Strain identifier

BacDive ID: 17858

Type strain: Yes

Species: Kordiimonas gwangyangensis

Strain Designation: GW14-5

Strain history: CIP <- 2005, JCM <- 2004, K.K. Kwon and S.J. Kim, Marine Biotechnol. Res. Cent., Ansan, Korea: strain GW14-5

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8014

BacDive-ID: 17858

DSM-Number: 19435

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

description: Kordiimonas gwangyangensis GW14-5 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediments of Gwangyang Bay of the South Sea.

NCBI tax id

NCBI tax idMatching level
288022species
1122137strain

strain history

@refhistory
8014<- JCM/RIKEN <- K. K. Kwon and S.-J. Kim, Korea Ocean Res. and Development Inst., Ansan; GW14-5
67770K. K. Kwon and S.-J. Kim GW14-5.
119755CIP <- 2005, JCM <- 2004, K.K. Kwon and S.J. Kim, Marine Biotechnol. Res. Cent., Ansan, Korea: strain GW14-5

doi: 10.13145/bacdive17858.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Kordiimonadales
  • family: Temperatibacteraceae
  • genus: Kordiimonas
  • species: Kordiimonas gwangyangensis
  • full scientific name: Kordiimonas gwangyangensis Kwon et al. 2005

@ref: 8014

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Kordiimonadales

family: Temperatibacteraceae

genus: Kordiimonas

species: Kordiimonas gwangyangensis

full scientific name: Kordiimonas gwangyangensis Kwon et al. 2005 emend. Yang et al. 2013

strain designation: GW14-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31494negative1.35 µm0.25 µmrod-shapedyes
69480yes90.405
69480negative99.987

pigmentation

  • @ref: 31494
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8014BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
36070Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119755CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
8014positivegrowth35mesophilic
31494positivegrowth17-44
31494positiveoptimum38.5mesophilic
36070positivegrowth37mesophilic
67770positivegrowth35mesophilic

culture pH

@refabilitytypepHPH range
31494positivegrowth6.0-8.5alkaliphile
31494positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31494
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
31494NaClpositivegrowth0.5-4 %
31494NaClpositiveoptimum2 %

observation

@refobservation
31494aggregates in clumps
67770quinones: MK-5, Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31494370543-hydroxybutyrate+carbon source
3149440585alpha-cyclodextrin+carbon source
3149435391aspartate+carbon source
3149417057cellobiose+carbon source
3149423652dextrin+carbon source
3149417234glucose+carbon source
3149429987glutamate+carbon source
3149415428glycine+carbon source
3149417306maltose+carbon source
3149451850methyl pyruvate+carbon source
31494506227N-acetylglucosamine+carbon source
3149417148putrescine+carbon source
3149426986threonine+carbon source
3149427082trehalose+carbon source
3149453423tween 40+carbon source
3149453426tween 80+carbon source

enzymes

@refvalueactivityec
31494catalase+1.11.1.6
31494cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
8014sediments of Gwangyang Bay of the South SeaRepublic of KoreaKORAsia
67770Sediment of Gwangyang BayRepublic of KoreaKORAsia
119755Environment, Estuarine sedimentRepublic of KoreaKORAsiaGwangyang bay

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4222.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16030;96_1039;97_2568;98_3182;99_4222&stattab=map
  • Last taxonomy: Kordiimonas gwangyangensis subclade
  • 16S sequence: AY682384
  • Sequence Identity:
  • Total samples: 115
  • soil counts: 3
  • aquatic counts: 90
  • animal counts: 20
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80141Risk group (German classification)
1197551Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8014
  • description: Kordiimonas gwangyangensis strain GW14-5 16S ribosomal RNA gene, partial sequence
  • accession: AY682384
  • length: 1448
  • database: ena
  • NCBI tax ID: 1122137

