Strain identifier
BacDive ID: 17109
Type strain: 
Species: Tsukamurella tyrosinosolvens
Strain Designation: Y2
Strain history: Y. M. Kim Y2.
NCBI tax ID(s): 57704 (species)
version 8.1 (current version)
General
@ref: 17643
BacDive-ID: 17109
DSM-Number: 45557
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive
description: Tsukamurella tyrosinosolvens Y2 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from subsurface soil from the side of a busy road at Yonsei University.
NCBI tax id
- NCBI tax id: 57704
- Matching level: species
strain history
| @ref | history |
|---|---|
| 17643 | <- JCM <- Y. M. Kim; Y2 |
| 67770 | Y. M. Kim Y2. |
doi: 10.13145/bacdive17109.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Tsukamurellaceae
- genus: Tsukamurella
- species: Tsukamurella tyrosinosolvens
- full scientific name: Tsukamurella tyrosinosolvens Yassin et al. 1997
synonyms
- @ref: 20215
- synonym: Tsukamurella carboxydivorans
@ref: 17643
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Tsukamurellaceae
genus: Tsukamurella
species: Tsukamurella tyrosinosolvens
full scientific name: Tsukamurella tyrosinosolvens Yassin et al. 1997 emend. Teng et al. 2016
strain designation: Y2
type strain: no
Morphology
cell morphology
| @ref | gram stain | motility | confidence |
|---|---|---|---|
| 29089 | positive | no | |
| 69480 | no | 93.626 | |
| 69480 | positive | 100 |
Culture and growth conditions
culture medium
- @ref: 17643
- 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 |
|---|---|---|---|---|
| 17643 | positive | growth | 28 | mesophilic |
| 29089 | positive | growth | 10-45 | |
| 29089 | positive | optimum | 30 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 29089
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 93 |
| 69480 | no | 99.976 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29089 | NaCl | positive | growth | 0-6 % |
| 29089 | NaCl | positive | optimum | 3 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29089 | 22599 | arabinose | + | carbon source |
| 29089 | 17057 | cellobiose | + | carbon source |
| 29089 | 28757 | fructose | + | carbon source |
| 29089 | 17306 | maltose | + | carbon source |
| 29089 | 29864 | mannitol | + | carbon source |
| 29089 | 33942 | ribose | + | carbon source |
| 29089 | 30911 | sorbitol | + | carbon source |
| 29089 | 16199 | urea | + | carbon source |
| 29089 | 18222 | xylose | + | carbon source |
enzymes
- @ref: 29089
- value: cytochrome oxidase
- activity: +
- ec: 1.9.3.1
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 17643 | subsurface soil (10cm depth) from the side of a busy road at Yonsei University | Seoul | Republic of Korea | KOR | Asia |
| 67770 | Subsurface soil (10 cm in depth) from the side of a busy road at Yonsei Univ. | Seoul | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_3845.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1974;97_2373;98_2929;99_3845&stattab=map
- Last taxonomy: Tsukamurella
- 16S sequence: EU521689
- Sequence Identity:
- Total samples: 12359
- soil counts: 3431
- aquatic counts: 2978
- animal counts: 5160
- plant counts: 790
Safety information
risk assessment
- @ref: 17643
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17643
- description: Tsukamurella carboxydivorans strain Y2 16S ribosomal RNA gene, partial sequence
- accession: EU521689
- length: 1512
- database: ena
- NCBI tax ID: 57704
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Tsukamurella tyrosinosolvens strain JCM 15482 | 57704.14 | wgs | patric | 57704 |
| 66792 | Tsukamurella tyrosinosolvens JCM 15482 | 2700989554 | draft | img | 57704 |
| 67770 | Tsukamurella tyrosinosolvens JCM 15482 | GCA_001575225 | contig | ncbi | 57704 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 17643 | 77 | high performance liquid chromatography (HPLC) |
| 29089 | 77 | |
| 17643 | 71.2 | sequence analysis |
| 67770 | 71 | genome sequence analysis |
| 67770 | 71.2 | genome sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 93 | no |
| gram-positive | yes | 89.579 | yes |
| anaerobic | no | 99.656 | yes |
| halophile | no | 93.618 | no |
| spore-forming | no | 78.129 | no |
| glucose-util | yes | 92.692 | no |
| motile | no | 92.615 | no |
| flagellated | no | 97.43 | yes |
| aerobic | yes | 93.134 | yes |
| thermophile | no | 99.162 | no |
| glucose-ferment | no | 90.285 | no |
External links
@ref: 17643
culture collection no.: DSM 45557, JCM 15482, KCCM 42885
straininfo link
- @ref: 86109
- straininfo: 404335
literature
- topic: Phylogeny
- Pubmed-ID: 19502350
- title: Tsukamurella carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete.
- authors: Park SW, Kim SM, Park ST, Kim YM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.005959-0
- year: 2009
- mesh: Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbon Monoxide/*metabolism, DNA, Bacterial/analysis, Fatty Acids/analysis, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17643 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45557) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45557 | |||
| 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 | |||
| 29089 | 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 | 25518 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 86109 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404335.1 | StrainInfo: A central database for resolving microbial strain identifiers |