Strain identifier
BacDive ID: 24870
Type strain: 
Species: Scopulibacillus darangshiensis
Strain Designation: DLS-06
Strain history: <- S. D. Lee, Cheju Natl. Univ.; DLS-06
NCBI tax ID(s): 442528 (species)
version 8.1 (current version)
General
@ref: 8080
BacDive-ID: 24870
DSM-Number: 19377
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, motile
description: Scopulibacillus darangshiensis DLS-06 is a spore-forming, mesophilic, motile bacterium that was isolated from scoria, volcanic ash.
NCBI tax id
- NCBI tax id: 442528
- Matching level: species
strain history
- @ref: 8080
- history: <- S. D. Lee, Cheju Natl. Univ.; DLS-06
doi: 10.13145/bacdive24870.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Sporolactobacillaceae
- genus: Scopulibacillus
- species: Scopulibacillus darangshiensis
- full scientific name: Scopulibacillus darangshiensis Lee and Lee 2015
@ref: 8080
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Sporolactobacillaceae
genus: Scopulibacillus
species: Scopulibacillus darangshiensis
full scientific name: Scopulibacillus darangshiensis Lee and Lee 2015
strain designation: DLS-06
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 94.366 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 8080
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
- @ref: 8080
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 8080
- sample type: scoria, volcanic ash
- geographic location: Jeju, Darangshi Oreum, 300 m above the sea level
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Dust |
| #Environmental | #Terrestrial | #Volcanic |
taxonmaps
- @ref: 69479
- File name: preview.99_156410.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_414;96_8908;97_24560;98_103110;99_156410&stattab=map
- Last taxonomy: Scopulibacillus darangshiensis subclade
- 16S sequence: AM711118
- Sequence Identity:
- Total samples: 45
- soil counts: 26
- aquatic counts: 4
- animal counts: 4
- plant counts: 11
Safety information
risk assessment
- @ref: 8080
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8080
- description: Scopulibacillus darangshiensis partial 16S rRNA gene, type strain DLS-06T
- accession: AM711118
- length: 1446
- database: ena
- NCBI tax ID: 442528
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Scopulibacillus darangshiensis DSM 19377 | GCA_004341035 | scaffold | ncbi | 442528 |
| 66792 | Scopulibacillus darangshiensis strain DSM 19377 | 442528.3 | wgs | patric | 442528 |
| 66792 | Scopulibacillus darangshiensis DSM 19377 | 2795385464 | draft | img | 442528 |
GC content
- @ref: 8080
- GC-content: 50.8
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| flagellated | yes | 58.566 | no |
| gram-positive | yes | 84.403 | no |
| anaerobic | no | 99.111 | no |
| aerobic | yes | 89.903 | no |
| halophile | no | 51.447 | no |
| spore-forming | yes | 93.928 | no |
| thermophile | no | 91.664 | yes |
| glucose-util | yes | 90.025 | no |
| motile | yes | 83.178 | no |
| glucose-ferment | no | 89.114 | no |
External links
@ref: 8080
culture collection no.: DSM 19377, KCTC 13161
straininfo link
- @ref: 88683
- straininfo: 402729
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20127464 | Scopulibacillus darangshiensis gen. nov., sp. nov., isolated from rock. | Lee SD, Lee DW | J Microbiol | 10.1007/s12275-009-0111-0 | 2010 | Bacillales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Temperature, Vitamin K 2/analysis | Genetics |
| Phylogeny | 27515245 | Scopulibacillus daqui sp. nov., a thermophilic bacterium isolated from high temperature daqu. | Yao S, Zhai L, Xin C, Liu Y, Xu L, Zhang X, Zhao T, Zhang L, Cheng C | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001417 | 2016 | Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Food Microbiology, Hot Temperature, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial, Vitamin K 2/chemistry | Biotechnology |
| Phylogeny | 29789976 | Scopulibacillus cellulosilyticus sp. nov., a cellulose-degrading bacterium isolated from tea. | Yan ZF, Lin P, Li CT, Kook M, Yi TH | Antonie Van Leeuwenhoek | 10.1007/s10482-018-1101-1 | 2018 | Bacteria/classification/genetics/*metabolism, Cellulose/*metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Tea/*microbiology | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8080 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19377) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19377 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 88683 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402729.1 | StrainInfo: A central database for resolving microbial strain identifiers |