Strain identifier
BacDive ID: 131419
Type strain: 
Species: Kocuria dechangensis
Strain Designation: NEAU-ST5-33
Strain history: CGMCC 1.12187 <-- J. Jiang; Northeast Agric. Univ., China; NEAU-ST5-33.
NCBI tax ID(s): 1176249 (species)
version 8.1 (current version)
General
@ref: 22646
BacDive-ID: 131419
DSM-Number: 25872
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Kocuria dechangensis NEAU-ST5-33 is a mesophilic bacterium that was isolated from saline and alkaline soils.
NCBI tax id
- NCBI tax id: 1176249
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22646 | <- J. Juquan, Northeast Agricultural Univ., Harbin, China <- Pan, Northeast Agricultural Univ., Harbin, China; NEAU-ST5-33 |
| 67770 | CGMCC 1.12187 <-- J. Jiang; Northeast Agric. Univ., China; NEAU-ST5-33. |
doi: 10.13145/bacdive131419.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Micrococcaceae
- genus: Kocuria
- species: Kocuria dechangensis
- full scientific name: Kocuria dechangensis Wang et al. 2015
@ref: 22646
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micrococcaceae
genus: Kocuria
species: Kocuria dechangensis
full scientific name: Kocuria dechangensis Wang et al. 2015
strain designation: NEAU-ST5-33
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 93.996 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 22646
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 22646 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.98
murein
- @ref: 22646
- murein short key: A11.06
- type: A3alpha L-Lys-L-Ala3
observation
- @ref: 67770
- observation: quinones: MK-8(H2)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 22646 | saline and alkaline soils | Heilongjiang Province, Dechang Township, Zhaodong City (45° 48' 59.28'' N 125° 41' 48.14'' E) | China | CHN | Asia | 45.8165 | 125.697 |
| 67770 | Saline and alkaline soil in Dechang Township | Zhaodong City, Heilongjiang Province | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Condition | #Alkaline | |
| #Condition | #Saline |
Safety information
risk assessment
- @ref: 22646
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22646
- description: Kocuria dechangensis strain NEAU-ST5-33 16S ribosomal RNA gene, partial sequence
- accession: JQ762279
- length: 1486
- database: ena
- NCBI tax ID: 1176249
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Kocuria dechangensis CGMCC 1.12187 | GCA_014636775 | scaffold | ncbi | 1176249 |
| 66792 | Kocuria dechangensis strain CGMCC 1.12187 | 1176249.3 | wgs | patric | 1176249 |
GC content
- @ref: 22646
- GC-content: 61.2
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 80 | no |
| flagellated | no | 98.03 | no |
| gram-positive | yes | 95.344 | no |
| anaerobic | no | 99.449 | no |
| aerobic | yes | 95.448 | no |
| halophile | yes | 51.438 | no |
| spore-forming | no | 90.726 | no |
| thermophile | no | 99.156 | yes |
| glucose-util | yes | 88.318 | no |
| motile | no | 92.42 | no |
| glucose-ferment | no | 87.428 | no |
External links
@ref: 22646
culture collection no.: DSM 25872, CGMCC 1.12187, JCM 31770
straininfo link
- @ref: 89847
- straininfo: 401750
literature
- topic: Phylogeny
- Pubmed-ID: 26048314
- title: Kocuria dechangensis sp. nov., an actinobacterium isolated from saline and alkaline soils.
- authors: Wang K, Zhang L, Liu Y, Pan Y, Meng L, Xu T, Zhang C, Liu H, Hong S, Huang H, Jiang J
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.000372
- year: 2015
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Micrococcaceae/classification, Molecular Sequence Data, Nucleic Acid Hybridization/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/analysis, Soil/chemistry, Soil Microbiology
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 22646 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25872 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25872) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 89847 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID401750.1 |