Strain identifier

BacDive ID: 3888

Type strain: Yes

Species: Deinococcus cellulosilyticus

Strain Designation: 5516J-15

Strain history: CIP <- 2008, DSMZ <- S. W. Kwon, KACC, Suwon, Korea: strain 5516J-15

NCBI tax ID(s): 1223518 (strain), 401558 (species)

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General

@ref: 7528

BacDive-ID: 3888

DSM-Number: 18568

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

description: Deinococcus cellulosilyticus 5516J-15 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from air sample.

NCBI tax id

NCBI tax idMatching level
1223518strain
401558species

strain history

@refhistory
7528<- Soon-Wo Kwon, strain 5516J-15
117241CIP <- 2008, DSMZ <- S. W. Kwon, KACC, Suwon, Korea: strain 5516J-15

doi: 10.13145/bacdive3888.20230509.8.1

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 cellulosilyticus
  • full scientific name: Deinococcus cellulosilyticus Weon et al. 2007

@ref: 7528

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus cellulosilyticus

full scientific name: Deinococcus cellulosilyticus Weon et al. 2007

strain designation: 5516J-15

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32091positive2.3 µm1.4 µmrod-shapedno
69480positive99.998
117241positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7528R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
38244MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
117241CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7528positivegrowth28mesophilic
32091positivegrowth5.0-45
32091positiveoptimum30mesophilic
38244positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32091positivegrowth4.0-9.0alkaliphile
32091positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32091
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
32091NaClpositivegrowth0.0-2.0 %
32091NaClpositiveoptimum1 %

murein

  • @ref: 7528
  • murein short key: A21.01
  • type: A3ß L-Orn-Gly2-3

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3209122599arabinose+carbon source
3209129864mannitol+carbon source
3209130911sorbitol+carbon source
3209153426tween 80+carbon source
320914853esculin+hydrolysis
3209117632nitrate+reduction
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin+builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
11724117632nitrate+reduction
11724116301nitrite-reduction

metabolite production

  • @ref: 117241
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32091catalase+1.11.1.6
32091cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
117241oxidase+
117241catalase+1.11.1.6
117241urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117241-++++++---++++-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117241+--+-+---++++-------+-++++++-++++-+++-++--------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7528air sampleSuwonRepublic of KoreaKORAsia
117241Environment, Air sampleJeju IslandRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Air

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75281Risk group (German classification)
1172411Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7528
  • description: Deinococcus cellulosilyticus strain 5516J-15 16S ribosomal RNA gene, partial sequence
  • accession: DQ883809
  • length: 1368
  • database: ena
  • NCBI tax ID: 401558

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus cellulosilyticus NBRC 106333 = KACC 11606GCA_007990775contigncbi1223518
66792Deinococcus cellulosilyticus NBRC 106333 = KACC 116061223518.3wgspatric1223518

GC content

  • @ref: 7528
  • GC-content: 61.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno83.013yes
gram-positiveyes82.537yes
anaerobicno99.221yes
aerobicyes92.464yes
halophileno93.907yes
spore-formingno87.722no
thermophileno93.763yes
glucose-utilyes87.163no
flagellatedno92.757yes
glucose-fermentno77.408no

External links

@ref: 7528

culture collection no.: DSM 18568, CIP 109796, KACC 11606

straininfo link

  • @ref: 73398
  • straininfo: 309440

literature

  • topic: Phylogeny
  • Pubmed-ID: 17684237
  • title: Deinococcus cellulosilyticus sp. nov., isolated from air.
  • authors: Weon HY, Kim BY, Schumann P, Son JA, Jang J, Go SJ, Kwon SW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64951-0
  • year: 2007
  • mesh: *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/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7528Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18568)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18568
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
32091Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2833728776041
38244Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7579
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
73398Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309440.1StrainInfo: A central database for resolving microbial strain identifiers
117241Curators of the CIPCollection of Institut Pasteur (CIP 109796)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109796