Strain identifier

BacDive ID: 5703

Type strain: Yes

Species: Chryseobacterium soli

Strain Designation: JS6-6

Strain history: CIP <- 2010, DSMZ <- KACC <- H.Y. Weon, Nat. Inst. Agric. Sci Technol., Suwon, Korea: strain JS6-6

NCBI tax ID(s): 445961 (species)

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

@ref: 8004

BacDive-ID: 5703

DSM-Number: 19298

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

description: Chryseobacterium soli JS6-6 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil sample.

NCBI tax id

  • NCBI tax id: 445961
  • Matching level: species

strain history

@refhistory
8004<- S.-W. Kwon, KACC; JS6-6 <- H.-Y. Weon, Natl. Inst. Agricult. Sci. and Technol., Suwon, Korea
122656CIP <- 2010, DSMZ <- KACC <- H.Y. Weon, Nat. Inst. Agric. Sci Technol., Suwon, Korea: strain JS6-6

doi: 10.13145/bacdive5703.20230509.8.1

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 soli
  • full scientific name: Chryseobacterium soli Weon et al. 2008

@ref: 8004

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium soli

full scientific name: Chryseobacterium soli Weon et al. 2008 emend. Hahnke et al. 2016

strain designation: JS6-6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32310negative2.25 µm0.7 µmrod-shapedno
69480no91.63
69480negative99.99
122656negativerod-shapedno

pigmentation

  • @ref: 32310
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8004R2A 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
40045MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
122656CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
8004positivegrowth30mesophilic
32310positivegrowth05-30
32310positiveoptimum29mesophilic
40045positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32310positivegrowth05-09alkaliphile
32310positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32310aerobe
122656facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

  • @ref: 32310
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3231028087glycogen+carbon source
3231017992sucrose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12265617632nitrate-reduction
12265616301nitrite-reduction

metabolite production

  • @ref: 122656
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
32310catalase+1.11.1.6
32310cytochrome oxidase+1.9.3.1
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
122656oxidase+
122656catalase+1.11.1.6
122656urease-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
122656-++++++++-++---+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122656+/-----+/-----+/-+/-+/----------+/--+/---+/---+/-+/----+/-+/--+/-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8004soil sampleJejuRepublic of KoreaKORAsia
122656Environment, Soil sampleJeju IslandRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5979.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_3508;98_4440;99_5979&stattab=map
  • Last taxonomy: Chryseobacterium soli subclade
  • 16S sequence: EF591302
  • Sequence Identity:
  • Total samples: 887
  • soil counts: 182
  • aquatic counts: 215
  • animal counts: 396
  • plant counts: 94

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80041Risk group (German classification)
1226561Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8004
  • description: Chryseobacterium soli strain JS6-6 16S ribosomal RNA gene, partial sequence
  • accession: EF591302
  • length: 1390
  • database: ena
  • NCBI tax ID: 445961

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium soli DSM 19298GCA_000737705contigncbi445961
66792Chryseobacterium soli strain DSM 19298445961.5wgspatric445961
66792Chryseobacterium soli DSM 192982617271210draftimg445961

GC content

@refGC-contentmethod
800439.9
800436.4sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.157yes
anaerobicno99.643yes
halophileno94.565no
spore-formingno94.72no
glucose-utilyes88.973no
aerobicyes92.784yes
flagellatedno97.123no
thermophileno99.521no
motileno93.554yes
glucose-fermentno91.476no

External links

@ref: 8004

culture collection no.: DSM 19298, KACC 12502, CIP 110182

straininfo link

  • @ref: 75185
  • straininfo: 323958

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18218951Chryseobacterium soli sp. nov. and Chryseobacterium jejuense sp. nov., isolated from soil samples from Jeju, Korea.Weon HY, Kim BY, Yoo SH, Kwon SW, Stackebrandt E, Go SJInt J Syst Evol Microbiol10.1099/ijs.0.65295-02008Bacterial Typing Techniques, Base Composition, Chryseobacterium/classification/genetics/*isolation & purification/physiology, DNA, Bacterial, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19643904Chryseobacterium piscicola sp. nov., isolated from diseased salmonid fish.Ilardi P, Fernandez J, Avendano-Herrera RInt J Syst Evol Microbiol10.1099/ijs.0.007021-02009Animals, Chryseobacterium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Fish Diseases/*microbiology, Flavobacteriaceae Infections/microbiology/*veterinary, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Salmonidae/microbiologyMetabolism
Phylogeny20656821Chryseobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a Rhus vernicifera-cultivated field.Im WT, Yang JE, Kim SY, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.023614-02010Aerobiosis, Base Composition, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ginsenosides/*metabolism, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhus/growth & development, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, beta-Glucosidase/metabolismMetabolism
Phylogeny20889766Chryseobacterium piperi sp. nov., isolated from a freshwater creek.Strahan BL, Failor KC, Batties AM, Hayes PS, Cicconi KM, Mason CT, Newman JDInt J Syst Evol Microbiol10.1099/ijs.0.027805-02010Bacterial Typing Techniques, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Molecular Sequence Data, Pennsylvania, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny34345976Chryseobacterium paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis.Zhang Z, Yang LL, Li CJ, Jiang XW, Zhi XYArch Microbiol10.1007/s00203-021-02504-22021Bacterial Typing Techniques, Base Composition, *Chryseobacterium/genetics, DNA, Bacterial/genetics, Fatty Acids, *Liliaceae, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2Transcriptome
Phylogeny35503093Chryseobacterium subflavum sp. nov., isolated from soil.Kong D, Wang Y, Li Q, Zhou Y, Jiang X, Xing Z, Wang Z, Ruan ZInt J Syst Evol Microbiol10.1099/ijsem.0.0053452022Bacterial Typing Techniques, Base Composition, *Chryseobacterium, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8004Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19298)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19298
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
32310Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2854828776041
40045Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8012
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)
68371Automatically annotated from API 50CH acid
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
75185Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323958.1StrainInfo: A central database for resolving microbial strain identifiers
122656Curators of the CIPCollection of Institut Pasteur (CIP 110182)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110182