Strain identifier

BacDive ID: 6660

Type strain: Yes

Species: Levilactobacillus zymae

Strain Designation: R-18615

Strain history: CIP <- 2005, CCM <- LMG <- P. Neyssen, IMDO, Vrije Univ., Brussels, Belgium: strain R-18615

NCBI tax ID(s): 1423817 (strain), 267363 (species)

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General

@ref: 8089

BacDive-ID: 6660

DSM-Number: 19395

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

description: Levilactobacillus zymae R-18615 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from artisanal wheat sourdough.

NCBI tax id

NCBI tax idMatching level
267363species
1423817strain

strain history

@refhistory
8089<- CCM <- M. Vancanneyt, R-18615 <- P. Neysens
67770LMG 22198 <-- M. Vancanneyt R-18615 <-- P. Neysens.
124040CIP <- 2005, CCM <- LMG <- P. Neyssen, IMDO, Vrije Univ., Brussels, Belgium: strain R-18615

doi: 10.13145/bacdive6660.20230509.8.1

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 zymae
  • full scientific name: Levilactobacillus zymae (Vancanneyt et al. 2005) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus zymae

@ref: 8089

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Levilactobacillus

species: Levilactobacillus zymae

full scientific name: Levilactobacillus zymae (Vancanneyt et al. 2005) Zheng et al. 2020

strain designation: R-18615

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31309positive11 µm1 µmrod-shapedno
69480no96.461
69480positive100
124040positiverod-shapedno

pigmentation

  • @ref: 31309
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8089PEDIOCOCCUS DAMNOSUS MEDIUM (DSMZ Medium 231)yeshttps://mediadive.dsmz.de/medium/231Name: PEDIOCOCCUS DAMNOSUS MEDIUM (DSMZ Medium 231) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Yeast extract 5.0 g/l Na-acetate 5.0 g/l K2HPO4 2.0 g/l (NH4)3 citrate 2.0 g/l Tween 80 1.0 g/l Cysteine hydrochloride 0.5 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
40644MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
124040CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8089positivegrowth30mesophilic
31309positiveoptimum7.5psychrophilic
40644positivegrowth37mesophilic
58766positivegrowth37mesophilic
67770positivegrowth30mesophilic
124040positivegrowth10-37
124040nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8089microaerophile
31309facultative anaerobe
58766anaerobe
124040facultative anaerobe

spore formation

@refspore formationconfidence
31309no
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
31309NaClpositivegrowth<7 %
31309NaClpositiveoptimum3.5 %

observation

  • @ref: 31309
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3130922599arabinose+carbon source
3130918403L-arabitol+carbon source
3130928757fructose+carbon source
3130924265gluconate+carbon source
3130917234glucose+carbon source
3130917306maltose+carbon source
31309506227N-acetylglucosamine+carbon source
3130933942ribose+carbon source
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol+builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12404017632nitrate-reduction
12404016301nitrite-reduction
12404017632nitrate+respiration

metabolite tests

  • @ref: 124040
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
124040oxidase-
124040alcohol dehydrogenase-1.1.1.1
124040catalase-1.11.1.6
124040lysine decarboxylase-4.1.1.18
124040ornithine decarboxylase-4.1.1.17

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8089----+++---+++-----+/----+--+--+++--------------+-+-+
8089----+++---+++-----+---+--+--++++-------------+-+-+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
8089artisanal wheat sourdoughBelgiumBELEurope
58766Wheat sourdoughBelgiumBELEurope
67770Wheat sourdough
124040Food, Wheat sourdoughBelgiumBELEurope2003

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6847.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_484;97_1758;98_2271;99_6847&stattab=map
  • Last taxonomy: Levilactobacillus
  • 16S sequence: LC480814
  • Sequence Identity:
  • Total samples: 2385
  • soil counts: 49
  • aquatic counts: 158
  • animal counts: 2008
  • plant counts: 170

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80891Risk group (German classification)
1240401Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8089Lactobacillus zymae 16S rRNA gene, type strain LMG 22198AJ6321571518ena267363
67770Lactobacillus zymae JCM 15957 gene for 16S ribosomal RNA, partial sequenceLC4808141505ena267363

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Levilactobacillus zymae NBRC 107157GCA_007991995contigncbi267363
66792Lactobacillus zymae DSM 193951423817.3wgspatric1423817
66792Lactobacillus zymae strain NBRC 107157267363.7wgspatric267363
66792Levilactobacillus zymae DSM 193952660238323draftimg1423817
67770Levilactobacillus zymae DSM 19395GCA_001434115scaffoldncbi1423817

GC content

@refGC-contentmethod
808953
3130954
6777053.6genome sequence analysis
6777053-54high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.059yes
gram-positiveyes96.536yes
anaerobicno80.161no
halophileyes89.944yes
spore-formingno93.314yes
glucose-utilyes92.634yes
thermophileno99.486yes
aerobicno97.169yes
flagellatedno97.946yes
glucose-fermentyes86.09no

External links

@ref: 8089

culture collection no.: DSM 19395, CCM 7241, LMG 22198, CCUG 50163, JCM 15957, BCRC 80776, CIP 108703, NBRC 107157

straininfo link

  • @ref: 76134
  • straininfo: 280627

literature

  • topic: Phylogeny
  • Pubmed-ID: 15774633
  • title: Lactobacillus acidifarinae sp. nov. and Lactobacillus zymae sp. nov., from wheat sourdoughs.
  • authors: Vancanneyt M, Neysens P, De Wachter M, Engelbeen K, Snauwaert C, Cleenwerck I, Van der Meulen R, Hoste B, Tsakalidou E, De Vuyst L, Swings J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63274-0
  • year: 2005
  • mesh: Bacterial Proteins/chemistry, Bacterial Typing Techniques, Base Composition, Bread/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Lactobacillus/*classification/genetics/growth & development/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Triticum/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8089Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19395)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19395
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
31309Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2762428776041
40644Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6361
58766Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50163)https://www.ccug.se/strain?id=50163
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
76134Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID280627.1StrainInfo: A central database for resolving microbial strain identifiers
124040Curators of the CIPCollection of Institut Pasteur (CIP 108703)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108703