Name: Oenococcus kitaharae DSM 17330
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6813

Type strain:

Species: Oenococcus kitaharae

Culture col. no.: DSM 17330, JCM 13282, NRIC 0645, CIP 109430

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

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

SI-ID 297270

DSM 17330, JCM 13282, CIP 109430, LMG 24489

Section

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

mesophilic
microaerophile
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Lactobacillaceae*
	Genus	*Oenococcus*
	Species	**Oenococcus kitaharae**
	Full Scientific Name (LPSN)	Oenococcus kitaharae Endo and Okada 2006

Information on morphological and physiological properties Morphology

[Ref.: #120448]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #120448]	Cell shape	coccus-shaped

[Ref.: #120448]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %97.977

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6898]

Culture medium

MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232)

[Ref.: #6898]

Culture medium growth

[Ref.: #6898]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6898]

Culture medium composition

expand / minimize

[Ref.: #37552]

Culture medium

MEDIUM 40- for Lactobacillus and Leuconostoc

[Ref.: #37552]

Culture medium growth

[Ref.: #37552]

Culture medium composition

expand / minimize

[Ref.: #120448]

Culture medium

CIP Medium 40

[Ref.: #120448]

Culture medium growth

[Ref.: #120448]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6898]		growth	30 °C
[Ref.: #37552]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #120448]		growth	15-37 °C
[Ref.: #120448]	no	growth	45 °C

[Ref.: #6898]	Temperature range	mesophilic
[Ref.: #37552]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #120448]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6898]	Oxygen tolerance	microaerophile
[Ref.: #120448]	Oxygen tolerance	facultative anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #120448]	nitrate ChEBI	-	reduction
[Ref.: #120448]	nitrate ChEBI	+	respiration
[Ref.: #120448]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #120448]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #120448]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120448]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #6898]	14359	-	-	-	-	-	+	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
[Ref.: #6898]	14358	-	-	-	-	-	+	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	-	-	+	-	-	+	+	+	+	+	-	-	-	+	-	-	+	-	-	-	-	-	-	-	+	-	+
[Ref.: #120448]	11557	not determinedn.d.	-	-	-	-	+	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	+/-	+/-	-	-	+	+/-	+/-	+	-	+	-	+	-	-	+/-	+/-	-	-	+	-	-	-	-	-	-	-	+	-	+

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #120448]	11859	-	-	+	-	-	+	+	+	-	+	+	+	+	-	-	+	+	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6898]	Sample type/isolated from	fermentation samples of distilled residue of shochu mashes
[Ref.: #6898]	Geographic location (country and/or sea, region)	Miyazaki
[Ref.: #6898]	Country	Japan
[Ref.: #6898]	Country ISO 3 Code	JPN
[Ref.: #6898]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Composting distilled shochu residue

[Ref.: #120448]	Sample type/isolated from	Environment, Composting distilled shochu residue
[Ref.: #120448]	Country	Japan
[Ref.: #120448]	Country ISO 3 Code	JPN
[Ref.: #120448]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Food production

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC483551 (>99% sequence identity) for Oenococcus kitaharae subclade from Microbeatlas

Aquatic Samples	98
Soil Samples	21
Animal Samples	284
Plant Samples	77
Total Samples	480

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #6898]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120448]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #6898]	Oenococcus kitaharae gene for 16S rRNA, partial sequence	AB221475	1494	ENA	1045004 tax ID
[Ref.: #67770]	Oenococcus kitaharae gene for 16S ribosomal RNA, partial sequence	LC483551	1486	ENA	336988 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Oenococcus kitaharae DSM 17330	GCA_000428085	scaffold	GenBank	1045004 tax ID
[Ref.: #66792]	Oenococcus kitaharae DSM 17330	GCA_000241055	complete	GenBank	1045004 tax ID	*
[Ref.: #66792]	Oenococcus kitaharae DSM 17330	1045004.5	wgs	PATRIC	1045004 tax ID	*
[Ref.: #66792]	Oenococcus kitaharae DSM 17330	1045004.4	wgs	PATRIC	1045004 tax ID	*
[Ref.: #66792]	Oenococcus kitaharae DSM 17330	1045004.6	plasmid	PATRIC	1045004 tax ID	*
[Ref.: #66792]	Oenococcus kitaharae NRIC 0645, DSM 17330	2524614648	draft	JGI IMG/M	1045004 tax ID	*

[Ref.: #6898]	GC-content	41 mol%
[Ref.: #67770]	GC-content	41 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Oenococcus kitaharae DSM 17330 DSM 17330 NCBI: GCA_000241055.1
[Ref.: #69481]	spore-forming	no	100	no

Availability in culture collections External links

[Ref.: #6898]

Culture collection no.

DSM 17330, JCM 13282, NRIC 0645, CIP 109430

[Ref.: #76279]

SI-ID 297270

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Processivity 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 C	J Biol Chem	10.1074/jbc.RA119.011995	2020	*
Metabolism	A 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 C	Carbohydr Polym	10.1016/j.carbpol.2017.09.056	2017	*
Genetics	Functional divergence in the genus Oenococcus as predicted by genome sequencing of the newly-described species, Oenococcus kitaharae.	Borneman AR, McCarthy JM, Chambers PJ, Bartowsky EJ	PLoS One	10.1371/journal.pone.0029626	2012	*
Phylogeny	Oenococcus kitaharae sp. nov., a non-acidophilic and non-malolactic-fermenting oenococcus isolated from a composting distilled shochu residue.	Endo A, Okada S	Int J Syst Evol Microbiol	10.1099/ijs.0.64288-0	2006	*

References

#6898

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17330

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#37552 ; Curators of the CIP;

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#69479

João 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76279

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID297270.1 )

#120448 Collection of Institut Pasteur ; Curators of the CIP; CIP 109430
* These data were automatically processed and therefore are not curated

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Oenococcus kitaharae DSM 17330 DSM 17330

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