Name: Virgibacillus dokdonensis DSW-10
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1484

Type strain:

Species: Virgibacillus dokdonensis

Strain Designation: DSW-10

Culture col. no.: DSM 16826, CIP 109001, KCTC 3933

Strain history: CIP <- 2005, DSMZ <- J.H. Yoon, KRIBB: strain DSW-10

NCBI tax ID(s): 302167 (species)

SI-ID 265636

DSM 16826, KCTC 3933, CIP 109001

Section

Virgibacillus dokdonensis DSW-10 is an aerobe, slightly halophilic, spore-forming bacterium that forms irregular colonies and was isolated from sea water of Dokdo Island.

colony-forming
Gram-variable
motile
rod-shaped
spore-forming
aerobe
mesophilic
slightly halophilic
16S sequence
Bacteria

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Virgibacillus*
	Species	**Virgibacillus dokdonensis**
	Full Scientific Name (LPSN)	Virgibacillus dokdonensis Yoon et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #23054]	Gram stain	variable
[Ref.: #67771]	Gram stain	variable
[Ref.: #118959]	Gram stain	positive

[Ref.: #23054]	Cell length	2.5-5.0 µm

[Ref.: #23054]	Cell width	0.6-0.8 µm

[Ref.: #23054]	Cell shape	rod-shaped
[Ref.: #118959]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #23054]	Motility	yes
[Ref.: #118959]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #23054]	Flagellum arrangement	peritrichous
[Ref.: #67771]	Flagellum arrangement	peritrichous

[Ref.: #118959]	Hemolysis ability	1

[Ref.: #23054]	Colony size	3.0-5.0 mm
[Ref.: #23054]	Colony shape	irregular
[Ref.: #23054]	Incubation period	2 days
[Ref.: #23054]	Cultivation medium used	MA supplemented with 3 % (w/v) NaCl

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6618]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #6618]

Culture medium growth

[Ref.: #6618]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6618]

Culture medium composition

expand / minimize

[Ref.: #23054]

Culture medium

MA supplemented with 3 % (w/v) NaCl

[Ref.: #23054]

Culture medium growth

[Ref.: #118959]

Culture medium

CIP Medium 13

[Ref.: #118959]

Culture medium growth

[Ref.: #118959]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6618]		growth	30 °C
[Ref.: #23054]		growth	15.0 °C
[Ref.: #23054]		growth	50.0 °C
[Ref.: #23054]	no	growth	10.0 °C
[Ref.: #23054]	no	growth	55.0 °C
[Ref.: #23054]		optimum	37.0 °C
[Ref.: #67771]		growth	37 °C

[Ref.: #6618]	Temperature range	mesophilic
[Ref.: #23054]	Temperature range	psychrophilic
[Ref.: #23054]	Temperature range	thermophilic
[Ref.: #23054]	Temperature range	psychrophilic
[Ref.: #23054]	Temperature range	thermophilic
[Ref.: #23054]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	Kind of pH		pH
[Ref.: #23054]		optimum	7.0-8.0
[Ref.: #23054]		growth	5.5
[Ref.: #23054]	no	growth	5.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #118959]	Oxygen tolerance	facultative anaerobe

[Ref.: #23054]	Spore description	terminal or subterminal, ellipsoidal or spherical, in swollen sporangia
[Ref.: #23054]	Type of spore	endospore
[Ref.: #23054]	Ability of spore formation	yes

[Ref.: #23054]

Halophily / tolerance level

slightly halophilic

	Salt	Tested relation		Salt conc.
[Ref.: #23054]	NaCl		optimum	4.0-5.0	%(w/v)
[Ref.: #23054]	NaCl		growth	0.0	%(w/v)
[Ref.: #23054]	NaCl		growth	23.0	%(w/v)
[Ref.: #23054]	NaCl	no	growth	>24.0	%(w/v)

[Ref.: #23054]	Murein short key	A31
[Ref.: #23054]	Murein types	A1gamma m-Dpm-direct

