Strain identifier
BacDive ID: 3889
Type strain: 
Species: Deinococcus misasensis
Strain Designation: TDMA-25
Strain history: D. Asker et al. TDMA-25.
NCBI tax ID(s): 1121382 (strain), 392413 (species)
version 8.1 (current version)
General
@ref: 16284
BacDive-ID: 3889
DSM-Number: 22328
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive
description: Deinococcus misasensis TDMA-25 is a mesophilic, Gram-positive bacterium that was isolated from Fresh water.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 392413 | species |
| 1121382 | strain |
strain history
| @ref | history |
|---|---|
| 16284 | <- CCUG <- D. Asker and K. Ueda, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; TDMA-25 |
| 67770 | D. Asker et al. TDMA-25. |
doi: 10.13145/bacdive3889.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/deinococcota
- domain: Bacteria
- phylum: Deinococcota
- class: Deinococci
- order: Deinococcales
- family: Deinococcaceae
- genus: Deinococcus
- species: Deinococcus misasensis
- full scientific name: Deinococcus misasensis Asker et al. 2008
@ref: 16284
domain: Bacteria
phylum: Deinococcus-Thermus
class: Deinococci
order: Deinococcales
family: Deinococcaceae
genus: Deinococcus
species: Deinococcus misasensis
full scientific name: Deinococcus misasensis Asker et al. 2008
strain designation: TDMA-25
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 99.72
Culture and growth conditions
culture medium
- @ref: 16284
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: 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 |
|---|---|---|---|---|
| 16284 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 40 | thermophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 99 |
| 69480 | no | 98.488 |
observation
- @ref: 67770
- observation: quinones: MK-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 16284 | Fresh water | Tottori, Misasa, a radioactive site in Japan | Japan | JPN | Asia |
| 67770 | Freshwater sample collected at Misasa | Tottori Pref. | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Freshwater
taxonmaps
- @ref: 69479
- File name: preview.99_7574.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_653;96_3530;97_4335;98_5549;99_7574&stattab=map
- Last taxonomy: Deinococcus
- 16S sequence: AB264135
- Sequence Identity:
- Total samples: 226
- soil counts: 8
- aquatic counts: 176
- animal counts: 42
Safety information
risk assessment
- @ref: 16284
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16284
- description: Deinococcus misasensis gene for 16S rRNA, partial sequence
- accession: AB264135
- length: 1403
- database: ena
- NCBI tax ID: 1121382
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Deinococcus misasensis DSM 22328 | 1121382.3 | wgs | patric | 1121382 |
| 66792 | Deinococcus misasensis DSM 22328 | 2571042005 | draft | img | 1121382 |
| 67770 | Deinococcus misasensis DSM 22328 | GCA_000745915 | scaffold | ncbi | 1121382 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16284 | 53.5 | |
| 67770 | 53.3-53.7 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| motile | no | 84.917 | no |
| flagellated | no | 91.383 | no |
| gram-positive | yes | 71.851 | no |
| anaerobic | no | 98.761 | no |
| aerobic | yes | 91.133 | no |
| halophile | no | 94.594 | no |
| spore-forming | no | 89.322 | no |
| thermophile | no | 89.297 | no |
| glucose-util | yes | 89.514 | no |
| glucose-ferment | no | 79.198 | no |
External links
@ref: 16284
culture collection no.: DSM 22328, CCUG 53610, JCM 14369, NBRC 102116
straininfo link
- @ref: 73399
- straininfo: 402024
literature
- topic: Phylogeny
- Pubmed-ID: 18096345
- title: Deinococcus misasensis and Deinococcus roseus, novel members of the genus Deinococcus, isolated from a radioactive site in Japan.
- authors: Asker D, Awad TS, Beppu T, Ueda K
- journal: Syst Appl Microbiol
- DOI: 10.1016/j.syapm.2007.10.002
- year: 2007
- mesh: Aerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deinococcus/*classification/genetics/*isolation & purification/radiation effects, Fatty Acids/analysis, Gamma Rays, Genes, rRNA, Japan, Molecular Sequence Data, Oxidoreductases/metabolism, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Ultraviolet Rays, *Water Microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 16284 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22328) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22328 | |
| 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 | |
| 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 | |
| 73399 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402024.1 | StrainInfo: A central database for resolving microbial strain identifiers |