Strain identifier
BacDive ID: 130494
Type strain: 
Species: Nocardioides deserti
Strain Designation: SC8A-24
Strain history: CGMCC 4.7183 <-- L. Tuo; Inst. of Med. Biotechnol., Chin. Acad. Med. Sci., China; SC8A-24.
NCBI tax ID(s): 1588644 (species)
version 8.1 (current version)
General
@ref: 21697
BacDive-ID: 130494
DSM-Number: 26045
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Nocardioides deserti SC8A-24 is a mesophilic bacterium that was isolated from saline–alkaline soil in the rhizosphere of Alhagi sparsifolia.
NCBI tax id
- NCBI tax id: 1588644
- Matching level: species
strain history
| @ref | history |
|---|---|
| 21697 | <- Chinese Acad. Med. Sciences & Peking Union Medical College; SC8A-24 <- Y. Dong |
| 67770 | CGMCC 4.7183 <-- L. Tuo; Inst. of Med. Biotechnol., Chin. Acad. Med. Sci., China; SC8A-24. |
doi: 10.13145/bacdive130494.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Nocardioidaceae
- genus: Nocardioides
- species: Nocardioides deserti
- full scientific name: Nocardioides deserti Tuo et al. 2015
@ref: 21697
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides deserti
full scientific name: Nocardioides deserti Tuo et al. 2015
strain designation: SC8A-24
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 90.171 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 21697 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
| 21697 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | 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 |
|---|---|---|---|---|
| 21697 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.793
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|---|
| 21697 | saline–alkaline soil in the rhizosphere of Alhagi sparsifolia | Alhagi sparsifolia | Xinjiang, Taklimakan desert (37° 02' 38'' N 80° 15' 1''E) | China | CHN | Asia | 37.0439 | 80.2503 |
| 67770 | Rhizosphere soil of Alhagis parsifolia from the Taklimakan desert | Alhagis parsifolia | Xinjiang Province, north-west China | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host Body-Site | #Plant | #Rhizosphere |
| #Condition | #Alkaline | |
| #Condition | #Saline |
Safety information
risk assessment
- @ref: 21697
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21697
- description: Nocardioides deserti strain SC8A-24 16S ribosomal RNA gene, partial sequence
- accession: KM816582
- length: 1482
- database: ena
- NCBI tax ID: 1588644
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Nocardioides deserti CGMCC 4.7183 | GCA_014646035 | scaffold | ncbi | 1588644 |
| 66792 | Nocardioides deserti SC8A-24 | GCA_014266025 | contig | ncbi | 1588644 |
| 66792 | Nocardioides deserti strain CGMCC 4.7183 | 1588644.4 | wgs | patric | 1588644 |
| 66792 | Nocardioides deserti SC8A-24 | 2921383071 | draft | img | 1588644 |
GC content
- @ref: 21697
- GC-content: 71
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 71 | no |
| flagellated | no | 94.714 | no |
| gram-positive | yes | 89.824 | no |
| anaerobic | no | 98.482 | no |
| aerobic | yes | 92.968 | no |
| halophile | no | 81.583 | no |
| spore-forming | no | 88.064 | no |
| glucose-util | yes | 92.236 | no |
| thermophile | no | 97.496 | yes |
| motile | no | 65.429 | no |
| glucose-ferment | no | 88.959 | no |
External links
@ref: 21697
culture collection no.: DSM 26045, CGMCC 4.7183, JCM 33040
straininfo link
- @ref: 89018
- straininfo: 404835
literature
- topic: Phylogeny
- Pubmed-ID: 25716951
- title: Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil.
- authors: Tuo L, Dong YP, Habden X, Liu JM, Guo L, Liu XF, Chen L, Jiang ZK, Liu SW, Zhang YB, Zhang YQ, Sun CH
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.000147
- year: 2015
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fabaceae/*microbiology, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
- 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 | |
| 21697 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26045 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26045) | |
| 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 | |
| 89018 | 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-ID404835.1 |