Strain identifier

BacDive ID: 138190

Type strain: Yes

Species: Halobacterium distributum

Strain history: CIP <- 1997, JCM <- VKM <- I.S. Zvyagintseva

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

@ref: 39236

BacDive-ID: 138190

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

description: Halobacterium distributum CIP 105238 is a mesophilic, Gram-negative, rod-shaped archaeon of the family Halobacteriaceae.

NCBI tax id

NCBI tax idMatching level
1227468strain
29283species
1227467strain

strain history

@refhistory
67770VKM B-1733 <-- I. S. Zvyagintseva 1m.
39236CIP <- 1997, JCM <- VKM <- I.S. Zvyagintseva

doi: 10.13145/bacdive138190.20230509.8.1

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 distributum
  • full scientific name: Halobacterium distributum corrig. Zvyagintseva and Tarasov 1989
  • synonyms

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

@ref: 39236

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halorubraceae

genus: Halorubrum

species: Halorubrum distributum

type strain: yes

Morphology

cell morphology

  • @ref: 39236
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
39236MEDIUM 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
39236CIP Medium 223yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=223
39236CIP Medium 232yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=232

culture temp

@refgrowthtypetemperaturerange
39236positivegrowth30mesophilic
67770positivegrowth37mesophilic
39236positivegrowth25-41
39236nogrowth5psychrophilic
39236nogrowth15psychrophilic
39236nogrowth45thermophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
39236606565hippurate+hydrolysis
3923617632nitrate-reduction
3923616301nitrite-reduction

antibiotic resistance

  • @ref: 39236
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 39236
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
39236oxidase+
39236beta-galactosidase+3.2.1.23
39236gelatinase-
39236catalase+1.11.1.6
39236gamma-glutamyltransferase-2.3.2.2
39236phenylalanine ammonia-lyase-4.3.1.24
39236tryptophan deaminase-
39236urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
39236-+++-+-+---+--------

Isolation, sampling and environmental information

isolation

@refcountrysample typeorigin.countrycontinent
39236USSR
67770TurkmenistanSalt soil crustTKMAsia
39236USSREnvironment, Salt soil crust in Turkmen

Safety information

risk assessment

  • @ref: 39236
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Halorubrum distributum 16S rRNA gene, complete sequenceD635721467ena29283
67770Halobacterium sp. (Halobacterium distributum) 16S ribosomal RNA sequenceL26170181ena29283

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halorubrum distributum JCM 10118GCA_000337335contigncbi1227468
67770Halorubrum distributum JCM 9100GCA_000337055contigncbi1227467
66792Halorubrum distributum JCM 91001227467.4wgspatric1227467
66792Halorubrum distributum JCM 101181227468.4wgspatric1227468

GC content

  • @ref: 67770
  • GC-content: 63.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno69.951no
gram-positiveno97.61no
anaerobicno97.356no
aerobicyes86.837no
halophileyes89.384no
spore-formingno93.995no
glucose-utilyes87.898no
flagellatedno95.521no
thermophileno95.18yes
glucose-fermentno83.266no

External links

@ref: 39236

culture collection no.: CIP 105238, ATCC 51197, JCM 9100, NCIMB 13203, VKM B-1733, CGMCC 1.3491, JCM 10118

straininfo link

@refstraininfo
9497046899
94971312081

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

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
39236Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105238Collection of Institut Pasteur (CIP 105238)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
94970Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID46899.1
94971Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID312081.1