Strain identifier
BacDive ID: 130492
Type strain: 
Species: Nocardioides rubriscoriae
Strain Designation: Sco-A25
Strain history: <- SD Lee, Cheju Univ.
NCBI tax ID(s): 642762 (species)
version 8.1 (current version)
General
@ref: 21695
BacDive-ID: 130492
DSM-Number: 23986
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive
description: Nocardioides rubriscoriae Sco-A25 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from red-coloured layer of scoria from a parasitic volcano.
NCBI tax id
- NCBI tax id: 642762
- Matching level: species
strain history
| @ref | history |
|---|---|
| 21695 | <- S. D. Lee, Jeju National Univ., Rep. of Korea; Sco-A25 <- D. W. Lee |
| 67771 | <- SD Lee, Cheju Univ. |
doi: 10.13145/bacdive130492.20230509.8.1
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 rubriscoriae
- full scientific name: Nocardioides rubriscoriae corrig. Lee and Lee 2014
synonyms
- @ref: 20215
- synonym: Nocardioides rubroscoriae
@ref: 21695
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides rubriscoriae
full scientific name: Nocardioides rubriscoriae Lee and Lee 2014
strain designation: Sco-A25
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 67771 | positive | |
| 69480 | positive | 99.999 |
Culture and growth conditions
culture medium
- @ref: 21695
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 21695 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.973
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 21695 | red-coloured layer of scoria (volcanic ash) from a parasitic volcano | Jeju | Republic of Korea | KOR | Asia |
| 67771 | From volcanic ash (scoria) | Jeju | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Dust |
| #Environmental | #Terrestrial | #Volcanic |
taxonmaps
- @ref: 69479
- File name: preview.99_177849.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_7953;97_17569;98_21830;99_177849&stattab=map
- Last taxonomy: Nocardioides rubriscoriae
- 16S sequence: FN386714
- Sequence Identity:
- Total samples: 58
- soil counts: 13
- aquatic counts: 9
- animal counts: 17
- plant counts: 19
Safety information
risk assessment
- @ref: 21695
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21695
- description: Nocardioides rubriscoriae partial 16S rRNA gene, type strain Sco-A25T
- accession: FN386714
- length: 1415
- database: ena
- NCBI tax ID: 642762
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Nocardioides rubriscoriae DSM 23986 | GCA_008087085 | contig | ncbi | 642762 |
| 66792 | Nocardioides rubriscoriae strain DSM 23986 | 642762.3 | wgs | patric | 642762 |
| 66792 | Nocardioides rubriscoriae DSM 23986 | 2899979250 | draft | img | 642762 |
GC content
- @ref: 21695
- GC-content: 71.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 57 | no |
| gram-positive | yes | 90.515 | yes |
| anaerobic | no | 98.238 | no |
| halophile | no | 96.871 | no |
| spore-forming | no | 77.011 | no |
| glucose-util | yes | 86.698 | no |
| thermophile | no | 97.918 | yes |
| flagellated | no | 94.175 | no |
| aerobic | yes | 89.415 | yes |
| motile | no | 76.41 | no |
| glucose-ferment | no | 88.033 | no |
External links
@ref: 21695
culture collection no.: DSM 23986, KCTC 19805, NBRC 107916
straininfo link
- @ref: 89016
- straininfo: 399824
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24696303 | Nocardioides rubroscoriae sp. nov., isolated from volcanic ash. | Lee SD, Lee DW | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0161-0 | 2014 | Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Volcanic Eruptions | Genetics |
| Phylogeny | 28777069 | Nocardioides litoris sp. nov., isolated from the Taean seashore. | Lee DW, Lee AH, Lee H, Kim JJ, Khim JS, Yim UH, Kim BS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001954 | 2017 | Actinomycetales/*classification/genetics/isolation & purification, Ammotherapy, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 32375979 | Nocardioides dongxiaopingii sp. nov., isolated from leaves of Lamiophlomis rotata on the Qinghai-Tibet Plateau. | Zhang S, Wang X, Yang J, Lu S, Lai XH, Jin D, Huang Y, Zhu W, Li J, Pu J, Huang Y, Tian Z, Dong K, Zhang G, Lei W, Wang S, Xu J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004161 | 2020 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lamiaceae/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
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 | |
| 21695 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23986 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23986) | |
| 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 | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 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 | |
| 89016 | 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-ID399824.1 |