Strain identifier

BacDive ID: 3863

Type strain: Yes

Species: Deinococcus deserti

Strain Designation: VCD115

Strain history: CIP <- 2006, DSMZ <- T. Heulin <- V. Chapon, VCD 115

NCBI tax ID(s): 310783 (species)

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General

@ref: 6732

BacDive-ID: 3863

DSM-Number: 17065

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Deinococcus deserti VCD115 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from desert soil.

NCBI tax id

  • NCBI tax id: 310783
  • Matching level: species

strain history

@refhistory
6732<- T. Heulin <- V. Chapon, VCD 115
118916CIP <- 2006, DSMZ <- T. Heulin <- V. Chapon, VCD 115

doi: 10.13145/bacdive3863.20230509.8.1

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 deserti
  • full scientific name: Deinococcus deserti de Groot et al. 2005

@ref: 6732

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus deserti

full scientific name: Deinococcus deserti de Groot et al. 2005

strain designation: VCD115

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31513negativerod-shapedno
118916positivecoccus-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6732TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
118916CIP Medium 331yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=331

culture temp

@refgrowthtypetemperaturerange
6732positivegrowth28mesophilic
31513positivegrowth23-37
31513positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
31513positivegrowth06-09alkaliphile
31513positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31513
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
31513NaClpositivegrowth<0.5 %
31513NaClpositiveoptimum0.25 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3151315740formate+carbon source
3151328757fructose+carbon source
3151328260galactose+carbon source
3151317234glucose+carbon source
3151327570histidine+carbon source
3151329864mannitol+carbon source
3151330911sorbitol+carbon source

enzymes

  • @ref: 31513
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6732desert soilSaharaTunisiaTUNAfrica
118916Environment, Gamma-irradiated mixed sand samplesSahara desertTunisiaTUNAfrica

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Soil
#Condition#Xerophilic

taxonmaps

  • @ref: 69479
  • File name: preview.99_6501.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_90;96_3075;97_3775;98_4795;99_6501&stattab=map
  • Last taxonomy: Deinococcus deserti subclade
  • 16S sequence: AY876378
  • Sequence Identity:
  • Total samples: 379
  • soil counts: 55
  • aquatic counts: 190
  • animal counts: 125
  • plant counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67321Risk group (German classification)
1189161Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6732
  • description: Deinococcus deserti strain VCD115 16S ribosomal RNA gene, partial sequence
  • accession: AY876378
  • length: 1406
  • database: ena
  • NCBI tax ID: 546414

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus deserti VCD115GCA_000020685completencbi546414
66792Deinococcus deserti VCD115546414.3completepatric546414
66792Deinococcus deserti VCD115546414.17plasmidpatric546414
66792Deinococcus deserti VCD115546414.19plasmidpatric546414
66792Deinococcus deserti VCD115546414.18plasmidpatric546414
66792Deinococcus deserti VCD115643692020completeimg546414

GC content

  • @ref: 6732
  • GC-content: 59.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.461yes
flagellatedno95.677no
gram-positiveyes79.498no
anaerobicno99.167yes
aerobicyes93.263yes
halophileno94.61yes
spore-formingno90.858no
thermophileno85.517no
glucose-utilyes90.279yes
glucose-fermentno88.621no

External links

@ref: 6732

culture collection no.: DSM 17065, CIP 109153, LMG 22923

straininfo link

  • @ref: 73373
  • straininfo: 134961

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16280508Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert.de Groot A, Chapon V, Servant P, Christen R, Saux MF, Sommer S, Heulin TInt J Syst Evol Microbiol10.1099/ijs.0.63717-02005Africa, Northern, Base Composition, DNA, Bacterial/analysis/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Deinococcus/classification/genetics/*isolation & purification/radiation effects, Desert Climate, Fatty Acids/analysis, *Gamma Rays, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Radiation Tolerance, TemperatureEnzymology
Phylogeny17684237Deinococcus cellulosilyticus sp. nov., isolated from air.Weon HY, Kim BY, Schumann P, Son JA, Jang J, Go SJ, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.64951-02007*Air Microbiology, Base Composition, DNA, Ribosomal/genetics, Deinococcus/chemistry/*classification/genetics/*isolation & purification, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Genetics19370165Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti.de Groot A, Dulermo R, Ortet P, Blanchard L, Guerin P, Fernandez B, Vacherie B, Dossat C, Jolivet E, Siguier P, Chandler M, Barakat M, Dedieu A, Barbe V, Heulin T, Sommer S, Achouak W, Armengaud JPLoS Genet10.1371/journal.pgen.10004342009Africa, Northern, Bacterial Proteins/chemistry/genetics/metabolism, Deinococcus/*chemistry/genetics/radiation effects, Desert Climate, Gamma Rays, Genome, Bacterial, *Genomics, Molecular Sequence Data, *Proteomics, Ultraviolet RaysMetabolism
Proteome23320389Major soluble proteome changes in Deinococcus deserti over the earliest stages following gamma-ray irradiation.Dedieu A, Sahinovic E, Guerin P, Blanchard L, Fochesato S, Meunier B, de Groot A, Armengaud JProteome Sci10.1186/1477-5956-11-32013
Phylogeny28108749Deinococcus malanensis sp. nov., isolated from radiation-polluted soil.Zhu J, Li SH, Tang QY, Chu M, Wang W, Salam N, Li L, Hozzein WN, Zhang ZD, Li WJArch Microbiol10.1007/s00203-016-1335-02017DNA, Bacterial/chemistry, Deinococcus/chemistry/*classification/genetics/isolation & purification, Fatty Acids/analysis, Genotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, *Soil Pollutants, RadioactiveGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6732Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17065)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17065
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
31513Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2780928776041
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)
69479João 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
73373Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134961.1StrainInfo: A central database for resolving microbial strain identifiers
118916Curators of the CIPCollection of Institut Pasteur (CIP 109153)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109153