Strain identifier
BacDive ID: 23074
Type strain:
Species: Companilactobacillus kimchiensis
Strain Designation: L133
Strain history: J.-W. Bae 133.
NCBI tax ID(s): 993692 (species)
General
@ref: 19296
BacDive-ID: 23074
DSM-Number: 24716
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped
description: Companilactobacillus kimchiensis L133 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from kimchi, fermented Korean food.
NCBI tax id
- NCBI tax id: 993692
- Matching level: species
strain history
@ref | history |
---|---|
19296 | <- J.-W. Bae, Kyung Hee Univ., Dept. of Biology, Seoul, Republic of Korea; L133 |
67770 | J.-W. Bae 133. |
doi: 10.13145/bacdive23074.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Lactobacillaceae
- genus: Companilactobacillus
- species: Companilactobacillus kimchiensis
- full scientific name: Companilactobacillus kimchiensis (Kim et al. 2013) Zheng et al. 2020
synonyms
- @ref: 20215
- synonym: Lactobacillus kimchiensis
@ref: 19296
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Companilactobacillus
species: Companilactobacillus kimchiensis
full scientific name: Companilactobacillus kimchiensis (Kim et al. 2013) Zheng et al. 2020
strain designation: L133
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell shape | motility | confidence |
---|---|---|---|---|---|
30505 | positive | 3 µm | rod-shaped | ||
69480 | no | 97.003 | |||
69480 | positive | 100 |
Culture and growth conditions
culture medium
- @ref: 19296
- 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
19296 | positive | growth | 25 | mesophilic |
30505 | positive | growth | 15-37 | |
30505 | positive | optimum | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30505 | positive | growth | 05-09 | alkaliphile |
30505 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 19296
- oxygen tolerance: microaerophile
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30505 | NaCl | positive | growth | 0-5 % |
30505 | NaCl | positive | optimum | 1.5 % |
murein
- @ref: 19296
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30505 | 17057 | cellobiose | + | carbon source |
30505 | 28757 | fructose | + | carbon source |
30505 | 28260 | galactose | + | carbon source |
30505 | 17234 | glucose | + | carbon source |
30505 | 17716 | lactose | + | carbon source |
30505 | 17306 | maltose | + | carbon source |
30505 | 37684 | mannose | + | carbon source |
30505 | 506227 | N-acetylglucosamine | + | carbon source |
30505 | 17814 | salicin | + | carbon source |
30505 | 17992 | sucrose | + | carbon source |
30505 | 27082 | trehalose | + | carbon source |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | + | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | + | builds acid from |
68371 | 28066 | gentiobiose | + | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | + | builds acid from |
68371 | 17992 | sucrose | + | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | + | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 4853 | esculin | + | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | + | builds acid from |
68371 | 59640 | N-acetylglucosamine | + | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | + | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19296 | - | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | + | + | - | + | - | + | + | + | - | + | + | - | - | - | - | - | - | + | + | - | + | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
19296 | kimchi, fermented Korean food | Republic of Korea | KOR | Asia |
67770 | Kimchi (traditional fermented food) | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Food production | #Vegetable (incl. Grains) |
#Engineered | #Food production | #Fermented |
taxonmaps
- @ref: 69479
- File name: preview.99_4555.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_954;97_1113;98_1324;99_4555&stattab=map
- Last taxonomy: Companilactobacillus kimchiensis
- 16S sequence: LC519996
- Sequence Identity:
- Total samples: 533
- soil counts: 102
- aquatic counts: 53
- animal counts: 281
- plant counts: 97
Safety information
risk assessment
- @ref: 19296
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
19296 | Lactobacillus kimchiensis strain L133 16S ribosomal RNA gene, partial sequence | HQ906500 | 1436 | ena | 993692 |
67770 | Lactobacillus kimchiensis JCM 17702 gene for 16S rRNA, partial sequence | LC519996 | 1498 | ena | 993692 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lactobacillus kimchiensis strain DSM 24716 | 993692.3 | wgs | patric | 993692 |
66792 | Companilactobacillus kimchiensis DSM 24716 | 2663763333 | draft | img | 993692 |
67770 | Companilactobacillus kimchiensis DSM 24716 | GCA_001438805 | contig | ncbi | 993692 |
GC content
@ref | GC-content | method |
---|---|---|
19296 | 35.7 | fluorimetric |
30505 | 35.7 | |
67770 | 35.7 | thermal denaturation, midpoint method (Tm) |
67770 | 35.5 | genome sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 95.32 | no |
flagellated | no | 98.39 | no |
gram-positive | yes | 95.315 | yes |
anaerobic | no | 90.811 | yes |
halophile | yes | 81.768 | yes |
spore-forming | no | 94.805 | no |
glucose-util | yes | 90.571 | yes |
aerobic | no | 96.184 | yes |
thermophile | no | 99.755 | yes |
glucose-ferment | yes | 88.505 | no |
External links
@ref: 19296
culture collection no.: DSM 24716, JCM 17702, KACC 15533
straininfo link
- @ref: 87312
- straininfo: 387798
literature
- topic: Phylogeny
- Pubmed-ID: 22798657
- title: Lactobacillus kimchiensis sp. nov., isolated from a fermented food.
- authors: Kim J, Kim JY, Kim MS, Roh SW, Bae JW
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.037572-0
- year: 2012
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, *Food Microbiology, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Biotechnology
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
19296 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24716) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24716 | |||
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 | |||
30505 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26837 | 28776041 | |
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
87312 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID387798.1 | StrainInfo: A central database for resolving microbial strain identifiers |