Halorubrum trapanicum (DSM 12287, CIP 105807, JCM 10477)

Name: Halorubrum trapanicum (DSM 12287, CIP 105807, JCM 10477)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5942

Type strain

Culture col. no. DSM 12287 CIP 105807 JCM 10477 NCIMB 13488 NRC 34021 1 more

NCBI tax ID(s) 29284

Special Collections DSMZ JCM CIP

History <- NCIMB <- W. D. Grant, Dept. Microbiol. and Immunol., Univ. Leicester, UK <- NRC, Ottawa, Canada <- LMD, Delft, Holland <- H.F.M. Petter, Delft, Holland. Is an authentic sub-culture of Petter's isolate. Other strains in circulation appear to be misidentified strains (Halococcus sp., D63786) or a strain incorrectly attributed to being NCIMB 767 (Natrinema sp., D14125, probably derived from NCIMB 784) NCIMB 13488 <-- W. D. Grant <-- NRC 34021. CIP <- 1998, NCIMB <- W.D. Grant, Leicester Univ., Leicester, UK: strain derived from NRC 34021

Links

Halorubrum trapanicum DSM 12287 is a Gram-negative, motile, rod-shaped archaeon that was isolated from Solar salt.

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

Name and taxonomic classification

SI-ID 46036

ATCC 43102,NCMB 767,CIP 105807,NCIMB 13488,JCM 8979,JCM 9742,NCIMB 767,VKM B-2026,JCM 10477,LMD 33.42,LMD 71.76,NCCB 71076,IAM 13173,IAM 13172,DSM 5647,CECT 397,DSM 12287

@ref 20215

Last LPSN update 2026-02-09 11:19:05

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloferacaceae

Genus Halorubrum

Species Halorubrum trapanicum

Full scientific name Halorubrum trapanicum (Petter 1931) McGenity and Grant 1996

Synonyms (2)

"Bacterium trapanicum"
Halobacterium trapanicum

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
123576	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
4673	HALOBACTERIA MEDIUM (DSMZ Medium 372)	Medium recipe at MediaDive	Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water
39355	MEDIUM 232 - for Halorubrum saccharovorum, Halorubrum distributum		Distilled water make up to (1000.000 ml);Sodium chloride (250.000 g);Iron (II) sulphate heptahydrate (0.050 g);Manganese II sulphate monohydrate (0.200 g);Magnesiumsulphate heptahydrate (20.000 g);Yeast extract (10.000 g);Casamino acids (7.500 g);Tri-sodi
123576	CIP Medium 232	Medium recipe at CIP
123576	CIP Medium 204	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
4673	positive	growth	37
39355	positive	growth	37
67770	positive	growth	37
123576	positive	growth	37-45
123576	negative	growth	5
123576	negative	growth	15
123576	negative	growth	25
123576	negative	growth	30

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		91.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
123576	606565 ChEBI	hippurate	-	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
123576	17632 ChEBI	nitrate	-	reduction
123576	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	+	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
123576	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123576	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
123576	15688 ChEBI	acetoin	-
123576	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
123576	alcohol dehydrogenase	-	1.1.1.1
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
123576	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
123576	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
123576	gamma-glutamyltransferase	-	2.3.2.2
123576	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
123576	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
123576	ornithine decarboxylase	-	4.1.1.17
123576	oxidase	+
123576	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
123576	tryptophan deaminase	-
123576	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

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
123576	-	+	+	+	-	+	-	-	+	+	-	+	-	-	-	-	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
123576	not determinedn.d.	+/-	-	-	-	+/-	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	+	+	-	-	+	-	-	-	+	-	-	-	+/-	+	-	-	+	-	-	-	-	-	-	+/-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Condition	#Saline

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4673	Solar salt	Sicily, Trapani	Italy	ITA	Europe
123576	Solar salt	Trapani, Sicily	Italy	ITA	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4673	1	Risk group (German classification) According to TRBA 466
123576	1	Risk group (French 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	ASM1787355v1 assembly for Halorubrum trapanicum DSM 12287	contig	GCA_017873555	29284.9	2913354236	29284	71.39
124043	ASM3952270v1 assembly for Halorubrum trapanicum JCM 10477	scaffold	GCA_039522705			29284	67.19

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Halorubrum trapanicum DNA for 16S rRNA	D63786	1472	228414
20218	Halococcus sp. JCM 8979 16S-23S ribosomal RNA intergenic spacer, partial sequence	EU984229	257	228414
20218	Halorubrum trapanicum gene for 16S rRNA, strain: NCMB 767	D14125	1472	29284
4673	H.trapanicum 16S rRNA gene	X82168	1460	29284
4673	Halorubrum trapanicum gene for 16S rRNA, complete sequence, strain: JCM 10477	AB663424	1470	29284
4673	Halorubrum trapanicum gene for 16S ribosomal RNA, partial sequence, strain: JCM 10477	AB477979	1430	29284

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halorubrum trapanicum DSM 12287
NCBI: GCA_017873555

