Strain identifier

BacDive ID: 6813

Type strain: Yes

Species: Oenococcus kitaharae

Strain history: CIP <- 2006, JCM <- 2005, A. Endo, NODAI, Tokyo, Japan: strain NRIC 0645

NCBI tax ID(s): 1045004 (strain), 336988 (species)

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General

@ref: 6898

BacDive-ID: 6813

DSM-Number: 17330

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic

description: Oenococcus kitaharae DSM 17330 is a microaerophile, mesophilic bacterium that was isolated from fermentation samples of distilled residue of shochu mashes.

NCBI tax id

NCBI tax idMatching level
336988species
1045004strain

strain history

@refhistory
6898<- A. Endo <- A. Endo and S. Okada
67770A. Endo NRIC 0645.
120448CIP <- 2006, JCM <- 2005, A. Endo, NODAI, Tokyo, Japan: strain NRIC 0645

doi: 10.13145/bacdive6813.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Oenococcus
  • species: Oenococcus kitaharae
  • full scientific name: Oenococcus kitaharae Endo and Okada 2006

@ref: 6898

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Oenococcus

species: Oenococcus kitaharae

full scientific name: Oenococcus kitaharae Endo and Okada 2006

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no97.977
69480100positive
120448nopositivecoccus-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6898MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232)yeshttps://mediadive.dsmz.de/medium/232Name: MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232; with strain-specific modifications) Composition: Tomato juice 100.0 g/l 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)2 citrate 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
37552MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
120448CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
6898positivegrowth30mesophilic
37552positivegrowth30mesophilic
67770positivegrowth30mesophilic
120448positivegrowth15-37
120448nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6898microaerophile
120448facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371melibiose+builds acid from28053
68371maltose+builds acid from17306
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120448nitrate-reduction17632
120448nitrite-reduction16301
120448nitrate+respiration17632

metabolite tests

  • @ref: 120448
  • 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
120448oxidase-
120448catalase-1.11.1.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120448--+--+++-++++--++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
6898-----+-----+++-----------+-++-+-+-----------------
6898-----+----++++--------+--+--+++++---+--+-------+-+
120448----+-----+++-------+/-+/---++/-+/-+-+-+--+/-+/---+-------+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6898fermentation samples of distilled residue of shochu mashesMiyazakiJapanJPNAsia
67770Composting distilled shochu residue
120448Environment, Composting distilled shochu residueJapanJPNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production

taxonmaps

  • @ref: 69479
  • File name: preview.99_148.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16020;96_109;97_116;98_129;99_148&stattab=map
  • Last taxonomy: Oenococcus kitaharae subclade
  • 16S sequence: LC483551
  • Sequence Identity:
  • Total samples: 480
  • soil counts: 21
  • aquatic counts: 98
  • animal counts: 284
  • plant counts: 77

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
68981Risk group (German classification)
1204481Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6898Oenococcus kitaharae gene for 16S rRNA, partial sequenceAB2214751494ena1045004
67770Oenococcus kitaharae gene for 16S ribosomal RNA, partial sequenceLC4835511486ena336988

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oenococcus kitaharae DSM 17330GCA_000241055completencbi1045004
66792Oenococcus kitaharae DSM 173301045004.5wgspatric1045004
66792Oenococcus kitaharae DSM 173301045004.4wgspatric1045004
66792Oenococcus kitaharae DSM 173301045004.6plasmidpatric1045004
66792Oenococcus kitaharae NRIC 0645, DSM 173302524614648draftimg1045004
66792Oenococcus kitaharae NRIC 0645, DSM 173302597489884completeimg1045004
67770Oenococcus kitaharae DSM 17330GCA_000428085scaffoldncbi1045004

GC content

@refGC-contentmethod
689841
6777041high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 100
  • training_data: no

External links

@ref: 6898

culture collection no.: DSM 17330, JCM 13282, NRIC 0645, CIP 109430

straininfo link

  • @ref: 76279
  • straininfo: 297270

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17012559Oenococcus kitaharae sp. nov., a non-acidophilic and non-malolactic-fermenting oenococcus isolated from a composting distilled shochu residue.Endo A, Okada SInt J Syst Evol Microbiol10.1099/ijs.0.64288-02006Alcoholic Beverages/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fermentation, Genes, rRNA, Gram-Positive Cocci/*classification/genetics/isolation & purification/physiology, Hordeum/*microbiology, Hydrogen-Ion Concentration, Ipomoea batatas/*microbiology, Japan, Lactic Acid/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Genetics22235313Functional divergence in the genus Oenococcus as predicted by genome sequencing of the newly-described species, Oenococcus kitaharae.Borneman AR, McCarthy JM, Chambers PJ, Bartowsky EJPLoS One10.1371/journal.pone.00296262012Amino Acids/biosynthesis, Carbohydrate Metabolism/genetics, Chromosomes, Bacterial/genetics, Genome, Bacterial/*genetics, Genomics, Lactic Acid/metabolism, Oenococcus/*genetics/metabolism/physiology, Phenotype, Reproduction/geneticsMetabolism
Metabolism29111031A dextran with unique rheological properties produced by the dextransucrase from Oenococcus kitaharae DSM 17330.Vuillemin M, Grimaud F, Claverie M, Rolland-Sabate A, Garnier C, Lucas P, Monsan P, Dols-Lafargue M, Remaud-Simeon M, Moulis CCarbohydr Polym10.1016/j.carbpol.2017.09.0562017Amino Acid Sequence, Biocatalysis, Carbohydrate Conformation, Databases, Protein, Dextrans/*biosynthesis, Glucosyltransferases/genetics/*metabolism, Oenococcus/*enzymology/genetics, Recombinant Proteins/genetics/*metabolism, Sucrose/chemistry/metabolism, ViscosityEnzymology
Metabolism32161118Processivity of dextransucrases synthesizing very-high-molar-mass dextran is mediated by sugar-binding pockets in domain V.Claverie M, Cioci G, Vuillemin M, Bondy P, Remaud-Simeon M, Moulis CJ Biol Chem10.1074/jbc.RA119.0119952020Bacterial Proteins/chemistry/*metabolism, Binding Sites, Biosynthetic Pathways, Dextrans/*metabolism, Glucosyltransferases/chemistry/*metabolism, Models, Molecular, Oenococcus/chemistry/*metabolism, Protein DomainsEnzymology

Reference

@idauthorscataloguedoi/urltitle
6898Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17330)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17330
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
37552Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7171
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
76279Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297270.1StrainInfo: A central database for resolving microbial strain identifiers
120448Curators of the CIPCollection of Institut Pasteur (CIP 109430)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109430