Strain identifier

BacDive ID: 13565

Type strain: Yes

Species: Kaistia soli

Strain Designation: 5YN9-8

Strain history: <- S.-W. Kwon, KACC; 5YN9-8 <- H.-Y. Weon, Natl. Inst. Agricult. Sci. and Technol., Suwon, Korea

NCBI tax ID(s): 1122133 (strain), 446684 (species)

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General

@ref: 8015

BacDive-ID: 13565

DSM-Number: 19436

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

description: Kaistia soli 5YN9-8 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from peat layer .

NCBI tax id

NCBI tax idMatching level
1122133strain
446684species

strain history

  • @ref: 8015
  • history: <- S.-W. Kwon, KACC; 5YN9-8 <- H.-Y. Weon, Natl. Inst. Agricult. Sci. and Technol., Suwon, Korea

doi: 10.13145/bacdive13565.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Kaistiaceae
  • genus: Kaistia
  • species: Kaistia soli
  • full scientific name: Kaistia soli Weon et al. 2008

@ref: 8015

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Kaistiaceae

genus: Kaistia

species: Kaistia soli

full scientific name: Kaistia soli Weon et al. 2008

strain designation: 5YN9-8

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32352negative1.5 µm1.05 µmrod-shapedno
69480negative99.968

pigmentation

  • @ref: 32352
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8015
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
8015positivegrowth28mesophilic
32352positivegrowth05-40
32352positiveoptimum29mesophilic

culture pH

@refabilitytypepH
32352positivegrowth05-08
32352positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32352
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.975

halophily

  • @ref: 32352
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3235222599arabinose+carbon source
3235233984fucose+carbon source
3235217234glucose+carbon source
3235228087glycogen+carbon source
3235224996lactate+carbon source
3235225115malate+carbon source
3235217306maltose+carbon source
3235229864mannitol+carbon source
3235237684mannose+carbon source
3235228053melibiose+carbon source
32352506227N-acetylglucosamine+carbon source
3235226546rhamnose+carbon source
3235233942ribose+carbon source
3235217814salicin+carbon source
3235230911sorbitol+carbon source
3235217992sucrose+carbon source

enzymes

@refvalueactivityec
32352acid phosphatase+3.1.3.2
32352catalase+1.11.1.6
32352cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 8015
  • sample type: peat layer (wetland located about 1200 m above sea level)
  • geographic location: Yongneup (38° 12' 53'' N 128° 07' 30'' E)
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 38.2147
  • longitude: 128.125

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Wetland (Swamp)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6464.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_3060;97_3758;98_4769;99_6464&stattab=map
  • Last taxonomy: Kaistia soli
  • 16S sequence: EF592609
  • Sequence Identity:
  • Total samples: 1232
  • soil counts: 597
  • aquatic counts: 358
  • animal counts: 124
  • plant counts: 153

Safety information

risk assessment

  • @ref: 8015
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8015
  • description: Kaistia soli strain 5YN9-8 16S ribosomal RNA gene, partial sequence
  • accession: EF592609
  • length: 1391
  • database: ena
  • NCBI tax ID: 1122133

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kaistia soli DSM 19436GCA_900129325scaffoldncbi1122133
66792Kaistia soli DSM 194361122133.4wgspatric1122133
66792Kaistia soli DSM 194362582581302draftimg1122133

GC content

@refGC-content
801567.0
3235267

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.648yes
flagellatedno96.741yes
gram-positiveno96.889yes
anaerobicno99.198no
aerobicyes90.17no
halophileno92.971no
spore-formingno96.295no
thermophileno96.355no
glucose-utilyes93.464no
glucose-fermentno90.61no

External links

@ref: 8015

culture collection no.: DSM 19436, KACC 12605

straininfo link

  • @ref: 82753
  • straininfo: 403754

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18599687Kaistia soli sp. nov., isolated from a wetland in Korea.Weon HY, Lee CM, Hong SB, Kim BY, Yoo SH, Kwon SW, Go SJInt J Syst Evol Microbiol10.1099/ijs.0.65366-02008Base Composition, DNA, Bacterial/chemistry, Fatty Acids/metabolism, Korea, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/chemistry/*classification/genetics/*isolation & purification, *Soil Microbiology, Species Specificity, *WetlandsGenetics
Phylogeny19661503Kaistia terrae sp. nov., isolated from a wetland in Korea.Kim SJ, Weon HY, Kim YS, Anandham R, Yoo SH, Park IC, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.011924-02009Alphaproteobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Species Specificity, *WetlandsGenetics
Phylogeny21131499Kaistia geumhonensis sp. nov. and Kaistia dalseonensis sp. nov., two members of the class Alphaproteobacteria.Jin L, Kim KK, Baek SH, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.028894-02010Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/*isolation & purification/metabolism, Rivers/*microbiologyMetabolism
Phylogeny22247212Kaistia defluvii sp. nov., isolated from river sediment.Jin L, Kim KK, Lee HG, Ahn CY, Oh HMInt J Syst Evol Microbiol10.1099/ijs.0.038687-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizobiaceae/*classification/genetics/isolation & purification, Rivers/*microbiology, Sequence Analysis, DNA, Sewage/microbiology, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny25013230Pseudoxanthobacter liyangensis sp. nov., isolated from dichlorodiphenyltrichloroethane-contaminated soil.Liu XM, Chen K, Meng C, Zhang L, Zhu JC, Huang X, Li SP, Jiang JDInt J Syst Evol Microbiol10.1099/ijs.0.056507-02014Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DDT/*chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/chemistry, Ubiquinone/chemistryGenetics
Phylogeny29683414Pinisolibacter ravus gen. nov., sp. nov., isolated from pine forest soil and allocation of the genera Ancalomicrobium and Pinisolibacter to the family Ancalomicrobiaceae fam. nov., and emendation of the genus Ancalomicrobium Staley 1968.Dahal RH, Chaudhary DK, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0027722018Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Phospholipids/chemistry, *Phylogeny, *Pinus, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny30063201Kaistia algarum sp. nov., isolated from a freshwater green alga Paulinella chromatophora.Lee Y, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0029432018Bacterial Typing Techniques, Base Composition, Chlorophyta/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizobiaceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8015Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19436)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19436
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
32352Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2858228776041
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
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
82753Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403754.1StrainInfo: A central database for resolving microbial strain identifiers