Strain identifier

BacDive ID: 131396

Type strain: Yes

Species: Leuconostoc rapi

Strain Designation: R-50029

Strain history: CIP <- 2015,BCCM LMG <- 2013, I. Snauwaert, Ghent Univ., Ghent, Belgium: strain R-50029 <- S. Pihlajaviita, Seinajoki Univ., Seinajoki, Finland: strain MHB 277

NCBI tax ID(s): 1406906 (species)

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General

@ref: 22623

BacDive-ID: 131396

DSM-Number: 27776

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive

description: Leuconostoc rapi R-50029 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from spoiled sous-vide-cooked rutabaga .

NCBI tax id

  • NCBI tax id: 1406906
  • Matching level: species

strain history

@refhistory
22623<- P. Vandamme, Lab. Microbiology, Ghent Univ., Belgium; LMG 27676 <- S. Pihlajaviita, Seinajoki Univ. of Applied Scs., Kaukajoki, Finland
122138CIP <- 2015,BCCM LMG <- 2013, I. Snauwaert, Ghent Univ., Ghent, Belgium: strain R-50029 <- S. Pihlajaviita, Seinajoki Univ., Seinajoki, Finland: strain MHB 277

doi: 10.13145/bacdive131396.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Leuconostoc
  • species: Leuconostoc rapi
  • full scientific name: Leuconostoc rapi Lyhs et al. 2015

@ref: 22623

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Leuconostoc

species: Leuconostoc rapi

full scientific name: Leuconostoc rapi Lyhs et al. 2015

strain designation: R-50029

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotilitycell shape
69480positive100
6948096.998no
122138positivenooval-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22623MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: 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
122138CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

  • @ref: 22623
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 22623
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no100

murein

  • @ref: 22623
  • murein short key: A11.05
  • type: A3alpha L-Lys-L-Ala2

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
22623----------+++--------+++-+++---++-------+---------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
22623spoiled sous-vide-cooked rutabaga (Brassica napobrassica)Brassica napobrassicaFinlandFINEurope
122138Spoiled packed sous-vide cooked rutabaga, Brassica napobrassicaFinlandFINEurope2012-01-02

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Decomposing plant
#Host#Plants#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
226231Risk group (German classification)
1221381Risk group (French classification)

Sequence information

16S sequences

  • @ref: 22623
  • description: Leuconostoc rapi partial 16S rRNA gene, type strain LMG 27676T
  • accession: HG515542
  • length: 1502
  • database: ena
  • NCBI tax ID: 1406906

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leuconostoc rapi DSM 27776GCA_016908715contigncbi1406906
66792Leuconostoc rapi DSM 27776GCA_019656095contigncbi1406906
66792Leuconostoc rapi strain DSM 277761406906.5wgspatric1406906
66792Leuconostoc rapi strain DSM 277761406906.3wgspatric1406906
66792Leuconostoc rapi DSM 277762901184053draftimg1406906

GC content

  • @ref: 22623
  • GC-content: 38
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.328no
gram-positiveyes96.991no
anaerobicno93.64yes
halophileyes95.838no
spore-formingno94.872no
thermophileno99.754yes
glucose-utilyes88.927no
aerobicno97.095no
flagellatedno97.785no
glucose-fermentyes91.22no

External links

@ref: 22623

culture collection no.: DSM 27776, LMG 27676, MHB 277, CIP 110986

straininfo link

  • @ref: 89829
  • straininfo: 390521

literature

  • topic: Phylogeny
  • Pubmed-ID: 25951860
  • title: Leuconostoc rapi sp. nov., isolated from sous-vide-cooked rutabaga.
  • authors: Lyhs U, Snauwaert I, Pihlajaviita S, Vuyst L, Vandamme P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.000305
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, Brassica napus/*microbiology, Cooking, DNA, Bacterial/genetics, Finland, *Food Microbiology, Genes, Bacterial, Leuconostoc/*classification/genetics/isolation & purification, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vegetables/microbiology
  • topic2: Biotechnology

Reference

@idauthorstitledoi/urlcatalogue
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
22623Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27776Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27776)
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
68371Automatically annotated from API 50CH acid
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
89829Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID390521.1
122138Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110986Collection of Institut Pasteur (CIP 110986)