Name: Secundilactobacillus kimchicus KCTC 12976
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133577

Type strain:

Species: Secundilactobacillus kimchicus

Culture col. no.: KCTC 12976, JCM 15530, DCY 51

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 528209 (species)

Section

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
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	*Secundilactobacillus*
	Species	**Secundilactobacillus kimchicus**
	Full Scientific Name (LPSN)	Secundilactobacillus kimchicus (Liang et al. 2011) Zheng et al. 2020

Synonym

Lactobacillus kimchicus

Information on morphological and physiological properties Morphology

[Ref.: #29632]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #29632]	Cell length	1.5 µm

[Ref.: #29632]	Cell width	0.55 µm

[Ref.: #29632]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #29632]	Motility	no
[Ref.: #67771]	Motility	no

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #29632]	growth	15-45 °C
[Ref.: #29632]	optimum	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

[Ref.: #29632]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29632]			optimum	6.5
[Ref.: #29632]			growth	06-07

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29632]	Oxygen tolerance	facultative aerobe
[Ref.: #67771]	Oxygen tolerance	facultative anaerobe

[Ref.: #29632]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29632]		NaCl		growth	0-8	%
[Ref.: #29632]		NaCl		optimum	4	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29632]	fructose ChEBI	+	carbon source
[Ref.: #29632]	galactose ChEBI	+	carbon source
[Ref.: #29632]	gluconate ChEBI	+	carbon source
[Ref.: #29632]	maltose ChEBI	+	carbon source
[Ref.: #29632]	mannitol ChEBI	+	carbon source
[Ref.: #29632]	mannose ChEBI	+	carbon source
[Ref.: #29632]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #29632]	ribose ChEBI	+	carbon source

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

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

[Ref.: #29632]	Sample type/isolated from	food product

[Ref.: #67770]	Sample type/isolated from	Kimchi
[Ref.: #67770]	Geographic location (country and/or sea, region)	Gyeonggi Province
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From kimchi
[Ref.: #67771]	Geographic location (country and/or sea, region)	Gyeonggi Province
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Food production

#Food

What are isolation sources categories?

[Ref.: #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

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.: #29632]	Lactobacillus kimchicus JCM 15530 strain DCY51 16S ribosomal RNA gene, partial sequence	EU678893	1499	GenBank	1302272 tax ID
[Ref.: #67771]	Lactobacillus kimchicus JCM 15530 gene for 16S ribosomal RNA, partial sequence	LC480811	1504	ENA	1302272 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]	Secundilactobacillus kimchicus JCM 15530	GCA_001433995	contig	GenBank	1302272 tax ID
[Ref.: #67771]	Secundilactobacillus kimchicus JCM 15530	GCA_001313205	contig	GenBank	1302272 tax ID
[Ref.: #66792]	Lactobacillus kimchicus JCM 15530	1302272.5	wgs	PATRIC	1302272 tax ID	*
[Ref.: #66792]	Lactobacillus kimchicus JCM 15530	1302272.4	wgs	PATRIC	1302272 tax ID	*
[Ref.: #66792]	Secundilactobacillus kimchicus JCM 15530	2657245468	draft	JGI IMG/M	1302272 tax ID	*
[Ref.: #66792]	Secundilactobacillus kimchicus JCM 15530	2734481936	draft	JGI IMG/M	1302272 tax ID	*

[Ref.: #29632]	GC-content	39.7 mol%
[Ref.: #67770]	GC-content	46.6 mol%	genome sequence analysis
[Ref.: #67771]	GC-content	39.7 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 Diaspora project based on: Lactobacillus kimchicus JCM 15530 PATRIC: 1302272.5
[Ref.: #69480]	motile	no	95.09	no
[Ref.: #69480]	gram-positive	yes	97.139	yes
[Ref.: #69480]	anaerobic	no	94.108	no
[Ref.: #69480]	halophile	yes	92.554	no
[Ref.: #69480]	spore-forming	no	94.058	no
[Ref.: #69480]	thermophile	no	99.212	yes
[Ref.: #69480]	glucose-util	yes	87.656	no
[Ref.: #69480]	aerobic	no	93.946	no
[Ref.: #69480]	flagellated	no	98.888	no
[Ref.: #69480]	glucose-ferment	yes	87.762	no

Availability in culture collections External links

[Ref.: #29632]

Culture collection no.

KCTC 12976, JCM 15530, DCY 51

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 )

#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 (see below)

#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) .

#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 .

#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) .

#26022

IJSEM 894 2011 ( DOI 10.1099/ijs.0.017418-0 , PubMed 20495030 )

* These data were automatically processed and therefore are not curated

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Lactobacillus kimchicus JCM 15530

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