Lentilactobacillus kisonensis (DSM 19906, JCM 15041, NRIC 0741)

Name: Lentilactobacillus kisonensis (DSM 19906, JCM 15041, NRIC 0741)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6684

Type strain

Culture col. no. DSM 19906 JCM 15041 NRIC 0741 YIT 11168 CIP 110026

NCBI tax ID(s) 481722

Special Collections DSMZ JCM CIP

Links

Lentilactobacillus kisonensis DSM 19906 is a microaerophile, mesophilic, Gram-positive prokaryote that was isolated from non-salted pickle solution used in production of sunki .

Gram-positive rod-shaped microaerophile mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 362306

DSM 19906,JCM 15041,CIP 110026

@ref 20215

Last LPSN update 2025-12-16 09:48:23

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Lentilactobacillus

Species Lentilactobacillus kisonensis

Full scientific name Lentilactobacillus kisonensis (Watanabe et al. 2009) Zheng et al. 2020

Synonyms (1)

Lactobacillus kisonensis

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
120447	positive	rod-shaped
125438	positive			93.411

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8378	MRS MEDIUM (DSMZ Medium 11)	Medium recipe at MediaDive	Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 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
33668	MEDIUM 20 - for Anaerobic bacteria		Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
120447	CIP Medium 40	Medium recipe at CIP
120447	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8378	positive	growth	30	mesophilic
33668	positive	growth	37	mesophilic
67770	positive	growth	30	mesophilic
120447	positive	growth	25-37	mesophilic
120447	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8378	microaerophile
120447	facultative anaerobe
125439	obligate aerobe	99.2

Spore formation

@ref	Spore formation	Confidence
125439		94.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	+	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
120447	17632 ChEBI	nitrate	-	reduction
120447	17632 ChEBI	nitrate	+	respiration
120447	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
120447	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
120447	alcohol dehydrogenase	+	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	+	3.2.1.31	from API zym
120447	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
120447	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
120447	ornithine decarboxylase	-	4.1.1.17
120447	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120447	-	-	-	-	-	+	-	-	-	-	-	-	+	+	+	+	+	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
8378	-	-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Vegetable (incl. Grains)
#Engineered	#Food production	#Fermented

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8378	non-salted pickle solution used in production of sunki (Japanese traditional fermented leaves and stems of red turnips)	Kiso county, Nagano prefecture	Japan	JPN	Asia
67770	Sunki, traditional Japanese pickles		Japan	JPN	Asia
120447	Sunki, non-salted pickle solution		Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8378	1	Risk group (German classification) According to TRBA 466
120447	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM143413v1 assembly for Lentilactobacillus kisonensis DSM 19906 = JCM 15041	contig	GCA_001434135	1423766.4	2663763466	1423766	54.63
67770	ASM131142v1 assembly for Lentilactobacillus kisonensis DSM 19906 = JCM 15041	contig	GCA_001311425	1423766.3	2728369685	1423766	21.06

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8378	Lentilactobacillus kisonensis gene for 16S rRNA, partial sequence, strain: YIT 11168 (= NRIC 0741, = JCM 15041, = DSM 19906)	AB366388	1565		481722
67770	Lactobacillus kisonensis JCM 15041 gene for 16S ribosomal RNA, partial sequence	LC480802	1509		481722

GC content

@ref	GC-content (mol%)	Method
8378	38.8
67770	38.8	high performance liquid chromatography (HPLC)
67770	41.7	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Lentilactobacillus kisonensis DSM 19906 = JCM 15041
NCBI: GCA_001434135

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.70	no
125439	motility	BacteriaNetⓘ	no	64.70	no
125439	gram_stain	BacteriaNetⓘ	positive	78.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus kisonensis DSM 19906 = JCM 15041
PATRIC: 1423766.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	93.41	no
125438	anaerobic	anaerobicⓘ	no	80.35	yes
125438	spore-forming	spore-formingⓘ	no	77.67	no
125438	aerobic	aerobicⓘ	no	87.12	yes
125438	thermophilic	thermophileⓘ	no	95.08	yes
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Insights into Systems for Iron-Sulfur Cluster Biosynthesis in Acidophilic Microorganisms.	Myriam P, Braulio P, Javiera RA, Claudia MV, Omar O, Renato C, Gloria L.	J Microbiol Biotechnol	10.4014/jmb.2206.06045	2022
Phylogeny	Halobacterium piscisalsi Yachai et al. 2008 is a later heterotypic synonym of Halobacterium salinarum Elazari-Volcani 1957.	Minegishi H, Echigo A, Shimane Y, Kamekura M, Tanasupawat S, Visessanguan W, Usami R.	Int J Syst Evol Microbiol	10.1099/ijs.0.036905-0	2012
	Fungal beta-glucan-facilitated cross-feeding activities between Bacteroides and Bifidobacterium species.	Fernandez-Julia P, Black GW, Cheung W, Van Sinderen D, Munoz-Munoz J.	Commun Biol	10.1038/s42003-023-04970-4	2023
Metabolism	Utilization of dietary mixed-linkage beta-glucans by the Firmicute Blautia producta.	Singh RP, Niharika J, Thakur R, Wagstaff BA, Kumar G, Kurata R, Patel D, Levy CW, Miyazaki T, Field RA.	J Biol Chem	10.1016/j.jbc.2023.104806	2023
Metabolism	Linear and branched beta-Glucans degrading enzymes from versatile Bacteroides uniformis JCM 13288^T and their roles in cooperation with gut bacteria.	Singh RP, Rajarammohan S, Thakur R, Hassan M.	Gut Microbes	10.1080/19490976.2020.1826761	2020
	Development of innovative pediocin PA-1 by DNA shuffling among class IIa bacteriocins.	Tominaga T, Hatakeyama Y.	Appl Environ Microbiol	10.1128/aem.00558-07	2007
Phylogeny	Analysis of Genomic and Characterization Features of Microbulbifer weihaiensis sp. nov., Isolated from Coastal Sediment.	Zhang YX, Liu AQ.	Microorganisms	10.3390/microorganisms13092005	2025
Phylogeny	Halobacterium litoreum sp. nov., isolated from a marine solar saltern.	Lu ZZ, Li Y, Zhou Y, Cui HL, Li ZR.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002259	2017
Metabolism	Lactobacillus concavus sp. nov., isolated from the walls of a distilled spirit fermenting cellar in China.	Tong H, Dong X.	Int J Syst Evol Microbiol	10.1099/ijs.0.63509-0	2005
Phylogeny	Lactobacillus kisonensis sp. nov., Lactobacillus otakiensis sp. nov., Lactobacillus rapi sp. nov. and Lactobacillus sunkii sp. nov., heterofermentative species isolated from sunki, a traditional Japanese pickle.	Watanabe K, Fujimoto J, Tomii Y, Sasamoto M, Makino H, Kudo Y, Okada S	Int J Syst Evol Microbiol	10.1099/ijs.0.004689-0	2009

References

#8378	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19906
#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 )
#33668	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#120447	Collection of Institut Pasteur ; Curators of the CIP; CIP 110026
#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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Lentilactobacillus kisonensis (DSM 19906, JCM 15041, NRIC 0741)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite tests

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001434135

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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