Strain identifier

BacDive ID: 6841

Type strain: Yes

Species: Leuconostoc miyukkimchii

Strain Designation: M2

Strain history: C. O. Jeon M2.

NCBI tax ID(s): 910540 (species)

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General

@ref: 18068

BacDive-ID: 6841

DSM-Number: 25624

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

description: Leuconostoc miyukkimchii M2 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from fermented brown algae L. kimchi.

NCBI tax id

  • NCBI tax id: 910540
  • Matching level: species

strain history

@refhistory
18068<- S. W. Kwon, KACC; KACC 15353
67770C. O. Jeon M2.

doi: 10.13145/bacdive6841.20230509.8.1

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 miyukkimchii
  • full scientific name: Leuconostoc miyukkimchii Lee et al. 2012

@ref: 18068

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Leuconostoc

species: Leuconostoc miyukkimchii

full scientific name: Leuconostoc miyukkimchii Lee et al. 2012

strain designation: M2

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30281positiveovoid-shapedno
69480no96.128
69480positive100

pigmentation

  • @ref: 30281
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 18068
  • 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
18068positivegrowth30mesophilic
30281positivegrowth04-35
30281positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

  • @ref: 30281
  • ability: positive
  • type: growth
  • pH: 05-09
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
18068microaerophile
30281facultative anaerobe

spore formation

@refspore formationconfidence
30281no
69481no100
69480no100

halophily

  • @ref: 30281
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-6 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3028117057cellobiose+carbon source
3028117306maltose+carbon source
3028129864mannitol+carbon source
3028133942ribose+carbon source
3028117814salicin+carbon source
3028127082trehalose+carbon source
3028118222xylose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
18068-----++----+++---------+++-+---++-------+---------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
18068fermented brown algae (Undaria pinnatifida) L. kimchiUndaria pinnatifidaRepublic of KoreaKORAsia
67770Brown algae kimchi (miyukkimchi)Republic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production
#Environmental#Aquatic#Marine
#Host#Algae#Brown Algae

Safety information

risk assessment

  • @ref: 18068
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
18068Leuconostoc miyukkimchii strain M2 16S ribosomal RNA gene, partial sequenceHQ2630241386ena910540
67770Leuconostoc miyukkimchii JCM 17445 gene for 16S rRNA, partial sequenceLC5199931483ena910540

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leuconostoc miyukkimchii JCM 17445GCA_019656055contigncbi910540
66792Leuconostoc miyukkimchii strain JCM 17445910540.4wgspatric910540

GC content

@refGC-contentmethod
1806842.5fluorimetric
3028142.5
6777042.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.207yes
flagellatedno97.718no
gram-positiveyes96.612yes
anaerobicno95.743yes
halophileyes93.969no
spore-formingno93.294no
thermophileno99.603no
glucose-utilyes89.079no
aerobicno95.361yes
glucose-fermentyes86.991no

External links

@ref: 18068

culture collection no.: DSM 25624, JCM 17445, KACC 15353

straininfo link

  • @ref: 76306
  • straininfo: 379816

literature

  • topic: Phylogeny
  • Pubmed-ID: 21705441
  • title: Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi.
  • authors: Lee SH, Park MS, Jung JY, Jeon CO
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.032367-0
  • year: 2011
  • mesh: Anaerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Food Microbiology, Hydrogen-Ion Concentration, Korea, Leuconostoc/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Undaria/*microbiology
  • topic2: Biotechnology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18068Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25624)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25624
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
30281Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2662228776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76306Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID379816.1StrainInfo: A central database for resolving microbial strain identifiers