Strain identifier

BacDive ID: 5682

Type strain: Yes

Species: Chryseobacterium wanjuense

Strain Designation: R2A 10-2

Strain history: CIP <- 2010, DSMZ <- S.W. Kwon, Nat. Inst. Agricul. Sci. Technol., Suwon, Korea: strain R2A 10-2 <- H.Y. Weon, KACC

NCBI tax ID(s): 356305 (species)

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General

@ref: 6920

BacDive-ID: 5682

DSM-Number: 17724

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

description: Chryseobacterium wanjuense R2A 10-2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from greenhouse soil cultivated with lettuce Lactuca sativa L..

NCBI tax id

  • NCBI tax id: 356305
  • Matching level: species

strain history

@refhistory
6920<- S.-W. Kwon, Natl. Inst. Agricult. Sci. and Technol., Suwon, Korea; R2A 10-2 <- H.-Y. Weon, KACC
123905CIP <- 2010, DSMZ <- S.W. Kwon, Nat. Inst. Agricul. Sci. Technol., Suwon, Korea: strain R2A 10-2 <- H.Y. Weon, KACC

doi: 10.13145/bacdive5682.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Chryseobacterium
  • species: Chryseobacterium wanjuense
  • full scientific name: Chryseobacterium wanjuense Weon et al. 2006

@ref: 6920

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium wanjuense

full scientific name: Chryseobacterium wanjuense Weon et al. 2006 emend. Montero-Calasanz et al. 2013

strain designation: R2A 10-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31750negative2-3.5 µm0.7-0.8 µmrod-shapedno
69480no91.915
69480negative99.993
123905negativerod-shapedno

pigmentation

  • @ref: 31750
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6920R2A 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
39758MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
123905CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
6920positivegrowth28mesophilic
31750positivegrowth05-37
31750positiveoptimum28mesophilic
39758positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31750positivegrowth05-09alkaliphile
31750positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31750aerobe
123905obligate aerobe

spore formation

@refspore formationconfidence
31750no
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
31750NaClpositivegrowth0-2 %
31750NaClpositiveoptimum0-1 %

observation

  • @ref: 31750
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3175017234glucose+carbon source
3175028087glycogen+carbon source
3175015792malonate+carbon source
3175017306maltose+carbon source
3175037684mannose+carbon source
3175026271proline+carbon source
68371Potassium 5-ketogluconate-builds acid from
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
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-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
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
12390517632nitrate-reduction
12390516301nitrite-reduction

metabolite production

  • @ref: 123905
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31750catalase+1.11.1.6
31750gelatinase+
31750cytochrome 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
123905oxidase+
123905catalase+1.11.1.6
123905urease-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
123905-++++++++-++---+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123905----------+/-+/-+/----------+/--+/---+/----+/-------+/-----------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
6920greenhouse soil cultivated with lettuce Lactuca sativa L.Lactuca sativaWanju ProvinceRepublic of KoreaKORAsia
123905Environment, Greenhouse soil cultivated with lettuce, Lactua sativaWanjuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Greenhouse
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_76791.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_1573;98_53676;99_76791&stattab=map
  • Last taxonomy: Chryseobacterium wanjuense subclade
  • 16S sequence: DQ256729
  • Sequence Identity:
  • Total samples: 307
  • soil counts: 27
  • aquatic counts: 24
  • animal counts: 3
  • plant counts: 253

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69201Risk group (German classification)
1239051Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6920
  • description: Chryseobacterium wanjuense strain R2A10-2 16S ribosomal RNA gene, partial sequence
  • accession: DQ256729
  • length: 1462
  • database: ena
  • NCBI tax ID: 356305

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium wanjuense DSM 17724GCA_900111495contigncbi356305
66792Chryseobacterium wanjuense strain DSM 17724356305.5wgspatric356305
66792Chryseobacterium wanjuense DSM 177242684622833draftimg356305

GC content

  • @ref: 6920
  • GC-content: 37.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.183yes
anaerobicno99.603yes
halophileno95.175yes
spore-formingno96.136yes
glucose-utilyes85.842yes
motileno92.794no
flagellatedno97.033yes
thermophileno98.778no
aerobicyes90.83yes
glucose-fermentno92.774no

External links

@ref: 6920

culture collection no.: DSM 17724, KACC 11468, CIP 110181

straininfo link

  • @ref: 75164
  • straininfo: 294440

literature

  • topic: Phylogeny
  • Pubmed-ID: 16825619
  • title: Chryseobacterium wanjuense sp. nov., isolated from greenhouse soil in Korea.
  • authors: Weon HY, Kim BY, Yoo SH, Kwon SW, Cho YH, Go SJ, Stackebrandt E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64179-0
  • year: 2006
  • mesh: Aerobiosis, Bacterial Typing Techniques, Chryseobacterium/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Gentian Violet, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Temperature, Vitamin K 2/analysis/chemistry
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6920Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17724)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17724
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
31750Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2802428776041
39758Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8011
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)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
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
75164Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID294440.1StrainInfo: A central database for resolving microbial strain identifiers
123905Curators of the CIPCollection of Institut Pasteur (CIP 110181)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110181