Halobacillus kuroshimensis (DSM 18393, JCM 14155, JS-Hb7)

Name: Halobacillus kuroshimensis (DSM 18393, JCM 14155, JS-Hb7)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1349

Type strain

Strain Designation JS-Hb7, IS-Hb7

Culture col. no. DSM 18393 JCM 14155 JS-Hb7 CIP 109650 IS-Hb7

NCBI tax ID(s) 1121938 302481

Special Collections DSMZ JCM CIP Literature strains

Links

Halobacillus kuroshimensis JS-Hb7 is a spore-forming, mesophilic, Gram-positive prokaryote that forms circular colonies and was isolated from carbonate rock collected from a 642 m-deep methane cold seep.

spore-forming Gram-positive rod-shaped colony-forming mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 309457

DSM 18393,JCM 14155,CIP 109650

@ref 20215

Last LPSN update 2025-12-16 09:47:05

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Halobacillus

Species Halobacillus kuroshimensis

Full scientific name Halobacillus kuroshimensis Hua et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
22985	positive	1.6-3.3 µm	0.5-1.0 µm	rod-shaped
120515	positive			ovoid-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period
22985	1.5-2.5 mm	yellow-orange	circular	3 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7522	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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
37807	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
120515	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7522	positive	growth	30	mesophilic
22985	positive	growth	9.0-48.0
22985	positive	optimum	25.0	mesophilic
37807	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
22985	positive	optimum	7.5-8.0
22985	positive	growth	5.5-10.0	alkaliphile

Physiology and metabolism

Spore formation

@ref	Spore description	Type of spore	Confidence
22985	spherical or ellipsoidal, terminal position	endospore
120515
125438			93.448
125439			93.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
22985	NaCl	positive	growth	0.5-25.0 %(w/v)
22985	NaCl		optimum	6.0 %

Murein

@ref	Murein short key	Type
7522	A21.04	A4ß L-Orn-D-Asp

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
22985	40585 ChEBI	alpha-cyclodextrin	-	hydrolysis
22985	17925 ChEBI	alpha-D-glucose	+	carbon source
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
22985		casein	+	hydrolysis
22985	17057 ChEBI	cellobiose	+	builds acid from
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
22985	15824 ChEBI	D-fructose	+	builds acid from
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
22985	12936 ChEBI	D-galactose	-	builds acid from
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
22985	17634 ChEBI	D-glucose	+	builds acid from
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
22985	16899 ChEBI	D-mannitol	-	builds acid from
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
22985	16024 ChEBI	D-mannose	+	carbon source
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
22985	16443 ChEBI	D-tagatose	-	builds acid from
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
22985	16551 ChEBI	D-trehalose	-	builds acid from
22985	65327 ChEBI	D-xylose	-	builds acid from
22985	65327 ChEBI	D-xylose	+	carbon source
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
22985	23652 ChEBI	dextrin	-	hydrolysis
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
22985	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
22985	5291 ChEBI	gelatin	+	hydrolysis
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
22985	17754 ChEBI	glycerol	+	builds acid from
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
22985	28087 ChEBI	glycogen	-	hydrolysis
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
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	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
22985	17306 ChEBI	maltose	+	builds acid from
22985	17306 ChEBI	maltose	+	carbon source
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
22985	37684 ChEBI	mannose	+	builds acid from
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
22985	28053 ChEBI	melibiose	-	builds acid from
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
22985	17268 ChEBI	myo-inositol	+	builds acid from
22985	17268 ChEBI	myo-inositol	+	carbon source
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
22985	506227 ChEBI	N-acetylglucosamine	+	builds acid from
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
22985	17632 ChEBI	nitrate	-	reduction
120515	17632 ChEBI	nitrate	-	reduction
120515	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
22985	17814 ChEBI	salicin	-	builds acid from
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
22985	28017 ChEBI	starch	+	hydrolysis
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
22985	17992 ChEBI	sucrose	+	builds acid from
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
22985	53424 ChEBI	tween 20	+	hydrolysis
22985	53423 ChEBI	tween 40	+	carbon source
22985	53423 ChEBI	tween 40	+	hydrolysis
22985	53426 ChEBI	tween 80	+	carbon source
22985	53426 ChEBI	tween 80	+	hydrolysis
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120515	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
22985	catalase	+	1.11.1.6
120515	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
22985	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120515	oxidase	+
22985	phenylalanine deaminase	-	4.3.1.5
68382	trypsin	-	3.4.21.4	from API zym
22985	urease	-	3.5.1.5
120515	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
120515	-	+	+	+	-	-	-	-	-	-	+	+	-	+	-	-	-	-	-	-

