Strain identifier

BacDive ID: 13566

Type strain: Yes

Species: Kaistia terrae

Strain Designation: 5YN7-3

Strain history: <- S.-W. Kwon, KACC; 5YN7-3 <- H.-Y. Weon

NCBI tax ID(s): 537017 (species)

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General

@ref: 15627

BacDive-ID: 13566

DSM-Number: 21341

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

description: Kaistia terrae 5YN7-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from wetland soil.

NCBI tax id

  • NCBI tax id: 537017
  • Matching level: species

strain history

  • @ref: 15627
  • history: <- S.-W. Kwon, KACC; 5YN7-3 <- H.-Y. Weon

doi: 10.13145/bacdive13566.20230509.8.1

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 terrae
  • full scientific name: Kaistia terrae Kim et al. 2010

@ref: 15627

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Kaistiaceae

genus: Kaistia

species: Kaistia terrae

full scientific name: Kaistia terrae Kim et al. 2010

strain designation: 5YN7-3

type strain: yes

Morphology

cell morphology

  • @ref: 29378
  • gram stain: negative
  • cell length: 1.2-1.4 µm
  • cell width: 0.8-0.9 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 29378
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15627
  • 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
15627positivegrowth28mesophilic
29378positivegrowth05-35
29378positiveoptimum30mesophilic

culture pH

@refabilitytypepH
29378positivegrowth05-08
29378positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29378
  • oxygen tolerance: aerobe

halophily

  • @ref: 29378
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29378168082-dehydro-D-gluconate+carbon source
29378581435-dehydro-D-gluconate+carbon source
2937816449alanine+carbon source
2937822599arabinose+carbon source
2937833984fucose+carbon source
2937817234glucose+carbon source
2937828087glycogen+carbon source
2937824996lactate+carbon source
2937817306maltose+carbon source
2937829864mannitol+carbon source
2937837684mannose+carbon source
2937828053melibiose+carbon source
2937826546rhamnose+carbon source
2937833942ribose+carbon source
2937817814salicin+carbon source
2937830911sorbitol+carbon source
2937817992sucrose+carbon source
293784853esculin+hydrolysis

enzymes

@refvalueactivityec
29378catalase+1.11.1.6
29378cytochrome oxidase+1.9.3.1
29378urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 15627
  • sample type: wetland soil
  • geographic location: Yongneup
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Wetland (Swamp)

Safety information

risk assessment

  • @ref: 15627
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15627
  • description: Kaistia terrae strain 5YN7-3 16S ribosomal RNA gene, partial sequence
  • accession: EU723082
  • length: 1371
  • database: ena
  • NCBI tax ID: 537017

Genome sequences

  • @ref: 66792
  • description: Kaistia terrae DSM 21341
  • accession: GCA_026344005
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 537017

GC content

@refGC-contentmethod
1562766.5high performance liquid chromatography (HPLC)
2937866.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno84.788yes
flagellatedno94.069yes
gram-positiveno97.602yes
anaerobicno98.59no
aerobicyes93.823no
halophileno93.227yes
spore-formingno96.213no
glucose-fermentno91.173no
thermophileno98.678no
glucose-utilyes91.039no

External links

@ref: 15627

culture collection no.: DSM 21341, KACC 12910

straininfo link

  • @ref: 82754
  • straininfo: 404202

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15627Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21341)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21341
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
29378Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2578628776041
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)
82754Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404202.1StrainInfo: A central database for resolving microbial strain identifiers