Strain identifier
BacDive ID: 1548
Type strain: 
Species: Salsuginibacillus kocurii
Strain Designation: CH9d
Strain history: <- A. Ventosa <- I.J. Carrasco, CH9d
NCBI tax ID(s): 1123239 (strain), 427078 (species)
version 8.1 (current version)
General
@ref: 7388
BacDive-ID: 1548
DSM-Number: 18087
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped
description: Salsuginibacillus kocurii CH9d is an aerobe, spore-forming, mesophilic bacterium that was isolated from sediment.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 427078 | species |
| 1123239 | strain |
strain history
- @ref: 7388
- history: <- A. Ventosa <- I.J. Carrasco, CH9d
doi: 10.13145/bacdive1548.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Salsuginibacillus
- species: Salsuginibacillus kocurii
- full scientific name: Salsuginibacillus kocurii Carrasco et al. 2007
@ref: 7388
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Salsuginibacillus
species: Salsuginibacillus kocurii
full scientific name: Salsuginibacillus kocurii Carrasco et al. 2007
strain designation: CH9d
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32212 | positive | 3.25 µm | 0.75 µm | rod-shaped | yes | |
| 69480 | yes | 96.854 | ||||
| 69480 | positive | 100 |
pigmentation
- @ref: 32212
- production: no
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_18087_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_18087_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_18087_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_18087_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_18087_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 7388
- name: HALOMONAS MAGADIENSIS MEDIUM (DSMZ Medium 971)
- growth: yes
- link: https://mediadive.dsmz.de/medium/971
- composition: Name: HALOMONAS MAGADIENSIS MEDIUM (DSMZ Medium 971; with strain-specific modifications) Composition: NaCl 80.0 g/l Agar 20.0 g/l Na2CO3 10.0 g/l Glucose 10.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 7388 | positive | growth | 30 | mesophilic |
| 32212 | positive | growth | 37 | mesophilic |
| 32212 | positive | optimum | 20-50 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32212 | positive | growth | 5.8-10.0 | alkaliphile |
| 32212 | positive | optimum | 8.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 32212
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32212 | yes | |
| 69481 | yes | 100 |
| 69480 | yes | 99.448 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32212 | NaCl | positive | growth | 03-20 % |
| 32212 | NaCl | positive | optimum | 10 % |
observation
- @ref: 32212
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32212 | 30089 | acetate | + | carbon source |
| 32212 | 17057 | cellobiose | + | carbon source |
| 32212 | 16947 | citrate | + | carbon source |
| 32212 | 16236 | ethanol | + | carbon source |
| 32212 | 15740 | formate | + | carbon source |
| 32212 | 17234 | glucose | + | carbon source |
| 32212 | 29864 | mannitol | + | carbon source |
| 32212 | 15361 | pyruvate | + | carbon source |
| 32212 | 33942 | ribose | + | carbon source |
| 32212 | 17992 | sucrose | + | carbon source |
| 32212 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 32212
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 7388
- sample type: sediment
- geographic location: Lake Chagannor, Inner Mongolia
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_175510.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4889;96_22575;97_28218;98_114817;99_175510&stattab=map
- Last taxonomy: Salsuginibacillus kocurii subclade
- 16S sequence: AM492160
- Sequence Identity:
- Total samples: 99
- soil counts: 10
- aquatic counts: 53
- animal counts: 35
- plant counts: 1
Safety information
risk assessment
- @ref: 7388
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7388
- description: Salsuginibacillus kocurii 16S rRNA gene, type strain CH9dT
- accession: AM492160
- length: 1502
- database: ena
- NCBI tax ID: 427078
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Salsuginibacillus kocurii DSM 18087 | GCA_000377705 | scaffold | ncbi | 1123239 |
| 66792 | Salsuginibacillus kocurii DSM 18087 | 1123239.3 | wgs | patric | 1123239 |
| 66792 | Salsuginibacillus kocurii DSM 18087 | 2517572235 | draft | img | 1123239 |
GC content
- @ref: 7388
- GC-content: 44.7
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 88.586 | yes |
| flagellated | yes | 51.993 | no |
| gram-positive | yes | 92.453 | yes |
| anaerobic | no | 98.315 | no |
| aerobic | yes | 93.46 | yes |
| halophile | yes | 93.458 | yes |
| spore-forming | yes | 84.655 | no |
| glucose-util | yes | 89.38 | no |
| thermophile | no | 97.031 | no |
| glucose-ferment | no | 90.014 | no |
External links
@ref: 7388
culture collection no.: DSM 18087, CCM 7365, CECT 7154, CGMCC 1.6287
straininfo link
- @ref: 71193
- straininfo: 310985
literature
- topic: Phylogeny
- Pubmed-ID: 17911315
- title: Salsuginibacillus kocurii gen. nov., sp. nov., a moderately halophilic bacterium from soda-lake sediment.
- authors: Carrasco IJ, Marquez MC, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65136-0
- year: 2007
- mesh: Bacillaceae/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids, Genes, rRNA, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Locomotion/physiology, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Spores, Bacterial/cytology, Temperature
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 7388 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18087) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18087 | ||||
| 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 | ||||
| 32212 | 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 | 28454 | 28776041 | ||
| 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) | ||||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
| 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 | ||||
| 71193 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID310985.1 | StrainInfo: A central database for resolving microbial strain identifiers |