Strain identifier

BacDive ID: 5689

Type strain: Yes

Species: Chryseobacterium daeguense

Strain Designation: K105

Strain history: CIP <- 2009, KCTC <- J.H. Yoon, KRIBB

NCBI tax ID(s): 1121286 (strain), 412438 (species)

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General

@ref: 8085

BacDive-ID: 5689

DSM-Number: 19388

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

description: Chryseobacterium daeguense K105 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from wastewater of a textile dye works.

NCBI tax id

NCBI tax idMatching level
1121286strain
412438species

strain history

@refhistory
8085<- J.-H. Yoon, Korea Res. Inst. of Biosci. and Biotechnol. (KRIBB); K105 <- J.-H. Yoon et al.
379002009, KCTC
67770J.-H. Yoon K105.
67771<- JH Yoon, KRIBB
118841CIP <- 2009, KCTC <- J.H. Yoon, KRIBB

doi: 10.13145/bacdive5689.20230509.8.1

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 daeguense
  • full scientific name: Chryseobacterium daeguense Yoon et al. 2007

@ref: 8085

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium daeguense

full scientific name: Chryseobacterium daeguense Yoon et al. 2007

strain designation: K105

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32084negative0.8-5 µm0.4-0.6 µmrod-shapedno
67771rod-shapedno
67771negative
69480no92.486
69480negative99.982
118841negativerod-shapedno

pigmentation

  • @ref: 32084
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8085TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
37900MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118841CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8085positivegrowth28mesophilic
32084positivegrowth10-41
32084positiveoptimum30-37mesophilic
37900positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30-37mesophilic

culture pH

@refabilitytypepHPH range
32084positivegrowth5-9.5alkaliphile
32084positiveoptimum6.5-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32084aerobe
67771aerobe
118841obligate aerobe

spore formation

@refspore formationconfidence
32084no
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
32084NaClpositivegrowth0-2 %
32084NaClpositiveoptimum0-1 %

observation

@refobservation
67770quinones: MK-6
67771quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3208422599arabinose+carbon source
3208417057cellobiose+carbon source
3208428757fructose+carbon source
3208417234glucose+carbon source
3208417306maltose+carbon source
3208426546rhamnose+carbon source
3208427082trehalose+carbon source
3208418222xylose+carbon source
11884117632nitrate-reduction
11884116301nitrite-reduction

metabolite production

  • @ref: 118841
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
32084catalase+1.11.1.6
32084cytochrome 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
118841oxidase+
118841catalase+1.11.1.6
118841urease-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
118841-+-+-+++++++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8085wastewater of a textile dye worksDaeguRepublic of KoreaKORAsia
67770Wastewater of a textile dye works in DaeguRepublic of KoreaKORAsia
67771From wastewaterRepublic of KoreaKORAsia
118841Environment, Wastewater of a textile dye worksDaeguRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial
#Engineered#Waste#Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_7792.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_225;98_5696;99_7792&stattab=map
  • Last taxonomy: Chryseobacterium daeguense subclade
  • 16S sequence: EF076759
  • Sequence Identity:
  • Total samples: 284
  • soil counts: 33
  • aquatic counts: 61
  • animal counts: 122
  • plant counts: 68

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80851Risk group (German classification)
1188411Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8085
  • description: Chryseobacterium daeguense strain K105 16S ribosomal RNA gene, partial sequence
  • accession: EF076759
  • length: 1472
  • database: ena
  • NCBI tax ID: 412438

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium daeguense DSM 193881121286.4wgspatric1121286
66792Chryseobacterium daeguense DSM 193882523533536draftimg1121286
67770Chryseobacterium daeguense DSM 19388GCA_000430825scaffoldncbi1121286

GC content

@refGC-contentmethod
808536.8high performance liquid chromatography (HPLC)
3208436.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.094no
flagellatedno95.616no
gram-positiveno98.751yes
anaerobicno99.248yes
aerobicyes89.242no
halophileno93.866no
spore-formingno96.837yes
thermophileno99.17no
glucose-utilyes89.025yes
glucose-fermentno92.679no

External links

@ref: 8085

culture collection no.: DSM 19388, JCM 14362, KCTC 12841, CIP 110016

straininfo link

  • @ref: 75171
  • straininfo: 309442

literature

  • topic: Phylogeny
  • Pubmed-ID: 17551058
  • title: Chryseobacterium daeguense sp. nov., isolated from wastewater of a textile dye works.
  • authors: Yoon JH, Kang SJ, Oh TK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64936-0
  • year: 2007
  • mesh: Bacterial Typing Techniques, Base Composition, Chryseobacterium/chemistry/*classification/genetics/*isolation & purification, Coloring Agents, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, *Industrial Waste, Korea, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Textile Industry, Waste Disposal, Fluid, *Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8085Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19388)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19388
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
32084Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2833028776041
37900Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7827
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
75171Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309442.1StrainInfo: A central database for resolving microbial strain identifiers
118841Curators of the CIPCollection of Institut Pasteur (CIP 110016)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110016