Strain identifier

BacDive ID: 13564

Type strain: Yes

Species: Kaistia granuli

Strain Designation: Ko04

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 1122132 (strain), 363259 (species)

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

@ref: 17223

BacDive-ID: 13564

DSM-Number: 23481

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

description: Kaistia granuli Ko04 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sludge.

NCBI tax id

NCBI tax idMatching level
1122132strain
363259species

strain history

@refhistory
17223<- KCTC; KCTC 12575 <- H.-W. Lee, KAIST
67771<- ST Lee, KAIST

doi: 10.13145/bacdive13564.20230509.8.1

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 granuli
  • full scientific name: Kaistia granuli Lee et al. 2007

@ref: 17223

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Kaistiaceae

genus: Kaistia

species: Kaistia granuli

full scientific name: Kaistia granuli Lee et al. 2007

strain designation: Ko04

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32136negative1.2 µm0.5 µmrod-shapedno
67771negative
69480negative99.977

pigmentation

  • @ref: 32136
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17223
  • 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
17223positivegrowth28mesophilic
32136positivegrowth18-30
32136positiveoptimum24psychrophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
32136positivegrowth5.0-8.0
32136positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32136aerobe
67771aerobe

spore formation

@refspore formationconfidence
32136no
69481no100
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
32136NaClpositivegrowth0-2 %
32136NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3213622599arabinose+carbon source
3213633984fucose+carbon source
3213617234glucose+carbon source
3213617306maltose+carbon source
3213629864mannitol+carbon source
3213637684mannose+carbon source
3213628053melibiose+carbon source
32136506227N-acetylglucosamine+carbon source
3213626546rhamnose+carbon source
3213633942ribose+carbon source
3213617814salicin+carbon source
3213630911sorbitol+carbon source
3213617992sucrose+carbon source
3213617632nitrate+reduction

enzymes

@refvalueactivityec
32136acid phosphatase+3.1.3.2
32136alpha-galactosidase+3.2.1.22
32136catalase+1.11.1.6
32136cytochrome oxidase+1.9.3.1
32136urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17223sludgewastewater treatment plant, GongjuRepublic of KoreaKORAsia
67771From sludgeRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7629.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_3060;97_4363;98_5583;99_7629&stattab=map
  • Last taxonomy: Kaistia
  • 16S sequence: AB244762
  • Sequence Identity:
  • Total samples: 1918
  • soil counts: 656
  • aquatic counts: 825
  • animal counts: 306
  • plant counts: 131

Safety information

risk assessment

  • @ref: 17223
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17223
  • description: Kaistia granuli gene for 16S rRNA, partial sequence
  • accession: AB244762
  • length: 1429
  • database: ena
  • NCBI tax ID: 363259

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kaistia granuli DSM 23481 Ko04GCA_000380505contigncbi1122132
66792Kaistia granuli DSM 23481 strain Ko041122132.6wgspatric1122132
66792Kaistia granuli DSM 234812521172615draftimg1122132

GC content

@refGC-contentmethod
1722367.8high performance liquid chromatography (HPLC)
3213667.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno86.569yes
flagellatedno95.39yes
gram-positiveno97.691yes
anaerobicno99.139no
halophileno91.107yes
spore-formingno96.737yes
thermophileno98.326yes
glucose-utilyes91.708yes
aerobicyes91.012no
glucose-fermentno91.263no

External links

@ref: 17223

culture collection no.: DSM 23481, KCTC 12575, LMG 23410

straininfo link

  • @ref: 82752
  • straininfo: 289785

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17911297Kaistia granuli sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor.Lee HW, Yu HS, Liu QM, Jung HM, An DS, Im WT, Jin FX, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.65023-02007Anaerobiosis/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Locomotion/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Organic Chemicals/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/chemistry/*classification/genetics/*isolation & purification, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sewage, Ubiquinone/analysis, *Water Microbiology, Water Purification/methodsGenetics
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17223Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23481)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23481
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
32136Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2838028776041
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
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
82752Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289785.1StrainInfo: A central database for resolving microbial strain identifiers