Virgibacillus halodenitrificans (DSM 10037, ATCC 49067, NBRC 102361)

Name: Virgibacillus halodenitrificans (DSM 10037, ATCC 49067, NBRC 102361)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1475

Type strain

Culture col. no. DSM 10037 ATCC 49067 NBRC 102361 LMG 9818 KCTC 3790 3 more

NCBI tax ID(s) 1236975 1482

Special Collections DSMZ JCM KCTC

History DSMZ <- J. Legall, Univ. Georgia, USA JCM <-- DSM 10037 <-- J. Le Gall.

Links

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

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 1123

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

@ref 20215

Last LPSN update 2026-05-29 08:25:16

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Virgibacillus

Species Virgibacillus halodenitrificans

Full scientific name Virgibacillus halodenitrificans (Denariaz et al. 1989) Yoon et al. 2004

Synonyms (1)

Bacillus halodenitrificans

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3759	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Soil extract 500.0 g/l NaCl 50.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
3759	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	96.495

Spore formation

@ref	Spore formation	Confidence
125438		93.941
125439		97.171

Observation

67770

Observationquinones: MK-7

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Condition	#Saline

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3759	solar saltern	L'étang de Berre	France	FRA	Europe
67770	Solar evaporation pond (saltern)	Strasburg	France	FRA	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3759	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	ASM131089v1 assembly for Virgibacillus halodenitrificans JCM 12304	contig	GCA_001310895	1236975.3	2728369661	1236975	58.72

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bacillus halodenitrificans gene for 16S ribosomal RNA	AB021186	1528	1482
20218	Bacillus halodenitrificans strain DSM 10037 16S ribosomal RNA gene, partial sequence	AY543169	1521	1482
20218	Virgibacillus halodenitrificans gene for 16S rRNA, partial sequence, strain: NBRC 102361	AB681753	1490	1482

GC content

3759

GC-content (mol%)38

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM131089v1 assembly for Virgibacillus halodenitrificans JCM 12304
NCBI: GCA_001310895

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.50	no
125439	gram_stain	BacteriaNetⓘ	variable	48.73	no
125439	motility	BacteriaNetⓘ	yes	84.07	no
125439	spore_formation	BacteriaNetⓘ	yes	97.17	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Virgibacillus halodenitrificans JCM 12304
PATRIC: 1236975.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	73.97	no
125438	anaerobic	anaerobicⓘ	no	91.44	no
125438	spore-forming	spore-formingⓘ	yes	93.94	no
125438	aerobic	aerobicⓘ	yes	71.35	no
125438	thermophilic	thermophileⓘ	no	91.44	yes
125438	flagellated	motile2+ⓘ	yes	82.65	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Carotegenic Virgibacillus halodenitrificans from Wadi El-Natrun Salt Lakes: Isolation, Optimization, Characterization and Biological Activities of Carotenoids.	Fayez D, Youssif A, Sabry S, Ghozlan H, Eltarahony M.	Biology (Basel)	10.3390/biology11101407	2022
Phylogeny	Characterization of halophilic bacterial communities in Turda Salt Mine (Romania).	Carpa R, Keul A, Muntean V, Dobrota C.	Orig Life Evol Biosph	10.1007/s11084-014-9375-4	2014
Phylogeny	Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert.	Piubeli F, de Lourdes Moreno M, Kishi LT, Henrique-Silva F, Garcia MT, Mellado E.	Indian J Microbiol	10.1007/s12088-015-0539-3	2015
Enzymology	Menaquinol-nitrate oxidoreductase of Bacillus halodenitrificans.	Ketchum PA, Denariaz G, LeGall J, Payne WJ.	J Bacteriol	10.1128/jb.173.8.2498-2505.1991	1991
	Phenomics and Genomics Reveal Adaptation of Virgibacillus dokdonensis Strain 21D to Its Origin of Isolation, the Seawater-Brine Interface of the Mediterranean Sea Deep Hypersaline Anoxic Basin Discovery.	Zeaiter Z, Marasco R, Booth JM, Prosdocimi EM, Mapelli F, Callegari M, Fusi M, Michoud G, Molinari F, Daffonchio D, Borin S, Crotti E.	Front Microbiol	10.3389/fmicb.2019.01304	2019
	Nitrogen and sulfur cycling driven by Campylobacterota in the sediment-water interface of deep-sea cold seep: a case in the South China Sea.	Sun QL, Xu K, Cao L, Du Z, Wang M, Sun L.	mBio	10.1128/mbio.00117-23	2023
	Identification of Trans-4-Hydroxy-L-Proline as a Compatible Solute and Its Biosynthesis and Molecular Characterization in Halobacillus halophilus.	Kim KH, Jia B, Jeon CO.	Front Microbiol	10.3389/fmicb.2017.02054	2017
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
Phylogeny	Virgibacillus tibetensis sp. nov., isolated from salt lake on the Tibetan plateau of China.	Li D, Phurbu D, Zhang X, Liu ZX, Wang R, Zheng YY, Zhou YG, Yu YJ, Xue L, Li AH.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006525	2024
Genetics	Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut.	Seck E, Rathored J, Khelaifia S, Croce O, Robert C, Couderc C, Di Pinto F, Sokhna C, Raoult D, Lagier JC.	New Microbes New Infect	10.1016/j.nmni.2015.09.014	2015
	Hymenobacter telluris sp. nov., isolated from soil in South Korea.	Damdintogtokh T, Park Y, Maeng S, Oh HJ, Bang M, Lee YK, Oh J, Bai J, Kim MK.	Arch Microbiol	10.1007/s00203-021-02692-x	2022
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

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 )
#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 )
#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 halodenitrificans (DSM 10037, ATCC 49067, NBRC 102361)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001310895

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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