Strain identifier
BacDive ID: 13399
Type strain: 
Species: Pseudonocardia carboxydivorans
Strain Designation: Y8
Strain history: Y. M. Kim Y8.
NCBI tax ID(s): 415010 (species)
version 8.1 (current version)
General
@ref: 16343
BacDive-ID: 13399
DSM-Number: 45349
keywords: 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped
description: Pseudonocardia carboxydivorans Y8 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 415010
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16343 | <- JCM/RIKEN <- Y. M. Kim; Y8 |
| 67770 | Y. M. Kim Y8. |
doi: 10.13145/bacdive13399.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Pseudonocardia
- species: Pseudonocardia carboxydivorans
- full scientific name: Pseudonocardia carboxydivorans Park et al. 2008
@ref: 16343
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Pseudonocardia
species: Pseudonocardia carboxydivorans
full scientific name: Pseudonocardia carboxydivorans Park et al. 2008
strain designation: Y8
type strain: yes
Morphology
cell morphology
- @ref: 32606
- gram stain: positive
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 32606
- production: yes
Culture and growth conditions
culture medium
- @ref: 16343
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16343 | positive | growth | 28 | mesophilic |
| 32606 | positive | growth | 03-37 | |
| 32606 | positive | optimum | 25 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 32606 | positive | growth | 7 |
| 32606 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32606
- oxygen tolerance: aerobe
spore formation
- @ref: 32606
- spore formation: yes
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32606 | NaCl | positive | growth | 0-4 % |
| 32606 | NaCl | positive | optimum | 0-4 % |
observation
| @ref | observation |
|---|---|
| 32606 | aggregates in chains |
| 67770 | quinones: MK-9 |
metabolite utilization
- @ref: 32606
- Chebi-ID: 506227
- metabolite: N-acetylglucosamine
- utilization activity: +
- kind of utilization tested: carbon source
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32606 | catalase | + | 1.11.1.6 |
| 32606 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 16343 | soil | Seoul | Republic of Korea | KOR | Asia |
| 67770 | Soil | Seoul | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_250.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_175;97_189;98_212;99_250&stattab=map
- Last taxonomy: Pseudonocardia
- 16S sequence: EF114314
- Sequence Identity:
- Total samples: 16902
- soil counts: 7999
- aquatic counts: 2199
- animal counts: 3094
- plant counts: 3610
Safety information
risk assessment
- @ref: 16343
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16343
- description: Pseudonocardia carboxydivorans strain Y8 16S ribosomal RNA gene, partial sequence
- accession: EF114314
- length: 1510
- database: ena
- NCBI tax ID: 415010
GC content
| @ref | GC-content | method |
|---|---|---|
| 16343 | 77 | |
| 67770 | 77 | high performance liquid chromatography (HPLC) |
External links
@ref: 16343
culture collection no.: DSM 45349, JCM 14827, KCCM 42678
straininfo link
- @ref: 82596
- straininfo: 399858
literature
- topic: Phylogeny
- Pubmed-ID: 18984679
- title: Pseudonocardia carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete, and an emended description of the genus Pseudonocardia.
- authors: Park SW, Park ST, Lee JE, Kim YM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65765-0
- year: 2008
- mesh: Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbon Monoxide/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16343 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45349) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45349 | |||
| 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 | |||
| 32606 | 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 | 28819 | 28776041 | |
| 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 | |||
| 82596 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399858.1 | StrainInfo: A central database for resolving microbial strain identifiers |