Name: Halorubrum xinjiangense BD-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5949

Type strain:

Species: Halorubrum xinjiangense

Strain Designation: BD-1

Culture col. no.: DSM 21996, CIP 108550, JCM 12388, AS 1.3527, CGMCC 1.3527

Strain history: CIP <- 2004, JCM <- P. Zhou: strain BD-1

NCBI tax ID(s): 261291 (species)

SI-ID 134289

AS 1.3527, JCM 12388, CIP 108550, CGMCC 1.3527, DSM 21996

Section

Halorubrum xinjiangense BD-1 is a mesophilic, Gram-negative archaeon that was isolated from Sludge samples of Xiao-Er-Kule saline lake.

Gram-negative
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 xinjiangense**
	Full Scientific Name (LPSN)	Halorubrum xinjiangense Feng et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #123980]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.968

[Ref.: #123980]	Cell shape	oval-shaped

[Ref.: #123980]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16090]

Culture medium

HALOBACTERIA MEDIUM (DSMZ Medium 372)

[Ref.: #16090]

Culture medium growth

[Ref.: #16090]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16090]

Culture medium composition

expand / minimize

[Ref.: #36748]

Culture medium

MEDIUM 204 - for Halorubrum, Marinococcus and Natrialba

[Ref.: #36748]

Culture medium growth

[Ref.: #36748]

Culture medium composition

expand / minimize

[Ref.: #123980]

Culture medium

CIP Medium 204

[Ref.: #123980]

Culture medium growth

[Ref.: #123980]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #16090]		growth	37 °C
[Ref.: #36748]		growth	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #123980]		growth	15-45 °C
[Ref.: #123980]	no	growth	5 °C

[Ref.: #16090]	Temperature range	mesophilic
[Ref.: #36748]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #123980]	Temperature range	psychrophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %94
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.983

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #123980]	hippurate ChEBI	-	hydrolysis
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #123980]	nitrate ChEBI	-	reduction
[Ref.: #123980]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #123980]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #123980]		acetoin ChEBI	-
[Ref.: #123980]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #123980]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #123980]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #123980]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #123980]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #123980]	oxidase	+
[Ref.: #123980]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #123980]	tryptophan deaminase	-
[Ref.: #123980]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #123980]	11322	not determinedn.d.	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #123980]	11275	-	+	+	+	-	+	-	-	+	+	-	+	-	-	-	-	-	-	-	-

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

[Ref.: #16090]	Sample type/isolated from	Sludge samples of Xiao-Er-Kule saline lake
[Ref.: #16090]	Geographic location (country and/or sea, region)	Xinjiang
[Ref.: #16090]	Country	China
[Ref.: #16090]	Country ISO 3 Code	CHN
[Ref.: #16090]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Xiao-Er-kule Lake in Xinjiang

[Ref.: #123980]	Sample type/isolated from	Environment, Sludge samples of saline lake
[Ref.: #123980]	Geographic location (country and/or sea, region)	Xinjiang
[Ref.: #123980]	Country	China
[Ref.: #123980]	Country ISO 3 Code	CHN
[Ref.: #123980]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Environmental	#Terrestrial	#Mud (Sludge)
#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.: #16090]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123980]	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.: #16090]	Halorubrum xinjiangense 16S ribosomal RNA gene, partial sequence	AY510707	1470	ENA	261291 tax ID
[Ref.: #20218]	Halorubrum xinjiangense gene for 16S rRNA, complete sequence, strain: JCM 12388	AB663426	1470	ENA	261291 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halorubrum xinjiangense CGMCC 1.3527	GCA_900102375	scaffold	GenBank	261291 tax ID	*
[Ref.: #66792]	Halorubrum xinjiangense CGMCC 1.3527	2617270761	draft	JGI IMG/M	261291 tax ID	*
[Ref.: #66792]	Halorubrum xinjiangense strain CGMCC 1.3527	261291.3	wgs	PATRIC	261291 tax ID	*

[Ref.: #16090]	GC-content	68.0 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	68 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 GenomeNet Sporulation v. 1 based on: Halorubrum xinjiangense CGMCC 1.3527 NCBI: GCA_900102375.1
[Ref.: #69481]	spore-forming	no	94	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halorubrum xinjiangense CGMCC 1.3527 NCBI: GCA_900102375.1
[Ref.: #69480]	motile	no	67.749	no
[Ref.: #69480]	flagellated	no	94.276	no
[Ref.: #69480]	gram-positive	no	97.826	no
[Ref.: #69480]	anaerobic	no	96.611	no
[Ref.: #69480]	aerobic	yes	82.342	no
[Ref.: #69480]	halophile	yes	88.185	no
[Ref.: #69480]	spore-forming	no	94.776	no
[Ref.: #69480]	glucose-ferment	no	80.398	no
[Ref.: #69480]	glucose-util	yes	89.277	no
[Ref.: #69480]	thermophile	no	93.144	yes

Availability in culture collections External links

[Ref.: #16090]

Culture collection no.

DSM 21996, CIP 108550, JCM 12388, AS 1.3527, CGMCC 1.3527

[Ref.: #75438]

SI-ID 134289

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halorubrum salinarum sp. nov., an extremely halophilic archaeon isolated from a saturated brine pond of a saltern.	Han HL, Danganan RE, Li Z, Shin NR, Bennett RM, Dedeles GR, Kim SG	Int J Syst Evol Microbiol	10.1099/ijsem.0.005231	2022	*
Phylogeny	Halorubrum californiense sp. nov., an extreme archaeal halophile isolated from a crystallizer pond at a solar salt plant in California, USA.	Pesenti PT, Sikaroodi M, Gillevet PM, Sanchez-Porro C, Ventosa A, Litchfield CD	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/002410-0	2008	*
Enzymology	Genetic cloning and functional expression in Escherichia coli of an archaerhodopsin gene from Halorubrum xinjiangense.	Feng J, Liu HC, Chu JF, Zhou PJ, Tang JA, Liu SJ	Extremophiles	10.1007/s00792-005-0468-x	2005	*
Phylogeny	Halorubrum xinjiangense sp. nov., a novel halophile isolated from saline lakes in China.	Feng J, Zhou PJ, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.63209-0	2004	*

References

#16090

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21996

#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 )

#36748 ; 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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75438

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-ID134289.1 )

#123980 Collection of Institut Pasteur ; Curators of the CIP; CIP 108550
* These data were automatically processed and therefore are not curated

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Halorubrum xinjiangense CGMCC 1.3527

Halorubrum xinjiangense CGMCC 1.3527

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