Strain identifier
BacDive ID: 6857
Type strain:
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)
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
@ref | history |
---|---|
6132 | <- D. Janssens, LMG <- G. Rusal <- J. J. Leisner; II-I-59 |
67770 | CCUG 41967 <-- LMG 17699 <-- J. Leisner II-I-59. |
67771 | <- CCUG <- LMG <- G Rusul <- J Leisner, II-I-59 |
118272 | CIP <- 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
@ref | cell shape | motility | gram stain | confidence |
---|---|---|---|---|
67771 | rod-shaped | no | ||
67771 | positive | |||
69480 | no | 93.879 | ||
69480 | positive | 100 | ||
118272 | rod-shaped | no | positive |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6132 | MRS MEDIUM (DSMZ Medium 11) | yes | https://mediadive.dsmz.de/medium/11 | 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 |
34935 | MEDIUM 40- for Lactobacillus and Leuconostoc | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g) | |
118272 | CIP Medium 40 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6132 | positive | growth | 30 | mesophilic |
34935 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
118272 | positive | growth | 15-37 | |
118272 | no | growth | 10 | psychrophilic |
118272 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
6132 | microaerophile |
67771 | microaerophile |
118272 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | + | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
118272 | nitrate | - | reduction | 17632 |
118272 | nitrite | - | reduction | 16301 |
118272 | nitrate | + | respiration | 17632 |
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
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
118272 | oxidase | - | |
118272 | alcohol dehydrogenase | + | 1.1.1.1 |
118272 | catalase | - | 1.11.1.6 |
118272 | lysine decarboxylase | - | 4.1.1.18 |
118272 | ornithine decarboxylase | - | 4.1.1.17 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118272 | - | + | - | - | - | - | - | - | - | - | + | + | - | + | - | - | + | - | - | - |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6132 | - | - | - | - | - | - | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | - | + | - | + | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location |
---|---|---|---|---|---|
6132 | chili bo | Malaysia | MYS | Asia | |
55282 | Chili Bo | Malaysia | MYS | Asia | |
67770 | Chilli Bo | Malaysia | MYS | Asia | |
67771 | From chili bo | Malaysia | MYS | Asia | |
118272 | Food | Malaysia | MYS | Asia | Chile 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
@ref | pathogenicity human | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|---|
6132 | yes, in single cases | yes, in single cases | 1 | Risk group (German classification) |
118272 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
6132 | Weissella cibaria partial 16S rRNA gene, strain LMG 17699T | AJ295989 | 1529 | ena | 137591 |
67771 | Weissella cibaria gene for 16S ribosomal RNA, partial sequence, strain: JCM 12495 | LC096236 | 1516 | ena | 137591 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Weissella cibaria strain JCM 12495 | 137591.149 | wgs | patric | 137591 |
67771 | Weissella cibaria JCM 12495 | GCA_005405525 | contig | ncbi | 137591 |
GC content
@ref | GC-content | method |
---|---|---|
6132 | 44-45 | |
67770 | 44 | thermal denaturation, midpoint method (Tm) |
67771 | 44.0-45.0 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 97.044 | yes |
gram-positive | yes | 95.722 | yes |
anaerobic | no | 92.818 | yes |
halophile | yes | 92.13 | no |
spore-forming | no | 96.083 | no |
thermophile | no | 99.787 | yes |
glucose-util | yes | 91.311 | no |
aerobic | no | 94.4 | yes |
flagellated | no | 98.399 | yes |
glucose-ferment | yes | 87.62 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15023961 | Genetic evidence that Weissella kimchii Choi et al. 2002 is a later heterotypic synonym of Weissella cibaria Bjorkroth et al. 2002. | Ennahar S, Cai Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.02783-0 | 2004 | Bacillus/*classification/*genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics | Genetics |
Biotechnology | 30954033 | Effect of Bacteriophages on Viability and Growth of Co-cultivated Weissella and Leuconostoc in Kimchi Fermentation. | Kong SJ, Park JH | J Microbiol Biotechnol | 10.4014/jmb.1902.02023 | 2019 | Bacteriophages/*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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6132 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15878) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15878 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
34935 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/4804 | ||||
55282 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 41967) | https://www.ccug.se/strain?id=41967 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
76322 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10764.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118272 | Curators of the CIP | Collection of Institut Pasteur (CIP 107376) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107376 |