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Strain identifier

BacDive ID: 1475

Type strain: Yes

Species: Virgibacillus halodenitrificans

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

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

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 3759

BacDive-ID: 1475

DSM-Number: 10037

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

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

NCBI tax id

NCBI tax idMatching level
1482species
1236975strain

strain history

doi: 10.13145/bacdive1475.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • 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

    • @ref: 20215
    • synonym: Bacillus halodenitrificans

@ref: 3759

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Virgibacillus

species: Virgibacillus halodenitrificans

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

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes66.852
6948091.58positive

Culture and growth conditions

culture medium

  • @ref: 3759
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: 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

@refgrowthtypetemperaturerange
3759positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 89.712

halophily

  • @ref: 69480
  • halophily level: halophilic
  • confidence: 97.098

observation

  • @ref: 67770
  • observation: quinones: MK-7

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3759solar salternL'étang de BerreFranceFRAEurope
67770Solar evaporation pond (saltern)StrasburgFranceFRAEurope

isolation source categories

  • Cat1: #Condition
  • Cat2: #Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_3814.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1959;97_2355;98_2906;99_3814&stattab=map
  • Last taxonomy: Virgibacillus halodenitrificans subclade
  • 16S sequence: AB681753
  • Sequence Identity:
  • Total samples: 5050
  • soil counts: 2809
  • aquatic counts: 693
  • animal counts: 1180
  • plant counts: 368

Safety information

risk assessment

  • @ref: 3759
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus halodenitrificans gene for 16S ribosomal RNAAB0211861528ena1482
20218Virgibacillus halodenitrificans genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 530AB367182530ena1482
20218Virgibacillus halodenitrificans genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 675AB367183675ena1482
20218Bacillus halodenitrificans strain DSM 10037 16S ribosomal RNA gene, partial sequenceAY5431691521ena1482
20218Virgibacillus halodenitrificans gene for 16S rRNA, partial sequence, strain: NBRC 102361AB6817531490ena1482

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Virgibacillus halodenitrificans JCM 123041236975.3wgspatric1236975
66792Virgibacillus halodenitrificans JCM 123042728369661draftimg1236975
67770Virgibacillus halodenitrificans JCM 12304 JCM 12304GCA_001310895contigncbi1236975

GC content

  • @ref: 3759
  • GC-content: 38

External links

@ref: 3759

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

straininfo link

@refpassport
20218http://www.straininfo.net/strains/161792
20218http://www.straininfo.net/strains/4651

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism12457847Three-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 WRJ Struct Biol10.1016/s1047-8477(02)00531-22002Amino Acid Sequence, Bacillus/*enzymology, Bacterial Proteins/*chemistry/metabolism, Binding Sites, Catalysis, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Quaternary, Salts/pharmacology, Sequence Homology, Amino Acid, Static Electricity, Structure-Activity Relationship, Superoxide Dismutase/*chemistry/metabolism, Zinc/metabolismGenetics
Enzymology12713952Crystal 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 JJ Struct Biol10.1016/s1047-8477(03)00014-52003Air, Amino Acid Sequence, Bacillus/*enzymology/growth & development, Binding Sites, Crystallography, X-Ray, Macromolecular Substances, Models, Molecular, Nucleoside-Diphosphate Kinase/biosynthesis/*chemistry, Protein Binding, Protein Conformation, Sequence Alignment, Superoxide Dismutase/biosynthesis
Phylogeny15545452Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.Yoon JH, Oh TK, Park YHInt J Syst Evol Microbiol10.1099/ijs.0.63196-02004Bacillaceae/*classification/cytology/*isolation & purification/physiology, Bacillus/classification/genetics, Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Gentian Violet, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic, Sequence Analysis, DNA, Spores, Bacterial/cytologyEnzymology
Phylogeny16403894Virgibacillus 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 CJInt J Syst Evol Microbiol10.1099/ijs.0.63734-02006Cyanoacrylates, Fatty Acids, Gram-Positive Endospore-Forming Bacteria/chemistry/*classification/isolation & purification/physiology, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity, TemperatureGenetics
Phylogeny21239563Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food.Kim J, Jung MJ, Roh SW, Nam YD, Shin KS, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.028191-02011Animals, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Fishes, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology, Sodium Chloride/metabolism, Virgibacillus/*classification/genetics/*isolation & purification/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3759Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10037)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10037
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)