Strain identifier

BacDive ID: 6854

Type strain: Yes

Species: Weissella koreensis

Strain Designation: S-5623

Strain history: CIP <- 2002, JCM <- 2001, J.S. Lee: strain S-5623

NCBI tax ID(s): 1123721 (strain), 165096 (species)

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General

@ref: 6042

BacDive-ID: 6854

DSM-Number: 15830

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

description: Weissella koreensis S-5623 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from kimchi, fermented vegetable food.

NCBI tax id

NCBI tax idMatching level
1123721strain
165096species

strain history

@refhistory
6042<- JCM <- J. S. Lee; S-5623
67770J.-S. Lee S-5623.
120492CIP <- 2002, JCM <- 2001, J.S. Lee: strain S-5623

doi: 10.13145/bacdive6854.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Weissella
  • species: Weissella koreensis
  • full scientific name: Weissella koreensis Lee et al. 2002

@ref: 6042

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Weissella

species: Weissella koreensis

full scientific name: Weissella koreensis Lee et al. 2002

strain designation: S-5623

type strain: yes

Morphology

cell morphology

  • @ref: 120492
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6042WEISSELA KOREENSIS MEDIUM (DSMZ Medium 232b)yeshttps://mediadive.dsmz.de/medium/232bName: WEISSELA KOREENSIS MEDIUM (DSMZ Medium 232b) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Yeast extract 5.0 g/l Na-acetate 5.0 g/l (NH4)2 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
39910MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
120492CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
6042positivegrowth30mesophilic
39910positivegrowth30mesophilic
57527positivegrowth30mesophilic
67770positivegrowth30mesophilic
120492positivegrowth10-37
120492nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6042anaerobe
57527anaerobe
120492facultative anaerobe

murein

  • @ref: 6042
  • murein short key: A11.13
  • type: A3alpha L-Lys-L-Ala-L-Ser

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
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
68371gentiobiose-builds acid from28066
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
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120492nitrate-reduction17632
120492nitrite-reduction16301
120492nitrate+respiration17632

antibiotic resistance

  • @ref: 120492
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite tests

  • @ref: 120492
  • 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
120492oxidase-
120492alcohol dehydrogenase-1.1.1.1
120492catalase-1.11.1.6
120492lysine decarboxylase-4.1.1.18
120492ornithine 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
120492-----+----++-+------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120492---++/-+----+++----+/----+------------------------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6042kimchi, fermented vegetable foodKoreaRepublic of KoreaKORAsia
57527Traditional Korean fermented-vegetable food
67770Traditional Korean fermented-vegetable food (Kimchi)
120492Food, Kimuchi, Fermented vegetable foodRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3027.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_155;96_1590;97_1897;98_2329;99_3027&stattab=map
  • Last taxonomy: Weissella koreensis subclade
  • 16S sequence: LC145573
  • Sequence Identity:
  • Total samples: 9681
  • soil counts: 523
  • aquatic counts: 1074
  • animal counts: 7440
  • plant counts: 644

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
60421Risk group (German classification)
1204921Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Weissella koreensis isolate S-5623 16S ribosomal RNA gene, partial sequenceAY0358911497ena165096
67770Weissella koreensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 11263LC1455731508ena165096

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Weissella koreensis KCTC 3621GCA_000277645contigncbi1123721
66792Weissella koreensis KCTC 36211123721.3wgspatric1123721

GC content

@refGC-contentmethod
604237
6777037high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno96.363no
flagellatedno98.821no
gram-positiveyes92.715no
anaerobicno87.883yes
aerobicno94.884yes
halophileyes91.848no
spore-formingno97.385no
thermophileno99.445yes
glucose-utilyes91.422no
glucose-fermentyes88.459no

External links

@ref: 6042

culture collection no.: DSM 15830, CCUG 47134, CIP 107634, JCM 11263, KCCM 41516, KCTC 3621

straininfo link

  • @ref: 76319
  • straininfo: 101064

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12148637Weissella koreensis sp. nov., isolated from kimchi.Lee JS, Lee KC, Ahn JS, Mheen TI, Pyun YR, Park YHInt J Syst Evol Microbiol10.1099/00207713-52-4-12572002Anaerobiosis, Base Composition, DNA, Ribosomal/analysis, Fermentation, Gram-Positive Bacteria/chemistry/*classification/metabolism, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vegetables/metabolism/microbiologyMetabolism
Genetics23012287Draft genome sequence of Weissella koreensis KCTC 3621T.Lee JH, Bae JW, Chun JJ Bacteriol10.1128/JB.01356-122012Amino Acids/metabolism, Anaerobiosis, DNA, Bacterial/*chemistry/*genetics, Food Microbiology, *Genome, Bacterial, Lactic Acid/metabolism, Molecular Sequence Data, *Sequence Analysis, DNA, Weissella/cytology/*genetics/isolation & purification/physiologyMetabolism
Phylogeny23396715Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana).Oh SJ, Shin NR, Hyun DW, Kim PS, Kim JY, Kim MS, Yun JH, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.047548-02013Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gastrointestinal Tract/microbiology, Gryllidae/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Weissella/*classification/genetics/isolation & purificationGenetics
Genetics30166128Genomic and metatranscriptomic analyses of Weissella koreensis reveal its metabolic and fermentative features during kimchi fermentation.Jeong SE, Chun BH, Kim KH, Park D, Roh SW, Lee SH, Jeon COFood Microbiol10.1016/j.fm.2018.04.0032018*Fermentation, Fermented Foods/*microbiology, Food Microbiology, Gene Expression Profiling, Genome, Bacterial, *Genomics, Lactic Acid/metabolism, Metabolic Networks and Pathways/*genetics, RNA, Ribosomal, 16S/genetics, Weissella/*genetics/*metabolismBiotechnology

Reference

@idauthorscataloguedoi/urltitle
6042Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15830)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15830
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
39910Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5091
57527Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47134)https://www.ccug.se/strain?id=47134
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
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
76319Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID101064.1StrainInfo: A central database for resolving microbial strain identifiers
120492Curators of the CIPCollection of Institut Pasteur (CIP 107634)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107634