Strain identifier

BacDive ID: 1970

Type strain: Yes

Species: Trinickia soli

Strain Designation: GP25-8

Strain history: CIP <- 2007, DSMZ <- S.W. Kwon, KACC, Korea: strain GP25-8 <- H.Y. Weon, Nat. Inst. Agric. Sci. Technol., Suwon, Korea

NCBI tax ID(s): 380675 (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: 7448

BacDive-ID: 1970

DSM-Number: 18235

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

description: Trinickia soli GP25-8 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil cultivated with Korea ginseng.

NCBI tax id

  • NCBI tax id: 380675
  • Matching level: species

strain history

@refhistory
7448<- S.-W. Kwon; GP25-8 <- H.-Y. Weon
67770KACC 11589 <-- S.-W. Kwon GP25-8.
122667CIP <- 2007, DSMZ <- S.W. Kwon, KACC, Korea: strain GP25-8 <- H.Y. Weon, Nat. Inst. Agric. Sci. Technol., Suwon, Korea

doi: 10.13145/bacdive1970.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Trinickia
  • species: Trinickia soli
  • full scientific name: Trinickia soli (Yoo et al. 2007) Estrada-de Los Santos et al. 2018

  • synonyms

    @refsynonym
    20215Burkholderia soli
    20215Paraburkholderia soli

@ref: 7448

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Trinickia

species: Trinickia soli

full scientific name: Trinickia soli (Yoo et al. 2007) Estrada-de Los Santos et al. 2018

strain designation: GP25-8

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31835negative2.75 µm0.625 µmrod-shapedno
69480yes94.731
69480negative99.993
122667negativerod-shapedno

colony morphology

  • @ref: 60402
  • incubation period: 2 days

pigmentation

  • @ref: 31835
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7448R2A 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
41984MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
122667CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7448positivegrowth28mesophilic
31835positivegrowth10-40
31835positiveoptimum28mesophilic
41984positivegrowth30mesophilic
60402positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31835positivegrowth04-08acidophile
31835positiveoptimum06-07

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31835aerobe
60402aerobe
122667obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
31835NaClpositivegrowth0-2 %
31835NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31835370543-hydroxybutyrate+carbon source
3183516449alanine+carbon source
3183522599arabinose+carbon source
3183533984fucose+carbon source
3183517234glucose+carbon source
3183528087glycogen+carbon source
3183527570histidine+carbon source
3183517240itaconate+carbon source
3183524996lactate+carbon source
3183529864mannitol+carbon source
3183517268myo-inositol+carbon source
31835506227N-acetylglucosamine+carbon source
3183526271proline+carbon source
3183517272propionate+carbon source
3183533942ribose+carbon source
3183530911sorbitol+carbon source
12266717632nitrate+reduction
12266716301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
12266735581indoleno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
31835catalase+1.11.1.6
31835cytochrome 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
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
122667oxidase+
122667catalase+1.11.1.6
122667urease-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
122667--++-+----++--------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7448--++--------------+----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
7448soil cultivated with Korea ginsengRepublic of KoreaKORAsia
60402Soil cultivated with Korean ginsengRepublic of KoreaKORAsia
67770Soil cultivated with Korean ginseng in the Eumseong region of Korea
122667Environment, Soil cultivated with Korean ginsengRepublic of KoreaKORAsiaEumseong region

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74481Risk group (German classification)
1226671Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7448
  • description: Burkholderia soli strain GP25-8 16S ribosomal RNA gene, partial sequence
  • accession: DQ465451
  • length: 1480
  • database: ena
  • NCBI tax ID: 380675

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Trinickia soli GP25-8GCA_002879855contigncbi380675
66792Trinickia soli strain LMG 24076380675.5wgspatric380675
66792Trinickia soli GP25-82889805101draftimg380675
67770Trinickia soli LMG 24076GCA_902859815contigncbi380675

GC content

@refGC-contentmethod
744865
3183564.9
6777064.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.51yes
anaerobicno99.002yes
halophileno95.338yes
spore-formingno93.957no
glucose-utilyes92.472no
aerobicyes87.692yes
motileyes79.038yes
flagellatedno86.422yes
thermophileno98.559yes
glucose-fermentno89.947no

External links

@ref: 7448

culture collection no.: DSM 18235, CIP 109628, KACC 11589, LMG 24076, CCUG 54942, JCM 16392

straininfo link

  • @ref: 71615
  • straininfo: 297152

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17220453Burkholderia soli sp. nov., isolated from soil cultivated with Korean ginseng.Yoo SH, Kim BY, Weon HY, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64471-02007Agriculture, Bacterial Typing Techniques, Burkholderia/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny22081715Burkholderia symbiotica sp. nov., isolated from root nodules of Mimosa spp. native to north-east Brazil.Sheu SY, Chou JH, Bontemps C, Elliott GN, Gross E, James EK, Sprent JI, Young JPW, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.037408-02011Bacterial Typing Techniques, Base Composition, Brazil, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Mimosa/*microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny23226514Burkholderia dabaoshanensis sp. nov., a heavy-metal-tolerant bacteria isolated from Dabaoshan mining area soil in China.Zhu H, Guo J, Chen M, Feng G, Yao QPLoS One10.1371/journal.pone.00502252012Burkholderia/drug effects/genetics/*isolation & purification/ultrastructure, China, DNA, Bacterial/genetics, Metals, Heavy/*toxicity, Microscopy, Electron, Transmission, *Mining, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction, *Soil Microbiology, Soil Pollutants/*toxicityEnzymology
Phylogeny30511914Trinickia diaoshuihuensis sp. nov., a plant growth promoting bacterium isolated from soil.Fu Y, Yan R, Liu D, Jiang S, Cui L, Guo X, Wang X, Zhang J, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0031552018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gram-Negative Aerobic Rods and Cocci/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7448Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18235)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18235
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
31835Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2810128776041
41984Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7393
60402Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54942)https://www.ccug.se/strain?id=54942
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
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
71615Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297152.1StrainInfo: A central database for resolving microbial strain identifiers
122667Curators of the CIPCollection of Institut Pasteur (CIP 109628)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109628