Strain identifier

BacDive ID: 5911

Type strain: No

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
478009strain
2242species

strain history

@refhistory
354<- D. Keradjopoulos <- W. Stoeckenius, R1
67770NCIMB 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

    @refsynonym
    20215Serratia cutirubra
    20215Halobacterium cutirubrum
    20215Halobacterium halobium
    20215Bacterium halobium
    20215Halobacterium salinarium
    20215Halobacterium piscisalsi
    20215Pseudomonas salinaria
    20215Halobacter salinaria
    20215Halobacter 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

@refnamegrowthlinkcomposition
354HALOBACTERIA MEDIUM (DSMZ Medium 372)yeshttps://mediadive.dsmz.de/medium/372Name: 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
354HALOBACTERIUM MEDIUM (DSMZ Medium 97)yeshttps://mediadive.dsmz.de/medium/97Name: 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

@refgrowthtypetemperaturerange
354positivegrowth37mesophilic
67770positivegrowth37mesophilic

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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halobacterium salinarum R1 DSM 671 = R1GCA_000069025completencbi478009
66792Halobacterium salinarum R1, DSM 671641522631completeimg478009
66792Halobacterium salinarum R1, DSM 6712596583691draftimg478009
66792Halobacterium salinarum R1 strain DSM 671 = R1478009.35plasmidpatric478009
66792Halobacterium salinarum R1 strain DSM 671 = R1478009.36plasmidpatric478009
66792Halobacterium salinarum R1 strain DSM 671 = R1478009.38plasmidpatric478009
66792Halobacterium salinarum R1 strain DSM 671 = R1478009.37plasmidpatric478009
66792Halobacterium salinarum R1478009.20completepatric478009

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno86no
motileno79.09no
flagellatedno95.658no
gram-positiveno97.349no
anaerobicno94.15yes
aerobicyes73.993no
halophileyes81.765no
spore-formingno93.576no
thermophileno91.852yes
glucose-utilyes86.591no
glucose-fermentno79.141no

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

@idauthorscataloguedoi/urltitle
354Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 671)https://www.dsmz.de/collection/catalogue/details/culture/DSM-671
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
47906Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 24034)https://www.ccug.se/strain?id=24034
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)
75391Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92941.1StrainInfo: A central database for resolving microbial strain identifiers