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23054]	cellobiose ChEBI	+	builds acid from
[Ref.: #23054]	D-fructose ChEBI	+	builds acid from
[Ref.: #23054]	D-fructose ChEBI	+	growth
[Ref.: #23054]	D-galactose ChEBI	+	builds acid from
[Ref.: #23054]	D-glucose ChEBI	+	builds acid from
[Ref.: #23054]	D-glucose ChEBI	+	growth
[Ref.: #23054]	D-mannitol ChEBI	-	builds acid from
[Ref.: #23054]	D-mannose ChEBI	+	builds acid from
[Ref.: #23054]	D-ribose ChEBI	+	builds acid from
[Ref.: #23054]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #23054]	D-trehalose ChEBI	-	builds acid from
[Ref.: #23054]	D-xylose ChEBI	-	builds acid from
[Ref.: #23054]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #23054]	L-arabinose ChEBI	-	builds acid from
[Ref.: #23054]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #23054]	lactose ChEBI	+	builds acid from
[Ref.: #23054]	maltose ChEBI	+	builds acid from
[Ref.: #23054]	melezitose ChEBI	-	builds acid from
[Ref.: #23054]	melibiose ChEBI	-	builds acid from
[Ref.: #23054]	myo-inositol ChEBI	+	builds acid from
[Ref.: #118959]	nitrate ChEBI	-	reduction
[Ref.: #118959]	nitrite ChEBI	-	reduction
[Ref.: #23054]	raffinose ChEBI	-	builds acid from
[Ref.: #23054]	starch ChEBI	+	hydrolysis
[Ref.: #23054]	sucrose ChEBI	+	builds acid from
[Ref.: #23054]	sucrose ChEBI	+	growth
[Ref.: #23054]	tween 20 ChEBI	+	hydrolysis
[Ref.: #23054]	tween 40 ChEBI	+	hydrolysis
[Ref.: #23054]	tween 60 ChEBI	+	hydrolysis
[Ref.: #23054]	tween 80 ChEBI	+	hydrolysis
[Ref.: #23054]	tyrosine ChEBI	-	hydrolysis
[Ref.: #23054]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #23054]	acetoin ChEBI	no
[Ref.: #23054]	indole ChEBI	no
[Ref.: #118959]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #23054]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #23054]	acid phosphatase	-	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #118959]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #23054]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #23054]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #23054]	alpha-fucosidase	-	3.2.1.51
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #23054]	alpha-galactosidase	-	3.2.1.22
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #23054]	alpha-glucosidase	+	3.2.1.20
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #23054]	alpha-mannosidase	-	3.2.1.24
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #23054]	arginine dihydrolase	-	3.5.3.6
[Ref.: #23054]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #23054]	beta-glucosidase	-	3.2.1.21
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #23054]	beta-glucuronidase	-	3.2.1.31
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #118959]	catalase	+	1.11.1.6
[Ref.: #23054]	cystine arylamidase	-	3.4.11.3
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #23054]	cytochrome oxidase	+	1.9.3.1
[Ref.: #23054]	esterase (C 4)	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #23054]	esterase lipase (C 8)	+
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #23054]	leucine arylamidase	-	3.4.11.1
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #23054]	lipase (C 14)	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #23054]	lysine decarboxylase	-	4.1.1.18
[Ref.: #118959]	lysine decarboxylase	-	4.1.1.18
[Ref.: #23054]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #23054]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #23054]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118959]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118959]	oxidase	+
[Ref.: #23054]	trypsin	-	3.4.21.4
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #23054]	urease	-	3.5.1.5
[Ref.: #118959]	urease	-	3.5.1.5
[Ref.: #23054]	valine arylamidase	-
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #118959]	11604	-	+	+	-	-	-	-	-	-	+	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #6618]	Sample type/isolated from	sea water of Dokdo Island
[Ref.: #6618]	Geographic location (country and/or sea, region)	east sea
[Ref.: #6618]	Country	Republic of Korea
[Ref.: #6618]	Country ISO 3 Code	KOR
[Ref.: #6618]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From seawater
[Ref.: #67771]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #118959]	Sample type/isolated from	Environment, Sea water
[Ref.: #118959]	Geographic location (country and/or sea, region)	Dokdo island
[Ref.: #118959]	Country	Republic of Korea
[Ref.: #118959]	Country ISO 3 Code	KOR
[Ref.: #118959]	Continent	Asia

[Ref.: #23054]	Enrichment culture	marine agar 2216 (MA; Difco)
[Ref.: #23054]	Enrichment culture temperature	30.0 ̊C
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY822043 (>99% sequence identity) for Virgibacillus from Microbeatlas

Aquatic Samples	178
Soil Samples	349
Animal Samples	356
Plant Samples	255
Total Samples	1138

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

[Ref.: #6618]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118959]	Biosafety level	1	Risk group (French classification)

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.: #23054]	Virgibacillus dokdonensis strain DSW-10 16S ribosomal RNA gene, partial sequence	AY822043	1520	GenBank	302167 tax ID
[Ref.: #20218]	Virgibacillus dokdonensis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 478	AB367176	478	ENA	302167 tax ID	*
[Ref.: #20218]	Virgibacillus dokdonensis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 628	AB367177	628	ENA	302167 tax ID	*
[Ref.: #20218]	Virgibacillus dokdonensis genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 735	AB367178	735	ENA	302167 tax ID	*

[Ref.: #23054]	GC-content	36.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	36.7 mol%

Availability in culture collections External links

[Ref.: #6618]

Culture collection no.

DSM 16826, CIP 109001, KCTC 3933

[Ref.: #71130]

SI-ID 265636

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Virgibacillus dokdonensis sp. nov., isolated from a Korean island, Dokdo, located at the edge of the East Sea in Korea.	Yoon JH, Kang SJ, Lee SY, Lee MH, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.63613-0	2005	*

References

#6618

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16826

#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 )

#23054

Jung-Hoon Yoon,So-Jung Kang,Soo-Young Lee,Mi-Hwa Lee,Tae-Kwang Oh: Virgibacillus dokdonensis sp. nov., isolated from a Korean island, Dokdo, located at the edge of the East Sea in Korea. IJSEM 55: 1833 - 1837 2005 ( DOI 10.1099/ijs.0.63613-0 , PubMed 16166674 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#71130

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID265636.1 )

#118959 Collection of Institut Pasteur ; Curators of the CIP; CIP 109001
* These data were automatically processed and therefore are not curated

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