Strain identifier

BacDive ID: 5669

Type strain: Yes

Species: Chryseobacterium taeanense

Strain Designation: PHA3-4

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

NCBI tax ID(s): 311334 (species)

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General

@ref: 6738

BacDive-ID: 5669

DSM-Number: 17071

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

description: Chryseobacterium taeanense PHA3-4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from roots of Elymus mollis growing on a coastal area.

NCBI tax id

  • NCBI tax id: 311334
  • Matching level: species

strain history

@refhistory
6738<- S. B. Kim; PHA3-4
367882006, KCTC
67771<- SB Kim, Chungnam Natl. Univ.
123408CIP <- 2006, KCTC <- S.B. Kim, Chungnam Natl. Univ.

doi: 10.13145/bacdive5669.20230509.8.1

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

@ref: 6738

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium taeanense

full scientific name: Chryseobacterium taeanense Park et al. 2006

strain designation: PHA3-4

type strain: yes

Morphology

cell morphology

@refgram staincell shapeconfidencemotility
31568negativerod-shaped
67771rod-shaped
67771negative
69480negative99.966
123408negativerod-shapedno

pigmentation

  • @ref: 31568
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6738R2A 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
36788MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123408CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6738positivegrowth30mesophilic
31568positivegrowth05-30
31568positiveoptimum25-30mesophilic
36788positivegrowth30mesophilic
59718positivegrowth30mesophilic
67771positivegrowth25-30mesophilic

culture pH

@refabilitytypepHPH range
31568positivegrowth05-09alkaliphile
31568positiveoptimum5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31568aerobe
59718aerobe
67771aerobe
123408obligate aerobe

spore formation

@refspore formationconfidence
31568no
67771no
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
31568NaClpositivegrowth0-6 %
31568NaClpositiveoptimum0-6 %

observation

  • @ref: 31568
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3156816449alanine+carbon source
3156840585alpha-cyclodextrin+carbon source
3156822599arabinose+carbon source
3156822653asparagine+carbon source
3156835391aspartate+carbon source
3156816947citrate+carbon source
3156823652dextrin+carbon source
3156815740formate+carbon source
3156828757fructose+carbon source
3156833984fucose+carbon source
3156828260galactose+carbon source
3156824265gluconate+carbon source
3156817234glucose+carbon source
3156829987glutamate+carbon source
3156824996lactate+carbon source
3156817716lactose+carbon source
3156825017leucine+carbon source
3156815792malonate+carbon source
3156817306maltose+carbon source
3156829864mannitol+carbon source
3156837684mannose+carbon source
3156818257ornithine+carbon source
3156828044phenylalanine+carbon source
3156826271proline+carbon source
3156817272propionate+carbon source
3156816634raffinose+carbon source
3156826546rhamnose+carbon source
3156817822serine+carbon source
3156830911sorbitol+carbon source
3156817992sucrose+carbon source
3156826986threonine+carbon source
3156827082trehalose+carbon source
12340817632nitrate-reduction
12340816301nitrite-reduction

metabolite production

  • @ref: 123408
  • 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
123408oxidase+
123408catalase+1.11.1.6
123408urease-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
123408-+-+-++-+-++---+++--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
6738roots of Elymus mollis growing on a coastal areaElymus mollisTae-anRepublic of KoreaKORAsia
67771From root of `Elymus mokkis`TaeahnRepublic of KoreaKORAsia
123408Environment, Roots of Elymus mokkisTaeanRepublic 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_36485.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_869;97_3271;98_26885;99_36485&stattab=map
  • Last taxonomy: Chryseobacterium taeanense subclade
  • 16S sequence: AY883416
  • Sequence Identity:
  • Total samples: 90
  • soil counts: 3
  • aquatic counts: 73
  • animal counts: 7
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67381Risk group (German classification)
1234081Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Chryseobacterium taeanense gene for 16S rRNA, partial sequence, strain: NBRC 100863AB6812691442ena311334
6738Chryseobacterium taeanense strain PHA3-4 16S ribosomal RNA gene, partial sequenceAY8834161424ena311334

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chryseobacterium taeanense DSM 17071GCA_900099685contigncbi311334
66792Chryseobacterium taeanense strain DSM 17071311334.6wgspatric311334
66792Chryseobacterium taeanense DSM 170712675903150draftimg311334

GC content

  • @ref: 6738
  • GC-content: 32.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.979yes
anaerobicno99.2yes
halophileno95.336no
spore-formingno94.56yes
glucose-utilyes86.876yes
motileno92.813no
flagellatedno95.984no
aerobicyes89.377yes
thermophileno99.401no
glucose-fermentno91.313no

External links

@ref: 6738

culture collection no.: CCUG 52900, DSM 17071, KCTC 12381, NBRC 100863, CIP 109195

straininfo link

  • @ref: 75151
  • straininfo: 138482

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
Phylogeny25273512Chryseobacterium takakiae sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides.Zhao R, Chen XY, Li XD, Chen ZL, Li YHInt J Syst Evol Microbiol10.1099/ijs.0.065888-02014Bacterial Typing Techniques, Base Composition, Bryophyta/*microbiology, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27902240Chryseobacterium lineare sp. nov., isolated from a limpid stream.Zhao Z, Tu YQ, Shen X, Han SB, Zhang CY, Sun C, Wu MInt J Syst Evol Microbiol10.1099/ijsem.0.0016292017Bacterial Typing Techniques, Base Composition, China, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny27902278Chryseobacterium endophyticum sp. nov., isolated from a maize leaf.Lin SY, Hameed A, Liu YC, Hsu YH, Hsieh YT, Lai WA, Young CCInt J Syst Evol Microbiol10.1099/ijsem.0.0016562017Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Taiwan, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6738Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17071)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17071
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
36788Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6910
59718Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52900)https://www.ccug.se/strain?id=52900
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
75151Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138482.1StrainInfo: A central database for resolving microbial strain identifiers
123408Curators of the CIPCollection of Institut Pasteur (CIP 109195)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109195