Strain identifier

BacDive ID: 6679

Type strain: Yes

Species: Levilactobacillus senmaizukei

Strain Designation: L13

Strain history: CIP <- 2008, NBRC <- K. Hiraga, Kyoto Inst. of Technol., Japan: strain L13

NCBI tax ID(s): 431273 (species)

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General

@ref: 15940

BacDive-ID: 6679

DSM-Number: 21775

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped

description: Levilactobacillus senmaizukei L13 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from pickles.

NCBI tax id

  • NCBI tax id: 431273
  • Matching level: species

strain history

@refhistory
15940<- NBRC <- K. Hiraga and K. Oda, Kyoto Inst. Technol., Graduate School, Dept. Appl. Biol., Kyoto, Japan; L13
122558CIP <- 2008, NBRC <- K. Hiraga, Kyoto Inst. of Technol., Japan: strain L13

doi: 10.13145/bacdive6679.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Levilactobacillus
  • species: Levilactobacillus senmaizukei
  • full scientific name: Levilactobacillus senmaizukei (Hiraga et al. 2008) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus senmaizukei

@ref: 15940

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Levilactobacillus

species: Levilactobacillus senmaizukei

full scientific name: Levilactobacillus senmaizukei (Hiraga et al. 2008) Zheng et al. 2020

strain designation: L13

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32553positive3 µm0.65 µmrod-shapedno
69480no96.067
69480positive100
122558positiverod-shapedno

pigmentation

  • @ref: 32553
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15940MRS 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
37666MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
122558CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
15940positivegrowth30mesophilic
32553positivegrowth15psychrophilic
37666positivegrowth30mesophilic
122558positivegrowth15-37
122558nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
15940anaerobe
15940microaerophile
32553facultative anaerobe
122558facultative anaerobe

spore formation

@refspore formationconfidence
32553no
69481no100
69480no99.992

halophily

  • @ref: 32553
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <8 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
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
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
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
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122558nitrate-reduction17632
122558nitrite-reduction16301
122558nitrate+respiration17632

metabolite tests

  • @ref: 122558
  • 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
122558oxidase-
122558alcohol dehydrogenase-1.1.1.1
122558catalase-1.11.1.6
122558lysine decarboxylase-4.1.1.18
122558ornithine 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
122558-++--+----++-+--+---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
15940-----++----++---------+--+--+------------------+--
122558----+/-+/----+/-+/-+/----------+/---+/---+/-------------------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
15940picklesUzumasa, KyotoJapanJPNAsia
122558Japanese pickleJapanJPNAsia2008

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6777.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_484;97_553;98_1175;99_6777&stattab=map
  • Last taxonomy: Levilactobacillus
  • 16S sequence: AB297927
  • Sequence Identity:
  • Total samples: 921
  • soil counts: 117
  • aquatic counts: 119
  • animal counts: 507
  • plant counts: 178

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
159401Risk group (German classification)
1225581Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus senmaizukei gene for 16S rRNA, partial sequence, strain: NBRC 103853AB6821401491ena1423803
15940Lactobacillus senmaizukei gene for 16S rRNA, partial sequenceAB2979271447ena1423803

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Levilactobacillus senmaizukei DSM 21775 = NBRC 103853GCA_001592085contigncbi1423803
66792Levilactobacillus senmaizukei DSM 21775 = NBRC 103853GCA_001436675scaffoldncbi1423803
66792Lactobacillus senmaizukei DSM 21775 = NBRC 1038531423803.3wgspatric1423803
66792Lactobacillus senmaizukei DSM 21775 = NBRC 1038531423803.4wgspatric1423803
66792Lactobacillus senmaizukei NBRC 1038532731957679draftimg1423803
66792Lactobacillus senmaizukei DSM 217752663763016draftimg1423803

GC content

@refGC-content
1594046.0
3255346

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno98.666yes
gram-positiveyes95.295no
anaerobicno90.879no
halophileyes92.361yes
spore-formingno94.936no
glucose-utilyes90.406no
motileno95.328yes
aerobicno96.421yes
thermophileno99.786yes
glucose-fermentyes84.596no

External links

@ref: 15940

culture collection no.: DSM 21775, NBRC 103853, TISTR 1847, CIP 109886

straininfo link

  • @ref: 76153
  • straininfo: 358817

literature

  • topic: Phylogeny
  • Pubmed-ID: 18599706
  • title: Lactobacillus senmaizukei sp. nov., isolated from Japanese pickle.
  • authors: Hiraga K, Ueno Y, Sukontasing S, Tanasupawat S, Oda K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65677-0
  • year: 2008
  • mesh: *Food Microbiology, Japan, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Biotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
15940Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21775)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21775
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
32553Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128771
37666Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7681
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)
68371Automatically annotated from API 50CH acid
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
76153Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID358817.1StrainInfo: A central database for resolving microbial strain identifiers
122558Curators of the CIPCollection of Institut Pasteur (CIP 109886)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109886