Name: Virgibacillus alimentarius J18
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 22931

Type strain:

Species: Virgibacillus alimentarius

Strain Designation: J18

Culture col. no.: DSM 26676, JCM 16994, KACC 14624

Strain history: J.-W. Bae J18.

NCBI tax ID(s): 698769 (species)

SI-ID 397593

DSM 26676

Section

Virgibacillus alimentarius J18 is an aerobe, halophilic, spore-forming bacterium that forms circular colonies and was isolated from Jeotgal, traditional salt-fermented seafood made of gizzard shad.

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

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 alimentarius**
	Full Scientific Name (LPSN)	Virgibacillus alimentarius Kim et al. 2011

Synonym

Virgibacillus campisalis

Information on morphological and physiological properties Morphology

[Ref.: #23056]	Gram stain	positive

[Ref.: #23056]	Cell length	1.2 µm

[Ref.: #23056]	Cell width	0.5 µm

[Ref.: #23056]	Cell shape	rod-shaped

[Ref.: #23056]	Motility	yes

[Ref.: #23056]	Colony size	1.0-2.0 mm
[Ref.: #23056]	Colony color	cream
[Ref.: #23056]	Colony shape	circular
[Ref.: #23056]	Incubation period	3 days
[Ref.: #23056]	Cultivation medium used	marine agar

[Ref.: #23056]	Pigment production	yes
[Ref.: #23056]	Pigmentation color	cream

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19130]

Culture medium

MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d)

[Ref.: #19130]

Culture medium growth

[Ref.: #19130]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19130]

Culture medium composition

expand / minimize

[Ref.: #23056]

Culture medium

Marine agar (MA)

[Ref.: #23056]

Culture medium growth

		Temperature
[Ref.: #19130]	growth	28 °C
[Ref.: #23056]	growth	4.0-40.0 °C
[Ref.: #23056]	optimum	37.0 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #19130]	Temperature range	mesophilic
[Ref.: #23056]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #23056]			optimum	10.0
[Ref.: #23056]			growth	7.0-11.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23056]

Oxygen tolerance

aerobe

[Ref.: #23056]	Spore description	ellipsoidal,terminal or subterminal
[Ref.: #23056]	Type of spore	endospore
[Ref.: #23056]	Ability of spore formation	yes

[Ref.: #23056]

Halophily / tolerance level

halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23056]		NaCl		growth	0.0-30.0	%
[Ref.: #23056]		NaCl		optimum	9.0-10.0	%

[Ref.: #23056]	Murein short key	A31
[Ref.: #23056]	Murein types	A1gamma m-Dpm-direct

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23056]	2-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #23056]	5-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #23056]	amygdalin ChEBI	-	builds acid from
[Ref.: #23056]	arbutin ChEBI	-	builds acid from
[Ref.: #23056]	cellobiose ChEBI	-	builds acid from
[Ref.: #23056]	citrate ChEBI	-	carbon source
[Ref.: #23056]	D-arabinose ChEBI	-	builds acid from
[Ref.: #23056]	D-arabitol ChEBI	-	builds acid from
[Ref.: #23056]	D-fructose ChEBI	-	builds acid from
[Ref.: #23056]	D-fucose ChEBI	-	builds acid from
[Ref.: #23056]	D-galactose ChEBI	-	builds acid from
[Ref.: #23056]	D-glucose ChEBI	+	builds acid from
[Ref.: #23056]	D-lyxose ChEBI	-	builds acid from
[Ref.: #23056]	D-mannitol ChEBI	-	builds acid from
[Ref.: #23056]	D-mannose ChEBI	-	builds acid from
[Ref.: #23056]	D-ribose ChEBI	+	builds acid from
[Ref.: #23056]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #23056]	D-tagatose ChEBI	+	builds acid from
[Ref.: #23056]	D-xylose ChEBI	-	builds acid from
[Ref.: #23056]	erythritol ChEBI	-	builds acid from
[Ref.: #23056]	esculin ChEBI	+	builds acid from
[Ref.: #23056]	galactitol ChEBI	-	builds acid from
[Ref.: #23056]	gluconate ChEBI	-	builds acid from
[Ref.: #23056]	glycerol ChEBI	+	builds acid from
[Ref.: #23056]	glycogen ChEBI	-	builds acid from
[Ref.: #23056]	inulin ChEBI	-	builds acid from
[Ref.: #23056]	L-arabinose ChEBI	-	builds acid from
[Ref.: #23056]	L-arabitol ChEBI	-	builds acid from
[Ref.: #23056]	L-fucose ChEBI	-	builds acid from
[Ref.: #23056]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #23056]	L-sorbose ChEBI	-	builds acid from
[Ref.: #23056]	L-xylose ChEBI	-	builds acid from
[Ref.: #23056]	lactose ChEBI	-	builds acid from
[Ref.: #23056]	maltose ChEBI	-	builds acid from
[Ref.: #23056]	melezitose ChEBI	-	builds acid from
[Ref.: #23056]	melibiose ChEBI	-	builds acid from
[Ref.: #23056]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #23056]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #23056]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #23056]	myo-inositol ChEBI	-	builds acid from
[Ref.: #23056]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #23056]	O-nitrophenyl-beta-D-galactopyranosid	-	hydrolysis
[Ref.: #23056]	raffinose ChEBI	-	builds acid from
[Ref.: #23056]	ribitol ChEBI	+	builds acid from
[Ref.: #23056]	salicin ChEBI	-	builds acid from
[Ref.: #23056]	starch ChEBI	-	builds acid from
[Ref.: #23056]	sucrose ChEBI	-	builds acid from
[Ref.: #23056]	trehalose ChEBI	-	builds acid from
[Ref.: #23056]	tryptophan ChEBI	-	energy source
[Ref.: #23056]	turanose ChEBI	-	builds acid from
[Ref.: #23056]	tween 20 ChEBI	+	hydrolysis
[Ref.: #23056]	tween 40 ChEBI	+	hydrolysis
[Ref.: #23056]	tween 60 ChEBI	+	hydrolysis
[Ref.: #23056]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #23056]	acetoin ChEBI	yes
[Ref.: #23056]	hydrogen sulfide ChEBI	no
[Ref.: #23056]	indole ChEBI	no

	Physiological tests	Metabolite	Indole test	Citrate test
[Ref.: #23056]		citrate ChEBI		-
[Ref.: #23056]		indole ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #23056]	arginine dihydrolase	-	3.5.3.6
[Ref.: #23056]	beta-galactosidase	-	3.2.1.23
[Ref.: #23056]	catalase	-	1.11.1.6
[Ref.: #23056]	cytochrome oxidase	+	1.9.3.1
[Ref.: #23056]	gelatinase	-
[Ref.: #23056]	lysine decarboxylase	-	4.1.1.18
[Ref.: #23056]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #23056]	tryptophan deaminase	-	4.1.99.1
[Ref.: #23056]	urease	-	3.5.1.5

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

[Ref.: #19130]	Sample type/isolated from	Jeotgal, traditional salt-fermented seafood made of gizzard shad
[Ref.: #19130]	Country	Republic of Korea
[Ref.: #19130]	Country ISO 3 Code	KOR
[Ref.: #19130]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Jeotgal, traditional salt-fermented seafood made of gizzard shad
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #23056]	Enrichment culture	marine agar (MA; BBL)
[Ref.: #23056]	Enrichment culture temperature	25.0 ̊C
[Ref.: #23056]	Isolation/enrichment procedure	dilution-plating method
* marker position based on {}

Isolation sources categories

#Engineered	#Food production	#Seafood
#Engineered	#Food production	#Fermented

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GU202420 (>99% sequence identity) for Virgibacillus from Microbeatlas

Aquatic Samples	6
Soil Samples	22
Animal Samples	34
Plant Samples	2
Total Samples	64

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

[Ref.: #19130]

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.: #19130]	Virgibacillus alimentarius strain J18 16S ribosomal RNA gene, partial sequence	GU202420	1458	ENA	698769 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Virgibacillus alimentarius J18	GCA_000709085	contig	GenBank	698769 tax ID

[Ref.: #19130]	GC-content	37.0 mol%
[Ref.: #23056]	GC-content	37.0 mol%	fluorimetric
[Ref.: #67770]	GC-content	37 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Virgibacillus alimentarius J18 NCBI: GCA_000709085.1
[Ref.: #69480]	motile	yes	86.822	yes
[Ref.: #69480]	flagellated	yes	67.253	no
[Ref.: #69480]	gram-positive	yes	92.839	yes
[Ref.: #69480]	anaerobic	no	99.632	no
[Ref.: #69480]	halophile	yes	95.619	yes
[Ref.: #69480]	spore-forming	yes	94.501	yes
[Ref.: #69480]	thermophile	no	97.312	yes
[Ref.: #69480]	glucose-util	yes	86.961	no
[Ref.: #69480]	aerobic	yes	94.521	no
[Ref.: #69480]	glucose-ferment	no	92.973	no

Availability in culture collections External links

[Ref.: #19130]

Culture collection no.

DSM 26676, JCM 16994, KACC 14624

[Ref.: #87179]

SI-ID 397593

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food.	Kim J, Jung MJ, Roh SW, Nam YD, Shin KS, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.028191-0	2011	*

References

#19130

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26676

#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 )

#23056

Jandi Kim,Mi-Ja Jung,Seong Woon Roh,Young-Do Nam,Kee-Sun Shin,Jin-Woo Bae: Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food. IJSEM 61: 2851 - 2855 2011 ( DOI 10.1099/ijs.0.028191-0 , PubMed 21239563 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#87179

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-ID397593.1 )

* These data were automatically processed and therefore are not curated

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