Cupriavidus numazuensis (DSM 15562, CIP 108892, LMG 26411)

Name: Cupriavidus numazuensis (DSM 15562, CIP 108892, LMG 26411)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2040

Type strain

Strain Designation TE26

Culture col. no. DSM 15562 CIP 108892 LMG 26411 CCUG 64483 NBRC 100056 1 more

NCBI tax ID(s) 1218073 221992

Special Collections DSMZ CCUG CIP Literature strains

Links

Cupriavidus numazuensis TE26 is an aerobe, mesophilic prokaryote that was isolated from pristine soil.

aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 200038

NBRC 100056,DSM 15562,CIP 108892,LMG 26411,CCUG 64483

@ref 20215

Last LPSN update 2025-12-16 09:47:14

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Cupriavidus

Species Cupriavidus numazuensis

Full scientific name Cupriavidus numazuensis (Kageyama et al. 2005) Martínez-Aguilar et al. 2013

Synonyms (2)

Wautersia numazuensis
Wautersia numadzuensis

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97
125439	negative	96.5

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6003	REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
6003	REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37397	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121371	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6003	positive	growth	25	mesophilic
37397	positive	growth	25	mesophilic
63132	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
63132	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		97.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30560	58143 ChEBI	5-dehydro-D-gluconate	+	carbon source
30560	17128 ChEBI	adipate	+	carbon source
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
30560	16947 ChEBI	citrate	+	carbon source
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
30560	27689 ChEBI	decanoate	+	carbon source
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
30560	33984 ChEBI	fucose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
30560	24265 ChEBI	gluconate	+	carbon source
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
30560	18403 ChEBI	L-arabitol	+	carbon source
30560	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
30560	urease	+	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
6003	+	-	-	-	+	-	-	-	+	-	-	-	-	-	+	+	+	+	+	+	+
6003	+	-	-	-	+	-	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6003	pristine soil	Shizuoka prefecture	Japan	JPN	Asia
63132	Pristine soil		Japan	JPN	Asia
121371	Environment, Pristine soil		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB104447 (>99% sequence identity) for Cupriavidus from Microbeatlas

Aquatic Samples	1798
Soil Samples	2258
Animal Samples	1650
Plant Samples	374
Total Samples	6080

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6003	1	Risk group (German classification) According to TRBA 466
121371	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
66792	LMG 26411 assembly for Cupriavidus numazuensis LMG 26411	contig	GCA_905397435	221992.4	3003465734	221992	41.3
124043	ASM4265182v1 assembly for Cupriavidus numazuensis CCUG 64483	scaffold	GCA_042651825			221992	37.18

Genome browser: GCA_905397435

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6003	Wautersia numazuensis gene for 16S rRNA, complete sequence, strain: TE26	AB104447	1529		221992
124043	Wautersia numazuensis gene for 16S rRNA, partial sequence, strain: NBRC 100056.	AB681139	1457		1218073

GC content

6003

GC-content (mol%)64

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Cupriavidus numazuensis LMG 26411
NCBI: GCA_905397435

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.10	no
125439	motility	BacteriaNetⓘ	yes	73.30	no
125439	gram_stain	BacteriaNetⓘ	negative	96.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cupriavidus numazuensis strain LMG 26411
PATRIC: 221992.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	no
125438	anaerobic	anaerobicⓘ	no	98.50	yes
125438	spore-forming	spore-formingⓘ	no	88.79	no
125438	aerobic	aerobicⓘ	yes	89.71	yes
125438	thermophilic	thermophileⓘ	no	99.50	yes
125438	flagellated	motile2+ⓘ	yes	82.99	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Mycotoxin Biodegradation Ability of the Cupriavidus Genus.	Al-Nussairawi M, Risa A, Garai E, Varga E, Szabo I, Csenki-Bakos Z, Kriszt B, Cserhati M.	Curr Microbiol	10.1007/s00284-020-02063-7	2020
Phylogeny	Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb. nov.	Martinez-Aguilar L, Caballero-Mellado J, Estrada-de Los Santos P	Int J Syst Evol Microbiol	10.1099/ijs.0.038729-0	2012

References

#6003	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15562
#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 )
#30560	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 #26891 (see below)
#37397	; Curators of the CIP;
#63132	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 64483
#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) .
#68369	Automatically annotated from API 20NE .
#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 .
#121371	Collection of Institut Pasteur ; Curators of the CIP; CIP 108892
#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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Cupriavidus numazuensis (DSM 15562, CIP 108892, LMG 26411)

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 production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_905397435

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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