Strain identifier

BacDive ID: 17029

Type strain: Yes

Species: Pyrobaculum calidifontis

Strain Designation: VA1

Strain history: T. Imanaka VA1.

NCBI tax ID(s): 410359 (strain), 181486 (species)

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General

@ref: 15444

BacDive-ID: 17029

DSM-Number: 21063

keywords: genome sequence, 16S sequence, Archaea, anaerobe, spore-forming, hyperthermophilic, Gram-negative

description: Pyrobaculum calidifontis VA1 is an anaerobe, spore-forming, hyperthermophilic archaeon that was isolated from terrestrial hot spring.

NCBI tax id

NCBI tax idMatching level
181486species
410359strain

strain history

@refhistory
15444<- JCM <- T. Imanaka; VA1
67770T. Imanaka VA1.

doi: 10.13145/bacdive17029.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/thermoproteota
  • domain: Archaea
  • phylum: Thermoproteota
  • class: Thermoprotei
  • order: Thermoproteales
  • family: Thermoproteaceae
  • genus: Pyrobaculum
  • species: Pyrobaculum calidifontis
  • full scientific name: Pyrobaculum calidifontis Amo et al. 2008

@ref: 15444

domain: Archaea

phylum: Crenarchaeota

class: Thermoprotei

order: Thermoproteales

family: Thermoproteaceae

genus: Pyrobaculum

species: Pyrobaculum calidifontis

full scientific name: Pyrobaculum calidifontis Amo et al. 2008

strain designation: VA1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.96

Culture and growth conditions

culture medium

  • @ref: 15444
  • name: PYROBACULUM CALIDIFONTIS MEDIUM (DSMZ Medium 1090)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1090
  • composition: Name: PYROBACULUM CALIDIFONTIS MEDIUM (DSMZ Medium 1090) Composition: Tryptone 10.0 g/l Na2S2O3 x 5 H2O 3.0 g/l Yeast extract 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
15444positivegrowth90hyperthermophilic
67770positivegrowth90hyperthermophilic
69480thermophilic99.999

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: anaerobe
  • confidence: 98.647

spore formation

@refspore formationconfidence
69481yes97
69480no99.971

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15444terrestrial hot springCalambaPhilippinesPHLAsia
67770Hot spring in CalambaLagunaPhilippinesPHLAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Environmental#Terrestrial
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_187621.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17852;96_68835;97_89480;98_122047;99_187621&stattab=map
  • Last taxonomy: Pyrobaculum calidifontis subclade
  • 16S sequence: AB078332
  • Sequence Identity:
  • Total samples: 16
  • aquatic counts: 15
  • animal counts: 1

Safety information

risk assessment

  • @ref: 15444
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15444
  • description: Pyrobaculum calidifontis gene for 16S rRNA, complete sequence
  • accession: AB078332
  • length: 1498
  • database: ena
  • NCBI tax ID: 410359

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pyrobaculum calidifontis JCM 11548GCA_000015805completencbi410359
66792Pyrobaculum calidifontis JCM 11548640069326completeimg410359
66792Pyrobaculum calidifontis JCM 11548410359.14completepatric410359

GC content

@refGC-contentmethod
1544457sequence analysis
6777051high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes97no
motileno75.926no
flagellatedno96.218no
gram-positiveno97.725no
anaerobicyes97.722no
halophileno80.73no
spore-formingno95.303no
thermophileyes100yes
glucose-utilyes75.735no
aerobicno92.773no
glucose-fermentno75.581no

External links

@ref: 15444

culture collection no.: DSM 21063, JCM 11548

straininfo link

  • @ref: 86030
  • straininfo: 231935

literature

  • topic: Enzymology
  • Pubmed-ID: 20936278
  • title: Characterization of a novel dye-linked L-proline dehydrogenase from an aerobic hyperthermophilic archaeon, Pyrobaculum calidifontis.
  • authors: Satomura T, Zhang XD, Hara Y, Doi K, Sakuraba H, Ohshima T
  • journal: Appl Microbiol Biotechnol
  • DOI: 10.1007/s00253-010-2914-7
  • year: 2010
  • mesh: Amino Acid Sequence, Chromatography, Cloning, Molecular, Coenzymes/metabolism, Enzyme Stability, Escherichia coli/genetics, Flavin-Adenine Dinucleotide/metabolism, Hot Temperature, Hydrogen-Ion Concentration, Kinetics, Molecular Sequence Data, Molecular Weight, Proline/metabolism, Proline Oxidase/chemistry/*genetics/isolation & purification/*metabolism, Protein Multimerization, Pyrobaculum/*enzymology, Sequence Alignment
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
15444Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21063)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21063
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86030Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID231935.1StrainInfo: A central database for resolving microbial strain identifiers