Strain identifier

BacDive ID: 7454

Type strain: Yes

Species: Microbacterium radiodurans

Strain history: <- NRRL; NRRL B-24799

NCBI tax ID(s): 661398 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refgram staincell lengthcell widthcell shapemotilityconfidence
29631positive0.5-0.8 µm0.4-0.6 µmrod-shapedyes
69480no90.437
69480positive100

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

@refgrowthtypetemperaturerange
18049positivegrowth28mesophilic
29631positivegrowth18-30
29631positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
29631positivegrowth06-10alkaliphile
29631positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29631
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
29631NaClpositivegrowth0-7 %
29631NaClpositiveoptimum0-7 %

observation

  • @ref: 29631
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2963117057cellobiose+carbon source
2963128757fructose+carbon source
2963117234glucose+carbon source
2963125115malate+carbon source
2963117306maltose+carbon source
2963129864mannitol+carbon source
2963137684mannose+carbon source
2963151850methyl pyruvate+carbon source
2963130911sorbitol+carbon source
2963127082trehalose+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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium radiodurans DSM 25564GCA_008710705contigncbi661398
66792Microbacterium radiodurans strain DSM 25564661398.3wgspatric661398

GC content

@refGC-content
1804967.7
2963167.74

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes93.156yes
anaerobicno99.54yes
halophileno84.906no
spore-formingno94.406no
glucose-utilyes85.393yes
thermophileno99.356yes
flagellatedno97.496no
motileno89.28yes
aerobicyes91.496no
glucose-fermentno85.04no

External links

@ref: 18049

culture collection no.: DSM 25564, CCTCC M208212, NRRL B-24799, GIMN 1.002

straininfo link

  • @ref: 76901
  • straininfo: 405960

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20061506Microbacterium 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 MInt J Syst Evol Microbiol10.1099/ijs.0.017400-02010Actinomycetales/*classification/genetics/*isolation & purification/radiation effects, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Ultraviolet RaysGenetics
Phylogeny33502309Microbacterium 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 JInt J Syst Evol Microbiol10.1099/ijsem.0.0046622021Animals, 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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18049Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25564)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25564
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29631Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2602128776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76901Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405960.1StrainInfo: A central database for resolving microbial strain identifiers