Strain identifier
BacDive ID: 1495
Type strain: 
Species: Virgibacillus litoralis
Strain history: <- YG Chen, Yunnan Inst., China
NCBI tax ID(s): 578221 (species)
version 8.1 (current version)
General
@ref: 15485
BacDive-ID: 1495
DSM-Number: 21085
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, motile, rod-shaped
description: Virgibacillus litoralis DSM 21085 is an aerobe, spore-forming, mesophilic bacterium that was isolated from saline soil.
NCBI tax id
- NCBI tax id: 578221
- Matching level: species
strain history
| @ref | history |
|---|---|
| 15485 | <- S.-K. Tang and Y.-G. Chen, YIM; JSM 089168 <- Y.-G. Chen and H.-D. Xiao |
| 67771 | <- YG Chen, Yunnan Inst., China |
doi: 10.13145/bacdive1495.20230509.8.1
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 litoralis
- full scientific name: Virgibacillus litoralis Chen et al. 2012
@ref: 15485
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Virgibacillus
species: Virgibacillus litoralis
full scientific name: Virgibacillus litoralis Chen et al. 2012
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | flagellum arrangement | gram stain | confidence |
|---|---|---|---|---|---|
| 67771 | rod-shaped | yes | peritrichous | ||
| 67771 | positive | ||||
| 69480 | yes | 97.16 | |||
| 69480 | positive | 100 |
Culture and growth conditions
culture medium
- @ref: 15485
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 15485 | positive | growth | 30 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | type of spore | spore formation | confidence |
|---|---|---|---|
| 67771 | endospore | yes | |
| 69481 | yes | 100 | |
| 69480 | yes | 100 |
observation
- @ref: 67771
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 15485 | saline soil | shore of Naozhou Island, Leizhou Bay, South China Sea | China | CHN | Asia |
| 67771 | From saline soil | the shore of Naozhou Island, Leizhou Bay, South China Sea | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Condition | #Saline |
Safety information
risk assessment
- @ref: 15485
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15485
- description: Virgibacillus litoralis strain JSM 089168 16S ribosomal RNA gene, partial sequence
- accession: FJ425909
- length: 1497
- database: ena
- NCBI tax ID: 578221
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Virgibacillus litoralis DSM 21085 | GCA_017873675 | contig | ncbi | 578221 |
| 66792 | Virgibacillus litoralis strain DSM 21085 | 578221.3 | wgs | patric | 578221 |
| 66792 | Virgibacillus litoralis DSM 21085 | 2913383645 | draft | img | 578221 |
GC content
- @ref: 15485
- GC-content: 40.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| gram-positive | yes | 77.626 | no |
| anaerobic | no | 98.759 | yes |
| halophile | yes | 89.068 | no |
| spore-forming | yes | 92.71 | yes |
| glucose-util | yes | 87.376 | no |
| thermophile | no | 97.303 | yes |
| motile | yes | 86.561 | no |
| flagellated | yes | 90.878 | yes |
| aerobic | yes | 90.751 | no |
| glucose-ferment | no | 87.818 | no |
External links
@ref: 15485
culture collection no.: DSM 21085, KCTC 13228, JSM 089168
straininfo link
- @ref: 71141
- straininfo: 401078
literature
- topic: Phylogeny
- Pubmed-ID: 19459062
- title: Virgibacillus litoralis sp. nov., a moderately halophilic bacterium isolated from saline soil.
- authors: Chen YG, Liu ZX, Peng DJ, Zhang YQ, Wang YX, Tang SK, Li WJ, Cui XL, Liu YQ
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-009-9349-0
- year: 2009
- mesh: Bacillaceae/classification/genetics/*isolation & purification/metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/*metabolism, *Soil Microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 15485 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21085) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21085 | |
| 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 | |
| 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 | ||
| 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 | |
| 71141 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401078.1 | StrainInfo: A central database for resolving microbial strain identifiers |