Name: Virgibacillus halophilus 5B73C
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1483

Type strain:

Species: Virgibacillus halophilus

Strain Designation: 5B73C

Culture col. no.: DSM 21623, IAM 15308, JCM 21758, KCTC 13935, CIP 109671

Strain history: <- A Yokota, IAM

NCBI tax ID(s): 361280 (species)

Other strains from Virgibacillus halophilus

V. halophilus CIP 108069

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Virgibacillus*
	Species	**Virgibacillus halophilus**
	Full Scientific Name (PNU)	Virgibacillus halophilus An et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #23055]	Gram stain	positive
[Ref.: #23055]	Cell length	1.75 µm
[Ref.: #23055]	Cell width	0.5 µm
[Ref.: #23055]	Cell shape	rod-shaped
[Ref.: #23055]	Motility	yes

[Ref.: #67771]	Gram stain	positive

[Ref.: #67771]	Cell shape	rod-shaped
[Ref.: #67771]	Motility	yes

[Ref.: #23055]	Colony color	pale yellow
[Ref.: #23055]	Colony shape	circular
[Ref.: #23055]	Cultivation medium used	trypticase soy agar containing 50 % Herbst’s artificial seawater

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15843]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #15843]

Culture medium growth

[Ref.: #15843]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #15843]

Culture medium composition

expand / minimize

[Ref.: #23055]

Culture medium

trypticase soy agar containing 50 % Herbst’s artificial seawater

[Ref.: #23055]

Culture medium growth

[Ref.: #36827]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #36827]

Culture medium growth

[Ref.: #36827]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15843]	growth	30 °C
[Ref.: #23055]	growth	5.0-45.0 °C
[Ref.: #36827]	growth	30 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #15843]	Temperature range	mesophilic
[Ref.: #36827]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #23055]			growth	5.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23055]	Oxygen tolerance	obligate aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #23055]	Spore description	ellipsoidal,subterminal
[Ref.: #23055]	Type of spore	endospore
[Ref.: #23055]	Ability of spore formation	yes
[Ref.: #67771]	Type of spore	spore
[Ref.: #67771]	Ability of spore formation	yes

[Ref.: #23055]

Halophily / tolerance level

halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23055]		NaCl		growth	0.0	%(w/v)
[Ref.: #23055]		NaCl		growth	18.0	%(w/v)

[Ref.: #23055]	Murein short key	A31
[Ref.: #23055]	Murein types	A1gamma m-Dpm-direct