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	91.70	no
125439	motility	BacteriaNetⓘ	yes	52.20	no
125439	gram_stain	BacteriaNetⓘ	negative	88.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	85.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic insights into Halorubrum ezzemoulense strain TC23: Genetic basis for halophilic traits and biotechnological potential.	Kesbic FI.	Sci Prog	10.1177/00368504251364316	2025
Genetics	Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations.	Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP, Papke RT.	Front Microbiol	10.3389/fmicb.2014.00143	2014
	Taxonomic and functional analysis of soil microbial communities in a mining site across a metal(loid) contamination gradient	Navas M, Perez-Esteban J, Torres M, Hontoria C, Moliner A.	European Journal of Soil Science.	10.1111/ejss.12979	2021
Metabolism	Deciphering Pathways for Carotenogenesis in Haloarchaea.	Giani M, Miralles-Robledillo JM, Peiro G, Pire C, Martinez-Espinosa RM.	Molecules	10.3390/molecules25051197	2020
	Deciphering archaeal glycolipids of an extremely halophilic archaeon of the genus Halobellus by MALDI-TOF/MS.	Lobasso S, Perez-Davo A, Vitale R, Sanchez MM, Corcelli A.	Chem Phys Lipids	10.1016/j.chemphyslip.2014.11.002	2015
Genetics	Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China-association with asthma, rhinitis and rhinoconjunctivitis in high school students.	Fu X, Ou Z, Zhang M, Meng Y, Li Y, Wen J, Hu Q, Zhang X, Norback D, Deng Y, Zhao Z, Sun Y.	Microbiome	10.1186/s40168-021-01091-0	2021
	Exploring tRNA gene cluster in archaea.	Morgado SM, Vicente ACP.	Mem Inst Oswaldo Cruz	10.1590/0074-02760180348	2019
Genetics	Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard.	Pratas D, Hosseini M, Grilo G, Pinho AJ, Silva RM, Caetano T, Carneiro J, Pereira F.	Genes (Basel)	10.3390/genes9090445	2018
	Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing.	Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT.	Genes (Basel)	10.3390/genes9030129	2018
	Metatranscriptomic and Metagenomic Analysis of Biological Diversity in Subglacial Lake Vostok (Antarctica).	Gura C, Rogers SO.	Biology (Basel)	10.3390/biology9030055	2020
	Archaeal Persisters: Persister Cell Formation as a Stress Response in Haloferax volcanii.	Megaw J, Gilmore BF.	Front Microbiol	10.3389/fmicb.2017.01589	2017
Metabolism	Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales.	Youssef NH, Savage-Ashlock KN, McCully AL, Luedtke B, Shaw EI, Hoff WD, Elshahed MS.	ISME J	10.1038/ismej.2013.165	2014
Proteome	Structural studies on archaeal phytanyl-ether lipids isolated from membranes of extreme halophiles by linear ion-trap multiple-stage tandem mass spectrometry with electrospray ionization.	Hsu FF, Lobasso S, Turk J, Corcelli A.	Anal Chim Acta	10.1016/j.aca.2013.02.010	2013
	Genotypic and Lipid Analyses of Strains From the Archaeal Genus Halorubrum Reveal Insights Into Their Taxonomy, Divergence, and Population Structure.	de la Haba RR, Corral P, Sanchez-Porro C, Infante-Dominguez C, Makkay AM, Amoozegar MA, Ventosa A, Papke RT.	Front Microbiol	10.3389/fmicb.2018.00512	2018
	Microbial diversity in Maras salterns, a hypersaline environment in the Peruvian Andes.	Maturrano L, Santos F, Rossello-Mora R, Anton J.	Appl Environ Microbiol	10.1128/aem.02214-05	2006
Phylogeny	Patterns and determinants of halophilic archaea (class halobacteria) diversity in tunisian endorheic salt lakes and sebkhet systems.	Najjari A, Elshahed MS, Cherif A, Youssef NH.	Appl Environ Microbiol	10.1128/aem.01097-15	2015
Phylogeny	Phylogenetic analyses of some extremely halophilic archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences.	Arahal DR, Dewhirst FE, Paster BJ, Volcani BE, Ventosa A.	Appl Environ Microbiol	10.1128/aem.62.10.3779-3786.1996	1996
Phylogeny	Strain NCIMB 13488 may serve as the type strain of Halorubrum trapanicum. Opinion 74.	Judicial Commission Of The International Committee On Systematics Of Prokaryotes	Int J Syst Evol Microbiol	10.1099/ijs.0.02497-0	2003
Phylogeny	Halorubrum ejinorense sp. nov., 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.0.65241-0	2007
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
	Characterization of Halorubrum sfaxense sp. nov., a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia.	Trigui H, Masmoudi S, Brochier-Armanet C, Maalej S, Dukan S.	Int J Microbiol	10.1155/2011/240191	2011
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

References

#4673	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12287
#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 )
#39355	; 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 .
#123576	Collection of Institut Pasteur ; Curators of the CIP; CIP 105807
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 trapanicum (DSM 12287, CIP 105807, JCM 10477)

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

Metabolite tests

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_017873555

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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