Strain identifier

BacDive ID: 6686

Type strain: Yes

Species: Lentilactobacillus rapi

Strain history: CIP <- 2009, JCM <- K. Watanabe, Yakult Central Inst. Microbiol. Res., Tokyo, Japan: strain YIT 11204

NCBI tax ID(s): 481723 (species)

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General

@ref: 8379

BacDive-ID: 6686

DSM-Number: 19907

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

description: Lentilactobacillus rapi DSM 19907 is a microaerophile, mesophilic bacterium that was isolated from non-salted pickle solution used in production of sunki .

NCBI tax id

  • NCBI tax id: 481723
  • Matching level: species

strain history

@refhistory
8379<- K. Watanabe, Yakult Central Inst. Microbiol. Res., Tokyo, Japan; YIT 11204
67770K. Watanabe YIT 11204.
122137CIP <- 2009, JCM <- K. Watanabe, Yakult Central Inst. Microbiol. Res., Tokyo, Japan: strain YIT 11204

doi: 10.13145/bacdive6686.20230509.8.1

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 rapi
  • full scientific name: Lentilactobacillus rapi (Watanabe et al. 2009) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus rapi

@ref: 8379

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lentilactobacillus

species: Lentilactobacillus rapi

full scientific name: Lentilactobacillus rapi (Watanabe et al. 2009) Zheng et al. 2020

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.197
69480100positive
122137nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8379MRS 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
33670MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
122137CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20
122137CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8379positivegrowth30mesophilic
33670positivegrowth37mesophilic
67770positivegrowth30mesophilic
122137positivegrowth15-37
122137nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8379microaerophile
122137facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12213717632nitrate-reduction
12213716301nitrite-reduction
12213717632nitrate+respiration

metabolite tests

  • @ref: 122137
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
122137oxidase-
122137alcohol dehydrogenase+1.1.1.1
122137catalase-1.11.1.6
122137lysine decarboxylase-4.1.1.18
122137ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122137---+-++---+++++++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8379non-salted pickle solution used in production of sunki (Japanese traditional fermented leaves and stems of red turnips)Kiso county, Nagano prefectureJapanJPNAsia
67770Sunki, traditional Japanese picklesJapanJPNAsia
122137Sunki, non-salted pickle solution

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Vegetable (incl. Grains)
#Engineered#Food production#Fermented

taxonmaps

  • @ref: 69479
  • File name: preview.99_7645.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_367;97_831;98_967;99_7645&stattab=map
  • Last taxonomy: Lentilactobacillus rapi
  • 16S sequence: LC480803
  • Sequence Identity:
  • Total samples: 922
  • soil counts: 196
  • aquatic counts: 87
  • animal counts: 478
  • plant counts: 161

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
83791Risk group (German classification)
1221371Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus rapi genes for 16S rRNA, intergenic spacer region, 23S rRNA, partial sequence, culture_collection: JCM:15042AB793776557ena481723
8379Lactobacillus rapi gene for 16S rRNA, partial sequence, strain: YIT 11204 (= NRIC 0743, = JCM 15042, = DSM 19907)AB3663891566ena481723
67770Lactobacillus rapi JCM 15042 gene for 16S ribosomal RNA, partial sequenceLC4808031510ena481723

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus rapi DSM 19907 = JCM 150421423795.5wgspatric1423795
66792Lactobacillus rapi DSM 19907 = JCM 150421423795.4wgspatric1423795
66792Lactobacillus rapi strain NBRC 109618481723.4wgspatric481723
66792Lentilactobacillus rapi JCM 150422728369686draftimg1423795
66792Lentilactobacillus rapi DSM 199072700989137draftimg1423795
67770Lentilactobacillus rapi DSM 19907 = JCM 15042GCA_001436255scaffoldncbi1423795
67770Lentilactobacillus rapi DSM 19907 = JCM 15042GCA_001311445contigncbi1423795
67770Lentilactobacillus rapi NBRC 109618GCA_007992555contigncbi481723

GC content

@refGC-contentmethod
837940.3high performance liquid chromatography (HPLC)
837939.2
6777043genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.663no
gram-positiveyes96.097no
anaerobicno92.945no
halophileyes84.619no
spore-formingno89.829no
glucose-utilyes84.542no
thermophileno99.304no
aerobicno93.525no
flagellatedno97.623no
glucose-fermentyes86.932no

External links

@ref: 8379

culture collection no.: DSM 19907, JCM 15042, NRIC 0743, YIT 11204, CIP 110029, NBRC 109618

straininfo link

  • @ref: 76160
  • straininfo: 362308

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19329601Lactobacillus kisonensis sp. nov., Lactobacillus otakiensis sp. nov., Lactobacillus rapi sp. nov. and Lactobacillus sunkii sp. nov., heterofermentative species isolated from sunki, a traditional Japanese pickle.Watanabe K, Fujimoto J, Tomii Y, Sasamoto M, Makino H, Kudo Y, Okada SInt J Syst Evol Microbiol10.1099/ijs.0.004689-02009Bacterial Typing Techniques, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, *Food Microbiology, Japan, Lactobacillus/*classification/*isolation & purification, Molecular Sequence Data, Polymorphism, Restriction Fragment Length, Rec A Recombinases/genetics, Sequence Analysis, DNABiotechnology
Phylogeny33174826Lentilactobacillus kribbianus sp. nov., isolated from the small intestine of a mini pig.Bai L, Paek J, Shin Y, Park HY, Chang YHInt J Syst Evol Microbiol10.1099/ijsem.0.0045602020Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Intestine, Small/*microbiology, Lactobacillaceae/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Swine, Swine, Miniature/*microbiologyTranscriptome
Phylogeny34913426Lentilactobacillus fungorum sp. nov., isolated from spent mushroom substrates.Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Ohkuma M, Kobayashi HInt J Syst Evol Microbiol10.1099/ijsem.0.0051842021*Agaricales, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Lactobacillaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny35522201Lentilactobacillus rapi subsp. dabitei subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product.Li Y, Li W, Luo R, Sakandar HA, Zhang H, Liu WInt J Syst Evol Microbiol10.1099/ijsem.0.0053592022Bacterial Typing Techniques, Base Composition, *Cultured Milk Products, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Lactic Acid, Lactobacillus, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny35576246Lentilactobacillus laojiaonis sp. nov., isolated from the mud in a fermentation cellar for the production of Chinese liquor.Zhao Q, Yang S, Bao G, Wang W, Miao L, Wang S, Shen C, Li YInt J Syst Evol Microbiol10.1099/ijsem.0.0053492022Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Ethanol, *Fatty Acids/chemistry, Fermentation, Humans, *Lactobacillaceae, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8379Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19907)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19907
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
33670Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7841
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/
68382Automatically annotated from API zym
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
76160Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362308.1StrainInfo: A central database for resolving microbial strain identifiers
122137Curators of the CIPCollection of Institut Pasteur (CIP 110029)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110029