Strain identifier

BacDive ID: 6567

Type strain: Yes

Species: Lentilactobacillus parakefiri

Strain Designation: 1731

Strain history: CIP <- 1994, JCM, Lactobacillus parakefir <- GCL: strain 1731

NCBI tax ID(s): 1423787 (strain), 152332 (species)

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General

@ref: 3924

BacDive-ID: 6567

DSM-Number: 10551

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Lentilactobacillus parakefiri 1731 is an anaerobe, mesophilic bacterium that was isolated from kefir grain.

NCBI tax id

NCBI tax idMatching level
1423787strain
152332species

strain history

@refhistory
3924<- JCM <- S. Takizawa, GCL 1731
67770S. Takizawa GCL 1731.
121564CIP <- 1994, JCM, Lactobacillus parakefir <- GCL: strain 1731

doi: 10.13145/bacdive6567.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lentilactobacillus
  • species: Lentilactobacillus parakefiri
  • full scientific name: Lentilactobacillus parakefiri (Takizawa et al. 1994) Zheng et al. 2020

  • synonyms

    @refsynonym
    20215Lactobacillus parakefir
    20215Lactobacillus parakefiri

@ref: 3924

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lentilactobacillus

species: Lentilactobacillus parakefiri

full scientific name: Lentilactobacillus parakefiri (Takizawa et al. 1994) Zheng et al. 2020

strain designation: 1731

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.635
69480100positive
121564nopositiverod-shaped

colony morphology

  • @ref: 54806
  • incubation period: 3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3924R - CW MEDIUM (DSMZ Medium 775)yeshttps://mediadive.dsmz.de/medium/775Name: R - CW MEDIUM (DSMZ Medium 775) Composition: Yeast extract 5.0 g/l Na-acetate 5.0 g/l KH2PO4 5.0 g/l Trypticase 5.0 g/l Tryptone 5.0 g/l (NH4)2 citrate 2.0 g/l MgSO4 x 7 H2O 0.5 g/l MnSO4 x H2O 0.2 g/l Tween 80 Cheese whey
41060MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
121564CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
3924positivegrowth30mesophilic
41060positivegrowth30mesophilic
54806positivegrowth30mesophilic
67770positivegrowth30mesophilic
121564positivegrowth15-37
121564nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
3924anaerobe
54806anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

murein

  • @ref: 3924
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

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
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
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
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
121564esculin-hydrolysis4853
121564nitrate-reduction17632
121564nitrite-reduction16301

enzymes

@refvalueactivityec
121564oxidase-
121564alcohol dehydrogenase+1.1.1.1
121564catalase-1.11.1.6
121564lysine decarboxylase+4.1.1.18
121564ornithine decarboxylase-4.1.1.17

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121564---++----+/-+----------------++/-+/----+/----------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
3924kefir grainDenmarkDNKEurope
54806Kefir grains from E.C.Hansen's lab.,Copenhagen,DKDenmarkDNKEurope
67770Kefir grains
121564Plant, Kefir grainsDenmarkDNKEuropeCopenhagen

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production

taxonmaps

  • @ref: 69479
  • File name: preview.99_3539.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_367;97_831;98_967;99_3539&stattab=map
  • Last taxonomy: Lentilactobacillus
  • 16S sequence: LC096211
  • Sequence Identity:
  • Total samples: 4525
  • soil counts: 442
  • aquatic counts: 432
  • animal counts: 3255
  • plant counts: 396

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
39241Risk group (German classification)
1215641Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus parakefiri gene for 16S rRNA, partial sequence, strain: JCM 8573AB289232610ena152332
20218Lactobacillus parakefiri gene for 16S ribosomal RNA, partial sequence, strain: JCM 8573AB3708791497ena152332
20218Lactobacillus parakefiri gene for 16S rRNA, partial sequence, strain: YIT 10382AB4293731533ena152332
20218Lactobacillus parakefiri 16S ribosomal RNA gene, partial sequenceAY0267501396ena152332
20218Lactobacillus parakefiri gene for 16S rRNA, partial sequence, strain: NBRC 15890AB6809911500ena152332
67770Lactobacillus parakefiri gene for 16S ribosomal RNA, partial sequence, strain: JCM 8573LC0962111514ena152332

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus parakefiri DSM 105511423787.3wgspatric1423787
66792Lactobacillus parakefiri strain DSM 10551152332.7wgspatric152332
66792Lactobacillus parakefiri strain JCM 8573152332.3wgspatric152332
66792Lentilactobacillus parakefiri DSM 105512660238146draftimg1423787
66792Lactobacillus parakefiri JCM 85732916479636draftimg152332
66792Lentilactobacillus parakefiri DSM 105512901596593draftimg1423787
67770Lentilactobacillus parakefiri DSM 10551GCA_001434215scaffoldncbi1423787
67770Lentilactobacillus parakefiri JCM 8573GCA_002157585scaffoldncbi152332
67770Lentilactobacillus parakefiri DSM 10551GCA_004354625scaffoldncbi152332

GC content

@refGC-contentmethod
392442thermal denaturation, midpoint method (Tm)
6777042.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.376no
gram-positiveyes97.53no
anaerobicno96.242no
halophileyes93.611no
spore-formingno92.376no
glucose-utilyes88.456no
thermophileno99.39yes
aerobicno91.049yes
flagellatedno98.431no
glucose-fermentyes85.635no

External links

@ref: 3924

culture collection no.: CCUG 39468, GCL 1731, ATCC 51648, DSM 10551, IFO 15890, JCM 8573, NBRC 15890, CGMCC 1.3400, CIP 104242, KCTC 5044, KCTC 5087, LMG 15133, NCIMB 13300, JCM 8753

straininfo link

  • @ref: 76041
  • straininfo: 13941

literature

  • Pubmed-ID: 28748134
  • title: Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiri.
  • authors: Tanizawa Y, Kobayashi H, Kaminuma E, Sakamoto M, Ohkuma M, Nakamura Y, Arita M, Tohno M
  • journal: Biosci Microbiota Food Health
  • DOI: 10.12938/bmfh.16-026
  • year: 2017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3924Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10551)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10551
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41060Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16129
54806Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39468)https://www.ccug.se/strain?id=39468
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76041Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13941.1StrainInfo: A central database for resolving microbial strain identifiers
121564Curators of the CIPCollection of Institut Pasteur (CIP 104242)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104242