Virgibacillus alimentarius (DSM 25790, CCUG 59308, KCTC 13727)

Name: Virgibacillus alimentarius (DSM 25790, CCUG 59308, KCTC 13727)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1496

Type strain

Strain Designation IDS-20

Culture col. no. DSM 25790 CCUG 59308 KCTC 13727 IDS-20

NCBI tax ID(s) 698769

Special Collections DSMZ CCUG KCTC Literature strains

History <- KCTC; KCTC 13727 <- JH Yoon, KRIBB

Links

Virgibacillus alimentarius IDS-20 is a facultative anaerobe, spore-forming, Gram-variable bacterium that was isolated from marine solar saltern, sediment.

spore-forming Gram-variable motile rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397970

KCTC 13727,DSM 25790,CCUG 59308

@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 alimentarius

Full scientific name Virgibacillus alimentarius Kim et al. 2011

Synonyms (1)

Virgibacillus campisalis

BacDive ID	Other strains from **Virgibacillus alimentarius** (1)	Type strain
22931	V. alimentarius J18, DSM 26676, JCM 16994, KACC 14624 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement
30306	variable	1.0-4.0 µm	0.5-1.0 µm	rod-shaped
67771				rod-shaped	monotrichous, polar
67771	variable

Colony morphology

61901

Incubation period2 days

Pigmentation

30306

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5489	CM + YE MEDIUM (DSMZ Medium 549)		Medium recipe at MediaDive	Name: CM + YE MEDIUM (DSMZ Medium 549; with strain-specific modifications) Composition: NaCl 50.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 15.0 g/l Yeast extract 10.0 g/l Casamino acids 7.5 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l FeSO4 x 7 H2O 0.01 g/l HCl 3.646e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
5489	positive	growth	28
30306	positive	growth	15-40
30306	positive	optimum	37
61901	positive	growth	37
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
30306	positive	optimum	7.5-8.0
30306	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30306	facultative anaerobe
61901	aerobe
67771	facultative anaerobe
125439	obligate aerobe	91

Spore formation

@ref	Type of spore	Confidence
30306
67771	endospore
125438		91.092

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30306	NaCl	positive	growth	0.5-20 %
30306	NaCl	positive	optimum	4-5 %

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30306	30089 ChEBI	acetate	+	carbon source
30306	16947 ChEBI	citrate	+	carbon source
30306	17234 ChEBI	glucose	+	carbon source
30306	25115 ChEBI	malate	+	carbon source
30306	15361 ChEBI	pyruvate	+	carbon source
30306	30031 ChEBI	succinate	+	carbon source
30306	53424 ChEBI	tween 20	+	carbon source
30306	53423 ChEBI	tween 40	+	carbon source
30306	53425 ChEBI	tween 60	+	carbon source
30306	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30306	catalase	+	1.11.1.6
30306	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Condition	#Saline	-

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
5489	marine solar saltern, sediment		West coast	Republic of Korea	KOR	Asia
61901	Marine solar saltern sediment	2007	west coast	Republic of Korea	KOR	Asia
67771	From sediment, marine solar saltern		Yellow Sea, the west coast of Korea	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence GU586225 (>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
5489	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
66792	ASM1787463v1 assembly for Virgibacillus alimentarius DSM 25790	contig	GCA_017874635	744463.3	2913450449	698769	62.01
124043	ASM4267620v1 assembly for Virgibacillus alimentarius CCUG 59308	scaffold	GCA_042676205			698769	60.96

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5489	Virgibacillus campisalis strain IDS-20 16S ribosomal RNA gene, partial sequence	GU586225	1523		744463

GC content

@ref	GC-content (mol%)	Method
5489	39.5	high performance liquid chromatography (HPLC)
30306	39.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Virgibacillus alimentarius DSM 25790
NCBI: GCA_017874635

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	74.50	no
125439	motility	BacteriaNetⓘ	yes	72.50	no
125439	gram_stain	BacteriaNetⓘ	variable	79.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	91.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Virgibacillus campisalis strain DSM 25790
PATRIC: 744463.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	65.96	yes
125438	anaerobic	anaerobicⓘ	no	98.13	yes
125438	spore-forming	spore-formingⓘ	yes	91.09	no
125438	aerobic	aerobicⓘ	yes	77.83	no
125438	thermophilic	thermophileⓘ	no	92.31	yes
125438	flagellated	motile2+ⓘ	yes	79.40	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Virgibacillus campisalis sp. nov., from a marine solar saltern.	Lee SY, Kang CH, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.033084-0	2011

References

#5489	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25790
#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 )
#26647	IJSEM 347 2012 ( DOI 10.1099/ijs.0.033084-0 , PubMed 21441379 )
#30306	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26647
#61901	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59308
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#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 25790, CCUG 59308, KCTC 13727)

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

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_017874635

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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