Strain identifier

BacDive ID: 1993

Type strain: Yes

Species: Chitinimonas koreensis

Strain Designation: R2A43-10, R2A 43-10

Strain history: CIP <- 2006, DSMZ <- KACC <- K.Y. Kim, Korea: strain R2A 43-10

NCBI tax ID(s): 1121278 (strain), 356302 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 6922

BacDive-ID: 1993

DSM-Number: 17726

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, motile, colony-forming

description: Chitinimonas koreensis R2A43-10 is a microaerophile, mesophilic, Gram-negative bacterium that forms irregular colonies and was isolated from greenhouse soil cultivated with cucumber.

NCBI tax id

NCBI tax idMatching level
356302species
1121278strain

strain history

@refhistory
6922<- S.-W. Kwon, KACC Korea <- K.-Y. Kim; R2A 43-10
120473CIP <- 2006, DSMZ <- KACC <- K.Y. Kim, Korea: strain R2A 43-10

doi: 10.13145/bacdive1993.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Chitinimonas
  • species: Chitinimonas koreensis
  • full scientific name: Chitinimonas koreensis Kim et al. 2006

@ref: 6922

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Chitinimonas

species: Chitinimonas koreensis

full scientific name: Chitinimonas koreensis Kim et al. 2006

strain designation: R2A43-10, R2A 43-10

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
23159negativeyes
69480yes96.01
69480negative99.999
120473negativeyesrod-shaped

colony morphology

  • @ref: 23159
  • colony shape: irregular

pigmentation

  • @ref: 23159
  • production: no
  • name: no pigments

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6922R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
36999MEDIUM 372 - for AquabacteriumyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.050 g);Agar (15.000 g);Glucose (0.500 g);Yeast extract (0.500 g);Pyruvic acid (0.300g);Tween 80 (1.000 ml);Casamino acids (0.500 g);Proteose Peptone N°3 (0.500 g);Di Potassium mon
120473CIP Medium 372yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=372

culture temp

@refgrowthtypetemperaturerange
6922positivegrowth28mesophilic
23159positivegrowth10-40
36999positivegrowth30mesophilic

culture pH

  • @ref: 23159
  • ability: positive
  • type: growth
  • pH: 5.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 120473
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.991

halophily

  • @ref: 23159
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23159168082-dehydro-D-gluconate-assimilation
23159167244-hydroxybutyrate-assimilation
2315917128adipate-assimilation
2315927689decanoate-assimilation
2315916899D-mannitol-assimilation
2315916988D-ribose-assimilation
2315917924D-sorbitol-assimilation
2315917268myo-inositol-assimilation
2315917240itaconate-assimilation
2315916977L-alanine-assimilation
2315930849L-arabinose-assimilation
2315962345L-rhamnose-assimilation
2315924996lactate-assimilation
2315915792malonate-assimilation
23159506227N-acetylglucosamine-assimilation
2315918401phenylacetate-assimilation
2315932032potassium gluconate-assimilation
2315932954sodium acetate-assimilation
2315953258sodium citrate-assimilation
231599300suberic acid-assimilation
2315927897tryptophan-energy source
2315917234glucose-fermentation
2315985146carboxymethylcellulose-hydrolysis
2315916991dna-hydrolysis
2315916199urea-hydrolysis
23159370543-hydroxybutyrate+assimilation
2315917634D-glucose+assimilation
2315917306maltose+assimilation
2315916024D-mannose+assimilation
2315928087glycogen+assimilation
2315915971L-histidine+assimilation
2315917203L-proline+assimilation
2315917115L-serine+assimilation
2315925115malate+assimilation
2315917992sucrose+assimilation
2315931011valerate+assimilation
23159casein+hydrolysis
2315917029chitin+hydrolysis
231595291gelatin+hydrolysis
2315928017starch+hydrolysis
2315918186tyrosine+hydrolysis
2315917632nitrate+reduction
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12047317632nitrate-reduction
12047316301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2315935581indoleno
6836935581indoleno
12047335581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
2315935581indole-
6836935581indole-

