Name: Halorubrum vacuolatum M24
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5943

Type strain:

Species: Halorubrum vacuolatum

Strain Designation: M24

Culture col. no.: DSM 8800, JCM 9060, NCIMB 13189, ATCC 51376, CGMCC 1.3563, CIP 104547

Strain history: CIP <- 1995, NCIMB <- W.D. Grant: strain M24

NCBI tax ID(s): 63740 (species)

SI-ID 93028

ATCC 51376, NCIMB 13189, CIP 104547, DSM 8800, JCM 9060

Section

Halorubrum vacuolatum M24 is a mesophilic archaeon of the family Halorubraceae.

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 vacuolatum**
	Full Scientific Name (LPSN)	Halorubrum vacuolatum (Mwatha and Grant 1993) Kamekura et al. 1997

	Synonym	Natronobacterium vacuolatum
	Synonym	Natronobacterium vacuolata

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3406]

Culture medium

ALKALOPHILIC HALOPHILE MEDIUM (DSMZ Medium 1431)

[Ref.: #3406]

Culture medium growth

[Ref.: #3406]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3406]

Culture medium composition

expand / minimize

[Ref.: #39036]

Culture medium

MEDIUM 136 - for Natronococcus occultus, Natrialba magadii and Halorubrum vacuolatum

[Ref.: #39036]

Culture medium growth

[Ref.: #39036]

Culture medium composition

expand / minimize

[Ref.: #123772]

Culture medium

CIP Medium 136

[Ref.: #123772]

Culture medium growth

[Ref.: #123772]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #3406]	growth	37 °C
[Ref.: #39036]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #3406]	Temperature range	mesophilic
[Ref.: #39036]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67770]

Observation

quinones: MK-8

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	75	9 of 12
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	pantothenate biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	NAD metabolism	61.11	11 of 18
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	vitamin B12 metabolism	50	17 of 34
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	oxidative phosphorylation	48.35	44 of 91
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	ubiquinone biosynthesis	28.57	2 of 7
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	acetate fermentation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #67770]	Sample type/isolated from	Brine from the Lake Magadi
[Ref.: #67770]	Country	Kenya
[Ref.: #67770]	Country ISO 3 Code	KEN
[Ref.: #67770]	Continent	Africa

[Ref.: #123772]	Sample type/isolated from	Environment, Soda lake, Magadi lake
[Ref.: #123772]	Country	Kenya
[Ref.: #123772]	Country ISO 3 Code	KEN
[Ref.: #123772]	Continent	Africa

[Ref.: #3406]	Geographic location (country and/or sea, region)	Lake Magadi
[Ref.: #3406]	Country	Kenya
[Ref.: #3406]	Country ISO 3 Code	KEN
[Ref.: #3406]	Continent	Africa
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence D87972 (>99% sequence identity) for Halorubrum vacuolatum subclade from Microbeatlas

Aquatic Samples	35
Soil Samples	1
Animal Samples
Plant Samples
Total Samples	36

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

[Ref.: #3406]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123772]	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.: #20218]	Halorubrum vacuolatum gene for 16S rRNA, complete sequence, strain: JCM 9060	AB663425	1471	ENA	63740 tax ID	*
[Ref.: #20218]	Halorubrum vacuolatum DNA for 16S rRNA	D87972	1468	ENA	63740 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Halorubrum vacuolatum DSM 8800	GCA_900188065	contig	GenBank	63740 tax ID
[Ref.: #66792]	Halorubrum vacuolatum DSM 8800	2724679803	draft	JGI IMG/M	63740 tax ID	*
[Ref.: #66792]	Halorubrum vacuolatum strain DSM 8800	63740.3	wgs	PATRIC	63740 tax ID	*

[Ref.: #67770]

GC-content

62.7 mol%

thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #3406]

Culture collection no.

DSM 8800, JCM 9060, NCIMB 13189, ATCC 51376, CGMCC 1.3563, CIP 104547

[Ref.: #75429]	SI-ID 93028	*
[Ref.: #75430]	SI-ID 312104	*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halorubrum orientale sp. nov., a halophilic archaeon 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.0.64420-0	2006	*

References

#3406

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 8800

#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 )

#39036 ; Curators of the CIP;

#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;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#75429

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-ID93028.1 )

#75430

#123772 Collection of Institut Pasteur ; Curators of the CIP; CIP 104547
* These data were automatically processed and therefore are not curated

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