Halorubrum distributum (DSM 23453, JCM 10247, VKM B-1739)

Name: Halorubrum distributum (DSM 23453, JCM 10247, VKM B-1739)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5946

Type strain

Strain Designation 4p

Culture col. no. DSM 23453 JCM 10247 VKM B-1739 CIP 108318 CGMCC 1.8971 2 more

NCBI tax ID(s) 1227486 29283

Special Collections DSMZ JCM CIP

History VKM B-1739 <-- I. S. Zvyagintseva 4p. CIP <- 2004, JCM <- 1998, VKM <- I. S. Zvyagintseva: strain 4p

Links

Halorubrum distributum 4p is a mesophilic, Gram-negative, ovoid-shaped prokaryote of the family Haloferacaceae.

Gram-negative ovoid-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 389474

JCM 10247,VKM B-1739,CIP 108318,DSM 23453

@ref 20215

Last LPSN update 2025-12-16 09:48:11

Domain Methanobacteriati

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloferacaceae

Genus Halorubrum

Species Halorubrum distributum

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

Synonyms (6)

Halobacterium distributum
Halorubrum arcis
Halorubrobacterium distributum
Halobacterium distributus
Halorubrum litoreum
Halorubrum terrestre

BacDive ID	Other strains from **Halorubrum distributum** (3)	Type strain
138190	H. distributum CIP 105238, ATCC 51197, JCM 9100, NCIMB 13203, ... (type strain)
5954	H. distributum DSM 23454, JCM 13916, CGMCC 1.5343, KCTC ...
5957	H. distributum Fa-1, DSM 23497, CGMCC 1.5336, JCM 13561

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
123471	negative	ovoid-shaped
125439	negative			91.4

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
17218	HALOBACTERIA MEDIUM (DSMZ Medium 372)	Medium recipe at MediaDive	Name: 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
39994	MEDIUM 223 - for Halorubrum saccharovorum and H. distributum		Distilled 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
123471	CIP Medium 223	Medium recipe at CIP
123471	CIP Medium 330	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17218	positive	growth	37	mesophilic
39994	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
123471	positive	growth	25-45
123471	negative	growth	5
123471	negative	growth	15

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		95.8

Halophily

@ref	Salt	Tested relation	Concentration
123471	NaCl	growth	0 %
123471	NaCl	growth	2 %
123471	NaCl	growth	4 %
123471	NaCl	growth	6 %
123471	NaCl	growth	8 %
123471	NaCl	growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
123471	606565 ChEBI	hippurate	+	hydrolysis
123471	17632 ChEBI	nitrate	-	reduction
123471	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123471	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
123471	15688 ChEBI	acetoin	-
123471	17234 ChEBI	glucose		-

Enzymes

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

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
123471	-	+	+	+	-	+	-	-	-	+	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
39994		Ashkhabad	USSR	TKM
67770	Salt crust	Ashgabat	Turkmenistan	TKM	Asia
123471	Salt crust	Ashkhabad	Turkmenistan	TKM	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17218	1	Risk group (German classification) According to TRBA 466
123471	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM33743v1 assembly for Halorubrum distributum JCM 10247	contig	GCA_000337435	1227486.3	2554235509	1227486	62.11

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Halorubrum terrestre gene for 16S rRNA, complete sequence, strain: JCM 10247	AB663422	1470	267368
20218	Halorubrum terrestre gene for 16S rRNA, partial sequence	AB090169	1467	267368
67770	Halobacterium distributum 16S ribosomal RNA (16S rRNA)	L26117	182	29283

GC content

@ref	GC-content (mol%)	Method
67770	64.4	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halorubrum terrestre JCM 10247
NCBI: GCA_000337435

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.80	no
125439	motility	BacteriaNetⓘ	yes	63.90	no
125439	gram_stain	BacteriaNetⓘ	negative	91.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	81.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic insights into Halorubrum ezzemoulense strain TC23: Genetic basis for halophilic traits and biotechnological potential.	Kesbic FI.	Sci Prog	10.1177/00368504251364316	2025
Genetics	Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations.	Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP, Papke RT.	Front Microbiol	10.3389/fmicb.2014.00143	2014
Metabolism	Dihydroxyacetone metabolism in Haloferax volcanii.	Ouellette M, Makkay AM, Papke RT.	Front Microbiol	10.3389/fmicb.2013.00376	2013
Transcriptome	Population and genomic analysis of the genus Halorubrum.	Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT.	Front Microbiol	10.3389/fmicb.2014.00140	2014
Phylogeny	Genome-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 A	Int J Syst Evol Microbiol	10.1099/ijsem.0.003956	2020
Phylogeny	[A new description of the type strain of Halobacterium distributum].	Zviagintseva IS, Kudriashova EB, Bulygina ES	Mikrobiologiia		1996
Phylogeny	Halorubrum lipolyticum sp. nov. and Halorubrum aidingense sp. nov., isolated from two salt lakes in Xin-Jiang, China.	Cui HL, Tohty D, Zhou PJ, Liu SJ.	Int J Syst Evol Microbiol	10.1099/ijs.0.64305-0	2006
Phylogeny	Halorubrum ejinorense sp. nov., isolated from Lake Ejinor, Inner Mongolia, China.	Castillo AM, Gutierrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A.	Int J Syst Evol Microbiol	10.1099/ijs.0.65241-0	2007
	Characterization of Halorubrum sfaxense sp. nov., a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia.	Trigui H, Masmoudi S, Brochier-Armanet C, Maalej S, Dukan S.	Int J Microbiol	10.1155/2011/240191	2011
Phylogeny	Taxonomic study of Halorubrum distributum and proposal of Halorubrum terrestre sp. nov.	Ventosa A, Gutierrez MC, Kamekura M, Zvyagintseva IS, Oren A	Int J Syst Evol Microbiol	10.1099/ijs.0.02621-0	2004

References

#17218	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23453
#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 )
#39994	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#123471	Collection of Institut Pasteur ; Curators of the CIP; CIP 108318
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Halorubrum distributum (DSM 23453, JCM 10247, VKM B-1739)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000337435

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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