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
120515	not determinedn.d.	+	-	-	-	+	-	-	-	-	+	+	+	+	-	+/-	-	-	+	-	-	-	+	-	-	-	-	+	+	-	-	+	+	-	-	+	+	+	-	-	+	-	-	-	-	+/-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	-
#Environmental	#Terrestrial	#Geologic
#Condition	#Psychrophilic (<10°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture
22985	carbonate rock collected from a 642 m-deep methane cold seep	Kuroshima Knoll	Japan	JPN	Asia	24.13	124.187 24.13/124.187	enrichment medium containing 0.5 % (w/v) Bacto-peptone (Difco),0.25 % yeast extract (Difco),0.1 % D-glucose (Wako) and 15 % NaCl
7522	deep-sea carbonate rock	Kuroshima Knoll	Japan	JPN	Asia
67770	Deep-sea carbonate rock at a methane cold seep in Kuroshima Knoll		Japan	JPN	Asia
120515	Environment, Deep sea carbonate rock	Carbonate rocks authentically formed in a methane seep of the Kuroshima Knoll, located at 642 m depth (Fujikuraet al., 2003, Inagakiet al., 2004), were collected with the remotely operated vehicle Dolphin 3K, operated by the Japan Agency for Marine Earth Science and Technology (JAMSTEC).	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7522	1	Risk group (German classification) According to TRBA 466
120515	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
67770	ASM42570v1 assembly for Halobacillus kuroshimensis DSM 18393	scaffold	GCA_000425705	1121938.3	2523533634	1121938	75.63

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7522	Halobacillus kuroshimensis gene for 16S rRNA, partial sequence	AB195680	1544		302481

GC content

@ref	GC-content (mol%)	Method
7522	42.1
67770	42.1	capillary zone electrophoresis (CZE)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halobacillus kuroshimensis DSM 18393 DSM 18393
NCBI: GCA_000425705

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	93.50	no
125439	motility	BacteriaNetⓘ	yes	85.10	no
125439	gram_stain	BacteriaNetⓘ	variable	85.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	82.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halobacillus kuroshimensis DSM 18393
PATRIC: 1121938.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	81.93	no
125438	anaerobic	anaerobicⓘ	no	97.86	no
125438	spore-forming	spore-formingⓘ	yes	93.45	no
125438	aerobic	aerobicⓘ	yes	76.57	no
125438	thermophilic	thermophileⓘ	no	97.27	yes
125438	flagellated	motile2+ⓘ	yes	84.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut.	Seck E, Rathored J, Khelaifia S, Croce O, Robert C, Couderc C, Di Pinto F, Sokhna C, Raoult D, Lagier JC.	New Microbes New Infect	10.1016/j.nmni.2015.09.014	2015
Phylogeny	Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov., moderately halophilic bacteria isolated from a deep-sea methane cold seep.	Hua NP, Kanekiyo A, Fujikura K, Yasuda H, Naganuma T	Int J Syst Evol Microbiol	10.1099/ijs.0.64817-0	2007

References

#7522	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18393
#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 )
#22985	Ngoc-Phuc Hua,Atsuko Kanekiyo,Katsunori Fujikura,Hisato Yasuda,Takeshi Naganuma: Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov., moderately halophilic bacteria isolated from a deep-sea methane cold seep. IJSEM 57: 1243 - 1249 2007 ( DOI 10.1099/ijs.0.64817-0 , PubMed 17551037 )
#37807	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#120515	Collection of Institut Pasteur ; Curators of the CIP; CIP 109650
#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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Halobacillus kuroshimensis (DSM 18393, JCM 14155, JS-Hb7)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

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_000425705

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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