Strain identifier

BacDive ID: 23022

Type strain: Yes

Species: Chryseobacterium koreense

Strain Designation: Chj707

Strain history: CIP <- 2005, IAM <- S.T. Lee, Kaist, Korea: strain Chj707

NCBI tax ID(s): 1304281 (strain), 232216 (species)

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General

@ref: 19094

BacDive-ID: 23022

DSM-Number: 25209

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

description: Chryseobacterium koreense Chj707 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from fresh mineral water.

NCBI tax id

NCBI tax idMatching level
232216species
1304281strain

strain history

@refhistory
19094<- CCUG <- P. Kämpfer, Univ. Giessen, Germany <- S. T. Lee, KAIST
67770IAM 15050 <-- S.-T. Lee Chj707.
67771<- ST Lee, KAIST
120466CIP <- 2005, IAM <- S.T. Lee, Kaist, Korea: strain Chj707

doi: 10.13145/bacdive23022.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Chryseobacterium
  • species: Chryseobacterium koreense
  • full scientific name: Chryseobacterium koreense (Kim et al. 2004) Kämpfer et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Kaistella koreensis

@ref: 19094

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium koreense

full scientific name: Chryseobacterium koreense (Kim et al. 2004) Kämpfer et al. 2009 emend. Hahnke et al. 2016

strain designation: Chj707

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30148negativerod-shapedno
67771rod-shaped
67771negative
69480no94.471
69480negative99.948
120466negativerod-shapedno

colony morphology

  • @ref: 120466
  • hemolysis ability: 1

pigmentation

@refproductionname
30148yes
120466noFlexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19094PLATE COUNT AGAR (DSMZ Medium 464)yeshttps://mediadive.dsmz.de/medium/464Name: PLATE COUNT AGAR (DSMZ Medium 464) Composition: Agar 15.0 g/l Tryptone 5.0 g/l Yeast extract 2.5 g/l Dextrose 1.0 g/l Distilled water
34328MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120466CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120466CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
19094positivegrowth28mesophilic
30148positiveoptimum30mesophilic
34328positivegrowth30mesophilic
58656positivegrowth22-37
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic
120466positivegrowth25-37mesophilic
120466nogrowth5psychrophilic
120466nogrowth15psychrophilic
120466nogrowth41thermophilic
120466nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30148aerobe
58656obligate aerobe
67771aerobe
120466obligate aerobe

spore formation

@refspore formationconfidence
30148no
67771no
69481no100
69480no99.984

halophily

@refsaltgrowthtested relationconcentration
120466NaClpositivegrowth0-2 %
120466NaClnogrowth4 %
120466NaClnogrowth6 %
120466NaClnogrowth8 %
120466NaClnogrowth10 %

observation

@refobservation
67770quinones: MK-6
67771quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3014817632nitrate+reduction
12046616947citrate-carbon source
1204664853esculin+hydrolysis
120466606565hippurate+hydrolysis
12046617632nitrate-builds gas from
12046617632nitrate+reduction
12046616301nitrite+builds gas from
12046616301nitrite-reduction
12046615792malonate-assimilation
12046617632nitrate-respiration

antibiotic resistance

  • @ref: 120466
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
3014835581indoleyes
12046635581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
3014835581indole+
12046615688acetoin-
12046617234glucose-

enzymes

@refvalueactivityec
30148catalase+1.11.1.6
30148cytochrome oxidase+1.9.3.1
120466oxidase+
120466beta-galactosidase-3.2.1.23
120466alcohol dehydrogenase+1.1.1.1
120466gelatinase+
120466amylase+
120466DNase+
120466caseinase+3.4.21.50
120466catalase+1.11.1.6
120466tween esterase+
120466gamma-glutamyltransferase+2.3.2.2
120466lecithinase+
120466lipase-
120466lysine decarboxylase-4.1.1.18
120466ornithine decarboxylase-4.1.1.17
120466phenylalanine ammonia-lyase-4.3.1.24
120466protease+
120466tryptophan deaminase+
120466urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120466-+++-++--+++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120466-------------------------------------------------+-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
19094fresh mineral waterRepublic of KoreaKORAsia
58656Fresh mineral waterRepublic of KoreaKORAsia
67770Natural mineral water from Daejeon CityRepublic of KoreaKORAsia
67771From fresh mineral waterRepublic of KoreaKORAsia
120466Environment, Freshwater streamRepublic of KoreaKORAsiaDaejeon City

