Strain identifier
BacDive ID: 5943
Type strain: 
Species: Halorubrum vacuolatum
Strain Designation: M24
Strain history: CIP <- 1995, NCIMB <- W.D. Grant: strain M24
NCBI tax ID(s): 63740 (species)
version 8.1 (current version)
General
@ref: 3406
BacDive-ID: 5943
DSM-Number: 8800
keywords: genome sequence, 16S sequence, Archaea, mesophilic
description: Halorubrum vacuolatum M24 is a mesophilic archaeon of the family Halorubraceae.
NCBI tax id
- NCBI tax id: 63740
- Matching level: species
strain history
| @ref | history |
|---|---|
| 3406 | <- NCIMB <- W. D. Grant <- W. E. Mwatha |
| 67770 | W. D. Grant M24. |
| 123772 | CIP <- 1995, NCIMB <- W.D. Grant: strain M24 |
doi: 10.13145/bacdive5943.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Haloferacales
- family: Halorubraceae
- genus: Halorubrum
- species: Halorubrum vacuolatum
- full scientific name: Halorubrum vacuolatum (Mwatha and Grant 1993) Kamekura et al. 1997
synonyms
@ref synonym 20215 Natronobacterium vacuolatum 20215 Natronobacterium vacuolata
@ref: 3406
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Halorubraceae
genus: Halorubrum
species: Halorubrum vacuolatum
full scientific name: Halorubrum vacuolatum (Mwatha and Grant 1993) Kamekura et al. 1997
strain designation: M24
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 3406 | ALKALOPHILIC HALOPHILE MEDIUM (DSMZ Medium 1431) | yes | https://mediadive.dsmz.de/medium/1431 | Name: ALKALOPHILIC HALOPHILE MEDIUM (DSMZ Medium 1431) Composition: NaCl 200.0 g/l Na2CO3 50.0 g/l Agar 20.0 g/l Yeast extract 10.0 g/l Casamino acids 7.5 g/l Trisodium citrate 3.0 g/l KCl 2.0 g/l MgSO4 x 7 H2O 1.0 g/l FeSO4 x 7 H2O 0.05 g/l MnCl2 x 4 H2O 0.00036 g/l |
| 39036 | MEDIUM 136 - for Natronococcus occultus, Natrialba magadii and Halorubrum vacuolatum | yes | Solution 2 - M0437 (600.000 ml);Solution 1 - M0437 (400.000 ml) | |
| 123772 | CIP Medium 136 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=136 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 3406 | positive | growth | 37 | mesophilic |
| 39036 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-8
Isolation, sampling and environmental information
isolation
| @ref | geographic location | country | origin.country | continent | sample type |
|---|---|---|---|---|---|
| 3406 | Lake Magadi | Kenya | KEN | Africa | |
| 67770 | Kenya | KEN | Africa | Brine from the Lake Magadi | |
| 123772 | Kenya | KEN | Africa | Environment, Soda lake, Magadi lake |
taxonmaps
- @ref: 69479
- File name: preview.99_191837.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17655;96_70840;97_92012;98_125037;99_191837&stattab=map
- Last taxonomy: Halorubrum vacuolatum subclade
- 16S sequence: D87972
- Sequence Identity:
- Total samples: 36
- soil counts: 1
- aquatic counts: 35
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 3406 | 1 | Risk group (German classification) |
| 123772 | 1 | Risk group (French classification) |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Halorubrum vacuolatum gene for 16S rRNA, complete sequence, strain: JCM 9060 | AB663425 | 1471 | ena | 63740 |
| 20218 | Halorubrum vacuolatum DNA for 16S rRNA | D87972 | 1468 | ena | 63740 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Halorubrum vacuolatum DSM 8800 | 2724679803 | draft | img | 63740 |
| 67770 | Halorubrum vacuolatum DSM 8800 | GCA_900188065 | contig | ncbi | 63740 |
| 66792 | Halorubrum vacuolatum strain DSM 8800 | 63740.3 | wgs | patric | 63740 |
GC content
- @ref: 67770
- GC-content: 62.7
- method: thermal denaturation, midpoint method (Tm)
External links
@ref: 3406
culture collection no.: DSM 8800, JCM 9060, NCIMB 13189, ATCC 51376, CGMCC 1.3563, CIP 104547
straininfo link
| @ref | straininfo |
|---|---|
| 75429 | 93028 |
| 75430 | 312104 |
literature
- topic: Phylogeny
- Pubmed-ID: 17082390
- title: Halorubrum orientale sp. nov., a halophilic archaeon isolated from Lake Ejinor, Inner Mongolia, China.
- authors: Castillo AM, Gutierrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64420-0
- year: 2006
- mesh: Base Composition, China, DNA, Archaeal/chemistry/genetics/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Halobacteriaceae/*classification/cytology/*isolation & purification/physiology, Lipids/analysis/chemistry, Magnesium/metabolism, Molecular Sequence Data, Movement, Phylogeny, Pigments, Biological/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/analysis/metabolism, Temperature, *Water Microbiology
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3406 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8800) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-8800 | |||
| 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 | |
| 39036 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16468 | ||||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 75429 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID93028.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 75430 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID312104.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 123772 | Curators of the CIP | Collection of Institut Pasteur (CIP 104547) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104547 |