Secundilactobacillus kimchicus (KCTC 12976, JCM 15530, DCY 51)

Name: Secundilactobacillus kimchicus (KCTC 12976, JCM 15530, DCY 51)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133577

Type strain

Culture col. no. KCTC 12976 JCM 15530 DCY 51

NCBI tax ID(s) 528209

Special Collections JCM KCTC Literature strains

History D.-C. Yang DCY51. <- DC Yang, Kyunghee Univ.

Links

Secundilactobacillus kimchicus KCTC 12976 is a facultative aerobe, Gram-positive, rod-shaped bacterium that was isolated from food product.

Gram-positive rod-shaped facultative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 272238

LMG 29609,KCTC 12976,JCM 15530

@ref 20215

Last LPSN update 2026-02-09 11:31:58

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Secundilactobacillus

Species Secundilactobacillus kimchicus

Full scientific name Secundilactobacillus kimchicus (Liang et al. 2011) Zheng et al. 2020

Synonyms (1)

Lactobacillus kimchicus

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29632	positive	1.5 µm	0.55 µm	rod-shaped
67771				rod-shaped
67771	positive
125438	positive				95.641

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29632	positive	growth	15-45
29632	positive	optimum	37
67770	positive	growth	37
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH
29632	positive	optimum	6.5
29632	positive	growth	06-07

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29632	facultative aerobe
67771	facultative anaerobe
125439	microaerophile	95.6

Spore formation

@ref	Spore formation
29632
67771

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29632	NaCl	positive	growth	0-8 %
29632	NaCl	positive	optimum	4 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29632	28757 ChEBI	fructose	+	carbon source
29632	28260 ChEBI	galactose	+	carbon source
29632	24265 ChEBI	gluconate	+	carbon source
29632	17306 ChEBI	maltose	+	carbon source
29632	29864 ChEBI	mannitol	+	carbon source
29632	37684 ChEBI	mannose	+	carbon source
29632	506227 ChEBI	N-acetylglucosamine	+	carbon source
29632	33942 ChEBI	ribose	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	L-lactaldehyde degradation	100	3 of 3
66794	acetoin degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	acetate fermentation	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	vitamin K metabolism	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	ribulose monophosphate pathway	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	teichoic acid biosynthesis	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	vitamin B1 metabolism	92.31	12 of 13
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	pyrimidine metabolism	82.22	37 of 45
66794	threonine metabolism	80	8 of 10
66794	Entner Doudoroff pathway	80	8 of 10
66794	purine metabolism	79.79	75 of 94
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	glutamate and glutamine metabolism	75	21 of 28
66794	photosynthesis	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	serine metabolism	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	formaldehyde oxidation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	d-xylose degradation	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	methylglyoxal degradation	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	methionine metabolism	57.69	15 of 26
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	degradation of pentoses	57.14	16 of 28
66794	cysteine metabolism	55.56	10 of 18
66794	non-pathway related	55.26	21 of 38
66794	alanine metabolism	55.17	16 of 29
66794	histidine metabolism	55.17	16 of 29
66794	proline metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	degradation of sugar acids	52	13 of 25
66794	oxidative phosphorylation	51.65	47 of 91
66794	lactate fermentation	50	2 of 4
66794	tryptophan metabolism	50	19 of 38
66794	adipate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	degradation of hexoses	50	9 of 18
66794	glutathione metabolism	50	7 of 14
66794	sulfopterin metabolism	50	2 of 4
66794	urea cycle	46.15	6 of 13
66794	lipid metabolism	45.16	14 of 31
66794	d-mannose degradation	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	citric acid cycle	42.86	6 of 14
66794	mevalonate metabolism	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	lysine metabolism	40.48	17 of 42
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	vitamin B6 metabolism	36.36	4 of 11
66794	cyanate degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	octane oxidation	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	flavin biosynthesis	33.33	5 of 15
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	starch degradation	30	3 of 10
66794	tyrosine metabolism	28.57	4 of 14
66794	ascorbate metabolism	27.27	6 of 22
66794	vitamin B12 metabolism	26.47	9 of 34
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	glycogen biosynthesis	25	1 of 4
66794	sulfate reduction	23.08	3 of 13
66794	allantoin degradation	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Food

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
29632	food product
67770	Kimchi	Gyeonggi Province	Republic of Korea	KOR	Asia
67771	From kimchi	Gyeonggi Province	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC480811 (>99% sequence identity) for Secundilactobacillus kimchicus subclade from Microbeatlas

Aquatic Samples	44
Soil Samples	35
Animal Samples	358
Plant Samples	50
Total Samples	487

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM143399v1 assembly for Secundilactobacillus kimchicus JCM 15530	contig	GCA_001433995	1302272.5	2657245468	1302272	70.4
67771	ASM131320v1 assembly for Secundilactobacillus kimchicus JCM 15530	contig	GCA_001313205	1302272.4	2734481936	1302272	31.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29632	Lactobacillus kimchicus JCM 15530 strain DCY51 16S ribosomal RNA gene, partial sequence	EU678893	1499		1302272
67771	Lactobacillus kimchicus JCM 15530 gene for 16S ribosomal RNA, partial sequence	LC480811	1504		1302272

GC content

@ref	GC-content (mol%)	Method
29632	39.7
67770	46.6	genome sequence analysis
67771	39.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Secundilactobacillus kimchicus JCM 15530
NCBI: GCA_001433995

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	76.10	no
125439	motility	BacteriaNetⓘ	no	70.30	no
125439	gram_stain	BacteriaNetⓘ	positive	89.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	95.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus kimchicus JCM 15530
PATRIC: 1302272.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	95.64	yes
125438	anaerobic	anaerobicⓘ	no	82.76	yes
125438	spore-forming	spore-formingⓘ	no	85.08	yes
125438	aerobic	aerobicⓘ	no	92.68	yes
125438	thermophilic	thermophileⓘ	no	94.86	yes
125438	flagellated	motile2+ⓘ	no	89.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Development of Lactobacillus kimchicus DCY51^T-mediated gold nanoparticles for delivery of ginsenoside compound K: in vitro photothermal effects and apoptosis detection in cancer cells.	Kim YJ, Perumalsamy H, Markus J, Balusamy SR, Wang C, Ho Kang S, Lee S, Park SY, Kim S, Castro-Aceituno V, Kim SH, Yang DC.	Artif Cells Nanomed Biotechnol	10.1080/21691401.2018.1541900	2019
Metabolism	Intracellular synthesis of gold nanoparticles with antioxidant activity by probiotic Lactobacillus kimchicus DCY51^T isolated from Korean kimchi.	Markus J, Mathiyalagan R, Kim YJ, Abbai R, Singh P, Ahn S, Perez ZEJ, Hurh J, Yang DC.	Enzyme Microb Technol	10.1016/j.enzmictec.2016.08.018	2016
	Microbial Nano-Factories: Synthesis and Biomedical Applications.	Ghosh S, Ahmad R, Zeyaullah M, Khare SK.	Front Chem	10.3389/fchem.2021.626834	2021

References

#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 )
#26022	IJSEM 894 2011 ( DOI 10.1099/ijs.0.017418-0 , PubMed 20495030 )
#29632	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26022
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Secundilactobacillus kimchicus (KCTC 12976, JCM 15530, DCY 51)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001433995

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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