Name: Virgibacillus halodenitrificans DSM 10037
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1475

Type strain:

Species: Virgibacillus halodenitrificans

Culture col. no.: DSM 10037, ATCC 49067, JCM 12304, CGMCC 1.8915, IAM 14938, KCTC 3790, LMG 9818, NBRC 102361

Strain history: DSM 10037 <-- J. Le Gall.

NCBI tax ID(s): 1236975 (strain), 1482 (species)

SI-ID 1123

LMG 9818, ATCC 49067, DSM 10037, KCTC 3790, BCRC 16037, CCRC 16037, IAM 14938, JCM 12304, NBRC 102361, CGMCC 1.3478

Special Collections

Section

Virgibacillus halodenitrificans DSM 10037 is a spore-forming bacterium that was isolated from solar saltern.

spore-forming
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 halodenitrificans**
	Full Scientific Name (LPSN)	Virgibacillus halodenitrificans (Denariaz et al. 1989) Yoon et al. 2004

Synonym

Bacillus halodenitrificans

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3759]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #3759]

Culture medium growth

[Ref.: #3759]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3759]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #3759]			growth	30 °C
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Ability of spore formation

yes Confidence in %93.941

[Ref.: #67770]

Observation

quinones: MK-7

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

[Ref.: #3759]	Sample type/isolated from	solar saltern
[Ref.: #3759]	Geographic location (country and/or sea, region)	L'étang de Berre
[Ref.: #3759]	Country	France
[Ref.: #3759]	Country ISO 3 Code	FRA
[Ref.: #3759]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Solar evaporation pond (saltern)
[Ref.: #67770]	Geographic location (country and/or sea, region)	Strasburg
[Ref.: #67770]	Country	France
[Ref.: #67770]	Country ISO 3 Code	FRA
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Condition

#Saline

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB681753 (>99% sequence identity) for Virgibacillus halodenitrificans subclade from Microbeatlas

Aquatic Samples	693
Soil Samples	2809
Animal Samples	1180
Plant Samples	368
Total Samples	5050

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

[Ref.: #3759]

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.: #20218]	Bacillus halodenitrificans gene for 16S ribosomal RNA	AB021186	1528	GenBank ENA	1482 tax ID	*
[Ref.: #20218]	Virgibacillus halodenitrificans genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 530	AB367182	530	GenBank ENA	1482 tax ID	*
[Ref.: #20218]	Virgibacillus halodenitrificans genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 675	AB367183	675	GenBank ENA	1482 tax ID	*
[Ref.: #20218]	Bacillus halodenitrificans strain DSM 10037 16S ribosomal RNA gene, partial sequence	AY543169	1521	GenBank ENA	1482 tax ID	*
[Ref.: #20218]	Virgibacillus halodenitrificans gene for 16S rRNA, partial sequence, strain: NBRC 102361	AB681753	1490	GenBank ENA	1482 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Virgibacillus halodenitrificans JCM 12304	GCA_001310895	contig	GenBank ENA	1236975 tax ID
[Ref.: #66792]	Virgibacillus halodenitrificans JCM 12304	1236975.3	wgs	PATRIC	1236975 tax ID	*
[Ref.: #66792]	Virgibacillus halodenitrificans JCM 12304	2728369661	draft	JGI IMG/M	1236975 tax ID	*

[Ref.: #3759]

GC-content

38 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Virgibacillus halodenitrificans JCM 12304 PATRIC: 1236975.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	73.968	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	91.443	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	93.941	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	71.345	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	91.435	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	82.653	no

Availability in culture collections External links

[Ref.: #3759]

Culture collection no.

DSM 10037, ATCC 49067, JCM 12304, CGMCC 1.8915, IAM 14938, KCTC 3790, LMG 9818, NBRC 102361

[Ref.: #71121]

SI-ID 1123

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	*
Phylogeny	Virgibacillus koreensis sp. nov., a novel bacterium from a salt field, and transfer of Virgibacillus picturae to the genus Oceanobacillus as Oceanobacillus picturae comb. nov. with emended descriptions.	Lee JS, Lim JM, Lee KC, Lee JC, Park YH, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.63734-0	2006	*
Phylogeny	Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.	Yoon JH, Oh TK, Park YH	Int J Syst Evol Microbiol	10.1099/ijs.0.63196-0	2004	*
Enzymology	Crystal structure of a nucleoside diphosphate kinase from Bacillus halodenitrificans: coexpression of its activity with a Mn-superoxide dismutase.	Chen CJ, Liu MY, Chang T, Chang WC, Wang BC, Le Gall J	J Struct Biol	10.1016/s1047-8477(03)00014-5	2003	*
Metabolism	Three-dimensional structure of manganese superoxide dismutase from Bacillus halodenitrificans, a component of the so-called "green protein".	Liao J, Liu MY, Chang T, Li M, Le Gall J, Gui LL, Zhang JP, Jiang T, Liang DC, Chang WR	J Struct Biol	10.1016/s1047-8477(02)00531-2	2002	*

References

#3759

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10037

#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 )

#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) .

#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) .

#71121

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-ID1123.1 )

* These data were automatically processed and therefore are not curated

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Virgibacillus halodenitrificans JCM 12304

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