Strain identifier
BacDive ID: 16654
Type strain: 
Species: Saccharolobus shibatae
Strain Designation: B12
Strain history: DSM 5389 <-- D. W. Grogan <-- W. Zillig strain B12.
NCBI tax ID(s): 2286 (species)
version 8.1 (current version)
General
@ref: 2133
BacDive-ID: 16654
DSM-Number: 5389
keywords: genome sequence, 16S sequence, Archaea, thermophilic
description: Saccharolobus shibatae B12 is a thermophilic archaeon that was isolated from geothermal mud hole.
NCBI tax id
- NCBI tax id: 2286
- Matching level: species
strain history
| @ref | history |
|---|---|
| 2133 | <- D.W. Grogan <- W. Zillig, B12 (Sulfolobus acidocaldarius) |
| 67770 | DSM 5389 <-- D. W. Grogan <-- W. Zillig strain B12. |
doi: 10.13145/bacdive16654.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/thermoproteota
- domain: Archaea
- phylum: Thermoproteota
- class: Thermoprotei
- order: Sulfolobales
- family: Sulfolobaceae
- genus: Saccharolobus
- species: Saccharolobus shibatae
- full scientific name: Saccharolobus shibatae (Grogan et al. 1991) Sakai and Kurosawa 2018
synonyms
- @ref: 20215
- synonym: Sulfolobus shibatae
@ref: 2133
domain: Archaea
phylum: Crenarchaeota
class: Thermoprotei
order: Sulfolobales
family: Sulfolobaceae
genus: Saccharolobus
species: Saccharolobus shibatae
full scientific name: Saccharolobus shibatae (Grogan et al. 1991) Sakai and Kurosawa 2018
strain designation: B12
type strain: yes
Culture and growth conditions
culture medium
- @ref: 2133
- name: SULFOLOBUS MEDIUM (DSMZ Medium 88)
- growth: yes
- link: https://mediadive.dsmz.de/medium/88
- composition: Name: SULFOLOBUS MEDIUM (DSMZ Medium 88) Composition: (NH4)2SO4 1.28713 g/l Yeast extract 0.990099 g/l KH2PO4 0.277228 g/l MgSO4 x 7 H2O 0.247525 g/l CaCl2 x 2 H2O 0.0693069 g/l FeCl3 x 6 H2O 0.019802 g/l Na2B4O7 x 10 H2O 0.00445545 g/l MnCl2 x 4 H2O 0.00178218 g/l ZnSO4 x 7 H2O 0.000217822 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Na2MoO4 x 2 H2O 2.9703e-05 g/l VOSO4 x 2 H2O 2.9703e-05 g/l CoSO4 x 7 H2O 9.90099e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 2133 | positive | growth | 75 | thermophilic |
| 67770 | positive | growth | 75 | thermophilic |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 2133 | geothermal mud hole | Kiushu island, Beppu | Japan | JPN | Asia |
| 67770 | Geothermal pools and bubbling 'mud pots' in Beppu | Kyushu | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Mud (Sludge)
taxonmaps
- @ref: 69479
- File name: preview.99_187114.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17810;96_68799;97_89441;98_121712;99_187114&stattab=map
- Last taxonomy: Sulfolobaceae
- 16S sequence: M32504
- Sequence Identity:
- Total samples: 139
- soil counts: 5
- aquatic counts: 131
- animal counts: 3
Safety information
risk assessment
- @ref: 2133
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 2133
- description: Sulfolobus shibatae strain B12 16S ribosomal RNA gene, partial sequence
- accession: M32504
- length: 1495
- database: ena
- NCBI tax ID: 523848
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Saccharolobus shibatae B12 | GCA_019175345 | complete | ncbi | 523848 |
| 66792 | Saccharolobus shibatae B12 | 523848.4 | complete | patric | 523848 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 2133 | 35.0 | |
| 67770 | 35.2 | high performance liquid chromatography (HPLC) |
| 67770 | 34 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | no | 97.211 | no |
| gram-positive | no | 91.678 | no |
| anaerobic | yes | 63.016 | no |
| aerobic | no | 61.894 | no |
| halophile | no | 83.905 | no |
| spore-forming | no | 95.589 | no |
| motile | no | 81.149 | no |
| thermophile | yes | 100 | yes |
| glucose-util | yes | 87.976 | no |
| glucose-ferment | no | 83.826 | no |
External links
@ref: 2133
culture collection no.: DSM 5389, ATCC 51178, JCM 8931, IFO 15437, NBRC 15437
straininfo link
- @ref: 85675
- straininfo: 42846
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 15999201 | Highly enantioselective stereo-inverting sec-alkylsulfatase activity of hyperthermophilic Archaea. | Wallner SR, Nestl BM, Faber K | Org Biomol Chem | 10.1039/b504883d | 2005 | Archaea/*enzymology, Molecular Conformation, Molecular Structure, Stereoisomerism, Sulfatases/*chemistry/metabolism, Temperature | Metabolism |
| Enzymology | 16233734 | Molecular cloning and characterization of a thermostable carboxylesterase from an archaeon, Sulfolobus shibatae DSM5389: non-linear kinetic behavior of a hormone-sensitive lipase family enzyme. | Ejima K, Liu J, Oshima Y, Hirooka K, Shimanuki S, Yokota Y, Hemmi H, Nakayama T, Nishino T | J Biosci Bioeng | 10.1016/S1389-1723(05)00310-5 | 2004 | ||
| Enzymology | 25043762 | Structural insights into the low pH adaptation of a unique carboxylesterase from Ferroplasma: altering the pH optima of two carboxylesterases. | Ohara K, Unno H, Oshima Y, Hosoya M, Fujino N, Hirooka K, Takahashi S, Yamashita S, Kusunoki M, Nakayama T | J Biol Chem | 10.1074/jbc.M113.521856 | 2014 | Carboxylesterase/chemistry/*metabolism, Crystallization, Euryarchaeota/*enzymology, Hydrogen Bonding, Hydrogen-Ion Concentration, Kinetics | Metabolism |
| Metabolism | 30387780 | Crystal structure of glycosyltrehalose synthase from Sulfolobus shibatae DSM5389. | Okazaki N, Blaber M, Kuroki R, Tamada T | Acta Crystallogr F Struct Biol Commun | 10.1107/S2053230X1801453X | 2018 | Amino Acid Sequence, Archaeal Proteins/chemistry/metabolism, Catalytic Domain, Conserved Sequence, Crystallography, X-Ray, Glucosyltransferases/*chemistry/metabolism, Models, Molecular, Sulfolobus/*enzymology, alpha-Amylases/chemistry | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 2133 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5389) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5389 | |
| 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 | |
| 85675 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42846.1 | StrainInfo: A central database for resolving microbial strain identifiers |