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kordiimonas gwangyangensis DSM 194351122137.3wgspatric1122137
66792Kordiimonas gwangyangensis JCM 128641236957.3wgspatric1122137
66792Kordiimonas gwangyangensis DSM 194352517093004draftimg1122137
66792Kordiimonas gwangyangensis JCM 128642585427871draftimg1122137
67770Kordiimonas gwangyangensis DSM 19435 = JCM 12864GCA_000375545contigncbi1122137
67770Kordiimonas gwangyangensis DSM 19435 = JCM 12864GCA_000616065contigncbi1122137

GC content

@refGC-contentmethod
801458.0high performance liquid chromatography (HPLC)
801439.3high performance liquid chromatography (HPLC)
3149439.3
6777055.3-55.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.836yes
flagellatedyes59.725no
gram-positiveno98.717yes
anaerobicno99.174yes
halophileno66.343no
spore-formingno93.938no
thermophileno98.791no
glucose-utilyes88.786yes
aerobicyes89.345yes
glucose-fermentno89.778no

External links

@ref: 8014

culture collection no.: DSM 19435, CIP 109032, JCM 12864, KCCM 42021

straininfo link

  • @ref: 86849
  • straininfo: 265605

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166706Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the 'Alphaproteobacteria'.Kwon KK, Lee HS, Yang SH, Kim SJInt J Syst Evol Microbiol10.1099/ijs.0.63684-02005Alphaproteobacteria/chemistry/*classification/genetics/isolation & purification, Benzopyrenes/*metabolism, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, Pyrenes/*metabolism, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAMetabolism
Phylogeny19187209Novel marine carbazole-degrading bacteria.Maeda R, Nagashima H, Widada J, Iwata K, Omori TFEMS Microbiol Lett10.1111/j.1574-6968.2009.01497.x2009Bacteria/*classification/isolation & purification/*metabolism, Bacterial Proteins/genetics, Biotransformation, Blotting, Southern, Carbazoles/*metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Japan, Molecular Sequence Data, Oxidoreductases/genetics, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, ortho-Aminobenzoates/metabolismMetabolism
Phylogeny22307506Kordiimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat.Math RK, Jeong SH, Jin HM, Park MS, Kim JM, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.038943-02012Alphaproteobacteria/*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
Phylogeny22427451Description of Kordiimonas aquimaris sp. nov., isolated from seawater, and emended descriptions of the genus Kordiimonas Kwon et al. 2005 emend. Xu et al. 2011 and of its existing species.Yang SH, Kim MR, Seo HS, Lee SH, Lee JH, Kim SJ, Kwon KKInt J Syst Evol Microbiol10.1099/ijs.0.038893-02012Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Glycolipids/analysis, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny23002050Eilatimonas milleporae gen. nov., sp. nov., a marine bacterium isolated from the hydrocoral Millepora dichotoma.Paramasivam N, Ben-Dov E, Arotsker L, Kushmaro AInt J Syst Evol Microbiol10.1099/ijs.0.043976-02012Alphaproteobacteria/*classification/genetics/isolation & purification, Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Indian Ocean, Israel, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Phylogeny25577204Emcibacter nanhaiensis gen. nov. sp. nov., isolated from sediment of the South China Sea.Liu X, Li G, Lai Q, Sun F, Du Y, Shao ZAntonie Van Leeuwenhoek10.1007/s10482-015-0381-y2015Aerobiosis, Alphaproteobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Glycolipids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Oceans and Seas, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny26936256Kordiimonas sediminis sp. nov., isolated from a sea cucumber culture pond.Zhang HX, Zhao JX, Chen GJ, Du ZJAntonie Van Leeuwenhoek10.1007/s10482-016-0671-z2016Alphaproteobacteria/*classification/genetics/growth & development/*isolation & purification, Animals, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Genotype, Geologic Sediments/microbiology, Phenotype, Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Sea Cucumbers/*microbiology, Seawater/*microbiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8014Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19435)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19435
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
31494Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2779228776041
36070Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6729
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/
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
86849Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265605.1StrainInfo: A central database for resolving microbial strain identifiers
119755Curators of the CIPCollection of Institut Pasteur (CIP 109032)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109032