Strain identifier

BacDive ID: 16874

Type strain: Yes

Species: Thermococcus aggregans

Strain Designation: TY

Strain history: F. Canganella TY.

NCBI tax ID(s): 110163 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

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

@refhistory
4834<- JCM <- F. Canganella
67770F. 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

@refgrowthtypetemperaturerange
4834positivegrowth85hyperthermophilic
67770positivegrowth85hyperthermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 4834
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4834hydrothermal vent site (2000 m)Gulf of California, Guaymas BasinUSAUSANorth America
67770Guaymas Basin hydrothermal ventGulf of CaliforniaPacific Ocean

isolation source categories

Cat1Cat2Cat3
#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

@refGC-contentmethod
483442thermal denaturation, midpoint method (Tm)
6777042high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno94.933no
gram-positiveno95.345no
anaerobicyes99.175yes
aerobicno96.924yes
halophileno70.353no
spore-formingno97.448no
motileno75.322no
glucose-fermentno53.726no
thermophileyes100no
glucose-utilyes84.786no

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

@idauthorscataloguedoi/urltitle
4834Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12819)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12819
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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
85882Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49367.1StrainInfo: A central database for resolving microbial strain identifiers