Strain identifier

BacDive ID: 6857

Type strain: Yes

Species: Weissella cibaria

Strain Designation: II-I-59

Strain history: CIP <- 2002, CCUG <- LMG <- J. Leisner, Weissella confusa: strain II-I-59

NCBI tax ID(s): 137591 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6132

BacDive-ID: 6857

DSM-Number: 15878

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, rod-shaped, human pathogen

description: Weissella cibaria II-I-59 is a microaerophile, mesophilic, rod-shaped human pathogen that was isolated from chili bo.

NCBI tax id

  • NCBI tax id: 137591
  • Matching level: species

strain history

@refhistory
6132<- D. Janssens, LMG <- G. Rusal <- J. J. Leisner; II-I-59
67770CCUG 41967 <-- LMG 17699 <-- J. Leisner II-I-59.
67771<- CCUG <- LMG <- G Rusul <- J Leisner, II-I-59
118272CIP <- 2002, CCUG <- LMG <- J. Leisner, Weissella confusa: strain II-I-59

doi: 10.13145/bacdive6857.20230509.8.1

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 cibaria
  • full scientific name: Weissella cibaria Björkroth et al. 2002
  • synonyms

    • @ref: 20215
    • synonym: Weissella kimchii

@ref: 6132

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Weissella

species: Weissella cibaria

full scientific name: Weissella cibaria Björkroth et al. 2002

strain designation: II-I-59

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771rod-shapedno
67771positive
69480no93.879
69480positive100
118272rod-shapednopositive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6132MRS 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
34935MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
118272CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
6132positivegrowth30mesophilic
34935positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic
118272positivegrowth15-37
118272nogrowth10psychrophilic
118272nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6132microaerophile
67771microaerophile
118272facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-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
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
68371D-mannitol-builds acid from16899
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
118272nitrate-reduction17632
118272nitrite-reduction16301
118272nitrate+respiration17632

antibiotic resistance

  • @ref: 118272
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite tests

  • @ref: 118272
  • 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
118272oxidase-
118272alcohol dehydrogenase+1.1.1.1
118272catalase-1.11.1.6
118272lysine decarboxylase-4.1.1.18
118272ornithine 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
118272-+--------++-+--+---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
6132-----------+++-----------+-++--+------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
6132chili boMalaysiaMYSAsia
55282Chili BoMalaysiaMYSAsia
67770Chilli BoMalaysiaMYSAsia
67771From chili boMalaysiaMYSAsia
118272FoodMalaysiaMYSAsiaChile Bo

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Food

taxonmaps

  • @ref: 69479
  • File name: preview.99_1159.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_155;96_519;97_786;98_910;99_1159&stattab=map
  • Last taxonomy: Weissella
  • 16S sequence: LC096236
  • Sequence Identity:
  • Total samples: 43874
  • soil counts: 2011
  • aquatic counts: 3467
  • animal counts: 36370
  • plant counts: 2026

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
6132yes, in single casesyes, in single cases1Risk group (German classification)
1182721Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6132Weissella cibaria partial 16S rRNA gene, strain LMG 17699TAJ2959891529ena137591
67771Weissella cibaria gene for 16S ribosomal RNA, partial sequence, strain: JCM 12495LC0962361516ena137591

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Weissella cibaria strain JCM 12495137591.149wgspatric137591
67771Weissella cibaria JCM 12495GCA_005405525contigncbi137591

GC content

@refGC-contentmethod
613244-45
6777044thermal denaturation, midpoint method (Tm)
6777144.0-45.0thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno97.044yes
gram-positiveyes95.722yes
anaerobicno92.818yes
halophileyes92.13no
spore-formingno96.083no
thermophileno99.787yes
glucose-utilyes91.311no
aerobicno94.4yes
flagellatedno98.399yes
glucose-fermentyes87.62no

External links

@ref: 6132

culture collection no.: DSM 15878, CCUG 41967, LMG 17699, CIP 107376, KCTC 3807, JCM 12495, NBRC 106073, KCTC 3817

straininfo link

  • @ref: 76322
  • straininfo: 10764

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023961Genetic evidence that Weissella kimchii Choi et al. 2002 is a later heterotypic synonym of Weissella cibaria Bjorkroth et al. 2002.Ennahar S, Cai YInt J Syst Evol Microbiol10.1099/ijs.0.02783-02004Bacillus/*classification/*genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Biotechnology30954033Effect of Bacteriophages on Viability and Growth of Co-cultivated Weissella and Leuconostoc in Kimchi Fermentation.Kong SJ, Park JHJ Microbiol Biotechnol10.4014/jmb.1902.020232019Bacteriophages/*physiology, Coculture Techniques/methods, *Fermentation, *Fermented Foods, Food Microbiology, Hydrogen-Ion Concentration, Lactobacillales, Leuconostoc/genetics/*growth & development/virology, Microbial Viability, Time Factors, Weissella/genetics/*growth & development/virology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6132Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15878)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15878
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
34935Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4804
55282Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 41967)https://www.ccug.se/strain?id=41967
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
76322Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10764.1StrainInfo: A central database for resolving microbial strain identifiers
118272Curators of the CIPCollection of Institut Pasteur (CIP 107376)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107376