Strain identifier
BacDive ID: 7454
Type strain:
Species: Microbacterium radiodurans
Strain history: <- NRRL; NRRL B-24799
NCBI tax ID(s): 661398 (species)
General
@ref: 18049
BacDive-ID: 7454
DSM-Number: 25564
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped
description: Microbacterium radiodurans DSM 25564 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from upper sand layers.
NCBI tax id
- NCBI tax id: 661398
- Matching level: species
strain history
- @ref: 18049
- history: <- NRRL; NRRL B-24799
doi: 10.13145/bacdive7454.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Microbacterium
- species: Microbacterium radiodurans
- full scientific name: Microbacterium radiodurans Zhang et al. 2010
@ref: 18049
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Microbacterium
species: Microbacterium radiodurans
full scientific name: Microbacterium radiodurans Zhang et al. 2010
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29631 | positive | 0.5-0.8 µm | 0.4-0.6 µm | rod-shaped | yes | |
69480 | no | 90.437 | ||||
69480 | positive | 100 |
pigmentation
- @ref: 29631
- production: yes
Culture and growth conditions
culture medium
- @ref: 18049
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
18049 | positive | growth | 28 | mesophilic |
29631 | positive | growth | 18-30 | |
29631 | positive | optimum | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29631 | positive | growth | 06-10 | alkaliphile |
29631 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29631
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.99 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29631 | NaCl | positive | growth | 0-7 % |
29631 | NaCl | positive | optimum | 0-7 % |
observation
- @ref: 29631
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29631 | 17057 | cellobiose | + | carbon source |
29631 | 28757 | fructose | + | carbon source |
29631 | 17234 | glucose | + | carbon source |
29631 | 25115 | malate | + | carbon source |
29631 | 17306 | maltose | + | carbon source |
29631 | 29864 | mannitol | + | carbon source |
29631 | 37684 | mannose | + | carbon source |
29631 | 51850 | methyl pyruvate | + | carbon source |
29631 | 30911 | sorbitol | + | carbon source |
29631 | 27082 | trehalose | + | carbon source |
enzymes
- @ref: 29631
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 18049
- sample type: upper sand layers
- geographic location: Xinjiang, Gobi desert
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Sandy
Safety information
risk assessment
- @ref: 18049
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18049
- description: Microbacterium radiodurans strain GIMN 1.002 16S ribosomal RNA gene, partial sequence
- accession: GQ329713
- length: 1430
- database: ena
- NCBI tax ID: 661398
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium radiodurans DSM 25564 | GCA_008710705 | contig | ncbi | 661398 |
66792 | Microbacterium radiodurans strain DSM 25564 | 661398.3 | wgs | patric | 661398 |
GC content
@ref | GC-content |
---|---|
18049 | 67.7 |
29631 | 67.74 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | yes | 93.156 | yes |
anaerobic | no | 99.54 | yes |
halophile | no | 84.906 | no |
spore-forming | no | 94.406 | no |
glucose-util | yes | 85.393 | yes |
thermophile | no | 99.356 | yes |
flagellated | no | 97.496 | no |
motile | no | 89.28 | yes |
aerobic | yes | 91.496 | no |
glucose-ferment | no | 85.04 | no |
External links
@ref: 18049
culture collection no.: DSM 25564, CCTCC M208212, NRRL B-24799, GIMN 1.002
straininfo link
- @ref: 76901
- straininfo: 405960
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20061506 | Microbacterium radiodurans sp. nov., a UV radiation-resistant bacterium isolated from soil. | Zhang W, Zhu HH, Yuan M, Yao Q, Tang R, Lin M, Yang SZ, Li ZK, Chen M | Int J Syst Evol Microbiol | 10.1099/ijs.0.017400-0 | 2010 | Actinomycetales/*classification/genetics/*isolation & purification/radiation effects, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Ultraviolet Rays | Genetics |
Phylogeny | 33502309 | Microbacterium caowuchunii sp. nov. and Microbacterium lushaniae sp. nov., isolated from plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau of PR China. | Tian Z, Yang J, Lai XH, Pu J, Jin D, Luo X, Huang Y, Li J, Zhang G, Wang S, Xu J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004662 | 2021 | Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Contents/microbiology, Lagomorpha/*microbiology, Microbacterium/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
18049 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25564) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25564 | |||
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 | |||
29631 | 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 | 26021 | 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) | |||
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 | |||
76901 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405960.1 | StrainInfo: A central database for resolving microbial strain identifiers |