Strain identifier

BacDive ID: 5946

Type strain: No

Species: Halorubrum distributum

Strain Designation: 4p

Strain history: CIP <- 2004, JCM <- 1998, VKM <- I. S. Zvyagintseva: strain 4p

NCBI tax ID(s): 267368 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 17218

BacDive-ID: 5946

DSM-Number: 23453

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

description: Halorubrum distributum 4p is a mesophilic, Gram-negative, ovoid-shaped archaeon of the family Halorubraceae.

NCBI tax id

  • NCBI tax id: 267368
  • Matching level: species

strain history

@refhistory
67770VKM B-1739 <-- I. S. Zvyagintseva 4p.
123471CIP <- 2004, JCM <- 1998, VKM <- I. S. Zvyagintseva: strain 4p

doi: 10.13145/bacdive5946.20230509.8.1

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 distributum
  • full scientific name: Halorubrum distributum (Zvyagintseva and Tarasov 1989) Oren and Ventosa 1996
  • synonyms

    @refsynonym
    20215Halobacterium distributus
    20215Halorubrum terrestre
    20215Halorubrum arcis
    20215Halorubrum litoreum
    20215Halorubrobacterium distributum
    20215Halobacterium distributum

@ref: 17218

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halorubraceae

genus: Halobacterium

species: Halobacterium distributum

full scientific name: Halorubrum distributum (Zvyagintseva and Tarasov 1989) Oren and Ventosa 1996

strain designation: 4p

type strain: no

Morphology

cell morphology

  • @ref: 123471
  • gram stain: negative
  • cell shape: ovoid-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17218HALOBACTERIA 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
39994MEDIUM 223 - for Halorubrum saccharovorum and H. distributumyesDistilled water make up to (1000.000 ml);Sodium chloride (250.000 g);Potassium chloride (2.000 g);Iron (II) sulphate heptahydrate (0.050 g);Manganese II sulphate monohydrate (0.200 mg);Magnesium sulphate heptahydrate (20.000 g);Agar (20.000 g);Yeast extra
123471CIP Medium 223yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=223
123471CIP Medium 330yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=330

culture temp

@refgrowthtypetemperaturerange
17218positivegrowth37mesophilic
39994positivegrowth37mesophilic
67770positivegrowth37mesophilic
123471positivegrowth25-45
123471nogrowth5psychrophilic
123471nogrowth15psychrophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
123471NaClnogrowth0 %
123471NaClnogrowth2 %
123471NaClnogrowth4 %
123471NaClnogrowth6 %
123471NaClnogrowth8 %
123471NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
123471606565hippurate+hydrolysis
12347117632nitrate-reduction
12347116301nitrite-reduction

metabolite production

  • @ref: 123471
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12347115688acetoin-
12347117234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
123471oxidase+
123471beta-galactosidase-3.2.1.23
123471alcohol dehydrogenase-1.1.1.1
123471gelatinase-
123471catalase+1.11.1.6
123471gamma-glutamyltransferase-2.3.2.2
123471lysine decarboxylase-4.1.1.18
123471ornithine decarboxylase-4.1.1.17
123471phenylalanine ammonia-lyase-4.3.1.24
123471tryptophan deaminase-
123471urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123471-+++-+---+-+--------

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrysample typecontinent
39994AshkhabadUSSRTKM
67770AshgabatTurkmenistanTKMSalt crustAsia
123471AshkhabadTurkmenistanTKMSalt crustAsia

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
172181Risk group (German classification)
1234711Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halorubrum terrestre gene for 16S rRNA, complete sequence, strain: JCM 10247AB6634221470ena267368
20218Halorubrum terrestre gene for 16S rRNA, partial sequenceAB0901691467ena267368
67770Halobacterium distributum 16S ribosomal RNA (16S rRNA)L26117182ena29283

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halorubrum terrestre JCM 102472554235509draftimg1227486
67770Halorubrum terrestre JCM 10247GCA_000337435contigncbi1227486
66792Halorubrum terrestre JCM 102471227486.3wgspatric1227486

GC content

  • @ref: 67770
  • GC-content: 64.4
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 17218

culture collection no.: DSM 23453, JCM 10247, CGMCC 1.5397, CGMCC 1.8971, CIP 108318, VKM B-1739

straininfo link

  • @ref: 75435
  • straininfo: 389474

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny8992245[A new description of the type strain of Halobacterium distributum].Zviagintseva IS, Kudriashova EB, Bulygina ESMikrobiologiia1996Base Sequence, Halobacteriaceae/classification/genetics, Halobacterium/*classification/genetics, Molecular Sequence Data, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/*genetics, RNA, Ribosomal, 5S/*genetics, Sequence Homology, Nucleic AcidGenetics
Phylogeny15023949Taxonomic study of Halorubrum distributum and proposal of Halorubrum terrestre sp. nov.Ventosa A, Gutierrez MC, Kamekura M, Zvyagintseva IS, Oren AInt J Syst Evol Microbiol2004Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Halobacteriaceae/*classification/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyGenetics10.1099/ijs.0.02621-0
Phylogeny31971502Genome-based analyses reveal a synonymy among Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996, Halorubrum terrestre Ventosa et al. 2004, Halorubrum arcis Xu et al. 2007 and Halorubrum litoreum Cui et al. 2007. Emended description of Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996.Infante-Dominguez C, de la Haba RR, Corral P, Sanchez-Porro C, Arahal DR, Ventosa AInt J Syst Evol Microbiol2020DNA, Archaeal/genetics, Genes, Archaeal, Halorubrum/*classification, Lipids/chemistry, Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome10.1099/ijsem.0.003956

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17218Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23453)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23453
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
39994Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5927
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/
68382Automatically annotated from API zym
75435Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389474.1StrainInfo: A central database for resolving microbial strain identifiers
123471Curators of the CIPCollection of Institut Pasteur (CIP 108318)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108318