Strain identifier

BacDive ID: 3779

Type strain: Yes

Species: Dyadobacter koreensis

Strain Designation: WPCB 159

Strain history: <- KS Baik, MicroID, Co. Ltd.

NCBI tax ID(s): 408657 (species)

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General

@ref: 15419

BacDive-ID: 3779

DSM-Number: 19938

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

description: Dyadobacter koreensis WPCB 159 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from fresh water.

NCBI tax id

  • NCBI tax id: 408657
  • Matching level: species

strain history

@refhistory
15419<- KCTC/KRIBB <- C. N. Seong, Sunchon Natl. Univ.; WPCB 159
67771<- KS Baik, MicroID, Co. Ltd.

doi: 10.13145/bacdive3779.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Dyadobacter
  • species: Dyadobacter koreensis
  • full scientific name: Dyadobacter koreensis Baik et al. 2007

@ref: 15419

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Dyadobacter

species: Dyadobacter koreensis

full scientific name: Dyadobacter koreensis Baik et al. 2007

strain designation: WPCB 159

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32063negativerod-shapedno
67771rod-shapedno
67771negative
69480negative99.997

pigmentation

  • @ref: 32063
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15419
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15419positivegrowth25mesophilic
32063positivegrowth04-30
32063positiveoptimum25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
32063positivegrowth05-11alkaliphile
32063positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32063aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.788

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3206322599arabinose+carbon source
3206328757fructose+carbon source
3206328260galactose+carbon source
3206317234glucose+carbon source
3206337684mannose+carbon source
3206328053melibiose+carbon source
3206317814salicin+carbon source
3206318222xylose+carbon source

enzymes

@refvalueactivityec
32063catalase+1.11.1.6
32063cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15419fresh waterWoopo wetlandRepublic of KoreaKORAsia
67771From freshwaterWoopo wetlandRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_77166.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_496;96_5222;97_6305;98_53937;99_77166&stattab=map
  • Last taxonomy: Dyadobacter koreensis subclade
  • 16S sequence: AB681383
  • Sequence Identity:
  • Total samples: 13
  • soil counts: 4
  • aquatic counts: 3
  • animal counts: 3
  • plant counts: 3

Safety information

risk assessment

  • @ref: 15419
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Dyadobacter koreensis gene for 16S rRNA, partial sequence, strain: NBRC 101116AB6813831433ena408657
15419Dyadobacter koreensis strain KCTC 12537 16S ribosomal RNA gene, partial sequenceEF0176601412ena408657

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyadobacter koreensis DSM 19938GCA_900108855scaffoldncbi408657
66792Dyadobacter koreensis strain DSM 19938408657.4wgspatric408657
66792Dyadobacter koreensis DSM 199382622736476draftimg408657

GC content

@refGC-content
3206344
6777144.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
glucose-fermentno85.99no
motileno93.117yes
flagellatedno97.479yes
gram-positiveno98.279yes
anaerobicno99.32yes
aerobicyes90.717yes
halophileno95.654no
spore-formingno93.793no
thermophileno99.667no
glucose-utilyes87.425no

External links

@ref: 15419

culture collection no.: DSM 19938, KCTC 12537, NBRC 101116

straininfo link

  • @ref: 73291
  • straininfo: 406258

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17551034Dyadobacter koreensis sp. nov., isolated from fresh water.Baik KS, Kim MS, Kim EM, Kim HR, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.64902-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/analysis, Cytophagaceae/*classification/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidEnzymology
Phylogeny19717578Dyadobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil.Zhang DC, Liu HC, Xin YH, Zhou YG, Schinner F, Margesin RInt J Syst Evol Microbiol10.1099/ijs.0.017236-02009Base Composition, Base Sequence, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny36006481Dyadobacter diqingensis sp. nov., isolated from Baima snow mountain of Diqing Tibetan Autonomous Prefecture in Yunnan province, south-west China.Ran L, Peng M, Wang WQ, Feng YZ, Wang J, Wang Y, Li CY, Liu XX, Chunyu WX, Tang SKArch Microbiol10.1007/s00203-022-03192-22022Bacterial Typing Techniques, China, Cytophagaceae, DNA, Bacterial/genetics, *Fatty Acids/analysis, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Snow, TibetTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
15419Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19938)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19938
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
32063Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128310
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
73291Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406258.1StrainInfo: A central database for resolving microbial strain identifiers