Strain identifier

BacDive ID: 133806

Type strain: Yes

Species: Kaistia defluvii

Strain Designation: B6-12

Strain history: <- L Jin, KRIBB

NCBI tax ID(s): 410841 (species)

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General

@ref: 30558

BacDive-ID: 133806

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

description: Kaistia defluvii B6-12 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from freshwater sediment .

NCBI tax id

  • NCBI tax id: 410841
  • Matching level: species

strain history

@refhistory
67770L. Jin B6-12.
67771<- L Jin, KRIBB

doi: 10.13145/bacdive133806.20230509.8.1

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 defluvii
  • full scientific name: Kaistia defluvii Jin et al. 2012

@ref: 30558

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Rhizobiaceae

genus: Kaistia

species: Kaistia defluvii

strain designation: B6-12

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30558negative1.5 µm0.65 µmrod-shapedno
67771negative

pigmentation

  • @ref: 30558
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
30558positivegrowth10-30
30558positiveoptimum29mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30558positivegrowth06-09alkaliphile
30558positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30558aerobe
67771aerobe

halophily

  • @ref: 30558
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30558168082-dehydro-D-gluconate+carbon source
30558581435-dehydro-D-gluconate+carbon source
3055822599arabinose+carbon source
3055833984fucose+carbon source
3055817234glucose+carbon source
3055824996lactate+carbon source
3055817306maltose+carbon source
3055829864mannitol+carbon source
3055837684mannose+carbon source
3055828053melibiose+carbon source
30558506227N-acetylglucosamine+carbon source
3055818401phenylacetate+carbon source
3055826546rhamnose+carbon source
3055833942ribose+carbon source
3055817814salicin+carbon source
3055830911sorbitol+carbon source
3055817992sucrose+carbon source
305584853esculin+hydrolysis
3055817632nitrate+reduction

enzymes

@refvalueactivityec
30558catalase+1.11.1.6
30558cytochrome oxidase+1.9.3.1
30558urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
30558freshwater sediment (river, lake, pond)
67770Sediment collected from the River GeumhoRepublic of KoreaKORAsia
67771From sedimentRepublic of KoreaKORAsiaDaegu

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Pond (small)
#Environmental#Aquatic#River (Creek)

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: AM409365
  • Sequence Identity:
  • Total samples: 1918
  • soil counts: 656
  • aquatic counts: 825
  • animal counts: 306
  • plant counts: 131

Sequence information

16S sequences

  • @ref: 30558
  • description: Kaistia defluvii partial 16S rRNA gene, type strain B6-12T
  • accession: AM409365
  • length: 1456
  • database: nuccore
  • NCBI tax ID: 410841

Genome sequences

  • @ref: 66792
  • description: Kaistia defluvii JCM 18034
  • accession: GCA_026343955
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 410841

GC content

@refGC-contentmethod
3055863
6777063high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno86.695yes
flagellatedno97.195yes
gram-positiveno97.897yes
anaerobicno99.201no
aerobicyes89.982yes
halophileno90.22no
spore-formingno96.615no
glucose-fermentno90.919no
thermophileno98.424yes
glucose-utilyes91.949yes

External links

@ref: 30558

culture collection no.: KCTC 23766, JCM 18034

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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

@idauthorstitledoi/urlID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
30558Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172688928776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/