Strain identifier
BacDive ID: 141151
Type strain:
Species: Companilactobacillus allii
Strain Designation: WiKim29, WiKim39
Strain history: <- Ji Yoon Chang, Wikim
NCBI tax ID(s): 1847728 (species)
General
@ref: 44072
BacDive-ID: 141151
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped, colony-forming
description: Companilactobacillus allii WiKim29 is a facultative anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from scallion kimchi.
NCBI tax id
- NCBI tax id: 1847728
- Matching level: species
strain history
@ref | history |
---|---|
67770 | J. Y. Chang; World Inst. of Kimchi, South Korea; WiKim39. |
67771 | <- Ji Yoon Chang, Wikim |
doi: 10.13145/bacdive141151.20230509.8.1
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 allii
- full scientific name: Companilactobacillus allii (Jung et al. 2017) Zheng et al. 2020
synonyms
- @ref: 20215
- synonym: Lactobacillus allii
@ref: 44072
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Lactobacillus
species: Lactobacillus allii
strain designation: WiKim29, WiKim39
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
44072 | positive | 1.8-2.5 µm | 0.6 µm | rod-shaped | no | |
67771 | rod-shaped | no | ||||
67771 | positive | |||||
69480 | no | 94.941 | ||||
69480 | positive | 100 |
colony morphology
- @ref: 44072
- colony size: 1 mm
- colony color: off-white
- colony shape: circular
- incubation period: 2 days
- medium used: MRS agar
Culture and growth conditions
culture medium
- @ref: 44072
- name: MRS agar
- growth: yes
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
44072 | positive | growth | 25-37 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
44072 | positive | growth | 4.5-9.0 | alkaliphile |
44072 | no | growth | 3.5-4.0 |
Physiology and metabolism
tolerance
- @ref: 44072
- compound: K2TeO3
- concentration: 0.04 %
oxygen tolerance
@ref | oxygen tolerance |
---|---|
44072 | facultative anaerobe |
67771 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
44072 | no | |
67771 | no | |
69481 | no | 100 |
69480 | no | 99.999 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
44072 | NaCl | positive | growth | 5 %(w/v) |
44072 | NaCl | no | growth | 7 %(w/v) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
44072 | 15963 | ribitol | - | builds acid from |
44072 | 22599 | arabinose | - | builds acid from |
44072 | 17108 | D-arabinose | - | builds acid from |
44072 | 18333 | D-arabitol | - | builds acid from |
44072 | 28847 | D-fucose | - | builds acid from |
44072 | 62318 | D-lyxose | - | builds acid from |
44072 | 16443 | D-tagatose | - | builds acid from |
44072 | 16813 | galactitol | - | builds acid from |
44072 | 17113 | erythritol | - | builds acid from |
44072 | 17754 | glycerol | - | builds acid from |
44072 | 28087 | glycogen | - | builds acid from |
44072 | 17268 | myo-inositol | - | builds acid from |
44072 | 15443 | inulin | - | builds acid from |
44072 | 30849 | L-arabinose | - | builds acid from |
44072 | 18403 | L-arabitol | - | builds acid from |
44072 | 18287 | L-fucose | - | builds acid from |
44072 | 29864 | mannitol | - | builds acid from |
44072 | 6731 | melezitose | - | builds acid from |
44072 | 28053 | melibiose | - | builds acid from |
44072 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
44072 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
44072 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
44072 | potassium 2-dehydro-D-gluconate | - | builds acid from | |
44072 | potassium 5-dehydro-D-gluconate | - | builds acid from | |
44072 | 32032 | potassium gluconate | - | builds acid from |
44072 | 16634 | raffinose | - | builds acid from |
44072 | 26546 | rhamnose | - | builds acid from |
44072 | 33942 | ribose | - | builds acid from |
44072 | 30911 | sorbitol | - | builds acid from |
44072 | 27922 | sorbose | - | builds acid from |
44072 | 28017 | starch | - | builds acid from |
44072 | 27082 | trehalose | - | builds acid from |
44072 | 32528 | turanose | - | builds acid from |
44072 | 17151 | xylitol | - | builds acid from |
44072 | 18222 | xylose | - | builds acid from |
44072 | 17234 | glucose | - | builds gas from |
44072 | 17632 | nitrate | - | reduction |
44072 | 27613 | amygdalin | + | builds acid from |
44072 | 18305 | arbutin | + | builds acid from |
44072 | 17057 | cellobiose | + | builds acid from |
44072 | 15824 | D-fructose | + | builds acid from |
44072 | 12936 | D-galactose | + | builds acid from |
44072 | 17634 | D-glucose | + | builds acid from |
44072 | 17716 | lactose | + | builds acid from |
44072 | 17306 | maltose | + | builds acid from |
44072 | esculin ferric citrate | + | builds acid from | |
44072 | 28066 | gentiobiose | + | builds acid from |
44072 | 506227 | N-acetylglucosamine | + | builds acid from |
44072 | 17814 | salicin | + | builds acid from |
