Strain identifier

BacDive ID: 130225

Type strain: Yes

Species: Variibacter gotjawalensis

Strain Designation: GJW-30

Strain history: <- JS Lee, KRIBB

NCBI tax ID(s): 1333996 (species)

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General

@ref: 22108

BacDive-ID: 130225

DSM-Number: 29671

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

description: Variibacter gotjawalensis GJW-30 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 1333996
  • Matching level: species

strain history

@refhistory
22108<- KCTC <- K. K. Kim et al., KRIBB
67771<- JS Lee, KRIBB

doi: 10.13145/bacdive130225.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Variibacter
  • species: Variibacter gotjawalensis
  • full scientific name: Variibacter gotjawalensis Kim et al. 2014

@ref: 22108

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Variibacter

species: Variibacter gotjawalensis

full scientific name: Variibacter gotjawalensis Kim et al. 2014

strain designation: GJW-30

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.947

multimedia

  • @ref: 22108
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_29671.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 22108
  • 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
22108positivegrowth28mesophilic
67771positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
22108forest soilAewol, Jeju, Gotjawal forestRepublic of KoreaKORAsia
67771From soilJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_164661.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_61727;97_79965;98_108173;99_164661&stattab=map
  • Last taxonomy: Variibacter gotjawalensis subclade
  • 16S sequence: HF970589
  • Sequence Identity:
  • Total samples: 2138
  • soil counts: 1524
  • aquatic counts: 195
  • animal counts: 357
  • plant counts: 62

Safety information

risk assessment

  • @ref: 22108
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22108
  • description: Variibacter gotjawalensis partial 16S rRNA gene, type strain GJW-30T
  • accession: HF970589
  • length: 1407
  • database: ena
  • NCBI tax ID: 1333996

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Variibacter gotjawalensis GJW-30GCA_002355335completencbi1333996
66792Variibacter gotjawalensis DSM 29671GCA_004216635scaffoldncbi1333996
66792Variibacter gotjawalensis CECT 8514GCA_011761465scaffoldncbi1333996
66792Variibacter gotjawalensis strain CECT 85141333996.5wgspatric1333996
66792Variibacter gotjawalensis strain DSM 296711333996.4wgspatric1333996
66792Variibacter gotjawalensis GJW-302775506837completeimg1333996
66792Variibacter gotjawalensis CECT 85142824472061draftimg1333996
66792Variibacter gotjawalensis DSM 296712795386120draftimg1333996

GC content

  • @ref: 22108
  • GC-content: 62.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.505no
gram-positiveno97.383no
anaerobicno98.741yes
aerobicyes95.309yes
halophileno88.891no
spore-formingno95.751no
glucose-utilyes78.404no
thermophileno96.835yes
glucose-fermentno92.689no
motileno78.087no

External links

@ref: 22108

culture collection no.: DSM 29671, CECT 8514, KCTC 32391, LMG 28093

straininfo link

  • @ref: 88767
  • straininfo: 391651

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24599521Variibacter gotjawalensis gen. nov., sp. nov., isolated from soil of a lava forest.Kim KK, Lee KC, Eom MK, Kim JS, Kim DS, Ko SH, Kim BH, Lee JSAntonie Van Leeuwenhoek10.1007/s10482-014-0146-z2014Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Forests, Gram-Negative Aerobic Rods and Cocci/*classification/genetics/*isolation & purification/physiology, Korea, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny26420766Pseudorhodoplanes sinuspersici gen. nov., sp. nov., isolated from oil-contaminated soil.Tirandaz H, Dastgheib SMM, Amoozegar MA, Shavandi M, de la Haba RR, Ventosa AInt J Syst Evol Microbiol10.1099/ijsem.0.0006432015Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Iran, Molecular Sequence Data, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Ubiquinone/chemistryGenetics
Genetics26656224Complete genome sequence of the Variibacter gotjawalensis GJW-30(T) from soil of lava forest, Gotjawal.Lee JS, Lee KC, Kim KK, Lee BJ Biotechnol10.1016/j.jbiotec.2015.11.0272015Alphaproteobacteria/*genetics, Base Composition, Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Forests, Genome Size, *Genome, Bacterial, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
22108Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29671Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29671)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88767Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID391651.1