Strain identifier

BacDive ID: 140557

Type strain: Yes

Species: Leuconostoc mesenteroides subsp. jonggajibkimchii

Strain Designation: DRC1506

Strain history: H. Y. Choi; Daesang, South Korea; DRC1506.

NCBI tax ID(s): 2026657 (subspecies)

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General

@ref: 43307

BacDive-ID: 140557

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, coccus-shaped, colony-forming

description: Leuconostoc mesenteroides subsp. jonggajibkimchii DRC1506 is a facultative anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from a commercial kimchi.

NCBI tax id

  • NCBI tax id: 2026657
  • Matching level: subspecies

strain history

  • @ref: 67770
  • history: H. Y. Choi; Daesang, South Korea; DRC1506.

doi: 10.13145/bacdive140557.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Leuconostoc
  • species: Leuconostoc mesenteroides subsp. jonggajibkimchii
  • full scientific name: Leuconostoc mesenteroides subsp. jonggajibkimchii Jeon et al. 2017

@ref: 43307

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Leuconostoc

species: Leuconostoc mesenteroides subsp. jonggajibkimchii

strain designation: DRC1506

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
43307positive0.6-1 µmcoccus-shapedno
69480no96.499
69480positive100

colony morphology

  • @ref: 43307
  • colony color: creamy white
  • colony shape: circular
  • medium used: MRS agar

Culture and growth conditions

culture medium

  • @ref: 43307
  • name: MRS agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43307positiveoptimum30-37mesophilic
43307positivegrowth10-40
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
43307positivegrowth4-9alkaliphile
43307positiveoptimum6.5-7

Physiology and metabolism

oxygen tolerance

  • @ref: 43307
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
43307no
69481no98
69480no100

halophily

@refsaltgrowthtested relationconcentration
43307NaClpositivegrowth0-7 %
43307NaClnogrowth8 %

observation

  • @ref: 43307
  • observation: Heterofermentative;gas and DL-lactic acid (98.1 : 1.9) are produced from glucose.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4330727613amygdalin+builds acid from
4330730849L-arabinose+builds acid from
4330718305arbutin+builds acid from
433074853esculin+builds acid from
4330712936D-galactose+builds acid from
4330717634D-glucose+builds acid from
4330717306maltose+builds acid from
4330716899D-mannitol+builds acid from
4330716024D-mannose+builds acid from
43307320061methyl alpha-D-glucopyranoside+builds acid from
43307506227N-acetylglucosamine+builds acid from
4330728053melibiose+builds acid from
4330717716lactose+builds acid from
4330716634raffinose+builds acid from
4330715824D-fructose+builds acid from
43307potassium 2-dehydro-D-gluconate+builds acid from
43307potassium 5-dehydro-D-gluconate+builds acid from
4330732032potassium gluconate+builds acid from
4330716988D-ribose+builds acid from
4330717814salicin+builds acid from
4330717992sucrose+builds acid from
4330727082trehalose+builds acid from
4330732528turanose+builds acid from
4330765327D-xylose+builds acid from
4330715963ribitol-builds acid from
4330717108D-arabinose-builds acid from
4330717151xylitol-builds acid from
4330722605arabinitol-builds acid from
4330716813galactitol-builds acid from
4330717113erythritol-builds acid from
4330733984fucose-builds acid from
4330717057cellobiose-builds acid from
4330728066gentiobiose-builds acid from
4330717754glycerol-builds acid from
4330728087glycogen-builds acid from
4330717268myo-inositol-builds acid from
4330715443inulin-builds acid from
4330762318D-lyxose-builds acid from
433076731melezitose-builds acid from
4330716443D-tagatose-builds acid from
4330717266L-sorbose-builds acid from
4330717924D-sorbitol-builds acid from
4330762345L-rhamnose-builds acid from
4330743943methyl alpha-D-mannoside-builds acid from
4330774863methyl beta-D-xylopyranoside-builds acid from

metabolite production

  • @ref: 43307
  • Chebi-ID: 52071
  • metabolite: dextran
  • production: yes

enzymes

@refvalueactivityec
43307catalase-1.11.1.6
43307cytochrome oxidase-1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43307C16:033.1
    43307C18:1ω9c14.7
    43307C19:0 cyclo ω8c13.6
    43307C16:1ω7c / C16:1ω6c12.3
  • type of FA analysis: whole cell analysis
  • incubation medium: MRS broth
  • agar/liquid: liquid
  • incubation temperature: 30
  • incubation pH: 6.50
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.0B
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43307a commercial kimchiDaesangRepublic of KoreaKORAsia
67770KimchiRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_41.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_22;96_35;97_36;98_39;99_41&stattab=map
  • Last taxonomy: Leuconostoc
  • 16S sequence: NR_157602
  • Sequence Identity:
  • Total samples: 44756
  • soil counts: 3647
  • aquatic counts: 6333
  • animal counts: 32069
  • plant counts: 2707

Sequence information

16S sequences

@refdescriptionaccessiondatabaselengthNCBI tax ID
4330716S rRNACP014611nuccore
67770Leuconostoc mesenteroides subsp. jonggajibkimchii strain DRC1506 16S ribosomal RNA, complete sequenceNR_157602nuccore15512026657

Genome sequences

  • @ref: 66792
  • description: Leuconostoc mesenteroides subsp. jonggajibkimchii DRC1506
  • accession: GCA_001886915
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 2026657

GC content

  • @ref: 43307
  • GC-content: 37.72
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
flagellatedno96.656yes
gram-positiveyes96.811yes
anaerobicno90.465yes
aerobicno95.554yes
halophileyes94.303no
spore-formingno95.397yes
glucose-utilyes87.65no
thermophileno99.209yes
motileno94.892yes
glucose-fermentyes91.317no

External links

@ref: 43307

culture collection no.: JCM 31787, KCCM 43249, BCRC 81165

literature

  • topic: Phylogeny
  • Pubmed-ID: 28671527
  • title: A proposal of Leuconostoc mesenteroides subsp. jonggajibkimchii subsp. nov. and reclassification of Leuconostoc mesenteroides subsp. suionicum (Gu et al., 2012) as Leuconostoc suionicum sp. nov. based on complete genome sequences.
  • authors: Jeon HH, Kim KH, Chun BH, Ryu BH, Han NS, Jeon CO
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001930
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Leuconostoc/*classification, Leuconostoc mesenteroides/*classification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
43307Hye Hee Jeon, Kyung Hyun Kim, Byung Hee Chun, Byung Hee Ryu, Nam Soo Han, Che Ok JeonA proposal of Leuconostoc mesenteroides subsp. jonggajibkimchii subsp. nov. and reclassification of Leuconostoc mesenteroides subsp. suionicum (Gu et al., 2012) as Leuconostoc suionicum sp. nov. based on complete genome sequences10.1099/ijsem.0.001930IJSEM 67: 2225-2230 201728671527
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