Strain identifier

BacDive ID: 6837

Type strain: Yes

Species: Leuconostoc inhae

Strain Designation: IH003

Strain history: CIP <- 2003, DSMZ <- H. Han <- B. Kim: strain IH003

NCBI tax ID(s): 927694 (strain), 178001 (species)

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General

@ref: 5712

BacDive-ID: 6837

DSM-Number: 15101

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, sphere-shaped

description: Leuconostoc inhae IH003 is an anaerobe, sphere-shaped bacterium that was isolated from kimchi .

NCBI tax id

NCBI tax idMatching level
927694strain
178001species

strain history

@refhistory
5712<- H. Han <- B. Kim; IH003
67770NRIC 0562 <-- DSM 15101 <-- H. Han <-- B. Kim IH003.
67771<- HU Han, Inha Univ.
120116CIP <- 2003, DSMZ <- H. Han <- B. Kim: strain IH003

doi: 10.13145/bacdive6837.20240916.9.1

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 inhae
  • full scientific name: Leuconostoc inhae Kim et al. 2003

@ref: 5712

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Leuconostoc

species: Leuconostoc inhae

full scientific name: Leuconostoc inhae Kim et al. 2003

strain designation: IH003

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771sphere-shapedno
67771positive
120116coccus-shapednopositive
69480no93.5
69480positive95.622

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5712MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: 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
39978MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
120116CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperature
5712positivegrowth28
39978positivegrowth25
67770positivegrowth30
67771positivegrowth25
120116positivegrowth10-25
120116nogrowth37
120116nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771anaerobe
120116facultative anaerobe

spore formation

@refspore formationconfidence
67771no
69481no100

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120116nitrate-reduction17632
120116nitrite-reduction16301
120116nitrate+respiration17632

antibiotic resistance

  • @ref: 120116
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite tests

  • @ref: 120116
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
120116oxidase-
120116alcohol dehydrogenase-1.1.1.1
120116catalase-1.11.1.6
120116lysine decarboxylase-4.1.1.18
120116ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120116--+--+---------+----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
5712----++-----+++----+--++--+-++--++------+--------+/--
120116---++-----+++----+/---++--+-++--++------+/---------+/--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
5712kimchi (fermented vegetable food in Korea)Republic of KoreaKORAsia
67770KimchiRepublic of KoreaKORAsia
67771From Kimchi(fermented vegetable food in Korea)Republic of KoreaKORAsia
120116Food, Kimchi, fermented vegetale food in KoreaRepublic of KoreaKORAsia1999

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_41680.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_22;96_35;97_36;98_457;99_41680&stattab=map
  • Last taxonomy: Leuconostoc
  • 16S sequence: LC519999
  • Sequence Identity:
  • Total samples: 831
  • soil counts: 148
  • aquatic counts: 66
  • animal counts: 575
  • plant counts: 42

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57121Risk group (German classification)
1201161Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5712Leuconostoc inhae 16S ribosomal RNA gene, partial sequenceAF4395601474nuccore927694
67770Leuconostoc inhae JCM 17833 gene for 16S rRNA, partial sequenceLC5199991486nuccore178001
124043Leuconostoc inhae DNA, 16S-23S rRNA intergenic spacer region, strain: NRIC 0562.AB290440380nuccore178001

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leuconostoc inhae DSM 15101GCA_019656015contigncbi178001
66792Leuconostoc inhae KCTC 3774927694.4wgspatric927694
66792Leuconostoc inhae strain DSM 15101178001.5wgspatric178001
66792Leuconostoc inhae Kim IH003, KCTC 3774651324069draftimg927694
67770Leuconostoc inhae KCTC 3774GCA_000166735contigncbi927694

GC content

@refGC-contentmethod
571239.9±0.5high performance liquid chromatography (HPLC)
6777039.9high performance liquid chromatography (HPLC)
6777139.9

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes95.622yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no87.92no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no94.732yes
69480spore-formingspore-formingAbility to form endo- or exosporesno86.199no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.6no
69480flagellatedmotile2+Ability to perform flagellated movementno93.5yes

External links

@ref: 5712

culture collection no.: DSM 15101, KCTC 3774, JCM 17833, CECT 7026, CIP 108081, LMG 22919, NRIC 0562

straininfo link

  • @ref: 76302
  • straininfo: 99904

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12892137Leuconostoc inhae sp. nov., a lactic acid bacterium isolated from kimchi.Kim B, Lee J, Jang J, Kim J, Han HInt J Syst Evol Microbiol10.1099/ijs.0.02463-02003Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fermentation, *Food Microbiology, Korea, Leuconostoc/*classification/genetics/*isolation & purification/metabolism, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Vegetables/microbiologyBiotechnology
Genetics21183671Genome sequence of Leuconostoc inhae KCTC 3774, isolated from Kimchi.Kim DS, Choi SH, Kim DW, Kim RN, Nam SH, Kang A, Kim A, Park HSJ Bacteriol10.1128/JB.01458-102010Food Microbiology, *Genome, Bacterial, Leuconostoc/classification/*genetics, Molecular Sequence DataBiotechnology
Phylogeny21705441Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi.Lee SH, Park MS, Jung JY, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.032367-02011Anaerobiosis, 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/*microbiologyBiotechnology

Reference

@idauthorscataloguedoi/urltitle
5712Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15101)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15101
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
39978Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5664
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
76302Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID99904.1StrainInfo: A central database for resolving microbial strain identifiers
120116Curators of the CIPCollection of Institut Pasteur (CIP 108081)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108081
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy