Strain identifier

BacDive ID: 396

Type strain: Yes

Species: Kangiella koreensis

Strain Designation: SW-125

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 523791 (strain), 261964 (species)

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General

@ref: 6255

BacDive-ID: 396

DSM-Number: 16069

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

description: Kangiella koreensis SW-125 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from sea water of tidal flat.

NCBI tax id

NCBI tax idMatching level
523791strain
261964species

strain history

@refhistory
6255<- J.-H. Yoon; SW-125
67770J.-H. Yoon SW-125.
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive396.20230509.8.1

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 koreensis
  • full scientific name: Kangiella koreensis Yoon et al. 2004

@ref: 6255

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Kangiellaceae

genus: Kangiella

species: Kangiella koreensis

full scientific name: Kangiella koreensis Yoon et al. 2004

strain designation: SW-125

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31263negative3 µm0.35 µmrod-shapedno
67771negative
69480negative99.997

pigmentation

  • @ref: 31263
  • production: yes

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_16069_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 6255
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6255positivegrowth30mesophilic
31263positivegrowth04-43
31263positiveoptimum33.5mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31263positivegrowth5.5-8.0
31263positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31263anaerobe
67771aerobe

spore formation

@refspore formationconfidence
31263no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
31263NaClpositivegrowth01-12 %
31263NaClpositiveoptimum2.5 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
312635291gelatin+carbon source
3126353424tween 20+carbon source
3126353423tween 40+carbon source
3126353425tween 60+carbon source
3126353426tween 80+carbon source
3126317632nitrate+reduction

enzymes

@refvalueactivityec
31263alkaline phosphatase+3.1.3.1
31263catalase+1.11.1.6
31263gelatinase+
31263cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
6255sea water of tidal flatRepublic of KoreaKORAsia
67770Tidal flat sediment collected from Daepo BeachRepublic of KoreaKORAsiaYellow Sea
67771From tidal flat sediment of the Yellow Sea in KoreaRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_4017.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15954;96_2042;97_2463;98_3045;99_4017&stattab=map
  • Last taxonomy: Kangiella koreensis
  • 16S sequence: AY520560
  • Sequence Identity:
  • Total samples: 1703
  • soil counts: 290
  • aquatic counts: 1130
  • animal counts: 230
  • plant counts: 53

Safety information

risk assessment

  • @ref: 6255
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6255Kangiella koreensis 16S ribosomal RNA gene, partial sequenceAY5205601494ena523791
67771Kangiella koreensis DSM 16069, complete genomeCP0017072852073ena523791

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kangiella koreensis DSM 16069GCA_000024085completencbi523791
66792Kangiella koreensis DSM 16069523791.5completepatric523791
66792Kangiella koreensis SW-125, DSM 16069644736377completeimg523791

GC content

@refGC-contentmethod
625544.0
3126344
6777044high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.009no
flagellatedno93.491yes
gram-positiveno98.856yes
anaerobicno99.171no
aerobicyes78.252no
halophileno76.675no
spore-formingno95.688no
thermophileno97.839yes
glucose-utilyes82.915no
glucose-fermentno85.177no

External links

@ref: 6255

culture collection no.: DSM 16069, KCTC 12182, JCM 12317

straininfo link

  • @ref: 70076
  • straininfo: 134292

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15388751Kangiella koreensis gen. nov., sp. nov. and Kangiella aquimarina sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.Yoon JH, Oh TK, Park YHInt J Syst Evol Microbiol10.1099/ijs.0.63156-02004Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Growth Inhibitors/pharmacology, Korea, Molecular Sequence Data, Movement, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic/pharmacology, Seawater/*microbiology, Sequence Analysis, DNA, Spores, Bacterial, Temperature, Ubiquinone/analysis, Water MicrobiologyEnzymology
Phylogeny20023058Kangiella japonica sp. nov., isolated from a marine environment.Romanenko LA, Tanaka N, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.017087-02009Alcanivoraceae/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyGenetics
Phylogeny20511465Kangiella spongicola sp. nov., a halophilic marine bacterium isolated from the sponge Chondrilla nucula.Ahn J, Park JW, McConnell JA, Ahn YB, Haggblom MMInt J Syst Evol Microbiol10.1099/ijs.0.021733-02010Aerobiosis, Animals, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Florida, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Genetics21304661Complete genome sequence of Kangiella koreensis type strain (SW-125).Han C, Sikorski J, Lapidus A, Nolan M, Glavina Del Rio T, Tice H, Cheng JF, Lucas S, Chen F, Copeland A, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Bruce D, Goodwin L, Pitluck S, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Brettin T, Goker M, Tindall BJ, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JCStand Genomic Sci10.4056/sigs.366352009
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6255Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16069)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16069
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
31263Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2758428776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
70076Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134292.1StrainInfo: A central database for resolving microbial strain identifiers