Halalkalibacterium halodurans (DSM 13666, CIP 107631, JCM 10945)

Name: Halalkalibacterium halodurans (DSM 13666, CIP 107631, JCM 10945)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1199

Type strain

Strain Designation No. 44, 44

Culture col. no. DSM 13666 CIP 107631 JCM 10945 GTC 854 No. 44 2 more

NCBI tax ID(s) 86665

Special Collections DSMZ JCM KCTC CIP

History DSMZ <- Z. Li; GTC 854 <- Shuzo and Yamagata; No. 44 JCM <-- GTC 854 <-- S. Yamagata No. 44. CIP <- 2011, DSMZ, Bacillus okuhidensis <- GTC <- Shuzo and Yamagata, Gifu, Japan: strain 44

Links

Halalkalibacterium halodurans No. 44 is an obligate aerobe, spore-forming, Gram-positive bacterium of the family Bacillaceae.

spore-forming Gram-positive motile rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49505

BCRC 80307,DSM 13666,JCM 10945,KCTC 3795,CIP 107631,LMG 22468

@ref 20215

Last LPSN update 2026-05-29 08:25:12

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Halalkalibacterium

Species Halalkalibacterium halodurans

Full scientific name Halalkalibacterium halodurans (Nielsen et al. 1995 ex Boyer et al. 1973) Joshi et al. 2022

Synonyms (5)

Alkalihalobacillus okuhidensis
Bacillus okuhidensis
Bacillus halodurans
"Bacillus alcalophilus subsp. halodurans"
Alkalihalobacillus halodurans

BacDive ID	Other strains from **Halalkalibacterium halodurans** (18)	Type strain
1112	H. halodurans PN 80, B-3881, DSM 497, ATCC 27557, NRRL ... (type strain)
1113	H. halodurans A-59, DSM 2513, ATCC 21591, JCM 9148, CGMCC ...
1114	H. halodurans PN 61, C 367, DSM 6939, NCIB 10313
1115	H. halodurans PN 62, C 371, DSM 6940, NCIB 10316
1116	H. halodurans BB 16, DSM 6944
1117	H. halodurans PN 30, C 364, DSM 8718, NCIB 10310
1118	H. halodurans PN 39, C 378, DSM 9774, NCIMB 10323
1119	H. halodurans C-125, DSM 18197, ATCC BAA-125, JCM 9153, ...
23692	H. halodurans PN 20, C 354, DSM 9757, NCIMB 10304
23693	H. halodurans PN 28, C 357, DSM 9758, NCIMB 10307
23694	H. halodurans PN 29, C 358, DSM 9759, NCIMB 10308
23695	H. halodurans PN 31, C 365, DSM 9760, NCIMB 10311
23696	H. halodurans PN 32, C 366, DSM 9761, NCIMB 10312
23697	H. halodurans PN 36, C 375, DSM 9762, NCIMB 10320
23698	H. halodurans PN 37, C 376, DSM 9773, NCIMB 10321
23699	H. halodurans PN 40, C 410, DSM 9775, NCIMB 10324
23700	H. halodurans PN 41, C 411, DSM 9776, NCIMB 10325
23701	H. halodurans PN 42, C 412, DSM 9777, NCIMB 10326

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
119802	positive	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
4948	BHI MEDIUM (DSMZ Medium 215)	Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215; with strain-specific modifications) Composition: Brain heart infusion 37.0 g/l MnSO4 0.01 g/l Distilled water
33150	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119802	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
4948	positive	growth	45
33150	positive	growth	45
67770	positive	growth	45
119802	positive	growth	22-55
119802	negative	growth	10

Culture pH

@ref	Ability	Type	PH
119802		growth	6

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
119802	obligate aerobe
125439	facultative anaerobe	96.877

Spore formation

@ref	Spore formation	Confidence
119802
125438		91.843

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119802	NaCl	positive	growth	0-10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
119802	16947 ChEBI	citrate	-	carbon source
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	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	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
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
119802	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
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
119802	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	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
119802	17632 ChEBI	nitrate	+	reduction
119802	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	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

