Strain identifier

BacDive ID: 141151

Type strain: Yes

Species: Companilactobacillus allii

Strain Designation: WiKim29, WiKim39

Strain history: <- Ji Yoon Chang, Wikim

NCBI tax ID(s): 1847728 (species)

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

@refhistory
67770J. 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
44072positive1.8-2.5 µm0.6 µmrod-shapedno
67771rod-shapedno
67771positive
69480no94.941
69480positive100

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

@refgrowthtypetemperaturerange
44072positivegrowth25-37mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
44072positivegrowth4.5-9.0alkaliphile
44072nogrowth3.5-4.0

Physiology and metabolism

tolerance

  • @ref: 44072
  • compound: K2TeO3
  • concentration: 0.04 %

oxygen tolerance

@refoxygen tolerance
44072facultative anaerobe
67771facultative anaerobe

spore formation

@refspore formationconfidence
44072no
67771no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
44072NaClpositivegrowth5 %(w/v)
44072NaClnogrowth7 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4407215963ribitol-builds acid from
4407222599arabinose-builds acid from
4407217108D-arabinose-builds acid from
4407218333D-arabitol-builds acid from
4407228847D-fucose-builds acid from
4407262318D-lyxose-builds acid from
4407216443D-tagatose-builds acid from
4407216813galactitol-builds acid from
4407217113erythritol-builds acid from
4407217754glycerol-builds acid from
4407228087glycogen-builds acid from
4407217268myo-inositol-builds acid from
4407215443inulin-builds acid from
4407230849L-arabinose-builds acid from
4407218403L-arabitol-builds acid from
4407218287L-fucose-builds acid from
4407229864mannitol-builds acid from
440726731melezitose-builds acid from
4407228053melibiose-builds acid from
44072320061methyl alpha-D-glucopyranoside-builds acid from
4407243943methyl alpha-D-mannoside-builds acid from
4407274863methyl beta-D-xylopyranoside-builds acid from
44072potassium 2-dehydro-D-gluconate-builds acid from
44072potassium 5-dehydro-D-gluconate-builds acid from
4407232032potassium gluconate-builds acid from
4407216634raffinose-builds acid from
4407226546rhamnose-builds acid from
4407233942ribose-builds acid from
4407230911sorbitol-builds acid from
4407227922sorbose-builds acid from
4407228017starch-builds acid from
4407227082trehalose-builds acid from
4407232528turanose-builds acid from
4407217151xylitol-builds acid from
4407218222xylose-builds acid from
4407217234glucose-builds gas from
4407217632nitrate-reduction
4407227613amygdalin+builds acid from
4407218305arbutin+builds acid from
4407217057cellobiose+builds acid from
4407215824D-fructose+builds acid from
4407212936D-galactose+builds acid from
4407217634D-glucose+builds acid from
4407217716lactose+builds acid from
4407217306maltose+builds acid from
44072esculin ferric citrate+builds acid from
4407228066gentiobiose+builds acid from
44072506227N-acetylglucosamine+builds acid from
4407217814salicin+builds acid from
4407217992sucrose+builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
4407216136hydrogen sulfideno
4407235581indoleno
4407216004(R)-lactateyes
4407216651(S)-lactateyes
4407215688acetoinyes

metabolite tests

  • @ref: 44072
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
44072catalase-1.11.1.6
44072cytochrome oxidase-1.9.3.1
44072alkaline phosphatase+3.1.3.1
44072esterase+
44072leucine arylamidase+3.4.11.1
44072valine arylamidase+
44072acid phosphatase+3.1.3.2
44072naphthol-AS-BI-phosphohydrolase+
44072alpha-glucosidase+3.2.1.20
44072beta-glucosidase+3.2.1.21
44072N-acetyl-beta-glucosaminidase+3.2.1.52

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44072C16:016.8
    44072C16:1ω9c1.2
    44072C18:02.4
    44072C18:1ω11c DMA1.5
    44072C18:1ω11c/9t/6t / unknown ECL 17.8348.1
    44072C18:1ω9c61.9
    44072C19:1 cyclo 9,101.1
    44072unknown ECL 18.199 C18:0 a DMA2.2
    44072unkown ECL 18.622 / isoC19:02.4
  • 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

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
44072scallion kimchiGwangjuRepublic of KoreaKORAsiaMRS agar2 days30anaerobic conditions
67770Scallion kimchi in GwangjuRepublic of KoreaKORAsia
67771From scallion kimchiRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Lactobacillus allii strain WiKim39 16S ribosomal RNA gene, partial sequenceKY4191641517ena1847728
67770Lactobacillus allii strain WiKim39 16S ribosomal RNA, complete sequenceNR_1590821577nuccore1847728
67771Companilactobacillus allii strain WiKim39 chromosome, complete genomeCP0193232506167ena1847728

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Companilactobacillus allii WiKim39GCA_001971585completencbi1847728
66792Lactobacillus allii strain JCM 319381847728.10wgspatric1847728
66792Companilactobacillus allii WiKim392767802141completeimg1847728
67770Companilactobacillus allii JCM 31938GCA_003946005contigncbi1847728
66792Companilactobacillus allii WiKim39GCA_023923085completencbi1847728

GC content

@refGC-contentmethod
4407235.3genome sequence analysis
6777135.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno98.211yes
gram-positiveyes95.678yes
anaerobicno86.544no
aerobicno97.183yes
halophileyes77.643no
spore-formingno95.809yes
glucose-utilyes90.925no
thermophileno98.959no
motileno94.595no
glucose-fermentyes87.881no

External links

@ref: 44072

culture collection no.: KCTC 21077, JCM 31938

literature

Pubmed-IDtitleauthorsjournalDOIyear
34829632UPLC-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 JYAntioxidants (Basel)10.3390/antiox101117612021
36453076Lactic 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 JYJ Microbiol Biotechnol10.4014/jmb.2209.090262022

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
44072Min Young Jung, Se Hee Lee, Moeun Lee, Jung Hee Song and Ji Yoon ChangLactobacillus allii sp. nov. isolated from scallion kimchi10.1099/ijsem.0.002327IJSEM 67: 4936-4942 201729043955
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic 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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1