Name: Halorubrum sodomense RD 26
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5939

Type strain:

Species: Halorubrum sodomense

Strain Designation: RD 26

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

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

NCBI tax ID(s): 35743 (species)

SI-ID 40673

ATCC 33755, DSM 3755, IFO 14740, NCMB 2197, CIP 105330, JCM 8880, NCIMB 2197, VKM B-1771, NBRC 14740, CGMCC 1.2206

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Methanobacteriota*
	Class	*Halobacteria*
	Order	*Haloferacales*
	Family	*Halorubraceae*
	Genus	*Halorubrum*
	Species	**Halorubrum sodomense**
	Full Scientific Name (LPSN)	Halorubrum sodomense (Oren 1983) McGenity and Grant 1996

	Synonym	Halobacterium sodomense
	Synonym	Halorubrobacterium sodomense

Information on morphological and physiological properties Morphology

[Ref.: #122649]	Gram stain	negative

[Ref.: #122649]	Cell shape	oval-shaped

[Ref.: #122649]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1341]

Culture medium

HALOBACTERIA MEDIUM (DSMZ Medium 372)

[Ref.: #1341]

Culture medium growth

[Ref.: #1341]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1341]

Culture medium composition

expand / minimize

[Ref.: #35812]

Culture medium

MEDIUM 204 - for Halorubrum, Marinococcus and Natrialba

[Ref.: #35812]

Culture medium growth

[Ref.: #35812]

Culture medium composition

expand / minimize

[Ref.: #122649]

Culture medium

CIP Medium 240

[Ref.: #122649]

Culture medium growth

[Ref.: #122649]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #122649]

Culture medium

CIP Medium 204

[Ref.: #122649]

Culture medium growth

[Ref.: #122649]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #1341]		growth	37 °C
[Ref.: #35812]		growth	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #122649]		growth	15-37 °C
[Ref.: #122649]	no	growth	5 °C
[Ref.: #122649]	no	growth	45 °C

[Ref.: #1341]	Temperature range	mesophilic
[Ref.: #35812]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #122649]	Temperature range	psychrophilic
[Ref.: #122649]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1341]	Name of produced compound	amyloglucosidase
[Ref.: #1341]	Name of produced compound	bacteriorhodopsin

[Ref.: #67770]

Observation

quinones: MK-8, MK-8(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #122649]	nitrate ChEBI	+	reduction
[Ref.: #122649]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122649]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #122649]		acetoin ChEBI	-
[Ref.: #122649]		glucose ChEBI		+

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #122649]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #122649]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #122649]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #122649]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122649]	oxidase	+
[Ref.: #122649]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122649]	tryptophan deaminase	-
[Ref.: #122649]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #122649]	10045	not determinedn.d.	-	-	+/-	+/-	+/-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	+/-	+/-	-	-	-	-	-	+

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122649]	8620	-	+	+	+	-	+	-	-	-	+	-	+	-	-	-	-	+	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #67770]	Sample type/isolated from	Surface water from the Dead Sea

[Ref.: #1341]	Geographic location (country and/or sea, region)	Dead Sea

[Ref.: #122649]	Geographic location (country and/or sea, region)	Dead Sea
[Ref.: #122649]	Country	Israel
[Ref.: #122649]	Country ISO 3 Code	ISR
[Ref.: #122649]	Continent	Asia
* marker position based on {}

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #1341]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122649]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #1341]	Halorubrum sodomense gene for 16S rRNA	D13379	1469	ENA	35743 tax ID
[Ref.: #20218]	H.sodomense 16S rRNA gene	X82169	1462	ENA	35743 tax ID	*
[Ref.: #20218]	Halorubrum sodomense gene for 16S rRNA, complete sequence, strain: JCM 8880	AB663420	1470	ENA	35743 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Halorubrum sodomense RD 26	GCA_900111935	scaffold	GenBank	35743 tax ID

[Ref.: #1341]	GC-content	67.4 mol%
[Ref.: #67770]	GC-content	68 mol%	Buoyant density centrifugation (BD)
[Ref.: #67770]	GC-content	67.4 mol%	Buoyant density centrifugation (BD)
[Ref.: #67770]	GC-content	66 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halorubrum sodomense RD 26 NCBI: GCA_900111935.1
[Ref.: #69480]	motile	no	66.523	no
[Ref.: #69480]	flagellated	no	94.73	no
[Ref.: #69480]	gram-positive	no	97.644	no
[Ref.: #69480]	anaerobic	no	97.293	no
[Ref.: #69480]	aerobic	yes	85.135	no
[Ref.: #69480]	halophile	yes	85.628	no
[Ref.: #69480]	spore-forming	no	94.653	no
[Ref.: #69480]	glucose-ferment	no	78.267	no
[Ref.: #69480]	thermophile	no	93.442	no
[Ref.: #69480]	glucose-util	yes	89.888	no

Availability in culture collections 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

[Ref.: #75423]	SI-ID 40673	*
[Ref.: #75424]	SI-ID 312178	*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halorubrum 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 SG	Int J Syst Evol Microbiol	10.1099/ijsem.0.005231	2022	*
Phylogeny	Halorubrum 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 CD	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/002410-0	2008	*
	Solar salt lake as natural environmental source for extraction halophilic pigments.	Khanafari A, Khavarinejad D, Mashinchian A	Iran J Microbiol		2010	*

References

#1341

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3755

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#35812 ; Curators of the CIP;
#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#75423

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID40673.1 )

#75424

#122649 Collection of Institut Pasteur ; Curators of the CIP; CIP 105330
* These data were automatically processed and therefore are not curated

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