Virgibacillus halophilus (DSM 21623, IAM 15308, JCM 21758)

Name: Virgibacillus halophilus (DSM 21623, IAM 15308, JCM 21758)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1483

Type strain

Strain Designation 5B73C

Culture col. no. DSM 21623 IAM 15308 JCM 21758 KCTC 13935 5B73C 1 more

NCBI tax ID(s) 361280

Special Collections DSMZ JCM KCTC CIP Literature strains

History <- JCM <- IAM <- S.-Y. An et al.; 5B73C IAM 15308 <-- S.-Y. An et al. 5B73C. <- A Yokota, IAM CIP <- 2007, JCM <- 2007, IAM <- S.Y. An, Tokyo Univ., Tokyo, Japan: strain 5B73C

Links

Virgibacillus halophilus 5B73C is an obligate aerobe, halophilic, spore-forming prokaryote that forms circular colonies and was isolated from Field soil.

spore-forming Gram-positive motile rod-shaped colony-forming obligate aerobe halophilic mesophilic 16S sequence

Name and taxonomic classification

SI-ID 309509

IAM 15308,KCTC 13935,JCM 21758,CIP 109671,DSM 21623

@ref 20215

Last LPSN update 2026-02-09 11:18:07

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Virgibacillus

Species Virgibacillus halophilus

Full scientific name Virgibacillus halophilus An et al. 2007

Synonyms (1)

Tigheibacillus halophilus

BacDive ID	Other strains from **Virgibacillus halophilus** (1)	Type strain
136929	V. halophilus CIP 108069, YIM 70118

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
23055	positive	1.75 µm	0.5 µm	rod-shaped
67771				rod-shaped
67771	positive
119821	positive			rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Medium used
23055	pale yellow	circular	trypticase soy agar containing 50 % Herbst’s artificial seawater

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15843	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: NaCl 20.0 g/l Agar 15.0 g/l Casein peptone 15.0 g/l Soy peptone 5.0 g/l Distilled water
23055	trypticase soy agar containing 50 % Herbst’s artificial seawater
36827	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119821	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15843	positive	growth	30	mesophilic
23055	positive	growth	5.0-45.0
36827	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
23055	positive	growth	5.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
23055	obligate aerobe
67771	aerobe
119821	obligate aerobe

Spore formation

@ref	Spore description	Type of spore	Spore formation
23055	ellipsoidal,subterminal	endospore
67771		spore

Halophily

@ref	Halophily level	Salt	Growth	Tested relation	Concentration
23055	halophilic	NaCl	positive	growth	0.0 %(w/v)
23055		NaCl	positive	growth	18.0 %(w/v)

Murein

@ref	Murein short key	Type
23055	A31	A1gamma m-Dpm-direct

Observation

@ref	Observation
67770	quinones: MK-7
67771	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23055	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
23055	17426 ChEBI	5-dehydro-D-gluconate	-	builds acid from
23055	27613 ChEBI	amygdalin	-	builds acid from
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
23055	18305 ChEBI	arbutin	+	builds acid from
23055	17057 ChEBI	cellobiose	+	builds acid from
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
23055	16947 ChEBI	citrate	-	carbon source
23055	17108 ChEBI	D-arabinose	-	builds acid from
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
23055	18333 ChEBI	D-arabitol	-	builds acid from
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
23055	28847 ChEBI	D-fucose	-	builds acid from
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
23055	62318 ChEBI	D-lyxose	-	builds acid from
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	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
23055	16443 ChEBI	D-tagatose	-	builds acid from
23055	65327 ChEBI	D-xylose	+	builds acid from
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
23055	17113 ChEBI	erythritol	-	builds acid from
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
23055	4853 ChEBI	esculin	+	builds acid from
23055	28757 ChEBI	fructose	+	builds acid from
23055	16813 ChEBI	galactitol	-	builds acid from
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
23055	28260 ChEBI	galactose	+	builds acid from
23055	5291 ChEBI	gelatin	+	hydrolysis
23055	28066 ChEBI	gentiobiose	+	builds acid from
23055	24265 ChEBI	gluconate	-	builds acid from
23055	17234 ChEBI	glucose	+	builds acid from
23055	17754 ChEBI	glycerol	+	builds acid from
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
23055	28087 ChEBI	glycogen	-	builds acid from
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
23055	15443 ChEBI	inulin	-	builds acid from
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
23055	30849 ChEBI	L-arabinose	+	builds acid from
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
23055	18403 ChEBI	L-arabitol	-	builds acid from
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
23055	18287 ChEBI	L-fucose	-	builds acid from
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
23055	65328 ChEBI	L-xylose	-	builds acid from
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
23055	17716 ChEBI	lactose	+	builds acid from
23055	17306 ChEBI	maltose	-	builds acid from
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
23055	29864 ChEBI	mannitol	+	builds acid from
23055	37684 ChEBI	mannose	+	builds acid from
23055	6731 ChEBI	melezitose	-	builds acid from
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
23055	28053 ChEBI	melibiose	-	builds acid from
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
23055	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
23055	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
23055	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
23055	17268 ChEBI	myo-inositol	-	builds acid from
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
23055	506227 ChEBI	N-acetylglucosamine	+	builds acid from
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
23055	17632 ChEBI	nitrate	+	reduction
119821	17632 ChEBI	nitrate	+	reduction
23055	16301 ChEBI	nitrite	-	reduction
119821	16301 ChEBI	nitrite	+	reduction
23055		O-nitrophenyl-beta-D-galactopyranosid	+	hydrolysis
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
23055	16634 ChEBI	raffinose	-	builds acid from
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
23055	26546 ChEBI	rhamnose	-	builds acid from
23055	15963 ChEBI	ribitol	-	builds acid from
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
23055	33942 ChEBI	ribose	+	builds acid from
23055	17814 ChEBI	salicin	+	builds acid from
23055	30911 ChEBI	sorbitol	-	builds acid from
23055	27922 ChEBI	sorbose	-	builds acid from
23055	28017 ChEBI	starch	-	builds acid from
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
23055	17992 ChEBI	sucrose	+	builds acid from
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
23055	27082 ChEBI	trehalose	+	builds acid from
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
23055	32528 ChEBI	turanose	-	builds acid from
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
23055	16199 ChEBI	urea	+	hydrolysis
23055	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite
23055	15688 ChEBI	acetoin
23055	16136 ChEBI	hydrogen sulfide
23055	35581 ChEBI	indole
119821	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Citrate test
23055	16947 ChEBI	citrate	-