[Ref.: #67770]	Observation	quinones: MK-7
[Ref.: #67771]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23055]	2-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #23055]	5-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #23055]	amygdalin ChEBI	-	builds acid from
[Ref.: #23055]	arbutin ChEBI	+	builds acid from
[Ref.: #23055]	cellobiose ChEBI	+	builds acid from
[Ref.: #23055]	citrate ChEBI	-	carbon source
[Ref.: #23055]	D-arabinose ChEBI	-	builds acid from
[Ref.: #23055]	D-arabitol ChEBI	-	builds acid from
[Ref.: #23055]	D-fucose ChEBI	-	builds acid from
[Ref.: #23055]	D-lyxose ChEBI	-	builds acid from
[Ref.: #23055]	D-tagatose ChEBI	-	builds acid from
[Ref.: #23055]	D-xylose ChEBI	+	builds acid from
[Ref.: #23055]	erythritol ChEBI	-	builds acid from
[Ref.: #23055]	esculin ChEBI	+	builds acid from
[Ref.: #23055]	fructose ChEBI	+	builds acid from
[Ref.: #23055]	galactitol ChEBI	-	builds acid from
[Ref.: #23055]	galactose ChEBI	+	builds acid from
[Ref.: #23055]	gelatin ChEBI	+	hydrolysis
[Ref.: #23055]	gentiobiose ChEBI	+	builds acid from
[Ref.: #23055]	gluconate ChEBI	-	builds acid from
[Ref.: #23055]	glucose ChEBI	+	builds acid from
[Ref.: #23055]	glycerol ChEBI	+	builds acid from
[Ref.: #23055]	glycogen ChEBI	-	builds acid from
[Ref.: #23055]	inulin ChEBI	-	builds acid from
[Ref.: #23055]	L-arabinose ChEBI	+	builds acid from
[Ref.: #23055]	L-arabitol ChEBI	-	builds acid from
[Ref.: #23055]	L-fucose ChEBI	-	builds acid from
[Ref.: #23055]	L-xylose ChEBI	-	builds acid from
[Ref.: #23055]	lactose ChEBI	+	builds acid from
[Ref.: #23055]	maltose ChEBI	-	builds acid from
[Ref.: #23055]	mannitol ChEBI	+	builds acid from
[Ref.: #23055]	mannose ChEBI	+	builds acid from
[Ref.: #23055]	melezitose ChEBI	-	builds acid from
[Ref.: #23055]	melibiose ChEBI	-	builds acid from
[Ref.: #23055]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #23055]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #23055]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #23055]	myo-inositol ChEBI	-	builds acid from
[Ref.: #23055]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #23055]	nitrate ChEBI	+	reduction
[Ref.: #23055]	nitrite ChEBI	-	reduction
[Ref.: #23055]	O-nitrophenyl-beta-D-galactopyranosid	+	hydrolysis
[Ref.: #23055]	raffinose ChEBI	-	builds acid from
[Ref.: #23055]	rhamnose ChEBI	-	builds acid from
[Ref.: #23055]	ribitol ChEBI	-	builds acid from
[Ref.: #23055]	ribose ChEBI	+	builds acid from
[Ref.: #23055]	salicin ChEBI	+	builds acid from
[Ref.: #23055]	sorbitol ChEBI	-	builds acid from
[Ref.: #23055]	sorbose ChEBI	-	builds acid from
[Ref.: #23055]	starch ChEBI	-	builds acid from
[Ref.: #23055]	sucrose ChEBI	+	builds acid from
[Ref.: #23055]	trehalose ChEBI	+	builds acid from
[Ref.: #23055]	turanose ChEBI	-	builds acid from
[Ref.: #23055]	urea ChEBI	+	hydrolysis
[Ref.: #23055]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite
[Ref.: #23055]		acetoin ChEBI
[Ref.: #23055]		hydrogen sulfide ChEBI
[Ref.: #23055]		indole ChEBI

	Physiological tests	Metabolite	Citrate test
[Ref.: #23055]		citrate ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #23055]	arginine dihydrolase	-	3.5.3.6
[Ref.: #23055]	beta-galactosidase	+	3.2.1.23
[Ref.: #23055]	catalase	+	1.11.1.6
[Ref.: #23055]	cytochrome oxidase	+	1.9.3.1
[Ref.: #23055]	gelatinase	+
[Ref.: #23055]	lysine decarboxylase	-	4.1.1.18
[Ref.: #23055]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #23055]	tryptophan deaminase	-	4.1.99.1
[Ref.: #23055]	urease	+	3.5.1.5

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

[Ref.: #15843]	Sample type/isolated from	Field soil
[Ref.: #15843]	Geographic location (country and/or sea, region)	Kakegawa, Shizuoka
[Ref.: #15843]	Country	Japan
[Ref.: #15843]	Country ISO 3 Code	JPN
[Ref.: #15843]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Field soil in Kakegawa
[Ref.: #67770]	Geographic location (country and/or sea, region)	Shizuoka
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From field soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Kakegawa, Shizuoka
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia

[Ref.: #23055]	Enrichment culture	plate count agar (Merck)
[Ref.: #23055]	Enrichment culture temperature	35.0 ̊C
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #15843]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #15843]	Virgibacillus halophilus rrs gene for 16S rRNA, partial sequence	AB243851	1519	ENA	361280 tax ID
[Ref.: #20218]	Virgibacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 524	AB367179	524	ENA	361280 tax ID	*
[Ref.: #20218]	Virgibacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 644	AB367180	644	ENA	361280 tax ID	*
[Ref.: #20218]	Virgibacillus halophilus genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 724	AB367181	724	ENA	361280 tax ID	*

[Ref.: #15843]	GC-content	42.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	42.6 mol%

Availability in culture collections External links

[Ref.: #15843]

Culture collection no.

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

[Ref.: #20218]

Associated Passport(s) in StrainInfo

720935, 721642, 720936

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 )

#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;

#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 .

* These data were automatically processed and therefore are not curated

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