Name: Halovivax ruber XH-70
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5888

Type strain:

Species: Halovivax ruber

Strain Designation: XH-70

Culture col. no.: DSM 18193, CGMCC 1.6204, JCM 13892

Strain history: A. Ventosa XH-70.

NCBI tax ID(s): 797302 (strain), 387341 (species)

SI-ID 308617

DSM 18193, JCM 13892, CGMCC 1.6204

Section

Halovivax ruber XH-70 is a mesophilic archaeon that was isolated from saline lake.

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	*Natrialbales*
	Family	*Natrialbaceae*
	Genus	*Halovivax*
	Species	**Halovivax ruber**
	Full Scientific Name (LPSN)	Halovivax ruber Castillo et al. 2007

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7417]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #7417]

Culture medium growth

[Ref.: #7417]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7417]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #7417]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #7417]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	100	8 of 8
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	pantothenate biosynthesis	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	purine metabolism	63.83	60 of 94
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	oxidative phosphorylation	49.45	45 of 91
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	degradation of sugar acids	36	9 of 25
[Ref.: #66794]	vitamin B12 metabolism	35.29	12 of 34
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	33.33	5 of 15
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #7417]	Sample type/isolated from	saline lake
[Ref.: #7417]	Geographic location (country and/or sea, region)	Lake Xilinhot, Inner Mongolia
[Ref.: #7417]	Country	China
[Ref.: #7417]	Country ISO 3 Code	CHN
[Ref.: #7417]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Saline Lake Xilinhot
[Ref.: #67770]	Geographic location (country and/or sea, region)	Inner Mongolia
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Condition	#Saline	-

What are isolation sources categories?

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

[Ref.: #7417]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #7417]	Halovivax ruber 16S rRNA gene, type strain XH-70T	AM269467	1379	ENA	797302 tax ID
[Ref.: #20218]	Halovivax ruber gene for 16S rRNA, complete sequence, strain: JCM 13892	AB663453	1474	ENA	797302 tax ID	*
[Ref.: #20218]	Halovivax ruber gene for 16S ribosomal RNA, partial sequence, strain: JCM 13892	AB477228	1434	ENA	797302 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halovivax ruber XH-70	GCA_000328525	complete	GenBank	797302 tax ID	*
[Ref.: #66792]	Halovivax ruber XH-70, DSM 18193	2506783009	complete	JGI IMG/M	797302 tax ID	*
[Ref.: #66792]	Halovivax ruber XH-70	797302.4	complete	PATRIC	797302 tax ID	*

[Ref.: #7417]

GC-content

65 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: Halovivax ruber XH-70 XH-70 NCBI: GCA_000328525.1
[Ref.: #69480]	motile	no	78.472	no
[Ref.: #69480]	flagellated	no	96.643	no
[Ref.: #69480]	gram-positive	no	95.741	no
[Ref.: #69480]	anaerobic	no	96.352	no
[Ref.: #69480]	aerobic	yes	84.248	no
[Ref.: #69480]	halophile	yes	86.682	no
[Ref.: #69480]	spore-forming	no	94.656	no
[Ref.: #69480]	thermophile	no	80.562	no
[Ref.: #69480]	glucose-util	yes	89.065	no
[Ref.: #69480]	glucose-ferment	no	82.108	no

Availability in culture collections External links

[Ref.: #7417]

Culture collection no.

DSM 18193, CGMCC 1.6204, JCM 13892

[Ref.: #75368]

SI-ID 308617

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halovivax cerinus sp. nov., an extremely halophilic archaeon from a hypersaline lake.	Amoozegar MA, Makhdoumi-Kakhki A, Mehrshad M, Rasooli M, Fazeli SAS, Sproer C, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.069757-0	2014	*
Phylogeny	Halovivax limisalsi sp. nov., an extremely halophilic archaeon from hypersaline mud.	Amoozegar MA, Makhdoumi-Kakhki A, Mehrshad M, Riazi S, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.063297-0	2014	*
Phylogeny	Halovivax ruber sp. nov., an extremely halophilic archaeon isolated from Lake Xilinhot, 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.0.64899-0	2007	*

References

#7417

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18193

#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 )

#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;

#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) .

#75368

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-ID308617.1 )

* These data were automatically processed and therefore are not curated

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Halovivax ruber XH-70 XH-70

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