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 Halorubraceae.

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/bacdive5939.20230509.8.1

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 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

  • @ref: 122649
  • gram stain: negative
  • cell shape: oval-shaped
  • motility: yes

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

@refgrowthtypetemperaturerange
1341positivegrowth37mesophilic
35812positivegrowth37mesophilic
67770positivegrowth37mesophilic
122649positivegrowth15-37
122649nogrowth5psychrophilic
122649nogrowth45thermophilic

Physiology and metabolism

compound production

@refcompound
1341amyloglucosidase
1341bacteriorhodopsin

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122649nitrate+reduction17632
122649nitrite-reduction16301

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
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
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

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 geneX821691462ena35743
20218Halorubrum sodomense gene for 16S rRNA, complete sequence, strain: JCM 8880AB6634201470ena35743
1341Halorubrum sodomense gene for 16S rRNAD133791469ena35743

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

traitpredictionconfidencetraining_data
motileno66.523no
flagellatedno94.73no
gram-positiveno97.644no
anaerobicno97.293no
aerobicyes85.135no
halophileyes85.628no
spore-formingno94.653no
glucose-fermentno78.267no
thermophileno93.442no
glucose-utilyes89.888no

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