Halorubrum distributum (CIP 105238, ATCC 51197, JCM 9100)

Name: Halorubrum distributum (CIP 105238, ATCC 51197, JCM 9100)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 138190

Type strain

Culture col. no. CIP 105238 ATCC 51197 JCM 9100 NCIMB 13203 VKM B-1733 2 more

NCBI tax ID(s) 1227467 1227468 29283

Special Collections JCM CIP

History VKM B-1733 <-- I. S. Zvyagintseva 1m. CIP <- 1997, JCM <- VKM <- I.S. Zvyagintseva

Links

Halorubrum distributum CIP 105238 is a Gram-negative, rod-shaped archaeon of the family Haloferacaceae.

Gram-negative rod-shaped genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 46899

ATCC 51197,NCIMB 13203,VKM B-1733,CIP 105238,JCM 9100,JCM 10118

@ref 20215

Last LPSN update 2026-02-09 11:33:03

Domain Archaea

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
5946	H. distributum 4p, DSM 23453, JCM 10247, CGMCC 1.5397, CGMCC ...
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
39236	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Composition	Medium link
39236	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
39236	CIP Medium 223		Medium recipe at CIP
39236	CIP Medium 232		Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
39236	positive	growth	30
39236	positive	growth	25-41
39236	negative	growth	5
39236	negative	growth	15
39236	negative	growth	45
67770	positive	growth	37

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		93.8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
39236	606565 ChEBI	hippurate	+	hydrolysis
39236	17632 ChEBI	nitrate	-	reduction
39236	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
39236	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
39236	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
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
39236	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
39236	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
39236	gamma-glutamyltransferase	-	2.3.2.2
39236	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
39236	oxidase	+
39236	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
39236	tryptophan deaminase	-
39236	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	denitrification	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	ethanol fermentation	100	2 of 2
66794	valine metabolism	88.89	8 of 9
66794	vitamin K metabolism	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylalanine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	citric acid cycle	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	starch degradation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	acetoin degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	non-pathway related	65.79	25 of 38
66794	purine metabolism	64.89	61 of 94
66794	proline metabolism	63.64	7 of 11
66794	pyrimidine metabolism	60	27 of 45
66794	propionate fermentation	60	6 of 10
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	threonine metabolism	60	6 of 10
66794	Entner Doudoroff pathway	60	6 of 10
66794	lipid metabolism	58.06	18 of 31
66794	cardiolipin biosynthesis	57.14	4 of 7
66794	glutathione metabolism	57.14	8 of 14
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	photosynthesis	57.14	8 of 14
66794	serine metabolism	55.56	5 of 9
66794	alanine metabolism	55.17	16 of 29
66794	glycolysis	52.94	9 of 17
66794	lysine metabolism	52.38	22 of 42
66794	coenzyme M biosynthesis	50	5 of 10
66794	glycogen biosynthesis	50	2 of 4
66794	degradation of sugar alcohols	50	8 of 16
66794	kanosamine biosynthesis II	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	toluene degradation	50	2 of 4
66794	myo-inositol biosynthesis	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	ketogluconate metabolism	50	4 of 8
66794	gluconeogenesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	C4 and CAM-carbon fixation	50	4 of 8
66794	tryptophan metabolism	47.37	18 of 38
66794	chorismate metabolism	44.44	4 of 9
66794	NAD metabolism	44.44	8 of 18
66794	lipid A biosynthesis	44.44	4 of 9
66794	cysteine metabolism	44.44	8 of 18
66794	arachidonic acid metabolism	44.44	8 of 18
66794	d-mannose degradation	44.44	4 of 9
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	heme metabolism	42.86	6 of 14
66794	methionine metabolism	42.31	11 of 26
66794	oxidative phosphorylation	41.76	38 of 91
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	bacilysin biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	leucine metabolism	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	degradation of sugar acids	36	9 of 25
66794	tyrosine metabolism	35.71	5 of 14
66794	degradation of pentoses	35.71	10 of 28
66794	histidine metabolism	34.48	10 of 29
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	carotenoid biosynthesis	31.82	7 of 22
66794	sulfate reduction	30.77	4 of 13
66794	urea cycle	30.77	4 of 13
66794	mevalonate metabolism	28.57	2 of 7
66794	tetrahydrofolate metabolism	28.57	4 of 14
66794	vitamin B6 metabolism	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	ppGpp biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	aspartate and asparagine metabolism	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	polyamine pathway	21.74	5 of 23

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
39236	-	+	+	+	-	+	-	+	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
39236		USSR
67770	Salt soil crust	Turkmenistan	TKM	Asia
39236	Environment, Salt soil crust in Turkmen	USSR

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
39236	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM33733v1 assembly for Halorubrum distributum JCM 10118	contig	GCA_000337335	1227468.4	2554235486	1227468	65.16
67770	ASM33705v1 assembly for Halorubrum distributum JCM 9100	contig	GCA_000337055	1227467.4	2554235487	1227467	62.17

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
67770	Halorubrum distributum 16S rRNA gene, complete sequence	D63572	1467	29283
67770	Halobacterium sp. (Halobacterium distributum) 16S ribosomal RNA sequence	L26170	181	29283
124043	Halorubrum distributum gene for 16S rRNA, complete sequence, strain: JCM 9100.	AB663410	1470	29283

GC content

@ref	GC-content (mol%)	Method
67770	63.9	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 distributum JCM 10118
NCBI: GCA_000337335

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	68.80	no
125439	gram_stain	BacteriaNetⓘ	positive	88.40	no
125439	motility	BacteriaNetⓘ	no	65.80	no
125439	spore_formation	BacteriaNetⓘ	no	93.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halorubrum distributum JCM 9100
PATRIC: 1227467.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	76.68	no
125438	anaerobic	anaerobicⓘ	no	86.96	no
125438	spore-forming	spore-formingⓘ	no	87.01	no
125438	aerobic	aerobicⓘ	yes	77.25	no
125438	thermophilic	thermophileⓘ	no	84.96	yes
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	[Interaction of halobacteria and cyanobacteria in a halophilic cyanobacterial community].	Zviagintseva IS, Gerasimenko LM, Kostrikina NA, Bulygina ES, Zavarzin GA.	Mikrobiologiia		1995
Phylogeny	[A new description of the type strain of Halobacterium distributum].	Zviagintseva IS, Kudriashova EB, Bulygina ES	Mikrobiologiia		1996
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

#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 )
#39236	Collection of Institut Pasteur ; Curators of the CIP; CIP 105238
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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 (CIP 105238, ATCC 51197, JCM 9100)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000337335

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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