Strain identifier

BacDive ID: 6661

Type strain: Yes

Species: Levilactobacillus acidifarinae

Strain Designation: R-19065, R-16065

Strain history: CIP <- 2005, CCM <- M. Vancanneyt, LMG <- P Neysens, IMDO, Vrije Univ., Brussels, Belgium: strain R-16065

NCBI tax ID(s): 1423715 (strain), 267364 (species)

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General

@ref: 8088

BacDive-ID: 6661

DSM-Number: 19394

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

description: Levilactobacillus acidifarinae R-19065 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from artisanal wheat sourdough.

NCBI tax id

NCBI tax idMatching level
1423715strain
267364species

strain history

@refhistory
8088<- CCM <- M. Vancanneyt, R-19065 <- P. Neysens
67770LMG 22200 <-- M. Vancanneyt R-19065 <-- P. Neysens.
115998CIP <- 2005, CCM <- M. Vancanneyt, LMG <- P Neysens, IMDO, Vrije Univ., Brussels, Belgium: strain R-16065

doi: 10.13145/bacdive6661.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus acidifarinae

@ref: 8088

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Levilactobacillus

species: Levilactobacillus acidifarinae

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

strain designation: R-19065, R-16065

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31309positive11 µm1 µmrod-shapedno
69480no95.803
69480positive100
115998positiverod-shapedno

pigmentation

  • @ref: 31309
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8088PEDIOCOCCUS 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
38291MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
115998CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8088positivegrowth30mesophilic
31309positiveoptimum7.5psychrophilic
38291positivegrowth37mesophilic
58765positivegrowth37mesophilic
67770positivegrowth30mesophilic
115998positivegrowth10-37
115998nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8088microaerophile
31309facultative anaerobe
58765anaerobe
115998facultative anaerobe

spore formation

@refspore formationconfidence
31309no
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
31309NaClpositivegrowth<5 %
31309NaClpositiveoptimum2.5 %

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
3130917234glucose+carbon source
3130917306maltose+carbon source
3130929864mannitol+carbon source
3130933942ribose+carbon source
3130918222xylose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-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
6837117992sucrose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-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
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11599817632nitrate-reduction
11599816301nitrite-reduction
11599817632nitrate+respiration

metabolite tests

  • @ref: 115998
  • 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
115998oxidase-
115998alcohol dehydrogenase-1.1.1.1
115998catalase-1.11.1.6
115998lysine decarboxylase-4.1.1.18
115998ornithine 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
115998-+--------+++++-+---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8088----+++---+++-----+---+--+--++/-+-+------------+-+--
115998---++/-+/----+/-++-----+/----+-----+---+/-------------+/--+/---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
8088artisanal wheat sourdoughBelgiumBELEurope
58765Wheat sourdoughBelgiumBELEurope
67770Wheat sourdough
115998Food, 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: LC483563
  • 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
80881Risk group (German classification)
1159981Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8088Lactobacillus acidifarinae 16S rRNA gene, type strain LMG 22200AJ6321581518ena267364
67770Lactobacillus acidifarinae gene for 16S ribosomal RNA, partial sequenceLC4835631508ena267364

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus acidifarinae DSM 193941423715.3wgspatric1423715
66792Lactobacillus acidifarinae strain NBRC 107156267364.3wgspatric267364
66792Levilactobacillus acidifarinae DSM 193942700989134draftimg1423715
67770Levilactobacillus acidifarinae DSM 19394GCA_001434835scaffoldncbi1423715
67770Levilactobacillus acidifarinae NBRC 107156GCA_007991975contigncbi267364

GC content

@refGC-contentmethod
808851
6777051high performance liquid chromatography (HPLC)
6777051.5genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.3yes
gram-positiveyes97.138no
anaerobicno78.091no
halophileyes86.869no
spore-formingno93.169yes
thermophileno99.747yes
glucose-utilyes89.387yes
aerobicno97.569yes
flagellatedno97.986yes
glucose-fermentyes85.149no

External links

@ref: 8088

culture collection no.: CCUG 50162, DSM 19394, CCM 7240, LMG 22200, JCM 15949, BCRC 80774, CIP 108702, NBRC 107156

straininfo link

  • @ref: 76135
  • straininfo: 10207

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
8088Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19394)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19394
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
38291Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6360
58765Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50162)https://www.ccug.se/strain?id=50162
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
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
76135Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10207.1StrainInfo: A central database for resolving microbial strain identifiers
115998Curators of the CIPCollection of Institut Pasteur (CIP 108702)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108702