Strain identifier

BacDive ID: 130365

Type strain: Yes

Species: Levilactobacillus yonginensis

Strain Designation: THK-V8

Strain history: T.-H. Yi THK-V8.

NCBI tax ID(s): 1054041 (species)

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General

@ref: 21901

BacDive-ID: 130365

DSM-Number: 29216

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped

description: Levilactobacillus yonginensis THK-V8 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from Korean fermented food, Kimchi.

NCBI tax id

  • NCBI tax id: 1054041
  • Matching level: species

strain history

@refhistory
21901<- KACC; KACC 16236
67770T.-H. Yi THK-V8.

doi: 10.13145/bacdive130365.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Levilactobacillus
  • species: Levilactobacillus yonginensis
  • full scientific name: Levilactobacillus yonginensis (Yi et al. 2013) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus yonginensis

@ref: 21901

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Levilactobacillus

species: Levilactobacillus yonginensis

full scientific name: Levilactobacillus yonginensis (Yi et al. 2013) Zheng et al. 2020

strain designation: THK-V8

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30845positiverod-shapedno
69480no95.352
69480positive100

pigmentation

  • @ref: 30845
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21901
  • name: MRS MEDIUM (DSMZ Medium 11)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/11
  • composition: Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21901positivegrowth30mesophilic
30845positivegrowth04-40
30845positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

  • @ref: 30845
  • ability: positive
  • type: growth
  • pH: 4.0-7.0
  • PH range: acidophile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
21901microaerophile
30845facultative anaerobe

spore formation

@refspore formationconfidence
30845no
69481no100
69480no99.999

halophily

  • @ref: 30845
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-7 %

observation

  • @ref: 30845
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3084522599arabinose+carbon source
3084518403L-arabitol+carbon source
3084516947citrate+carbon source
3084528757fructose+carbon source
3084528260galactose+carbon source
3084524265gluconate+carbon source
3084517234glucose+carbon source
3084517306maltose+carbon source
30845506227N-acetylglucosamine+carbon source
3084533942ribose+carbon source
3084517814salicin+carbon source
3084518222xylose+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21901Korean fermented food, KimchiYonginRepublic of KoreaKORAsia
67770KimchiYonginRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Vegetable (incl. Grains)
#Engineered#Food production#Fermented

taxonmaps

  • @ref: 69479
  • File name: preview.99_3900.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_484;97_553;98_1175;99_3900&stattab=map
  • Last taxonomy: Levilactobacillus
  • 16S sequence: LC520003
  • Sequence Identity:
  • Total samples: 1243
  • soil counts: 164
  • aquatic counts: 140
  • animal counts: 727
  • plant counts: 212

Safety information

risk assessment

  • @ref: 21901
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
21901Lactobacillus yonginensis strain THK-V8 16S ribosomal RNA gene, partial sequenceJN1286401451ena1054041
67770Lactobacillus yonginensis JCM 18023 gene for 16S rRNA, partial sequenceLC5200031509ena1054041

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus yonginensis strain JCM 180231054041.3wgspatric1054041
66792Levilactobacillus yonginensis JCM 180232881698443draftimg1054041
67770Levilactobacillus yonginensis JCM 18023GCA_003946265contigncbi1054041

GC content

@refGC-contentmethod
2190147.8
6777047.9genome sequence analysis
6777047.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.131no
flagellatedno98.607no
gram-positiveyes97.327yes
anaerobicno87.834yes
aerobicno94.71yes
halophileyes91.215no
spore-formingno94.247yes
thermophileno99.712yes
glucose-utilyes90.188yes
glucose-fermentyes81.932no

External links

@ref: 21901

culture collection no.: DSM 29216, JCM 18023, KACC 16236, BCRC 81079

straininfo link

  • @ref: 88897
  • straininfo: 377908

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23475345Lactobacillus yonginensis sp. nov., a lactic acid bacterium with ginsenoside converting activity isolated from Kimchi.Yi EJ, Yang JE, Lee JM, Park Y, Park SY, Shin HS, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.045799-02013Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, *Food Microbiology, Ginsenosides/*metabolism, Lactic Acid, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNABiotechnology
Phylogeny28867002Lactobacillus cerevisiae sp. nov., isolated from a spoiled brewery sample.Koob J, Jacob F, Wenning M, Hutzler MInt J Syst Evol Microbiol10.1099/ijsem.0.0021392017Bacterial Typing Techniques, Base Composition, Beer/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Germany, Lactobacillus/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny32129738Lactobacillus enshiensis sp. nov., a novel arsenic-resistant bacterium.Zhang Z, Wang Y, Hou Q, Zhao H, Li W, Sun Z, Guo ZInt J Syst Evol Microbiol10.1099/ijsem.0.0040722020*Arsenic, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Fermented Foods/*microbiology, *Food Microbiology, Lactic Acid/biosynthesis, Lactobacillus/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNABiotechnology

Reference

@idauthorstitledoi/urlcatalogueID_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
21901Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29216Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29216)
30845Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172717528776041
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/
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
88897Reimer, 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-ID377908.1