Lentilactobacillus rapi (DSM 19907, JCM 15042, NRIC 0743)

Name: Lentilactobacillus rapi (DSM 19907, JCM 15042, NRIC 0743)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6686

Type strain

Culture col. no. DSM 19907 JCM 15042 NRIC 0743 YIT 11204 NBRC 109618 1 more

NCBI tax ID(s) 481723

Special Collections DSMZ JCM CIP

History <- K. Watanabe, Yakult Central Inst. Microbiol. Res., Tokyo, Japan; YIT 11204 K. Watanabe YIT 11204. CIP <- 2009, JCM <- K. Watanabe, Yakult Central Inst. Microbiol. Res., Tokyo, Japan: strain YIT 11204

Links

Lentilactobacillus rapi DSM 19907 is a microaerophile, Gram-positive, rod-shaped bacterium that was isolated from non-salted pickle solution used in production of sunki .

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

Name and taxonomic classification

SI-ID 362308

LMG 29246,NBRC 109618,DSM 19907,JCM 15042,CIP 110029

@ref 20215

Last LPSN update 2026-02-09 11:19:17

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Lentilactobacillus

Species Lentilactobacillus rapi

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

Synonyms (1)

Lactobacillus rapi

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
122137	positive	rod-shaped
125438	positive			94.087

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8379	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
33670	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)
122137	CIP Medium 20	Medium recipe at CIP
122137	CIP Medium 40	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
8379	positive	growth	30
33670	positive	growth	37
67770	positive	growth	30
122137	positive	growth	15-37
122137	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8379	microaerophile
122137	facultative anaerobe
125439	obligate aerobe	95.7

Spore formation

@ref	Spore formation	Confidence
125439		96.2

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
122137	17632 ChEBI	nitrate	-	reduction
122137	17632 ChEBI	nitrate	+	respiration
122137	16301 ChEBI	nitrite	-	reduction

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
122137	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122137	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
122137	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
122137	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
122137	ornithine decarboxylase	-	4.1.1.17
122137	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
122137	-	-	-	+	-	+	+	-	-	-	+	+	+	+	+	+	+	-	-	-

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
8379	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
122137	Sunki, non-salted pickle solution

Taxonmaps

69479

Global distribution of 16S sequence LC480803 (>99% sequence identity) for Lentilactobacillus rapi from Microbeatlas

Aquatic Samples	87
Soil Samples	196
Animal Samples	478
Plant Samples	161
Total Samples	922

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8379	1	Risk group (German classification) According to TRBA 466
122137	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	ASM143625v1 assembly for Lentilactobacillus rapi DSM 19907 = JCM 15042	scaffold	GCA_001436255	1423795.5	2700989137	1423795	59.82
67770	ASM799255v1 assembly for Lentilactobacillus rapi NBRC 109618	contig	GCA_007992555	481723.4	2967514140	481723	43.77
67770	ASM131144v1 assembly for Lentilactobacillus rapi DSM 19907 = JCM 15042	contig	GCA_001311445	1423795.4	2728369686	1423795	20.15

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Lactobacillus rapi genes for 16S rRNA, intergenic spacer region, 23S rRNA, partial sequence, culture_collection: JCM:15042	AB793776	557	481723
8379	Lentilactobacillus rapi gene for 16S rRNA, partial sequence, strain: YIT 11204 (= NRIC 0743, = JCM 15042, = DSM 19907)	AB366389	1566	481723
67770	Lactobacillus rapi JCM 15042 gene for 16S ribosomal RNA, partial sequence	LC480803	1510	481723

GC content

@ref	GC-content (mol%)	Method
8379	40.3	high performance liquid chromatography (HPLC)
8379	39.2
67770	43	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Lentilactobacillus rapi DSM 19907 = JCM 15042
NCBI: GCA_001436255

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.20	no
125439	motility	BacteriaNetⓘ	no	79.40	no
125439	gram_stain	BacteriaNetⓘ	positive	68.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus rapi DSM 19907 = JCM 15042
PATRIC: 1423795.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	94.09	no
125438	anaerobic	anaerobicⓘ	no	84.22	yes
125438	spore-forming	spore-formingⓘ	no	80.90	no
125438	aerobic	aerobicⓘ	no	90.86	yes
125438	thermophilic	thermophileⓘ	no	94.94	yes
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Exploring microbial communities of Spanish-style green table olives of Conservolea and Halkidiki cultivars during modified atmosphere packaging in multi-layered pouches through culture-dependent techniques and metataxonomic analysis	Tzamourani AP, Kasimati A, Karagianni E, Manthou E, Panagou EZ.	Food Microbiol		2022
	Exploring microbial communities of Spanish-style green table olives of Conservolea and Halkidiki cultivars during modified atmosphere packaging in multi-layered pouches through culture-dependent techniques and metataxonomic analysis.	Tzamourani AP, Kasimati A, Karagianni E, Manthou E, Panagou EZ.	Food Microbiol	10.1016/j.fm.2022.104063	2022
Genetics	Metagenomic and physicochemical profiling reveal microbial functions in pit mud for Jiang-Nong Jianxiang Baijiu fermentation.	Cao L, Sun H, Xu Z, Xu X, Shi G, Zhang J, Liang C, Li T, Liu C, Wang M, Tian S, Li E.	BMC Microbiol	10.1186/s12866-025-03884-x	2025
Phylogeny	Elevation of Lentilactobacillus rapi subsp. dabitei Li et al. 2022 to the species level as Lentilactobacillus dabitei sp. nov.	Wang TY, Gu CT.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006149	2023
Phylogeny	Lentilactobacillus laojiaonis sp. nov., isolated from the mud in a fermentation cellar for the production of Chinese liquor.	Zhao Q, Yang S, Bao G, Wang W, Miao L, Wang S, Shen C, Li Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.005349	2022
Phylogeny	Lentilactobacillus rapi subsp. dabitei subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product.	Li Y, Li W, Luo R, Sakandar HA, Zhang H, Liu W	Int J Syst Evol Microbiol	10.1099/ijsem.0.005359	2022
Phylogeny	Lentilactobacillus fungorum sp. nov., isolated from spent mushroom substrates.	Tohno M, Tanizawa Y, Kojima Y, Sakamoto M, Ohkuma M, Kobayashi H	Int J Syst Evol Microbiol	10.1099/ijsem.0.005184	2021
Phylogeny	Lentilactobacillus kribbianus sp. nov., isolated from the small intestine of a mini pig.	Bai L, Paek J, Shin Y, Park HY, Chang YH	Int J Syst Evol Microbiol	10.1099/ijsem.0.004560	2020
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

#8379	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19907
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#33670	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#122137	Collection of Institut Pasteur ; Curators of the CIP; CIP 110029
#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 rapi (DSM 19907, JCM 15042, NRIC 0743)

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

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001436255

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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