Strain identifier

BacDive ID: 133675

Type strain: Yes

Species: Kangiella geojedonensis

Strain Designation: YCS-5

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 914150 (species)

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General

@ref: 30094

BacDive-ID: 133675

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

description: Kangiella geojedonensis YCS-5 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 914150
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- JH Yoon, KRIBB

doi: 10.13145/bacdive133675.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Kangiellaceae
  • genus: Kangiella
  • species: Kangiella geojedonensis
  • full scientific name: Kangiella geojedonensis Yoon et al. 2012

@ref: 30094

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Kangiellaceae

genus: Kangiella

species: Kangiella geojedonensis

strain designation: YCS-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30094negative0.8-6.5 µm0.2-0.4 µmrod-shapedno
67771negative
69480negative99.988

colony morphology

  • @ref: 62342
  • incubation period: 1 day

pigmentation

  • @ref: 30094
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30094positivegrowth10-40
30094positiveoptimum30mesophilic
62342positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

  • @ref: 30094
  • ability: positive
  • type: optimum
  • pH: 7-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30094aerobe
62342aerobe
67771aerobe

spore formation

@refspore formationconfidence
30094no
69481no100
69480no100

halophily

@refsaltgrowthtested relationconcentration
30094NaClpositivegrowth0.5-16 %
30094NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3009453424tween 20+carbon source
3009453423tween 40+carbon source
3009453425tween 60+carbon source
3009453426tween 80+carbon source

enzymes

@refvalueactivityec
30094acid phosphatase+3.1.3.2
30094alkaline phosphatase+3.1.3.1
30094catalase+1.11.1.6
30094gelatinase+
30094cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinent
30094seawater
62342Seawater2009GeojedoRepublic of KoreaKORAsia
67771From seawaterGeoje-doRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6392.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15954;96_2042;97_3722;98_4721;99_6392&stattab=map
  • Last taxonomy: Kangiella geojedonensis
  • 16S sequence: HQ340606
  • Sequence Identity:
  • Total samples: 269
  • soil counts: 4
  • aquatic counts: 250
  • animal counts: 13
  • plant counts: 2

Sequence information

16S sequences

  • @ref: 30094
  • description: Kangiella geojedonensis strain YCS-5 16S ribosomal RNA gene, partial sequence
  • accession: HQ340606
  • length: 1461
  • database: nuccore
  • NCBI tax ID: 914150

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kangiella geojedonensis YCS-5GCA_000981765completencbi914150
66792Kangiella geojedonensis strain YCS-5914150.17completepatric914150
66792Kangiella geojedonensis KCTC 234202630968673completeimg914150

GC content

  • @ref: 30094
  • GC-content: 47

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.759no
flagellatedno92.845yes
gram-positiveno99.002no
anaerobicno99.141yes
aerobicyes82.473no
halophileno67.818no
spore-formingno95.824yes
thermophileno99.191yes
glucose-utilyes79.106no
glucose-fermentno86.52no

External links

@ref: 30094

culture collection no.: KCTC 23420, CCUG 60526

straininfo link

  • @ref: 91553
  • straininfo: 411908

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21478391Kangiella geojedonensis sp. nov., isolated from seawater.Yoon JH, Kang SJ, Lee SY, Lee JS, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.029314-02011Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Korea, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ubiquinone/analysisGenetics
Phylogeny22685109Kangiella sediminilitoris sp. nov., isolated from a tidal flat sediment.Lee SY, Park S, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.040691-02012Alcanivoraceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Genetics26044616Complete genome of Kangiella geojedonensis KCTC 23420(T), putative evidence for recent genome reduction in marine environments.Choe H, Kim S, Oh J, Nasir A, Kim BK, Kim KMMar Genomics10.1016/j.margen.2015.05.0152015Chromosome Mapping, Chromosomes, Bacterial, Gammaproteobacteria/*genetics, *Genome, Bacterial, Oceans and Seas, PhylogenyPhylogeny

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcataloguejournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
30094Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172645128776041
62342Curators of the CCUGhttps://www.ccug.se/strain?id=60526Culture Collection University of Gothenburg (CCUG) (CCUG 60526)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91553Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID411908.1