Workshop and Q&A October 6th

Strain identifier

BacDive ID: 24133

Type strain: Yes

Species: Secundilactobacillus oryzae

Strain history: <- DSM <- M Tohno, National Agriculture and Food Res Org (NARO), Nat. Inst. of Livestock and Grassland Science, Tochigi, Japan, SG293

NCBI tax ID(s): 1202668 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 7 (current version):
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 7 (current version)

General

@ref: 20993

BacDive-ID: 24133

DSM-Number: 26518

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

description: Secundilactobacillus oryzae DSM 26518 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from fermented rice grains.

NCBI tax id

  • NCBI tax id: 1202668
  • Matching level: species

strain history

doi: 10.13145/bacdive24133.20220920.7

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Secundilactobacillus
  • species: Secundilactobacillus oryzae
  • full scientific name: Secundilactobacillus oryzae (Tohno et al. 2013) Zheng et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus oryzae

@ref: 20993

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Secundilactobacillus

species: Secundilactobacillus oryzae

full scientific name: Secundilactobacillus oryzae (Tohno et al. 2013) Zheng et al. 2020

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30984positive5 µm1 µmrod-shapedno
67771rod-shapedno
67771positive

pigmentation

  • @ref: 30984
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33558MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
20993MRS MEDIUM (DSMZ Medium 11)yesName: 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 waterhttps://bacmedia.dsmz.de/medium/11

culture temp

@refgrowthtypetemperaturerange
20993positivegrowth30mesophilic
30984positivegrowth04-45
30984positiveoptimum30mesophilic
33558positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

  • @ref: 30984
  • ability: positive
  • type: growth
  • pH: 5.0-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
20993microaerophile
30984facultative anaerobe
67771microaerophile

spore formation

@refspore formation
30984no
67771no

halophily

  • @ref: 30984
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 04-08 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30984168082-dehydro-D-gluconate+carbon source
3098424265gluconate+carbon source
3098417234glucose+carbon source
3098417306maltose+carbon source
30984506227N-acetylglucosamine+carbon source
3098433942ribose+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
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

enzymes

@refvalueactivityec
30984acid phosphatase+3.1.3.2
30984alkaline phosphatase+3.1.3.1

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
20993-----+-----+-------------+--+---------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
20993fermented rice grainsTochigi, OhtawaraJapanJPNAsia
67770Fermented rice grain (Oryza sativa L. subsp. japonica)Ohtawara, TochigiJapanJPNAsiaOryza sativa L. subsp. japonica
67771From fermented rice grainsTochigi, OhtawaraJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 20993
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20993Lactobacillus oryzae gene for 16S ribosomal RNA, partial sequence, strain: SG293AB7316601488ena1291743
67770Lactobacillus oryzae JCM 18671 gene for 16S rRNA, partial sequenceLC5219921502ena1291743

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Schleiferilactobacillus oryzae JCM 18671 SG293GCA_000740055contigncbi1291743
66792Schleiferilactobacillus oryzae JCM 18671 JCM 18671GCA_001311525contigncbi1291743
66792Lactobacillus oryzae JCM 186711291743.4wgspatric1291743
66792Lactobacillus oryzae JCM 186711291743.3wgspatric1291743
66792Secundilactobacillus oryzae JCM 186712728369689draftimg1291743
67771Schleiferilactobacillus oryzae JCM 18671 strain SG293, whole genome shotgun sequencing projectBBJM00000000ncbi1291743

GC content

@refGC-contentmethod
2099343.4high performance liquid chromatography (HPLC)
3098443.4
6777042.8genome sequence analysis

External links

@ref: 20993

culture collection no.: DSM 26518, JCM 18671, KCTC 21047, SG 293

straininfo link

@refpassport
20218http://www.straininfo.net/strains/890449
20218http://www.straininfo.net/strains/890448

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23378109Lactobacillus oryzae sp. nov., isolated from fermented rice grain (Oryza sativa L. subsp. japonica).Tohno M, Kitahara M, Irisawa T, Inoue H, Uegaki R, Ohkuma M, Tajima KInt J Syst Evol Microbiol10.1099/ijs.0.048918-02013Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, *Fermentation, Food Microbiology, Japan, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNABiotechnology
Genetics25169865Draft Genome Sequence of Lactobacillus oryzae Strain SG293T.Tanizawa Y, Fujisawa T, Mochizuki T, Kaminuma E, Nakamura Y, Tohno MGenome Announc10.1128/genomeA.00861-142014

Reference

@idauthorstitledoi/urljournalpubmedcatalogueID_cross_reference
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
20993Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26518Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26518)
2731410.1099/ijs.0.048918-023378109
30984Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604127314
33558Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30383
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid