Virgibacillus alimentarius (DSM 26676, JCM 16994, KACC 14624)

Name: Virgibacillus alimentarius (DSM 26676, JCM 16994, KACC 14624)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 22931

Type strain

Strain Designation J18

Culture col. no. DSM 26676 JCM 16994 KACC 14624 J18

NCBI tax ID(s) 698769

Special Collections DSMZ JCM Literature strains

History DSMZ <- JCM <- J.-W. Bae; J18 JCM <-- J.-W. Bae J18.

Links

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

Name and taxonomic classification

SI-ID 397593

JCM 16994,DSM 26676

@ref 20215

Last LPSN update 2026-05-29 08:30:20

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Virgibacillus

Species Virgibacillus alimentarius

Full scientific name Virgibacillus alimentarius Kim et al. 2011

Synonyms (1)

Virgibacillus campisalis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
23056	positive	1.2 µm	0.5 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
23056	1.0-2.0 mm	cream	circular	3 days	marine agar

Pigmentation

@ref	Production	Color
23056		cream

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19130	MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d)		Medium recipe at MediaDive	Name: MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d) Composition: Difco marine broth 37.4 g/l Agar 15.0 g/l Malt extract 1.0 g/l Soy peptone 1.0 g/l Pancreatic digest of casein 1.0 g/l Distilled water
23056	Marine agar (MA)

Culture temp

@ref	Growth	Type	Temperature (°C)
19130	positive	growth	28
23056	positive	growth	4.0-40.0
23056	positive	optimum	37.0
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
23056	positive	optimum	10.0
23056	positive	growth	7.0-11.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

23056

Oxygen toleranceaerobe

Spore formation

@ref	Spore description	Type of spore	Spore formation	Confidence
23056	ellipsoidal,terminal or subterminal	endospore
125438				90.553

Halophily

@ref	Halophily level	Salt	Growth	Tested relation	Concentration
23056	halophilic	NaCl	positive	growth	0.0-30.0 %
23056		NaCl		optimum	9.0-10.0 %

Murein

@ref	Murein short key	Type
23056	A31	A1gamma m-Dpm-direct

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23056	16808 ChEBI	2-dehydro-D-gluconate	+	builds acid from
23056	17426 ChEBI	5-dehydro-D-gluconate	+	builds acid from
23056	27613 ChEBI	amygdalin	-	builds acid from
23056	18305 ChEBI	arbutin	-	builds acid from
23056	17057 ChEBI	cellobiose	-	builds acid from
23056	16947 ChEBI	citrate	-	carbon source
23056	17108 ChEBI	D-arabinose	-	builds acid from
23056	18333 ChEBI	D-arabitol	-	builds acid from
23056	15824 ChEBI	D-fructose	-	builds acid from
23056	28847 ChEBI	D-fucose	-	builds acid from
23056	12936 ChEBI	D-galactose	-	builds acid from
23056	17634 ChEBI	D-glucose	+	builds acid from
23056	62318 ChEBI	D-lyxose	-	builds acid from
23056	16899 ChEBI	D-mannitol	-	builds acid from
23056	16024 ChEBI	D-mannose	-	builds acid from
23056	16988 ChEBI	D-ribose	+	builds acid from
23056	17924 ChEBI	D-sorbitol	-	builds acid from
23056	16443 ChEBI	D-tagatose	+	builds acid from
23056	65327 ChEBI	D-xylose	-	builds acid from
23056	17113 ChEBI	erythritol	-	builds acid from
23056	4853 ChEBI	esculin	+	builds acid from
23056	16813 ChEBI	galactitol	-	builds acid from
23056	24265 ChEBI	gluconate	-	builds acid from
23056	17754 ChEBI	glycerol	+	builds acid from
23056	28087 ChEBI	glycogen	-	builds acid from
23056	15443 ChEBI	inulin	-	builds acid from
23056	30849 ChEBI	L-arabinose	-	builds acid from
23056	18403 ChEBI	L-arabitol	-	builds acid from
23056	18287 ChEBI	L-fucose	-	builds acid from
23056	62345 ChEBI	L-rhamnose	-	builds acid from
23056	17266 ChEBI	L-sorbose	-	builds acid from
23056	65328 ChEBI	L-xylose	-	builds acid from
23056	17716 ChEBI	lactose	-	builds acid from
23056	17306 ChEBI	maltose	-	builds acid from
23056	6731 ChEBI	melezitose	-	builds acid from
23056	28053 ChEBI	melibiose	-	builds acid from
23056	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
23056	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
23056	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
23056	17268 ChEBI	myo-inositol	-	builds acid from
23056	506227 ChEBI	N-acetylglucosamine	+	builds acid from
23056		O-nitrophenyl-beta-D-galactopyranosid	-	hydrolysis
23056	16634 ChEBI	raffinose	-	builds acid from
23056	15963 ChEBI	ribitol	+	builds acid from
23056	17814 ChEBI	salicin	-	builds acid from
23056	28017 ChEBI	starch	-	builds acid from
23056	17992 ChEBI	sucrose	-	builds acid from
23056	27082 ChEBI	trehalose	-	builds acid from
23056	27897 ChEBI	tryptophan	-	energy source
23056	32528 ChEBI	turanose	-	builds acid from
23056	53424 ChEBI	tween 20	+	hydrolysis
23056	53423 ChEBI	tween 40	+	hydrolysis
23056	53425 ChEBI	tween 60	+	hydrolysis
23056	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite
23056	15688 ChEBI	acetoin
23056	16136 ChEBI	hydrogen sulfide
23056	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Citrate test	Indole test
23056	16947 ChEBI	citrate	-
23056	35581 ChEBI	indole		-

Enzymes

@ref	Value	Activity	Ec
23056	arginine dihydrolase	-	3.5.3.6
23056	beta-galactosidase	-	3.2.1.23
23056	catalase	-	1.11.1.6
23056	cytochrome oxidase	+	1.9.3.1
23056	gelatinase	-
23056	lysine decarboxylase	-	4.1.1.18
23056	ornithine decarboxylase	-	4.1.1.17
23056	tryptophan deaminase	-	4.1.99.1
23056	urease	-	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Seafood
#Engineered	#Food production	#Fermented

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture temperature	Isolation procedure
19130	Jeotgal, traditional salt-fermented seafood made of gizzard shad	Republic of Korea	KOR	Asia
23056					marine agar (MA; BBL)	25.0	dilution-plating method
67770	Jeotgal, traditional salt-fermented seafood made of gizzard shad	Republic of Korea	KOR	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19130	1	Risk group (German 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	Virgibacillus alimentarius J18 assembly for Virgibacillus alimentarius J18	contig	GCA_000709085	698769.3	2609460047	698769	44.69

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19130	Virgibacillus alimentarius strain J18 16S ribosomal RNA gene, partial sequence	GU202420	1458		698769

GC content

@ref	GC-content (mol%)	Method
19130	37.0
23056	37.0	fluorimetric
67770	37	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Virgibacillus alimentarius J18
NCBI: GCA_000709085.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	67.55	no
125438	anaerobic	anaerobicⓘ	no	98.06	yes
125438	aerobic	aerobicⓘ	yes	78.31	yes
125438	spore-forming	spore-formingⓘ	yes	90.55	yes
125438	thermophilic	thermophileⓘ	no	91.05	yes
125438	flagellated	motile2+ⓘ	yes	76.90	no

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 .
#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 )
#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 alimentarius (DSM 26676, JCM 16994, KACC 14624)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

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

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000709085

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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