Strain identifier
BacDive ID: 1496
Type strain: 
Species: Virgibacillus alimentarius
Strain Designation: IDS-20
Strain history: <- JH Yoon, KRIBB
NCBI tax ID(s): 698769 (species)
version 8.1 (current version)
General
@ref: 5489
BacDive-ID: 1496
DSM-Number: 25790
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-variable, motile, rod-shaped
description: Virgibacillus alimentarius IDS-20 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from marine solar saltern, sediment.
NCBI tax id
- NCBI tax id: 698769
- Matching level: species
strain history
| @ref | history |
|---|---|
| 5489 | <- KCTC; KCTC 13727 |
| 67771 | <- JH Yoon, KRIBB |
doi: 10.13145/bacdive1496.20230509.8.1
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 alimentarius
- full scientific name: Virgibacillus alimentarius Kim et al. 2011
synonyms
- @ref: 20215
- synonym: Virgibacillus campisalis
@ref: 5489
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Virgibacillus
species: Virgibacillus campisalis
full scientific name: Virgibacillus campisalis Lee et al. 2012
strain designation: IDS-20
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
|---|---|---|---|---|---|---|---|
| 30306 | variable | 1.0-4.0 µm | 0.5-1.0 µm | rod-shaped | yes | ||
| 67771 | rod-shaped | yes | monotrichous, polar | ||||
| 67771 | variable | ||||||
| 69480 | yes | 97.106 | |||||
| 69480 | positive | 100 |
colony morphology
- @ref: 61901
- incubation period: 2 days
pigmentation
- @ref: 30306
- production: yes
Culture and growth conditions
culture medium
- @ref: 5489
- name: CM + YE MEDIUM (DSMZ Medium 549)
- growth: yes
- link: https://mediadive.dsmz.de/medium/549
- composition: 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 | range |
|---|---|---|---|---|
| 5489 | positive | growth | 28 | mesophilic |
| 30306 | positive | growth | 15-40 | |
| 30306 | positive | optimum | 37 | mesophilic |
| 61901 | positive | growth | 37 | mesophilic |
| 67771 | positive | growth | 37 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30306 | positive | growth | 6.0-9.0 | alkaliphile |
| 30306 | positive | optimum | 7.5-8.0 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 30306 | facultative anaerobe |
| 61901 | aerobe |
| 67771 | facultative anaerobe |
spore formation
| @ref | spore formation | type of spore | confidence |
|---|---|---|---|
| 30306 | yes | ||
| 67771 | yes | endospore | |
| 69481 | yes | 100 | |
| 69480 | yes | 99.999 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30306 | NaCl | positive | growth | 0.5-20 % |
| 30306 | NaCl | positive | optimum | 4-5 % |
observation
- @ref: 67771
- observation: quinones: MK-7
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30306 | 30089 | acetate | + | carbon source |
| 30306 | 16947 | citrate | + | carbon source |
| 30306 | 17234 | glucose | + | carbon source |
| 30306 | 25115 | malate | + | carbon source |
| 30306 | 15361 | pyruvate | + | carbon source |
| 30306 | 30031 | succinate | + | carbon source |
| 30306 | 53424 | tween 20 | + | carbon source |
| 30306 | 53423 | tween 40 | + | carbon source |
| 30306 | 53425 | tween 60 | + | carbon source |
| 30306 | 53426 | 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
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 5489 | marine solar saltern, sediment | West coast | Republic of Korea | KOR | Asia | |
| 61901 | Marine solar saltern sediment | west coast | Republic of Korea | KOR | Asia | 2007 |
| 67771 | From sediment, marine solar saltern | Yellow Sea, the west coast of Korea | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
| #Condition | #Saline |
taxonmaps
- @ref: 69479
- File name: preview.99_3806.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1954;97_2350;98_2899;99_3806&stattab=map
- Last taxonomy: Virgibacillus
- 16S sequence: GU586225
- Sequence Identity:
- Total samples: 64
- soil counts: 22
- aquatic counts: 6
- animal counts: 34
- plant counts: 2
Safety information
risk assessment
- @ref: 5489
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5489
- description: Virgibacillus campisalis strain IDS-20 16S ribosomal RNA gene, partial sequence
- accession: GU586225
- length: 1523
- database: ena
- NCBI tax ID: 744463
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Virgibacillus alimentarius DSM 25790 | GCA_017874635 | contig | ncbi | 698769 |
| 66792 | Virgibacillus campisalis strain DSM 25790 | 744463.3 | wgs | patric | 744463 |
| 66792 | Virgibacillus campisalis DSM 25790 | 2913450449 | draft | img | 744463 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 5489 | 39.5 | high performance liquid chromatography (HPLC) |
| 30306 | 39.5 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 86.139 | no |
| flagellated | yes | 68.928 | no |
| gram-positive | yes | 91.671 | yes |
| anaerobic | no | 99.665 | no |
| aerobic | yes | 93.459 | no |
| halophile | yes | 96.593 | no |
| spore-forming | yes | 94.686 | yes |
| thermophile | no | 96.434 | yes |
| glucose-util | yes | 88.762 | yes |
| glucose-ferment | no | 93.444 | no |
External links
@ref: 5489
culture collection no.: DSM 25790, CCUG 59308, KCTC 13727
straininfo link
- @ref: 71142
- straininfo: 397970
literature
- topic: Phylogeny
- Pubmed-ID: 21441379
- title: Virgibacillus campisalis sp. nov., from a marine solar saltern.
- authors: Lee SY, Kang CH, Oh TK, Yoon JH
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.033084-0
- year: 2011
- mesh: Bacillaceae/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Lipids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, *Sodium Chloride, Species Specificity
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 5489 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25790) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25790 | |||
| 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 | |||
| 30306 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26647 | 28776041 | |
| 61901 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 59308) | https://www.ccug.se/strain?id=59308 | |||
| 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) | |||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/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. | 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) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 71142 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397970.1 | StrainInfo: A central database for resolving microbial strain identifiers |