Strain identifier

BacDive ID: 5677

Type strain: Yes

Species: Chryseobacterium daecheongense

Strain Designation: CPW406

Strain history: CIP <- 2010, DSMZ <- K.K. Kim, KAIST: strain CPW406 <- H.S. Bae

NCBI tax ID(s): 192389 (species)

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General

@ref: 5774

BacDive-ID: 5677

DSM-Number: 15235

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

description: Chryseobacterium daecheongense CPW406 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from sediment in sewage.

NCBI tax id

  • NCBI tax id: 192389
  • Matching level: species

strain history

@refhistory
5774<- K. K. Kim, KAIST; CPW406 <- H.-S. Bae
67771<- KK Kim <- HS Bae
118840CIP <- 2010, DSMZ <- K.K. Kim, KAIST: strain CPW406 <- H.S. Bae

doi: 10.13145/bacdive5677.20230509.8.1

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 daecheongense
  • full scientific name: Chryseobacterium daecheongense Kim et al. 2005

@ref: 5774

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium daecheongense

full scientific name: Chryseobacterium daecheongense Kim et al. 2005 emend. Montero-Calasanz et al. 2014

strain designation: CPW406

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771rod-shapedno
67771negative
69480no90.196
69480negative99.977
118840rod-shapednonegative

colony morphology

  • @ref: 59714
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5774NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37591MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
118840CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
5774positivegrowth30mesophilic
37591positivegrowth30mesophilic
59714positivegrowth30-37mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59714aerobe
67771aerobe
118840obligate aerobe

spore formation

@refspore formationconfidence
67771no
69481no100
69480no99.998

observation

  • @ref: 67771
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
11884017632nitrate+reduction
11884016301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11884035581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
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
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
118840oxidase+
118840catalase+1.11.1.6
118840urease-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
59714-+-+-++-+-++---+-+--
118840-+-+-++-+-++---+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
59714+----++-------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5774sediment in sewageKorea, Cheongju Industrial ComplexRepublic of KoreaKORAsia
67771From sedimentRepublic of KoreaKORAsia
118840Environment, Sediment in sewageCheongju Industrial ComplexRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_26695.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_1573;98_20005;99_26695&stattab=map
  • Last taxonomy: Chryseobacterium daecheongense
  • 16S sequence: AJ457206
  • Sequence Identity:
  • Total samples: 224
  • soil counts: 64
  • aquatic counts: 26
  • animal counts: 107
  • plant counts: 27

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57741Risk group (German classification)
1188401Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5774
  • description: Chryseobacterium sp. CPW406 16S rRNA gene
  • accession: AJ457206
  • length: 1446
  • database: ena
  • NCBI tax ID: 192389

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium daecheongense DSM 15235GCA_003729955contigncbi192389
66792Chryseobacterium daecheongense DSM 15235GCA_004365465contigncbi192389
66792Chryseobacterium daecheongense strain DSM 15235192389.5wgspatric192389
66792Chryseobacterium daecheongense DSM 152352681812956draftimg192389

GC content

@refGC-content
577438.3
6777136.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.396yes
gram-positiveno98.673no
anaerobicno99.661no
aerobicyes89.37yes
halophileno97.006no
spore-formingno95.654no
glucose-utilyes80.927yes
flagellatedno95.57yes
thermophileno98.568yes
glucose-fermentno93.372yes

External links

@ref: 5774

culture collection no.: DSM 15235, CCUG 52896, KCTC 12088, NBRC 102008, CIP 110173

straininfo link

  • @ref: 75159
  • straininfo: 107090

literature

  • topic: Phylogeny
  • Pubmed-ID: 15653865
  • title: Chryseobacterium daecheongense sp. nov., isolated from freshwater lake sediment.
  • authors: Kim KK, Bae HS, Schumann P, Lee ST
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02931-0
  • year: 2005
  • mesh: Chryseobacterium/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
5774Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15235)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15235
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
37591Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8003
59714Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52896)https://www.ccug.se/strain?id=52896
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
75159Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID107090.1StrainInfo: A central database for resolving microbial strain identifiers
118840Curators of the CIPCollection of Institut Pasteur (CIP 110173)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110173