Strain identifier

BacDive ID: 5912

Type strain: Yes

Species: Halobacterium salinarum

Strain Designation: 91-R6

Strain history: CIP <- 2016, DSMZ <- B.J. Tindall <- NRC <- N.E. Gibbons <- A.G. Lochhead: strain 91-R6

NCBI tax ID(s): 2597657 (strain), 2242 (species)

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General

@ref: 1340

BacDive-ID: 5912

DSM-Number: 3754

keywords: genome sequence, 16S sequence, Archaea, mesophilic, Gram-negative, rod-shaped

description: Halobacterium salinarum 91-R6 is a mesophilic, Gram-negative, rod-shaped archaeon that was isolated from salted cow hide.

NCBI tax id

NCBI tax idMatching level
2597657strain
2242species

strain history

@refhistory
1340<- B.J. Tindall <- NRC <- N.E. Gibbons <- A.G. Lochhead, 91-R6
67770NCIMB 764 <-- N. E. Gibbons <-- A. G. Lochhead.
122383CIP <- 2016, DSMZ <- B.J. Tindall <- NRC <- N.E. Gibbons <- A.G. Lochhead: strain 91-R6

doi: 10.13145/bacdive5912.20230509.8.1

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: 1340

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: 91-R6

type strain: yes

Morphology

cell morphology

  • @ref: 122383
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1340HALOBACTERIA 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
1340HALOBACTERIUM 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
122383CIP Medium 330yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=330
122383CIP Medium 204yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=204

culture temp

@refgrowthtypetemperaturerange
1340positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-8, MK-8(H2)

Isolation, sampling and environmental information

isolation

@refsample type
1340salted cow hide
67770Salted cowhide
122383Salted cow hide

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Organ#Skin, Nail, Hair
#Condition#Saline

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: AB663362
  • Sequence Identity:
  • Total samples: 33
  • soil counts: 5
  • aquatic counts: 26
  • animal counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
13401Risk group (German classification)
1223831Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halobacterium salinarum gene for 16S rRNA, complete sequence, strain: JCM 8978AB6633621473ena2242
1340Halobacterium salinarum 16S rRNA gene, type strain DSM 3754TAJ4961851473ena2597657

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halobacterium salinarum 91-R6GCA_004799605completencbi2242
66792Halobacterium salinarum DSM 37542597490337draftimg2242
67770Halobacterium salinarum DSM 3754GCA_008124605contigncbi2597657
66792Halobacterium salinarum strain 91-R62242.21completepatric2242
66792Halobacterium salinarum DSM 37542597657.4wgspatric2597657

GC content

  • @ref: 67770
  • GC-content: 66.4
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno78.53no
flagellatedno95.249no
gram-positiveno97.5no
anaerobicno93.959no
aerobicyes76.327no
halophileyes84.22no
spore-formingno93.943no
glucose-utilyes86.989no
thermophileno87.276yes
glucose-fermentno79.994no

External links

@ref: 1340

culture collection no.: DSM 3754, ATCC 33171, JCM 8978, NCMB 764, NRC 34002, CGMCC 1.3519, CIP 104033, IAM 13166, NBRC 102687, NCIMB 764, NCMB 766, VKM B-1769

straininfo link

@refstraininfo
7539240375
75393312097

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17012561Halobacterium jilantaiense sp. nov., a halophilic archaeon isolated from a saline lake in Inner Mongolia, China.Yang Y, Cui HL, Zhou PJ, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.64437-02006Bacterial Typing Techniques, Base Composition, China, DNA, Archaeal/analysis, DNA, Ribosomal/analysis, Fresh Water/chemistry/*microbiology, Genes, rRNA, Halobacterium/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
Phylogeny18768619Halobacterium piscisalsi sp. nov., from fermented fish (pla-ra) in Thailand.Yachai M, Tanasupawat S, Itoh T, Benjakul S, Visessanguan W, Valyasevi RInt J Syst Evol Microbiol10.1099/ijs.0.65592-02008Base Composition, Carbohydrate Metabolism, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fish Products/*microbiology, Genes, rRNA, Halobacterium/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Hypotonic Solutions/toxicity, Locomotion, Microbial Viability, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature, ThailandMetabolism
Phylogeny22058320Halobacterium piscisalsi Yachai et al. 2008 is a later heterotypic synonym of Halobacterium salinarum Elazari-Volcani 1957.Minegishi H, Echigo A, Shimane Y, Kamekura M, Tanasupawat S, Visessanguan W, Usami RInt J Syst Evol Microbiol10.1099/ijs.0.036905-02011DNA, Archaeal/genetics, DNA-Directed RNA Polymerases/genetics, *Food Microbiology, Halobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, ThailandBiotechnology
23057712Biofilm formation by haloarchaea.Frols S, Dyall-Smith M, Pfeifer FEnviron Microbiol10.1111/j.1462-2920.2012.02895.x2012Bacterial Adhesion, *Biofilms, Halobacteriaceae/*physiology/*ultrastructure, Microscopy, Confocal, Microscopy, Electron, Transmission
Phylogeny23525908Haloferax chudinovii sp. nov., a halophilic archaeon from Permian potassium salt deposits.Saralov AI, Baslerov RV, Kuznetsov BBExtremophiles10.1007/s00792-013-0534-82013Archaeal Proteins/analysis, Base Composition, Carbohydrates/analysis, DNA, Archaeal/chemistry, Geologic Sediments/*microbiology, Haloferax/chemistry/cytology/genetics/*isolation & purification, Lipids/analysis, Phylogeny, Potassium, SiberiaEnzymology
Phylogeny28901903Halobacterium litoreum sp. nov., isolated from a marine solar saltern.Lu ZZ, Li Y, Zhou Y, Cui HL, Li ZRInt J Syst Evol Microbiol10.1099/ijsem.0.0022592017Base Composition, China, DNA, Archaeal/genetics, Genes, Archaeal, Glycolipids/analysis, Halobacterium/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, *Water MicrobiologyTranscriptome
Genetics31296677The Genome Sequence of the Halobacterium salinarum Type Strain Is Closely Related to That of Laboratory Strains NRC-1 and R1.Pfeiffer F, Marchfelder A, Habermann B, Dyall-Smith MLMicrobiol Resour Announc10.1128/MRA.00429-192019
Genetics31797576Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754(T) ) and the laboratory strains R1 and NRC-1.Pfeiffer F, Losensky G, Marchfelder A, Habermann B, Dyall-Smith MMicrobiologyopen10.1002/mbo3.9742019Archaeal Proteins/genetics/metabolism, Biological Evolution, Computational Biology/methods, Gene Order, Genetic Heterogeneity, *Genome, Archaeal, *Genomics/methods, Halobacterium salinarum/*genetics, Molecular Sequence Annotation, PlasmidsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1340Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3754)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3754
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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
75392Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40375.1StrainInfo: A central database for resolving microbial strain identifiers
75393Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312097.1StrainInfo: A central database for resolving microbial strain identifiers
122383Curators of the CIPCollection of Institut Pasteur (CIP 104033)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104033