Strain identifier

BacDive ID: 133577

Type strain: Yes

Species: Secundilactobacillus kimchicus

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 528209 (species)

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General

@ref: 29632

BacDive-ID: 133577

keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, Gram-positive, rod-shaped

description: Secundilactobacillus kimchicus KCTC 12976 is a facultative aerobe, Gram-positive, rod-shaped bacterium that was isolated from food product.

NCBI tax id

  • NCBI tax id: 528209
  • Matching level: species

strain history

@refhistory
67770D.-C. Yang DCY51.
67771<- DC Yang, Kyunghee Univ.

doi: 10.13145/bacdive133577.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Secundilactobacillus
  • species: Secundilactobacillus kimchicus
  • full scientific name: Secundilactobacillus kimchicus (Liang et al. 2011) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus kimchicus

@ref: 29632

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lactobacillus

species: Lactobacillus kimchicus

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29632positive1.5 µm0.55 µmrod-shapedno
67771rod-shapedno
67771positive

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29632positivegrowth15-45
29632positiveoptimum37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepH
29632positivegrowth06-07
29632positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29632facultative aerobe
67771facultative anaerobe

spore formation

@refspore formation
29632no
67771no

halophily

@refsaltgrowthtested relationconcentration
29632NaClpositivegrowth0-8 %
29632NaClpositiveoptimum4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2963228757fructose+carbon source
2963228260galactose+carbon source
2963224265gluconate+carbon source
2963217306maltose+carbon source
2963229864mannitol+carbon source
2963237684mannose+carbon source
29632506227N-acetylglucosamine+carbon source
2963233942ribose+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
29632food product
67770KimchiGyeonggi ProvinceRepublic of KoreaKORAsia
67771From kimchiGyeonggi ProvinceRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_8304.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_750;97_873;98_6042;99_8304&stattab=map
  • Last taxonomy: Secundilactobacillus kimchicus subclade
  • 16S sequence: LC480811
  • Sequence Identity:
  • Total samples: 487
  • soil counts: 35
  • aquatic counts: 44
  • animal counts: 358
  • plant counts: 50

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
29632Lactobacillus kimchicus JCM 15530 strain DCY51 16S ribosomal RNA gene, partial sequenceEU6788931499nuccore1302272
67771Lactobacillus kimchicus JCM 15530 gene for 16S ribosomal RNA, partial sequenceLC4808111504ena1302272

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus kimchicus JCM 155301302272.5wgspatric1302272
66792Lactobacillus kimchicus JCM 155301302272.4wgspatric1302272
66792Secundilactobacillus kimchicus JCM 155302657245468draftimg1302272
66792Secundilactobacillus kimchicus JCM 155302734481936draftimg1302272
67770Secundilactobacillus kimchicus JCM 15530GCA_001433995contigncbi1302272
67771Secundilactobacillus kimchicus JCM 15530GCA_001313205contigncbi1302272

GC content

@refGC-contentmethod
2963239.7
6777046.6genome sequence analysis
6777139.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.09no
gram-positiveyes97.139yes
anaerobicno94.108no
halophileyes92.554no
spore-formingno94.058no
thermophileno99.212yes
glucose-utilyes87.656no
aerobicno93.946no
flagellatedno98.888no
glucose-fermentyes87.762no

External links

@ref: 29632

culture collection no.: KCTC 12976, JCM 15530, DCY 51

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournal
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
29632Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172602228776041
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/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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/