Halovivax ruber (DSM 18193, CGMCC 1.6204, JCM 13892)

Name: Halovivax ruber (DSM 18193, CGMCC 1.6204, JCM 13892)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5888

Type strain

Strain Designation XH-70

Culture col. no. DSM 18193 CGMCC 1.6204 JCM 13892 XH-70

NCBI tax ID(s) 797302 387341

Special Collections DSMZ JCM

History DSMZ <- A. Ventosa, Univ. of Sevilla; XH-70 <- A. M. Castillo JCM <-- A. Ventosa XH-70.

Links

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

genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 308617

DSM 18193,JCM 13892,CGMCC 1.6204

@ref 20215

Last LPSN update 2026-05-29 08:26:16

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Natrialbaceae

Genus Halovivax

Species Halovivax ruber

Full scientific name Halovivax ruber Castillo et al. 2007

Morphology

Cell morphology

@ref	Motility	Confidence
125438		91.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7417	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 100.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7417	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	90.967

Spore formation

@ref	Spore formation	Confidence
125439		95.407

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7417	saline lake	Lake Xilinhot, Inner Mongolia	China	CHN	Asia
67770	Saline Lake Xilinhot	Inner Mongolia	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7417	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM32852v1 assembly for Halovivax ruber XH-70	complete	GCA_000328525	797302.4	2506783009	797302	98.85

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Halovivax ruber gene for 16S ribosomal RNA, partial sequence, strain: JCM 13892	AB477228	1434	797302
20218	Halovivax ruber gene for 16S rRNA, complete sequence, strain: JCM 13892	AB663453	1474	797302
7417	Halovivax ruber 16S rRNA gene, type strain XH-70T	AM269467	1379	797302

GC content

@ref	GC-content (mol%)	Method
7417	65	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: ASM32852v1 assembly for Halovivax ruber XH-70
BV-BRC: 797302.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	90.97	no
125439	gram_stain	BacteriaNetⓘ	negative	51.24	no
125439	motility	BacteriaNetⓘ	yes	45.71	no
125439	spore_formation	BacteriaNetⓘ	no	95.41	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halovivax ruber XH-70 XH-70
NCBI: GCA_000328525.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	71.79	no
125438	anaerobic	anaerobicⓘ	no	84.90	no
125438	aerobic	aerobicⓘ	yes	76.70	no
125438	spore-forming	spore-formingⓘ	no	85.43	no
125438	thermophilic	thermophileⓘ	no	83.82	yes
125438	flagellated	motile2+ⓘ	no	91.50	no

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;
#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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Halovivax ruber (DSM 18193, CGMCC 1.6204, JCM 13892)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000328525

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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