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/bacdive6660.20250331.9.3

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
124040positiverod-shapedno
125438no90
125438positive93.214

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

@refgrowthtypetemperature
8089positivegrowth30
31309positiveoptimum7.5
40644positivegrowth37
58766positivegrowth37
67770positivegrowth30
124040positivegrowth10-37
124040nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8089microaerophile
31309facultative anaerobe
58766anaerobe
124040facultative anaerobe
125439anaerobe96.8

spore formation

@refspore formationconfidence
31309no
125439no94

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
12404017632nitrate-reduction
12404016301nitrite-reduction
12404017632nitrate+respiration
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
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
6837159640N-acetylglucosamine+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
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

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 22198AJ6321571518nuccore267363
67770Lactobacillus zymae JCM 15957 gene for 16S ribosomal RNA, partial sequenceLC4808141505nuccore267363
124043Lactobacillus zymae gene for 16S rRNA, partial sequence, strain: NBRC 107157.AB6260711491nuccore267363

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes93.214yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no81.953no
125438spore-formingspore-formingAbility to form endo- or exosporesno79.525no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no94.864yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.577yes
125438motile2+flagellatedAbility to perform flagellated movementno90yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94
125439BacteriaNetmotilityAbility to perform movementno82.9
125439BacteriaNetgram_stainReaction to gram-stainingpositive81.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe96.8

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
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
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1