Companilactobacillus nodensis (DSM 19682, CIP 109958, JCM 14932)

Name: Companilactobacillus nodensis (DSM 19682, CIP 109958, JCM 14932)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6674

Type strain

Strain Designation IZ4B, iz4b-1

Culture col. no. DSM 19682 CIP 109958 JCM 14932 NBRC 107160 IZ4B 1 more

NCBI tax ID(s) 460870

Special Collections DSMZ JCM CIP Literature strains

History DSMZ <- T. Kashiwagi, Tokyo University of Science;IZ4B JCM <-- T. Kashiwagi iz4b-1. CIP <- 2009, DSMZ <- T. Kashiwagi, Tokyo Univ. of Science, Chiba, Japan: strain IZ4B

Links

Companilactobacillus nodensis IZ4B is a microaerophile, Gram-positive, rod-shaped bacterium that was isolated from Japanese pickles.

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

Name and taxonomic classification

SI-ID 360509

NBRC 107160,DSM 19682,JCM 14932,LMG 25508,CIP 109958

@ref 20215

Last LPSN update 2026-05-29 08:26:28

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Companilactobacillus

Species Companilactobacillus nodensis

Full scientific name Companilactobacillus nodensis (Kashiwagi et al. 2009) Zheng et al. 2020

Synonyms (1)

Lactobacillus nodensis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32611	positive	5 µm	1.8 µm	rod-shaped
121322	positive			rod-shaped
125438					92.5
125438	positive				92.316

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8253	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
40607	MEDIUM 40- for Lactobacillus and Leuconostoc		Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
121322	CIP Medium 40	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
8253	positive	growth	30
32611	positive	growth	15-37
32611	positive	optimum	26
40607	positive	growth	37
67770	positive	growth	30
121322	positive	growth	15-37
121322	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8253	microaerophile
32611	anaerobe
121322	facultative anaerobe
125439	facultative anaerobe	93.91

Spore formation

32611

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32611	NaCl	positive	growth	0-15 %
32611	NaCl	positive	optimum	7.5 %

Murein

@ref	Murein short key	Type
8253	A11.31	A4alpha L-Lys-D-Asp

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
32611	22599 ChEBI	arabinose	+	carbon source
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
32611	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
32611	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
32611	28260 ChEBI	galactose	+	carbon source
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
32611	17234 ChEBI	glucose	+	carbon source
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
32611	37684 ChEBI	mannose	+	carbon source
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
32611	506227 ChEBI	N-acetylglucosamine	+	carbon source
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
121322	17632 ChEBI	nitrate	-	reduction
121322	17632 ChEBI	nitrate	+	respiration
121322	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	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
32611	33942 ChEBI	ribose	+	carbon source
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 production

@ref	Chebi-ID	Metabolite	Production
121322	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
121322	15688 ChEBI	acetoin	+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121322	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
121322	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
121322	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
121322	ornithine decarboxylase	-	4.1.1.17
121322	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
121322	urease	-	3.5.1.5
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
121322	-	+	-	-	-	+	-	-	-	-	+	+	-	-	-	+	+	-	-	-

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
8253	-	-	-	+	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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
8253	Japanese pickles	Tochigi prefecture, Utsunomiya city	Japan	JPN	Asia
67770	Rice bran
121322	Food, Rice bran, Japanse pickles	Utsunomiya	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC258158 (>99% sequence identity) for Companilactobacillus from Microbeatlas

Aquatic Samples	22
Soil Samples	37
Animal Samples	270
Plant Samples	28
Total Samples	357

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8253	1	Risk group (German classification) According to TRBA 466
121322	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	ASM159206v1 assembly for Companilactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160	contig	GCA_001592065	1423775.5	2681812987	1423775	74.63
67770	ASM143555v1 assembly for Companilactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160	scaffold	GCA_001435555	1423775.4	2690315703	1423775	73.83
67770	ASM61590v1 assembly for Companilactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160	contig	GCA_000615905	1236953.3	2585427881	1423775	62.83

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
8253	Lactobacillus nodensis gene for 16S ribosomal RNA, partial sequence	AB332024	1556	460870
67770	Lactobacillus nodensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 14932	LC258158	1513	460870
124043	Lactobacillus nodensis gene for 16S rRNA, partial sequence, strain: NBRC 107160.	AB626074	1499	460870

GC content

@ref	GC-content (mol%)	Method
8253	40.6
67770	37.6	genome sequence analysis
67770	40.6	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: ASM159206v1 assembly for Companilactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160
BV-BRC: 1423775.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	93.91	no
125439	gram_stain	BacteriaNetⓘ	positive	67.04	no
125439	motility	BacteriaNetⓘ	no	61.04	no
125439	spore_formation	BacteriaNetⓘ	no	71.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus nodensis DSM 19682 = JCM 14932 = NBRC 107160
PATRIC: 1423775.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.32	yes
125438	anaerobic	anaerobicⓘ	no	84.07	no
125438	spore-forming	spore-formingⓘ	no	84.47	yes
125438	aerobic	aerobicⓘ	no	93.87	yes
125438	thermophilic	thermophileⓘ	no	96.50	yes
125438	flagellated	motile2+ⓘ	no	92.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lactobacillus terrae sp. nov., a novel species isolated from soil samples in the Republic of Korea.	Kim HJ, Lee HJ, Lim B, Kim E, Kim HY, Suh M, Hur M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002918	2018
Phylogeny	Lactobacillus insicii sp. nov., isolated from fermented raw meat.	Ehrmann MA, Krockel L, Lick S, Radmann P, Bantleon A, Vogel RF	Int J Syst Evol Microbiol	10.1099/ijsem.0.000705	2015
Phylogeny	Lactobacillus nodensis sp. nov., isolated from rice bran.	Kashiwagi T, Suzuki T, Kamakura T	Int J Syst Evol Microbiol	10.1099/ijs.0.65772-0	2009

References

#8253	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19682
#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 )
#28824	IJSEM 83 2009 ( DOI 10.1099/ijs.0.65772-0 , PubMed 19126729 )
#32611	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 #28824
#40607	; 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 .
#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 .
#121322	Collection of Institut Pasteur ; Curators of the CIP; CIP 109958
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Companilactobacillus nodensis (DSM 19682, CIP 109958, JCM 14932)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001592065

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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