Name: Weissella koreensis S-5623
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6854

Type strain:

Species: Weissella koreensis

Strain Designation: S-5623

Culture col. no.: DSM 15830, CCUG 47134, CIP 107634, JCM 11263, KCCM 41516, KCTC 3621

Strain history: CIP <- 2002, JCM <- 2001, J.S. Lee: strain S-5623

NCBI tax ID(s): 1123721 (strain), 165096 (species)

SI-ID 101064

JCM 11263, KCTC 3621, CCUG 47134, CIP 107634, DSM 15830, CECT 7110

Special Collections

Other strains from Weissella koreensis

Section

When using BacDive for research please cite our paper

Weissella koreensis S-5623 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from kimchi, fermented vegetable food.

Gram-positive
rod-shaped
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Lactobacillaceae*
	Genus	*Weissella*
	Species	**Weissella koreensis**
	Full Scientific Name (LPSN)	Weissella koreensis Lee et al. 2002

Information on morphological and physiological properties Morphology

[Ref.: #120492]	Gram stain	positive
[Ref.: #125438]	Gram stain	positive Confidence in %93.06

[Ref.: #120492]	Cell shape	rod-shaped

[Ref.: #120492]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %95.5

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6042]

Culture medium

WEISSELA KOREENSIS MEDIUM (DSMZ Medium 232b)

[Ref.: #6042]

Culture medium growth

[Ref.: #6042]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6042]

Culture medium composition

expand / minimize

[Ref.: #39910]

Culture medium

MEDIUM 40- for Lactobacillus and Leuconostoc

[Ref.: #39910]

Culture medium growth

[Ref.: #39910]

Culture medium composition

expand / minimize

[Ref.: #120492]

Culture medium

CIP Medium 40

[Ref.: #120492]

Culture medium growth

[Ref.: #120492]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6042]		growth	30 °C
[Ref.: #39910]		growth	30 °C
[Ref.: #57527]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #120492]		growth	10-37 °C
[Ref.: #120492]	negative	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6042]	Oxygen tolerance	anaerobe
[Ref.: #57527]	Oxygen tolerance	anaerobe
[Ref.: #120492]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	facultative anaerobe Confidence in %94.8

[Ref.: #125438]

Ability of spore formation

no Confidence in %92.707

[Ref.: #6042]	Murein short key	A11.13
[Ref.: #6042]	Murein types	A3alpha L-Lys-L-Ala-L-Ser

	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]	cellobiose 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-galactose 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-mannose 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]	gentiobiose 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]	lactose 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-glucopyranoside 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.: #68371]	N-acetylglucosamine ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #120492]	nitrate ChEBI	-	reduction
[Ref.: #120492]	nitrate ChEBI	+	respiration
[Ref.: #120492]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose 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.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #120492]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #120492]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120492]	alcohol dehydrogenase	-	1.1.1.1
[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.: #120492]	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.: #120492]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120492]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120492]	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.: #120492]	11068	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.: #120492]	10525	-	-	-	-	-	+	-	-	-	-	+	+	-	+	-	-	-	-	-	-

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

[Ref.: #6042]	Sample type/isolated from	kimchi, fermented vegetable food
[Ref.: #6042]	Geographic location (country and/or sea, region)	Korea
[Ref.: #6042]	Country	Republic of Korea
[Ref.: #6042]	Country ISO 3 Code	KOR
[Ref.: #6042]	Continent	Asia

[Ref.: #57527]	Sample type/isolated from	Traditional Korean fermented-vegetable food

[Ref.: #67770]	Sample type/isolated from	Traditional Korean fermented-vegetable food (Kimchi)

[Ref.: #120492]	Sample type/isolated from	Food, Kimuchi, Fermented vegetable food
[Ref.: #120492]	Country	Republic of Korea
[Ref.: #120492]	Country ISO 3 Code	KOR
[Ref.: #120492]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Food production	#Vegetable (incl. Grains)
#Engineered	#Food production	#Fermented

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC145573 (>99% sequence identity) for Weissella koreensis subclade from Microbeatlas

Aquatic Samples	1074
Soil Samples	523
Animal Samples	7440
Plant Samples	644
Total Samples	9681

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

[Ref.: #6042]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120492]	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.: #67770]	Weissella koreensis isolate S-5623 16S ribosomal RNA gene, partial sequence	AY035891	1497	GenBank ENA	165096 tax ID
[Ref.: #67770]	Weissella koreensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 11263	LC145573	1508	GenBank ENA	165096 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Weissella koreensis KCTC 3621	GCA_000277645	contig	GenBank ENA	1123721 tax ID	*
[Ref.: #66792]	Weissella koreensis KCTC 3621	1123721.3	wgs	PATRIC	1123721 tax ID	*

[Ref.: #6042]	GC-content	37 mol%
[Ref.: #67770]	GC-content	37 mol%	high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Weissella koreensis KCTC 3621 PATRIC: 1123721.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	93.06	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	81.022	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	92.707	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	92.969	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	95.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Weissella koreensis KCTC 3621 NCBI: GCA_000277645
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	facultative anaerobe	94.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	86.3
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	62.9
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	64.4

Availability in culture collections External links

[Ref.: #6042]

Culture collection no.

DSM 15830, CCUG 47134, CIP 107634, JCM 11263, KCCM 41516, KCTC 3621

[Ref.: #76319]

SI-ID 101064

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic and metatranscriptomic analyses of Weissella koreensis reveal its metabolic and fermentative features during kimchi fermentation.	Jeong SE, Chun BH, Kim KH, Park D, Roh SW, Lee SH, Jeon CO	Food Microbiol	10.1016/j.fm.2018.04.003	2018	*
Phylogeny	Weissella diestrammenae sp. nov., isolated from the gut of a camel cricket (Diestrammena coreana).	Oh SJ, Shin NR, Hyun DW, Kim PS, Kim JY, Kim MS, Yun JH, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.047548-0	2013	*
Genetics	Draft genome sequence of Weissella koreensis KCTC 3621T.	Lee JH, Bae JW, Chun J	J Bacteriol	10.1128/JB.01356-12	2012	*
Phylogeny	Weissella koreensis sp. nov., isolated from kimchi.	Lee JS, Lee KC, Ahn JS, Mheen TI, Pyun YR, Park YH	Int J Syst Evol Microbiol	10.1099/00207713-52-4-1257	2002	*

References

#6042

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15830

#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 )

#39910 ; Curators of the CIP;
#57527 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 47134

#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 .

#76319

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-ID101064.1 )

#120492 Collection of Institut Pasteur ; Curators of the CIP; CIP 107634

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* These data were automatically processed and therefore are not curated

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Weissella koreensis KCTC 3621

Weissella koreensis KCTC 3621

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