Strain identifier

BacDive ID: 23077

Type strain: Yes

Species: Weissella oryzae

Strain history: M. Tohno SG25.

NCBI tax ID(s): 1129792 (species)

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General

@ref: 19278

BacDive-ID: 23077

DSM-Number: 25784

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

description: Weissella oryzae DSM 25784 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from fermented grice grains.

NCBI tax id

  • NCBI tax id: 1129792
  • Matching level: species

strain history

@refhistory
19278<- M. Tohno, National Agriculture and Food Res. Org. (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan; SG25
67770M. Tohno SG25.

doi: 10.13145/bacdive23077.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Weissella
  • species: Weissella oryzae
  • full scientific name: Weissella oryzae Tohno et al. 2013

@ref: 19278

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Weissella

species: Weissella oryzae

full scientific name: Weissella oryzae Tohno et al. 2013

type strain: yes

Morphology

cell morphology

  • @ref: 30752
  • gram stain: positive
  • cell length: 1.95 µm
  • cell width: 0.8 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 30752
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19278
  • name: MRS MEDIUM (DSMZ Medium 11)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/11
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
19278positivegrowth30mesophilic
30752positivegrowth10-42
67770positivegrowth30mesophilic

culture pH

  • @ref: 30752
  • ability: positive
  • type: growth
  • pH: 3.9-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
19278microaerophile
30752facultative anaerobe

spore formation

  • @ref: 30752
  • spore formation: no

halophily

  • @ref: 30752
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 4-6.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3075222599arabinose+carbon source
3075228757fructose+carbon source
3075228260galactose+carbon source
3075224265gluconate+carbon source
3075217234glucose+carbon source
3075217306maltose+carbon source
3075237684mannose+carbon source
3075228053melibiose+carbon source
30752506227N-acetylglucosamine+carbon source
3075233942ribose+carbon source
3075227082trehalose+carbon source
3075218222xylose+carbon source
68371Potassium 5-ketogluconate-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
6837117992sucrose-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
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
19278----+++----++---------+-----+---+-----------------
19278----+++----+++--------+-----+---+-----------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19278fermented grice grainsNasushiobara, TochigiJapanJPNAsia
67770Fermented rice grainsTochigiJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Vegetable (incl. Grains)
#Host#Plants#Herbaceous plants (Grass,Crops)
#Engineered#Food production#Fermented

taxonmaps

  • @ref: 69479
  • File name: preview.99_3901.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_155;96_519;97_786;98_2966;99_3901&stattab=map
  • Last taxonomy: Weissella
  • 16S sequence: LC521985
  • Sequence Identity:
  • Total samples: 2541
  • soil counts: 138
  • aquatic counts: 227
  • animal counts: 1907
  • plant counts: 269

Safety information

risk assessment

  • @ref: 19278
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
19278Weissella oryzae gene for 16S ribosomal RNA, partial sequence, strain: SG25AB6903451474ena1329250
67770Weissella oryzae JCM 18191 gene for 16S rRNA, partial sequenceLC5219851488ena1129792

GC content

@refGC-contentmethod
1927840.6high performance liquid chromatography (HPLC)
3075240.6

External links

@ref: 19278

culture collection no.: DSM 25784, JCM 18191, SG 25, LMG 30913

straininfo link

  • @ref: 87315
  • straininfo: 397106

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22843715Weissella oryzae sp. nov., isolated from fermented rice grains.Tohno M, Kitahara M, Inoue H, Uegaki R, Irisawa T, Ohkuma M, Tajima KInt J Syst Evol Microbiol10.1099/ijs.0.043612-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, Molecular Sequence Data, Oryza/*microbiology, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Weissella/*classification/genetics/isolation & purificationGenetics
Genetics25013139Draft Genome Sequence of Weissella oryzae SG25T, Isolated from Fermented Rice Grains.Tanizawa Y, Fujisawa T, Mochizuki T, Kaminuma E, Suzuki Y, Nakamura Y, Tohno MGenome Announc10.1128/genomeA.00667-142014Phylogeny
Enzymology25541486Botulinum neurotoxin homologs in non-Clostridium species.Mansfield MJ, Adams JB, Doxey ACFEBS Lett10.1016/j.febslet.2014.12.0182014Botulinum Toxins/*genetics/isolation & purification, Clostridium/chemistry/*genetics, Evolution, Molecular, Gene Transfer, Horizontal, Molecular Sequence Data, Multigene Family, Protein Structure, Tertiary, Tetanus Toxin/*genetics/isolation & purification, Weissella/chemistry/*geneticsPhylogeny
Pathogenicity27443638The first non Clostridial botulinum-like toxin cleaves VAMP within the juxtamembrane domain.Zornetta I, Azarnia Tehran D, Arrigoni G, Anniballi F, Bano L, Leka O, Zanotti G, Binz T, Montecucco CSci Rep10.1038/srep302572016Amino Acid Sequence/genetics, Botulinum Toxins/*chemistry/genetics, Cell Membrane/chemistry/genetics, Clostridium botulinum/genetics, Genome, Bacterial, Metalloproteases/*chemistry/genetics, Models, Molecular, Molecular Dynamics Simulation, Neurotoxins/*chemistry/genetics, Protein Binding, Protein Domains, Protein Folding, Weissella/chemistry/*geneticsGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19278Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25784)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25784
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
30752Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2708328776041
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
87315Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397106.1StrainInfo: A central database for resolving microbial strain identifiers