Cupriavidus necator (DSM 13513, ATCC 43291, CCUG 52238)

Name: Cupriavidus necator (DSM 13513, ATCC 43291, CCUG 52238)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2033

Type strain

Strain Designation N-1, Jr N-1

Culture col. no. DSM 13513 ATCC 43291 CCUG 52238 CIP 103161 LMG 8453 3 more

NCBI tax ID(s) 106590

Special Collections DSMZ CCUG CIP

Links

Cupriavidus necator N-1 is an aerobe, mesophilic prokaryote that was isolated from soil.

aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 2100

LMG 8453,ATCC 43291,LMG 11253,JCM 36303,CIP 103161,DSM 13513,BCRC 14873,CCRC 14873,CCUG 52238

@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 necator

Full scientific name Cupriavidus necator Makkar and Casida 1987

BacDive ID	Other strains from **Cupriavidus necator** (40)	Type strain
330	C. necator 1978, DSM 2625, CCUG 52964, ATCC 33178, LMG ...
1998	C. necator H 1, CCUG 52966, LMG 1200, ATCC 23442, DSM ...
1999	C. necator H 20, DSM 530, ATCC 17700
2001	C. necator H 16 G+1, H 16 G⁺1, DSM 538
2002	C. necator H 16 F 34, DSM 539
2003	C. necator H 16 F 29, DSM 540
2004	C. necator H 16 PHB-4, H 16 PHB^-4, DSM 541
2005	C. necator LH-7, LH^-7, DSM 416
2006	C. necator PH-9, PH^-9, DSM 418
2007	C. necator PH-4, PH^-4, DSM 422
2008	C. necator pHG1, H 16, H16, Wilde H16, strain S-10-1, ...
2009	C. necator H16 25/1, DSM 430
2010	C. necator B 19, DSM 515, JCM 20894, CCUG 13796, IAM ...
2011	C. necator G 27, DSM 516
2012	C. necator G 29, DSM 517
2013	C. necator DSM 518
2014	C. necator H 16 G+7, H 16 G⁺7, DSM 542
2015	C. necator G 29 G+1, G 29 G⁺1, DSM 543
2016	C. necator H 20 G+3, H 20 G⁺3, DSM 544
2017	C. necator H 1 G+3, H 1 G⁺3, DSM 545
2018	C. necator H 1 G+4, H 1 G⁺4, DSM 546
2019	C. necator H 20 G+1, H 20 G⁺1, DSM 547
2020	C. necator H 16 G+3, H 16 G⁺3, DSM 551
2021	C. necator H16 pHS4, DSM 3102
2022	C. necator JMP363 Smr, pJP2, DSM 4056
2023	C. necator JMP364, pJP3, JMP364 Smr, DSM 4057
2024	C. necator JMP134, pJP4, DSM 4058, NCIB 12592
2025	C. necator JMP365, pJP5, JMP365 Smr, DSM 4059
2026	C. necator JMP366, pJP7, JMP366 Smr, DSM 4060
2027	C. necator TA06, DSM 4182
2028	C. necator H850, DSM 5536, NRRL B-15940
2031	C. necator Bo, Tfa 17, DSM 11098
2032	C. necator H850-4LT, DSM 13439
2034	C. necator C145, DSM 15443
2035	C. necator HF39, DSM 15444
2036	C. necator DSM 30029, ATCC 25207, NRRL B-2804, CCUG ...
100613	C. necator STI05003(IMET), pS3,
162984	C. necator JCM 20695, IAM 12628
163005	C. necator JCM 20908, ATCC 17702, IAM 13548, LMG 1203
163006	C. necator JCM 20909, ATCC 17708, IAM 13549, LMG 1208

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.5
125439	negative	98.4

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5069	BHI MEDIUM (DSMZ Medium 215)	Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
5069	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37118	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
121251	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5069	positive	growth	26	mesophilic
5069	positive	growth	28
37118	positive	growth	30	mesophilic
59481	positive	growth	30-37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
59481	aerobe
125438	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125438		90.121
125439		97.8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
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
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
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

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

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
5069	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	+	-	+	+
5069	+	-	-	-	+	-	-	-	-	-	-	-	-	-	+	+	-	+	+	+	+

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
5069	soil	Pensylvania	USA	USA	North America
59481	Soil	PA,University Park	USA	USA	North America
121251	Environment, Soil		United States of America	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence AF191737 (>99% sequence identity) for Cupriavidus from Microbeatlas

Aquatic Samples	5686
Soil Samples	15055
Animal Samples	7044
Plant Samples	2775
Total Samples	30560

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5069	1	Risk group (German classification) According to TRBA 466
121251	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	ASM21921v1 assembly for Cupriavidus necator N-1	complete	GCA_000219215	1042878.5	650716031	1042878	96.08
124043	ASM3384274v1 assembly for Cupriavidus necator ATCC 43291	contig	GCA_033842745	106590.40		106590	76.86

