Strain identifier

BacDive ID: 5683

Type strain: Yes

Species: Chryseobacterium soldanellicola

Strain Designation: PSD1-4

Strain history: CIP <- 2006, KCTC <- S.B. Kim, Chungnam Natl. Univ.

NCBI tax ID(s): 311333 (species)

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General

@ref: 6739

BacDive-ID: 5683

DSM-Number: 17072

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

description: Chryseobacterium soldanellicola PSD1-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from roots of Calystegia soldanella growing on a coastal area.

NCBI tax id

  • NCBI tax id: 311333
  • Matching level: species

strain history

@refhistory
6739<- S. B. Kim; PSD1-4
374752006, KCTC
67771<- SB Kim, Chungnam Natl. Univ.
122653CIP <- 2006, KCTC <- S.B. Kim, Chungnam Natl. Univ.

doi: 10.13145/bacdive5683.20230509.8.1

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 soldanellicola
  • full scientific name: Chryseobacterium soldanellicola Park et al. 2006

@ref: 6739

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium soldanellicola

full scientific name: Chryseobacterium soldanellicola Park et al. 2006

strain designation: PSD1-4

type strain: yes

Morphology

cell morphology

@refgram staincell shapeconfidencemotility
31568negativerod-shaped
67771rod-shaped
67771negative
69480negative99.997
122653negativerod-shapedno

pigmentation

  • @ref: 31568
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6739R2A 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
37475MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122653CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6739positivegrowth30mesophilic
31568positivegrowth05-30
31568positiveoptimum25-30mesophilic
37475positivegrowth25mesophilic
59722positivegrowth30-37mesophilic
67771positivegrowth25-30mesophilic

culture pH

@refabilitytypepH
31568positivegrowth05-07
31568positiveoptimum5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31568aerobe
59722aerobe
67771aerobe
122653obligate aerobe

spore formation

@refspore formationconfidence
31568no
67771no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
31568NaClpositivegrowth0-4 %
31568NaClpositiveoptimum0-4 %

observation

  • @ref: 31568
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3156830089acetate+carbon source
3156816449alanine+carbon source
3156840585alpha-cyclodextrin+carbon source
3156822599arabinose+carbon source
3156822653asparagine+carbon source
3156835391aspartate+carbon source
3156823652dextrin+carbon source
3156828757fructose+carbon source
3156817234glucose+carbon source
3156829987glutamate+carbon source
3156817754glycerol+carbon source
3156817306maltose+carbon source
3156837684mannose+carbon source
3156828044phenylalanine+carbon source
3156826271proline+carbon source
3156817272propionate+carbon source
3156826546rhamnose+carbon source
3156817822serine+carbon source
3156826986threonine+carbon source
3156827082trehalose+carbon source
315684853esculin+hydrolysis
12265317632nitrate-reduction
12265316301nitrite-reduction

metabolite production

  • @ref: 122653
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
31568gelatinase+
31568cytochrome 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
122653oxidase-
122653alcohol dehydrogenase-1.1.1.1
122653catalase+1.11.1.6
122653lysine decarboxylase-4.1.1.18
122653ornithine decarboxylase-4.1.1.17
122653urease-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
122653-+++-++-++++---+++--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
6739roots of Calystegia soldanella growing on a coastal areaCalystegia soldanellaTae-anRepublic of KoreaKORAsia
59722Root of Calystegia soldanellaTaeahnRepublic of KoreaKORAsia
67771From root of `Calystegia soldanella`TaeahnRepublic of KoreaKORAsia
122653Plant, Roots of Calystegia soldanellaTaeanRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_36486.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_3508;98_5156;99_36486&stattab=map
  • Last taxonomy: Chryseobacterium soldanellicola
  • 16S sequence: AY883415
  • Sequence Identity:
  • Total samples: 30
  • soil counts: 3
  • aquatic counts: 14
  • animal counts: 11
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67391Risk group (German classification)
1226531Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Chryseobacterium soldanellicola gene for 16S rRNA, partial sequence, strain: NBRC 100864AB6812701442ena311333
6739Chryseobacterium soldanellicola strain PSD1-4 16S ribosomal RNA gene, partial sequenceAY8834151415ena311333

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium soldanellicola DSM 17072GCA_900100115contigncbi311333
66792Chryseobacterium soldanellicola strain DSM 17072311333.10wgspatric311333
66792Chryseobacterium soldanellicola DSM 170722684622906draftimg311333

GC content

  • @ref: 6739
  • GC-content: 28.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.17yes
anaerobicno99.501yes
halophileno94.025no
spore-formingno95.628no
glucose-utilyes86.977yes
motileno90.503no
flagellatedno96.021no
aerobicyes89.323yes
thermophileno99.224yes
glucose-fermentno91.214no

External links

@ref: 6739

culture collection no.: DSM 17072, KCTC 12382, NBRC 100864, CCUG 52904, CIP 109194

straininfo link

  • @ref: 75165
  • straininfo: 232858

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16449453Chryseobacterium soldanellicola sp. nov. and Chryseobacterium taeanense sp. nov., isolated from roots of sand-dune plants.Park MS, Jung SR, Lee KH, Lee MS, Do JO, Kim SB, Bae KSInt J Syst Evol Microbiol10.1099/ijs.0.63825-02006Bacterial Typing Techniques, Calystegia/growth & development/*microbiology, Chryseobacterium/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Ecosystem, Elymus/growth & development/*microbiology, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, *Soil MicrobiologyGenetics
Phylogeny18319450Chryseobacterium aquaticum sp. nov., isolated from a water reservoir.Kim KK, Lee KC, Oh HM, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.65491-02008Bacterial Typing Techniques, Chryseobacterium/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny18450690Chryseobacterium gregarium sp. nov., isolated from decaying plant material.Behrendt U, Ulrich A, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.65544-02008Bacterial Typing Techniques, Chryseobacterium/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, Poaceae/*metabolism/*microbiology, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA, 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
Phylogeny25450189Chryseobacterium polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Chryseobacterium.Chen XY, Zhao R, Chen ZL, Liu L, Li XD, Li YHAntonie Van Leeuwenhoek10.1007/s10482-014-0338-62014Bacterial Typing Techniques, Base Composition, Bryophyta/growth & development/*microbiology, Chryseobacterium/*classification/genetics/*isolation & purification, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ice Cover, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analysisGenetics
Phylogeny25878202Chryseobacterium solani sp. nov., isolated from field-grown eggplant rhizosphere soil.Du J, Ngo HTT, Won K, Kim KY, Jin FX, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.0002662015Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Solanum melongena/*microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
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/urltitlejournalpubmedID_cross_reference
6739Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17072)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17072
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
31568Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127858
37475Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6909
59722Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52904)https://www.ccug.se/strain?id=52904
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)
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
75165Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232858.1StrainInfo: A central database for resolving microbial strain identifiers
122653Curators of the CIPCollection of Institut Pasteur (CIP 109194)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109194