Strain identifier
BacDive ID: 11239
Type strain: 
Species: Nocardiopsis nikkonensis
Strain Designation: YU 1183-22
Strain history: <- T Tamura, NBRC, Japan <- Y Akaike & M Hayakawa, Univ. of Yamanashi
NCBI tax ID(s): 629485 (species)
version 8.1 (current version)
General
@ref: 18019
BacDive-ID: 11239
DSM-Number: 45662
keywords: 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped
description: Nocardiopsis nikkonensis YU 1183-22 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil .
NCBI tax id
- NCBI tax id: 629485
- Matching level: species
strain history
| @ref | history |
|---|---|
| 18019 | <- NBRC; NBRC 102170 <- Y. Akaike and M. Hayakawa, Univ. Yamanashi; YU 1183-22 |
| 67771 | <- T Tamura, NBRC, Japan <- Y Akaike & M Hayakawa, Univ. of Yamanashi |
doi: 10.13145/bacdive11239.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Nocardiopsidaceae
- genus: Nocardiopsis
- species: Nocardiopsis nikkonensis
- full scientific name: Nocardiopsis nikkonensis Yamamura et al. 2010
@ref: 18019
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiopsaceae
genus: Nocardiopsis
species: Nocardiopsis nikkonensis
full scientific name: Nocardiopsis nikkonensis Yamamura et al. 2010
strain designation: YU 1183-22
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility |
|---|---|---|---|
| 29612 | positive | rod-shaped | no |
| 67771 | positive |
pigmentation
- @ref: 29612
- production: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 18019 | YIM MEDIUM + 10 % NACL (DSMZ Medium 1302) | yes | https://mediadive.dsmz.de/medium/1302 | Name: YIM MEDIUM + 10 % NaCl (DSMZ Medium 1302) Composition: NaCl 100.0 g/l Agar 20.0 g/l Yeast extract 2.0 g/l CaCO3 1.0 g/l Glucose 1.0 g/l Tryptone 0.5 g/l Distilled water |
| 18019 | GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159) | yes | https://mediadive.dsmz.de/medium/1159 | Name: GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159) Composition: NaCl 100.0 g/l Agar 15.0 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 |
|---|---|---|---|---|
| 18019 | positive | growth | 28 | mesophilic |
| 29612 | positive | growth | 10-37 | |
| 29612 | positive | optimum | 30 | mesophilic |
| 67771 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29612 | positive | growth | 06-11 | alkaliphile |
| 29612 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 29612 | aerobe |
| 67771 | aerobe |
spore formation
- @ref: 29612
- spore formation: yes
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29612 | NaCl | positive | growth | 0-20 % |
| 29612 | NaCl | positive | optimum | 0-10 % |
observation
- @ref: 29612
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29612 | 22599 | arabinose | + | carbon source |
| 29612 | 28757 | fructose | + | carbon source |
| 29612 | 28260 | galactose | + | carbon source |
| 29612 | 17234 | glucose | + | carbon source |
| 29612 | 17992 | sucrose | + | carbon source |
| 29612 | 18222 | xylose | + | carbon source |
enzymes
- @ref: 29612
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 18019 | soil (compost) | Japan | JPN | Asia |
| 67771 | From soil | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Biodegradation | #Composting |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_42853.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_1154;98_31125;99_42853&stattab=map
- Last taxonomy: Nocardiopsis nikkonensis
- 16S sequence: AB491226
- Sequence Identity:
- Total samples: 98
- soil counts: 28
- aquatic counts: 11
- animal counts: 58
- plant counts: 1
Safety information
risk assessment
- @ref: 18019
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18019
- description: Nocardiopsis nikkonensis gene for 16S ribosomal RNA, partial sequence
- accession: AB491226
- length: 1488
- database: ena
- NCBI tax ID: 629485
GC content
- @ref: 18019
- GC-content: 72.3
External links
@ref: 18019
culture collection no.: DSM 45662, KCTC 19666, NBRC 102170
straininfo link
- @ref: 80474
- straininfo: 407083
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20118291 | Nocardiopsis nikkonensis sp. nov., isolated from a compost sample. | Yamamura H, Ohkubo SY, Ishida Y, Otoguro M, Tamura T, Hayakawa M | Int J Syst Evol Microbiol | 10.1099/ijs.0.016956-0 | 2010 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry | Genetics |
| Phylogeny | 27613380 | Nocardiopsis rhizosphaerae sp. nov., isolated from rhizosphere soil of Halocnermum strobilaceum (Pall.) Bieb. | Zhang YG, Lu XH, Ding YB, Zhou XK, Wang HF, Guo JW, Liu YH, Duan YQ, Li WJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001483 | 2016 | Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 18019 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45662) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45662 | |||
| 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 | |||
| 29612 | 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 | 26002 | 28776041 | |
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 80474 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407083.1 | StrainInfo: A central database for resolving microbial strain identifiers |