enzymes

@refvalueactivityec
23159acid phosphatase+3.1.3.2
23159alkaline phosphatase+3.1.3.1
23159alpha-chymotrypsin-3.4.21.1
23159alpha-fucosidase-3.2.1.51
23159alpha-galactosidase+3.2.1.22
23159alpha-glucosidase-3.2.1.20
23159alpha-mannosidase-3.2.1.24
23159arginine dihydrolase-3.5.3.6
23159beta-galactosidase3.2.1.23
23159beta-glucosidase-3.2.1.21
23159beta-glucuronidase-3.2.1.31
23159catalase+1.11.1.6
23159cystine arylamidase-3.4.11.3
23159cytochrome oxidase+1.9.3.1
23159esterase (C 4)+
23159esterase lipase (C 8)+
23159leucine arylamidase+3.4.11.1
23159lipase (C 14)-
23159N-acetyl-beta-glucosaminidase-3.2.1.52
23159naphthol-AS-BI-phosphohydrolase+
23159trypsin-3.4.21.4
23159tryptophan deaminase-4.1.99.1
23159urease-3.5.1.5
23159valine arylamidase-
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
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120473oxidase+/-
120473gelatinase+
120473catalase+1.11.1.6
120473urease-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
120473-+++++++--++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6922+----+/-+++----+---+--+
6922+-----+-+----+---+--+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
6922greenhouse soil cultivated with cucumberRepublic of KoreaKORAsia
23159Sangju Province
120473Environment, Greenhouse soil cultivated with cucumberRepublic of KoreaKORAsiaSangju Province

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Greenhouse
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6728.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16429;96_3181;97_3899;98_4957;99_6728&stattab=map
  • Last taxonomy: Chitinimonas koreensis subclade
  • 16S sequence: DQ256728
  • Sequence Identity:
  • Total samples: 2386
  • soil counts: 370
  • aquatic counts: 395
  • animal counts: 1310
  • plant counts: 311

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69221Risk group (German classification)
1204731Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6922
  • description: Chitinimonas koreensis strain R2A43-10 16S ribosomal RNA gene, partial sequence
  • accession: DQ256728
  • length: 1494
  • database: ena
  • NCBI tax ID: 356302

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chitinimonas koreensis DSM 17726GCA_000428465scaffoldncbi1121278
66792Chitinimonas koreensis DSM 177261121278.3wgspatric1121278
66792Chitinimonas koreensis DSM 177262524614556draftimg1121278
66792Chitinimonas koreensis R2A43-10GCA_014353015completencbi356302

GC content

  • @ref: 23159
  • GC-content: 65.0
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes73.741no
gram-positiveno98.93yes
anaerobicno98.888no
aerobicyes77.465no
halophileno97.807yes
spore-formingno94.623no
thermophileno99.436no
glucose-utilyes88.617yes
motileyes88.804yes
glucose-fermentno90.052yes

External links

@ref: 6922

culture collection no.: DSM 17726, KACC 11467, CIP 109380

straininfo link

  • @ref: 71640
  • straininfo: 297145

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16902004Chitinimonas koreensis sp. nov., isolated from greenhouse soil in Korea.Kim BY, Weon HY, Yoo SH, Chen WM, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64163-02006Base Composition, Betaproteobacteria/chemistry/*classification/isolation & purification/physiology, Culture Media, DNA, Bacterial/chemistry, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, TemperatureCultivation
Phylogeny24907265Chitinimonas prasina sp. nov., isolated from lake water.Li Y, Zhu H, Lai Q, Lei X, Chen Z, Zhang H, Tian Y, Zheng W, Zheng TInt J Syst Evol Microbiol10.1099/ijs.0.061234-02014Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny28434214Chitinimonas naiadis sp. nov., Isolated from a Freshwater River.Padakandla SR, Chae JCJ Microbiol Biotechnol10.4014/jmb.1703.030752017Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/*genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Genome, Bacterial, Phosphatidylethanolamines/analysis, Phylogeny, RNA, Ribosomal, 16S, Republic of Korea, Rivers/*microbiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6922Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17726)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17726
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
23159Byung-Yong Kim, Hang-Yeon Weon, Seung-Hee Yoo, Wen-Ming Chen, Soon-Wo Kwon, Seung-Joo Go, Erko Stackebrandt10.1099/ijs.0.64163-0Chitinimonas koreensis sp. nov., isolated from greenhouse soil in KoreaIJSEM 56: 1761-1764 200616902004
36999Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7115
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)
68369Automatically annotated from API 20NE
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
71640Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297145.1StrainInfo: A central database for resolving microbial strain identifiers
120473Curators of the CIPCollection of Institut Pasteur (CIP 109380)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109380