44072 | 17992 | sucrose | + | builds acid from |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
44072 | 16136 | hydrogen sulfide | no |
44072 | 35581 | indole | no |
44072 | 16004 | (R)-lactate | yes |
44072 | 16651 | (S)-lactate | yes |
44072 | 15688 | acetoin | yes |
metabolite tests
- @ref: 44072
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
44072 | catalase | - | 1.11.1.6 |
44072 | cytochrome oxidase | - | 1.9.3.1 |
44072 | alkaline phosphatase | + | 3.1.3.1 |
44072 | esterase | + | |
44072 | leucine arylamidase | + | 3.4.11.1 |
44072 | valine arylamidase | + | |
44072 | acid phosphatase | + | 3.1.3.2 |
44072 | naphthol-AS-BI-phosphohydrolase | + | |
44072 | alpha-glucosidase | + | 3.2.1.20 |
44072 | beta-glucosidase | + | 3.2.1.21 |
44072 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
fatty acid profile
fatty acids
@ref fatty acid percentage 44072 C16:0 16.8 44072 C16:1ω9c 1.2 44072 C18:0 2.4 44072 C18:1ω11c DMA 1.5 44072 C18:1ω11c/9t/6t / unknown ECL 17.834 8.1 44072 C18:1ω9c 61.9 44072 C19:1 cyclo 9,10 1.1 44072 unknown ECL 18.199 C18:0 a DMA 2.2 44072 unkown ECL 18.622 / isoC19:0 2.4 - type of FA analysis: whole cell analysis
- incubation medium: MRS agar
- incubation temperature: 30
- incubation time: 2
- library/peak naming table: BHIBLA
- system: MIS MIDI
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture duration | enrichment culture temperature | isolation procedure |
---|---|---|---|---|---|---|---|---|---|
44072 | scallion kimchi | Gwangju | Republic of Korea | KOR | Asia | MRS agar | 2 days | 30 | anaerobic conditions |
67770 | Scallion kimchi in Gwangju | Republic of Korea | KOR | Asia | |||||
67771 | From scallion kimchi | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Food production | #Vegetable (incl. Grains) |
#Engineered | #Food production | #Food |
#Engineered | #Food production | #Fermented |
taxonmaps
- @ref: 69479
- File name: preview.99_53813.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_1756;97_2100;98_2579;99_53813&stattab=map
- Last taxonomy: Companilactobacillus allii
- 16S sequence: NR_159082
- Sequence Identity:
- Total samples: 517
- soil counts: 47
- aquatic counts: 60
- animal counts: 382
- plant counts: 28
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
67770 | Lactobacillus allii strain WiKim39 16S ribosomal RNA gene, partial sequence | KY419164 | 1517 | ena | 1847728 |
67770 | Lactobacillus allii strain WiKim39 16S ribosomal RNA, complete sequence | NR_159082 | 1577 | nuccore | 1847728 |
67771 | Companilactobacillus allii strain WiKim39 chromosome, complete genome | CP019323 | 2506167 | ena | 1847728 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Companilactobacillus allii WiKim39 | GCA_001971585 | complete | ncbi | 1847728 |
66792 | Lactobacillus allii strain JCM 31938 | 1847728.10 | wgs | patric | 1847728 |
66792 | Companilactobacillus allii WiKim39 | 2767802141 | complete | img | 1847728 |
67770 | Companilactobacillus allii JCM 31938 | GCA_003946005 | contig | ncbi | 1847728 |
66792 | Companilactobacillus allii WiKim39 | GCA_023923085 | complete | ncbi | 1847728 |
GC content
@ref | GC-content | method |
---|---|---|
44072 | 35.3 | genome sequence analysis |
67771 | 35.3 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 98.211 | yes |
gram-positive | yes | 95.678 | yes |
anaerobic | no | 86.544 | no |
aerobic | no | 97.183 | yes |
halophile | yes | 77.643 | no |
spore-forming | no | 95.809 | yes |
glucose-util | yes | 90.925 | no |
thermophile | no | 98.959 | no |
motile | no | 94.595 | no |
glucose-ferment | yes | 87.881 | no |
External links
@ref: 44072
culture collection no.: KCTC 21077, JCM 31938
literature
Pubmed-ID | title | authors | journal | DOI | year |
---|---|---|---|---|---|
34829632 | UPLC-QTOF-MS/MS and GC-MS Characterization of Phytochemicals in Vegetable Juice Fermented Using Lactic Acid Bacteria from Kimchi and Their Antioxidant Potential. | Lee M, Song JH, Choi EJ, Yun YR, Lee KW, Chang JY | Antioxidants (Basel) | 10.3390/antiox10111761 | 2021 |
36453076 | Lactic Acid Bacteria Strains Used as Starters for Kimchi Fermentation Protect the Disruption of Tight Junctions in the Caco-2 Cell Monolayer Model. | Kang JY, Lee M, Song JH, Choi EJ, Kim DU, Lim SK, Kim N, Chang JY | J Microbiol Biotechnol | 10.4014/jmb.2209.09026 | 2022 |
Reference
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | ||
44072 | Min Young Jung, Se Hee Lee, Moeun Lee, Jung Hee Song and Ji Yoon Chang | Lactobacillus allii sp. nov. isolated from scallion kimchi | 10.1099/ijsem.0.002327 | IJSEM 67: 4936-4942 2017 | 29043955 |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 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 | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |