Strain identifier
BacDive ID: 1475
Type strain: 
Species: Virgibacillus halodenitrificans
Strain history: DSM 10037 <-- J. Le Gall.
NCBI tax ID(s): 1236975 (strain), 1482 (species)
version 9.2 (current version)
General
@ref: 3759
BacDive-ID: 1475
DSM-Number: 10037
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Virgibacillus halodenitrificans DSM 10037 is a spore-forming, mesophilic bacterium that was isolated from solar saltern.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1482 | species |
| 1236975 | strain |
strain history
| @ref | history |
|---|---|
| 3759 | <- J. Legall, Univ. Georgia, USA |
| 67770 | DSM 10037 <-- J. Le Gall. |
doi: 10.13145/bacdive1475.20241212.9.2
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
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
| @ref | growth | type | temperature |
|---|---|---|---|
| 3759 | positive | growth | 30 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: yes
- confidence: 93.941
observation
- @ref: 67770
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 3759 | solar saltern | L'étang de Berre | France | FRA | Europe |
| 67770 | Solar evaporation pond (saltern) | Strasburg | France | FRA | Europe |
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
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Bacillus halodenitrificans gene for 16S ribosomal RNA | AB021186 | 1528 | nuccore | 1482 |
| 20218 | Virgibacillus halodenitrificans genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 530 | AB367182 | 530 | nuccore | 1482 |
| 20218 | Virgibacillus halodenitrificans genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 675 | AB367183 | 675 | nuccore | 1482 |
| 20218 | Bacillus halodenitrificans strain DSM 10037 16S ribosomal RNA gene, partial sequence | AY543169 | 1521 | nuccore | 1482 |
| 20218 | Virgibacillus halodenitrificans gene for 16S rRNA, partial sequence, strain: NBRC 102361 | AB681753 | 1490 | nuccore | 1482 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Virgibacillus halodenitrificans JCM 12304 | 1236975.3 | wgs | patric | 1236975 |
| 66792 | Virgibacillus halodenitrificans JCM 12304 | 2728369661 | draft | img | 1236975 |
| 67770 | Virgibacillus halodenitrificans JCM 12304 | GCA_001310895 | contig | ncbi | 1236975 |
GC content
- @ref: 3759
- GC-content: 38
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 73.968 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 91.443 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 93.941 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 71.345 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 91.435 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 82.653 | no |
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
- @ref: 71121
- straininfo: 1123
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 12457847 | 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 | Amino 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/metabolism | Genetics |
| Enzymology | 12713952 | 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 | Air, 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 | |
| Phylogeny | 15545452 | 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 | Bacillaceae/*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/cytology | Enzymology |
| Phylogeny | 16403894 | 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 | Cyanoacrylates, 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, Temperature | Genetics |
| Phylogeny | 21239563 | 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 | Animals, 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/metabolism | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3759 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10037) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10037 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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. | 10.60712/SI-ID1123.1 | StrainInfo: A central database for resolving microbial strain identifiers |