Strain identifier

BacDive ID: 5939

Type strain: Yes

Species: Halorubrum sodomense

Strain Designation: RD 26

Strain history: CIP <- 1997, JCM <- IFO <- ATCC <- A. Oren RD-26

NCBI tax ID(s): 35743 (species)

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General

@ref: 1341

BacDive-ID: 5939

DSM-Number: 3755

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

description: Halorubrum sodomense RD 26 is a mesophilic, Gram-negative, motile archaeon of the family Haloferacaceae.

NCBI tax id

  • NCBI tax id: 35743
  • Matching level: species

strain history

@refhistory
1341<- B.J. Tindall <- NCMB <- ATCC <- A. Oren, RD 26
67770IFO 14740 <-- ATCC 33755 <-- A. Oren RD-26.
122649CIP <- 1997, JCM <- IFO <- ATCC <- A. Oren RD-26

doi: 10.13145/bacdive5939.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Halobacteriales
  • family: Haloferacaceae
  • genus: Halorubrum
  • species: Halorubrum sodomense
  • full scientific name: Halorubrum sodomense (Oren 1983) McGenity and Grant 1996

  • synonyms

    @refsynonym
    20215Halobacterium sodomense
    20215Halorubrobacterium sodomense

@ref: 1341

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halorubraceae

genus: Halorubrum

species: Halorubrum sodomense

full scientific name: Halorubrum sodomense (Oren 1983) McGenity and Grant 1996

strain designation: RD 26

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
122649negativeoval-shapedyes
125439negative98

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1341HALOBACTERIA 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
35812MEDIUM 204 - for Halorubrum, Marinococcus and NatrialbayesDistilled water make up to (1000.000 ml);Sodium chloride (200.000 g);Potassium chloride (2.000 g);ManganeseII chloride tetrahydrate (0.360 mg);Magnesium sulphate heptahydrate (20.000 g);Agar (20.000 g);Yeast extract (5.000 g);Ferrous chloride tetrahydrate
122649CIP Medium 240yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=240
122649CIP Medium 204yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=204

culture temp

@refgrowthtypetemperature
1341positivegrowth37
35812positivegrowth37
67770positivegrowth37
122649positivegrowth15-37
122649nogrowth5
122649nogrowth45

Physiology and metabolism

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 96.7

compound production

@refcompound
1341amyloglucosidase
1341bacteriorhodopsin

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12264917632nitrate+reduction
12264916301nitrite-reduction
68371Potassium 5-ketogluconate+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

metabolite production

  • @ref: 122649
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12264915688acetoin-
12264917234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
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
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
122649oxidase+
122649beta-galactosidase-3.2.1.23
122649gelatinase-
122649catalase+1.11.1.6
122649gamma-glutamyltransferase-2.3.2.2
122649phenylalanine ammonia-lyase-4.3.1.24
122649tryptophan deaminase-
122649urease-3.5.1.5
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122649-+++-+---+-+----+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122649--+/-+/-+/-+/-----------------------------------+/-+/-+/------+

Isolation, sampling and environmental information

isolation

@refgeographic locationsample typecountryorigin.countrycontinent
1341Dead Sea
67770Surface water from the Dead Sea
122649Dead SeaIsraelISRAsia

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
13411Risk group (German classification)
1226491Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218H.sodomense 16S rRNA geneX821691462nuccore35743
20218Halorubrum sodomense gene for 16S rRNA, complete sequence, strain: JCM 8880AB6634201470nuccore35743
1341Halorubrum sodomense gene for 16S rRNAD133791469nuccore35743

Genome sequences

  • @ref: 67770
  • description: Halorubrum sodomense RD 26
  • accession: GCA_900111935
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 35743

GC content

@refGC-contentmethod
134167.4
6777068Buoyant density centrifugation (BD)
6777067.4Buoyant density centrifugation (BD)
6777066thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno79.694no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no84.039no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.356no
125438spore-formingspore-formingAbility to form endo- or exosporesno88.398no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno82.791yes
125438motile2+flagellatedAbility to perform flagellated movementno88no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.7
125439BacteriaNetmotilityAbility to perform movementyes64.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative98
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe88.3

External links

@ref: 1341

culture collection no.: DSM 3755, ATCC 33755, NCMB 2197, JCM 8880, CGMCC 1.2928, CIP 105330, IFO 14740, NBRC 14740, NCIMB 2197, VKM B-1771

straininfo link

@refstraininfo
7542340673
75424312178

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19060045Halorubrum californiense sp. nov., an extreme archaeal halophile isolated from a crystallizer pond at a solar salt plant in California, USA.Pesenti PT, Sikaroodi M, Gillevet PM, Sanchez-Porro C, Ventosa A, Litchfield CDInt J Syst Evol Microbiol10.1099/ijs.0.2008/002410-02008California, Crystallization, Halorubrum/*classification/genetics/*physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Species SpecificityGenetics
22347558Solar salt lake as natural environmental source for extraction halophilic pigments.Khanafari A, Khavarinejad D, Mashinchian AIran J Microbiol2010
Phylogeny35037851Halorubrum salinarum sp. nov., an extremely halophilic archaeon isolated from a saturated brine pond of a saltern.Han HL, Danganan RE, Li Z, Shin NR, Bennett RM, Dedeles GR, Kim SGInt J Syst Evol Microbiol10.1099/ijsem.0.0052312022Base Composition, DNA, Archaeal/genetics, Fatty Acids/chemistry, *Halorubrum/classification/isolation & purification, Philippines, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, *Salts, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1341Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3755)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3755
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
35812Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17338
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
75423Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40673.1StrainInfo: A central database for resolving microbial strain identifiers
75424Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312178.1StrainInfo: A central database for resolving microbial strain identifiers
122649Curators of the CIPCollection of Institut Pasteur (CIP 105330)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105330
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1