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6534.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_3096;97_3797;98_4822;99_6534&stattab=map
  • Last taxonomy: Chryseobacterium koreense subclade
  • 16S sequence: AB681907
  • Sequence Identity:
  • Total samples: 6230
  • soil counts: 1091
  • aquatic counts: 2278
  • animal counts: 2512
  • plant counts: 349

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
190941Risk group (German classification)
1204661Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Chryseobacterium koreense gene for 16S rRNA, partial sequence, strain: NBRC 103027AB6819071442ena232216
19094Kaistella koreensis strain Chj707 16S ribosomal RNA gene, partial sequenceAF3441791472ena232216

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium koreense DSM 25209GCA_014201785scaffoldncbi232216
66792Chryseobacterium koreense CCUG 49689GCA_001045435contigncbi1304281
66792Chryseobacterium koreense CCUG 496891304281.5wgspatric1304281
66792Chryseobacterium koreense strain DSM 25209232216.8wgspatric232216
66792Chryseobacterium koreense DSM 252092861269263draftimg232216
66792Chryseobacterium koreense CCUG 496892648501397draftimg1304281

GC content

@refGC-contentmethod
3014842.3
1909440.1sequence analysis
6777042.3high performance liquid chromatography (HPLC)
6777141.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.507no
gram-positiveno98.079no
anaerobicno97.724yes
halophileno96.381no
spore-formingno96.651yes
thermophileno98.872yes
glucose-utilyes85.667no
aerobicyes85.598yes
flagellatedno97.585no
glucose-fermentno89.212no

External links

@ref: 19094

culture collection no.: DSM 25209, CCUG 49689, IAM 15050, JCM 21512, KCTC 12107, NBRC 103027, CIP 108606

straininfo link

  • @ref: 87262
  • straininfo: 107101

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545478Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium-Bergeyella-Riemerella branch.Kim MK, Im WT, Shin YK, Lim JH, Kim SH, Lee BC, Park MY, Lee KY, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.02998-02004Bacterial Typing Techniques, Base Composition, Chryseobacterium/genetics, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Flavobacteriaceae/*classification/cytology/*isolation & purification/physiology, Fresh Water/*microbiology, Genes, rRNA, Gentian Violet, Korea, Molecular Sequence Data, Phenazines, Phylogeny, Pigments, Biological, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial, Water MicrobiologyEnzymology
Phylogeny19622666Description of Chryseobacterium anthropi sp. nov. to accommodate clinical isolates biochemically similar to Kaistella koreensis and Chryseobacterium haifense, proposal to reclassify Kaistella koreensis as Chryseobacterium koreense comb. nov. and emended description of the genus Chryseobacterium.Kampfer P, Vaneechoutte M, Lodders N, De Baere T, Avesani V, Janssens M, Busse HJ, Wauters GInt J Syst Evol Microbiol10.1099/ijs.0.008250-02009Bacterial Typing Techniques, Chryseobacterium/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Flavobacteriaceae/*classification/genetics/isolation & purification, Flavobacteriaceae Infections/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology
Phylogeny36201336Chryseobacterium oryzae sp. nov. and Chryseobacterium suipulveris sp. nov., isolated from Andong sikhye and pigpen dust, respectively.Heo J, Won M, Lee D, Kim JS, Han BH, Kim SJ, Hong SB, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0055322022Bacterial Typing Techniques, Base Composition, *Chryseobacterium, DNA, Bacterial/genetics, Dust, Fatty Acids/chemistry, Nucleotides, Phosphatidylethanolamines, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
19094Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25209)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25209
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
30148Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126499
34328Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6254
58656Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49689)https://www.ccug.se/strain?id=49689
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
87262Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID107101.1StrainInfo: A central database for resolving microbial strain identifiers
120466Curators of the CIPCollection of Institut Pasteur (CIP 108606)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108606