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
23055	arginine dihydrolase	-	3.5.3.6
23055	beta-galactosidase	+	3.2.1.23
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
23055	catalase	+	1.11.1.6
119821	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
23055	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
23055	gelatinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
23055	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
23055	ornithine decarboxylase	-	4.1.1.17
119821	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
23055	tryptophan deaminase	-	4.1.99.1
23055	urease	+	3.5.1.5
119821	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
119821	-	-	+	+	-	+	-	+	-	+	+	+	+	+	-	+	-	+	-	-

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
119821	not determinedn.d.	+	-	-	+	+	+	-	-	-	+/-	+	+	+	-	-	-	-	+	-	-	-	+	-	+/-	+/-	+/-	+	-	+/-	-	+	+	-	-	-	-	-	+/-	+/-	-	-	+/-	-	+/-	+/-	-	+/-	-	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture temperature
15843	Field soil	Kakegawa, Shizuoka	Japan	JPN	Asia
23055						plate count agar (Merck)	35.0
67770	Field soil in Kakegawa	Shizuoka	Japan	JPN	Asia
67771	From field soil	Kakegawa, Shizuoka	Japan	JPN	Asia
119821	Environment, Soil	Kakegawa, Shizuoka	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB243851 (>99% sequence identity) for Virgibacillus halophilus subclade from Microbeatlas

Aquatic Samples	3
Soil Samples	17
Animal Samples	21
Plant Samples	7
Total Samples	48

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15843	1	Risk group (German classification) According to TRBA 466
119821	1	Risk group (French classification) According to TRBA 466

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15843	Virgibacillus halophilus rrs gene for 16S rRNA, partial sequence	AB243851	1519		361280

GC content

@ref	GC-content (mol%)	Method
15843	42.6	high performance liquid chromatography (HPLC)
67771	42.6

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Validation List no. 219. Valid publication of new names and new combinations effectively published outside the IJSEM.	Oren A, Goker M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006452	2024
	Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.	Miliotis G, Sengupta P, Hameed A, Chuvochina M, McDonagh F, Simpson AC, Parker CW, Singh NK, Rekha PD, Morris D, Raman K, Kyrpides NC, Hugenholtz P, Venkateswaran K.	mBio	10.1128/mbio.00181-24	2024
Phylogeny	Virgibacillus halophilus sp. nov., spore-forming bacteria isolated from soil in Japan.	An SY, Asahara M, Goto K, Kasai H, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.64307-0	2007

References

#15843	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21623
#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 )
#23055	Sun-Young An,Mika Asahara,Keiichi Goto,Hiroaki Kasai,Akira Yokota: Virgibacillus halophilus sp. nov., spore-forming bacteria isolated from soil in Japan. IJSEM 57: 1607 - 1611 2007 ( DOI 10.1099/ijs.0.64307-0 , PubMed 17625203 )
#36827	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#119821	Collection of Institut Pasteur ; Curators of the CIP; CIP 109671
#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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Virgibacillus halophilus (DSM 21623, IAM 15308, JCM 21758)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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