Strain identifier
BacDive ID: 23285
Type strain:
Species: Stakelama sediminis
Strain Designation: CJ70
Strain history: C.-J. Cha CJ70.
NCBI tax ID(s): 463200 (species)
General
@ref: 19228
BacDive-ID: 23285
DSM-Number: 27203
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Stakelama sediminis CJ70 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.
NCBI tax id
- NCBI tax id: 463200
- Matching level: species
strain history
@ref | history |
---|---|
19228 | <- C.-J. Cha, Chung-Ang Univ., Seoul, Republic of Korea; CJ70 <- C. N. Thawng |
67770 | C.-J. Cha CJ70. |
doi: 10.13145/bacdive23285.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Stakelama
- species: Stakelama sediminis
- full scientific name: Stakelama sediminis Thawng et al. 2013
@ref: 19228
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Stakelama
species: Stakelama sediminis
full scientific name: Stakelama sediminis Thawng et al. 2013
strain designation: CJ70
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
30603 | negative | rod-shaped | no | |
69480 | negative | 99.907 |
pigmentation
- @ref: 30603
- production: yes
multimedia
- @ref: 19228
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27203.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 19228
- 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 | growth | type | temperature | range |
---|---|---|---|---|
19228 | positive | growth | 28 | mesophilic |
30603 | positive | growth | 20-37 | |
30603 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30603 | positive | growth | 05-10 | alkaliphile |
30603 | positive | optimum | 6 |
Physiology and metabolism
oxygen tolerance
- @ref: 30603
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.989 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30603 | NaCl | positive | growth | 0-5 % |
30603 | NaCl | positive | optimum | 0.5 % |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30603 | 21217 | L-alaninamide | + | carbon source |
30603 | 16449 | alanine | + | carbon source |
30603 | 22599 | arabinose | + | carbon source |
30603 | 17057 | cellobiose | + | carbon source |
30603 | 23652 | dextrin | + | carbon source |
30603 | 28757 | fructose | + | carbon source |
30603 | 28260 | galactose | + | carbon source |
30603 | 17234 | glucose | + | carbon source |
30603 | 32323 | glucuronamide | + | carbon source |
30603 | 29987 | glutamate | + | carbon source |
30603 | 24996 | lactate | + | carbon source |
30603 | 17306 | maltose | + | carbon source |
30603 | 37684 | mannose | + | carbon source |
30603 | 37657 | methyl D-glucoside | + | carbon source |
30603 | 26271 | proline | + | carbon source |
30603 | 51850 | methyl pyruvate | + | carbon source |
30603 | 17822 | serine | + | carbon source |
30603 | 30031 | succinate | + | carbon source |
30603 | 27082 | trehalose | + | carbon source |
30603 | 53426 | tween 80 | + | carbon source |
30603 | 4853 | esculin | + | hydrolysis |
30603 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30603 | acid phosphatase | + | 3.1.3.2 |
30603 | alkaline phosphatase | + | 3.1.3.1 |
30603 | catalase | + | 1.11.1.6 |
30603 | cytochrome oxidase | + | 1.9.3.1 |
30603 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
19228 | tidal flat sediment | Republic of Korea | KOR | Asia |
67770 | Tidal flat sediment | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Tidal flat |
#Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_116517.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_46188;97_59272;98_78722;99_116517&stattab=map
- Last taxonomy: Stakelama sediminis subclade
- 16S sequence: EU099873
- Sequence Identity:
- Total samples: 14
- soil counts: 1
- aquatic counts: 9
- animal counts: 1
- plant counts: 3
Safety information
risk assessment
- @ref: 19228
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19228
- description: Stakelama sediminis strain CJ70 16S ribosomal RNA gene, partial sequence
- accession: EU099873
- length: 1410
- database: ena
- NCBI tax ID: 463200
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Stakelama sediminis DSM 27203 | GCA_014199335 | contig | ncbi | 463200 |
66792 | Stakelama sediminis strain DSM 27203 | 463200.5 | wgs | patric | 463200 |
66792 | Stakelama sediminis DSM 27203 | 2828395373 | draft | img | 463200 |
GC content
@ref | GC-content | method |
---|---|---|
19228 | 61.4 | |
67770 | 61.4 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 97.084 | no |
anaerobic | no | 99.134 | yes |
halophile | no | 91.467 | yes |
spore-forming | no | 94.694 | no |
glucose-util | yes | 91.352 | yes |
aerobic | yes | 91.837 | yes |
flagellated | no | 87.167 | yes |
motile | yes | 70.533 | yes |
thermophile | no | 94.819 | yes |
glucose-ferment | no | 90.837 | no |
External links
@ref: 19228
culture collection no.: DSM 27203, JCM 18079, KACC 16559
straininfo link
- @ref: 87506
- straininfo: 397254
literature
- topic: Phylogeny
- Pubmed-ID: 22523167
- title: Stakelama sediminis sp. nov., isolated from tidal flat sediment.
- authors: Thawng CN, Park SJ, Cha JH, Cha CJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.039743-0
- year: 2012
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analysis
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
19228 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27203) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27203 | |||
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 | |||
30603 | 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 | 26934 | 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) | |||
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) | |||
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 | |||
87506 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397254.1 | StrainInfo: A central database for resolving microbial strain identifiers |