
- topic: Phylogeny
- Pubmed-ID: 9828419
- title: Thermococcus guaymasensis sp. nov. and Thermococcus aggregans sp. nov., two novel thermophilic archaea isolated from the Guaymas Basin hydrothermal vent site.
- authors: Canganella F, Jones WJ, Gambacorta A, Antranikian G
- journal: Int J Syst Bacteriol
- DOI: 10.1099/00207713-48-4-1181
- year: 1998
- mesh: DNA, Archaeal/chemistry, DNA, Ribosomal/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Terminology as Topic, Thermococcus/*classification/cytology/isolation & purification/physiology, *Water Microbiology
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
4834 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12819) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12819 | |
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/ | ||
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 | |
85882 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49367.1 | StrainInfo: A central database for resolving microbial strain identifiers |