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119802	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
119802	15688 ChEBI	acetoin	-
119802	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
119802	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
119802	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
119802	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
119802	caseinase	+	3.4.21.50
119802	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
119802	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
119802	gamma-glutamyltransferase	-	2.3.2.2
119802	gelatinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
119802	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
119802	ornithine decarboxylase	-	4.1.1.17
119802	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
119802	tween esterase	+
119802	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
119802	-	-	+	-	-	+	-	-	-	-	-	+	+	+	-	+	-	-	-	-

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
119802	not determinedn.d.	+/-	-	-	+	+	+	-	-	-	+/-	+/-	+/-	+/-	-	-	-	-	+/-	-	-	-	+/-	+/-	+/-	+	+/-	+/-	+/-	+/-	+	+/-	+/-	-	-	+/-	+/-	+/-	-	-	-	-	-	-	-	-	-	+/-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
119802	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	-	-	-	-	-	+	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	+	+	-	-	+	+	-	-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	-	-	+	-	+	-	-	-	-	+	-	-	-	-	-	+	-	+	+	+	-	+	+	+	-	+	-	+

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4948		Gifu, Okuhida Spa area	Japan	JPN	Asia
67770	Water sample obtained from the Okuhida hot spa area	Gifu Pref.	Japan	JPN	Asia
119802	Environment, Water	Okuhida hot spa area	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC379066 (>99% sequence identity) for Alkalihalobacillus halodurans from Microbeatlas

Aquatic Samples	1519
Soil Samples	1545
Animal Samples	3493
Plant Samples	429
Total Samples	6986

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4948	1	Risk group (German classification) According to TRBA 466
119802	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	ASM127491v2 assembly for Halalkalibacterium halodurans DSM 13666	contig	GCA_001274915	136160.3	2648501690	86665	53.79

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Alkalihalobacillus halodurans gene for 16S rRNA, partial sequence	AB047684	1452		136160
67770	Alkalihalobacillus halodurans gene for 16S rRNA, partial sequence, strain: JCM 10945	LC379066	1472		86665

GC content

@ref	GC-content (mol%)	Method
4948	41
67770	41	high performance liquid chromatography (HPLC)
67770	43.4	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM127491v2 assembly for Halalkalibacterium halodurans DSM 13666
BV-BRC: 136160.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	96.88	no
125439	gram_stain	BacteriaNetⓘ	variable	73.49	no
125439	motility	BacteriaNetⓘ	yes	55.13	no
125439	spore_formation	BacteriaNetⓘ	yes	74.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacillus okuhidensis strain DSM 13666
PATRIC: 136160.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	78.83	no
125438	anaerobic	anaerobicⓘ	no	88.07	yes
125438	spore-forming	spore-formingⓘ	yes	91.84	no
125438	aerobic	aerobicⓘ	yes	76.30	no
125438	thermophilic	thermophileⓘ	no	81.42	no
125438	flagellated	motile2+ⓘ	yes	84.44	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genome-based reclassification of Bacillus okuhidensis as a later heterotypic synonym of Bacillus halodurans.	Liu GH, Narsing Rao MP, Dong ZY, Wang JP, Che JM, Chen QQ, Sengonca C, Liu B, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003666	2019
Phylogeny	Bacillus oceani sp. nov., isolated from seawater.	Song L, Liu H, Wang J, Huang Y, Dai X, Han X, Zhou Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.000793	2015
Phylogeny	Bacillus okuhidensis sp. nov., isolated from the Okuhida spa area of Japan.	Li Z, Kawamura Y, Shida O, Yamagata S, Deguchi T, Ezaki T	Int J Syst Evol Microbiol	10.1099/00207713-52-4-1205	2002

References

#4948	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13666
#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 )
#33150	; 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 .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#119802	Collection of Institut Pasteur ; Curators of the CIP; CIP 107631
#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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Halalkalibacterium halodurans (DSM 13666, CIP 107631, JCM 10945)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001274915

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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