Strain identifier
BacDive ID: 5911
Type strain:
Species: Halobacterium salinarum
Strain Designation: R1
Strain history: NCIMB 2080 <-- ATCC 29341 <-- L. I. Hochstein R-1 <-- L. Briggs.
NCBI tax ID(s): 478009 (strain), 2242 (species)
General
@ref: 354
BacDive-ID: 5911
DSM-Number: 671
keywords: genome sequence, 16S sequence, Archaea, aerobe, mesophilic, Gram-negative
description: Halobacterium salinarum R1 is an aerobe, mesophilic, Gram-negative archaeon of the family Halobacteriaceae.
NCBI tax id
NCBI tax id | Matching level |
---|---|
478009 | strain |
2242 | species |
strain history
@ref | history |
---|---|
354 | <- D. Keradjopoulos <- W. Stoeckenius, R1 |
67770 | NCIMB 2080 <-- ATCC 29341 <-- L. I. Hochstein R-1 <-- L. Briggs. |
doi: 10.13145/bacdive5911.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Halobacteria
- order: Halobacteriales
- family: Halobacteriaceae
- genus: Halobacterium
- species: Halobacterium salinarum
- full scientific name: Halobacterium salinarum corrig. (Harrison and Kennedy 1922) Elazari-Volcani 1957 (Approved Lists 1980)
synonyms
@ref synonym 20215 Serratia cutirubra 20215 Halobacterium cutirubrum 20215 Halobacterium halobium 20215 Bacterium halobium 20215 Halobacterium salinarium 20215 Halobacterium piscisalsi 20215 Pseudomonas salinaria 20215 Halobacter salinaria 20215 Halobacter cutirubrum
@ref: 354
domain: Archaea
phylum: Euryarchaeota
class: Halobacteria
order: Halobacteriales
family: Halobacteriaceae
genus: Halobacterium
species: Halobacterium salinarum
full scientific name: Halobacterium salinarum (Harrison and Kennedy 1922) Elazari-Volcani 1957 emend. Gruber et al. 2004
strain designation: R1
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.982
colony morphology
- @ref: 47906
- incubation period: 4 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
354 | HALOBACTERIA MEDIUM (DSMZ Medium 372) | yes | https://mediadive.dsmz.de/medium/372 | Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water |
354 | HALOBACTERIUM MEDIUM (DSMZ Medium 97) | yes | https://mediadive.dsmz.de/medium/97 | Name: HALOBACTERIUM MEDIUM (DSMZ Medium 97) Composition: NaCl 250.0 g/l Agar 20.0 g/l MgSO4 x 7 H2O 20.0 g/l Yeast extract 10.0 g/l Casamino acids 7.5 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l FeSO4 x 7 H2O 0.05 g/l MnSO4 x H2O 0.0002 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
354 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 47906
- oxygen tolerance: aerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.965
observation
- @ref: 67770
- observation: quinones: MK-8, MK-8(H2)
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_187322.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17654;96_68930;97_89585;98_121877;99_187322&stattab=map
- Last taxonomy: Halobacterium salinarum
- 16S sequence: M11583
- Sequence Identity:
- Total samples: 33
- soil counts: 5
- aquatic counts: 26
- animal counts: 2
Safety information
risk assessment
- @ref: 354
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 67770
- description: Halobacterium halobium 16S rRNA gene, complete cds
- accession: M11583
- length: 1473
- database: ena
- NCBI tax ID: 2242
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Halobacterium salinarum R1 DSM 671 = R1 | GCA_000069025 | complete | ncbi | 478009 |
66792 | Halobacterium salinarum R1, DSM 671 | 641522631 | complete | img | 478009 |
66792 | Halobacterium salinarum R1, DSM 671 | 2596583691 | draft | img | 478009 |
66792 | Halobacterium salinarum R1 strain DSM 671 = R1 | 478009.35 | plasmid | patric | 478009 |
66792 | Halobacterium salinarum R1 strain DSM 671 = R1 | 478009.36 | plasmid | patric | 478009 |
66792 | Halobacterium salinarum R1 strain DSM 671 = R1 | 478009.38 | plasmid | patric | 478009 |
66792 | Halobacterium salinarum R1 strain DSM 671 = R1 | 478009.37 | plasmid | patric | 478009 |
66792 | Halobacterium salinarum R1 | 478009.20 | complete | patric | 478009 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 86 | no |
motile | no | 79.09 | no |
flagellated | no | 95.658 | no |
gram-positive | no | 97.349 | no |
anaerobic | no | 94.15 | yes |
aerobic | yes | 73.993 | no |
halophile | yes | 81.765 | no |
spore-forming | no | 93.576 | no |
thermophile | no | 91.852 | yes |
glucose-util | yes | 86.591 | no |
glucose-ferment | no | 79.141 | no |
External links
@ref: 354
culture collection no.: DSM 671, CCUG 24034, JCM 9409, ATCC 29341, NCIMB 2080
straininfo link
- @ref: 75391
- straininfo: 92941
literature
- topic: Enzymology
- Pubmed-ID: 15619297
- title: Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation.
- authors: Tebbe A, Klein C, Bisle B, Siedler F, Scheffer B, Garcia-Rizo C, Wolfertz J, Hickmann V, Pfeiffer F, Oesterhelt D
- journal: Proteomics
- DOI: 10.1002/pmic.200400910
- year: 2005
- mesh: Bacterial Proteins/*chemistry/isolation & purification, Base Composition, Chromosomes, Bacterial/genetics, Cytosol/chemistry, Electrophoresis, Gel, Two-Dimensional, Genome, Bacterial, Halobacterium salinarum/*chemistry/genetics, Membrane Proteins/analysis, Open Reading Frames, Proteome/*analysis, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- topic2: Proteome
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
354 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 671) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-671 | |
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 | |
47906 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 24034) | https://www.ccug.se/strain?id=24034 | |
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 | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
75391 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92941.1 | StrainInfo: A central database for resolving microbial strain identifiers |