Genome browser: GCA_000219215

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Cupriavidus necator 16S ribosomal RNA gene, partial sequence	AF191737	1356		106590

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Cupriavidus necator N-1
NCBI: GCA_000219215

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.00	no
125439	gram_stain	BacteriaNetⓘ	negative	98.40	no
125439	motility	BacteriaNetⓘ	yes	76.60	no
125439	spore_formation	BacteriaNetⓘ	no	97.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cupriavidus necator N-1 N-1
NCBI: GCA_000219215.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	no
125438	anaerobic	anaerobicⓘ	no	96.97	yes
125438	aerobic	aerobicⓘ	yes	90.40	yes
125438	spore-forming	spore-formingⓘ	no	90.12	no
125438	thermophilic	thermophileⓘ	no	98.99	yes
125438	flagellated	motile2+ⓘ	yes	87.66	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Functional expression of a Mo-dependent formate dehydrogenase in Escherichia coli under aerobic conditions.	Schulz M, Berger A, Roche D, Pateau E, Dubois I, Delmas VA, Cadillon M, Bouzon M, Doring V.	PLoS One	10.1371/journal.pone.0334613	2025
	A Review on Enhancing Cupriavidus necator Fermentation for Poly(3-hydroxybutyrate) (PHB) Production From Low-Cost Carbon Sources.	Zhang L, Jiang Z, Tsui TH, Loh KC, Dai Y, Tong YW.	Front Bioeng Biotechnol	10.3389/fbioe.2022.946085	2022
Genetics	Complete genome sequence of Photobacterium ganghwense C2.2: A new polyhydroxyalkanoate production candidate.	Lascu I, Mereuta I, Chiciudean I, Hansen H, Avramescu SM, Tanase AM, Stoica I.	Microbiologyopen	10.1002/mbo3.1182	2021
	Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass.	Lyu X, Nuhu M, Candry P, Wolfanger J, Betenbaugh M, Saldivar A, Zuniga C, Wang Y, Shrestha S.	J Ind Microbiol Biotechnol	10.1093/jimb/kuae025	2024
Genetics	The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living polynucleobacter population.	Hahn MW, Scheuerl T, Jezberova J, Koll U, Jezbera J, Simek K, Vannini C, Petroni G, Wu QL.	PLoS One	10.1371/journal.pone.0032772	2012
	Beyond Intracellular Accumulation of Polyhydroxyalkanoates: Chiral Hydroxyalkanoic Acids and Polymer Secretion.	Yanez L, Conejeros R, Vergara-Fernandez A, Scott F.	Front Bioeng Biotechnol	10.3389/fbioe.2020.00248	2020
Genetics	Mining of Microbial Genomes for the Novel Sources of Nitrilases.	Sharma N, Thakur N, Raj T, Savitri, Bhalla TC.	Biomed Res Int	10.1155/2017/7039245	2017
Metabolism	Secondary compound hypothesis revisited: Selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE).	Fraraccio S, Strejcek M, Dolinova I, Macek T, Uhlik O.	Sci Rep	10.1038/s41598-017-07760-1	2017
Metabolism	Anaerobic production of medium-chain fatty alcohols via a beta-reduction pathway.	Mehrer CR, Incha MR, Politz MC, Pfleger BF.	Metab Eng	10.1016/j.ymben.2018.05.011	2018
	Response in Soil of Cupriavidus necator and Other Copper-Resistant Bacterial Predators of Bacteria to Addition of Water, Soluble Nutrients, Various Bacterial Species, or Bacillus thuringiensis Spores and Crystals.	Casida LE.	Appl Environ Microbiol	10.1128/aem.54.9.2161-2166.1988	1988
Genetics	Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico).	Gonzalez-Sanchez A, Lozano-Aguirre L, Jimenez-Flores G, Lopez-Samano M, Garcia-de Los Santos A, Cevallos MA, Le Borgne S.	Microorganisms	10.3390/microorganisms13040809	2025
Metabolism	Factors affecting poly(3-hydroxybutyrate) production from oil palm frond juice by Cupriavidus necator (CCUG52238(T)).	Mohd Zahari MA, Ariffin H, Mokhtar MN, Salihon J, Shirai Y, Hassan MA	J Biomed Biotechnol	10.1155/2012/125865	2012
Enzymology	Renewable sugars from oil palm frond juice as an alternative novel fermentation feedstock for value-added products.	Zahari MA, Zakaria MR, Ariffin H, Mokhtar MN, Salihon J, Shirai Y, Hassan MA	Bioresour Technol	10.1016/j.biortech.2012.01.119	2012
Phylogeny	Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge.	Sun LN, Wang DS, Yang ED, Fang LC, Chen YF, Tang XY, Hua RM	Int J Syst Evol Microbiol	10.1099/ijsem.0.001034	2016

References

#5069	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13513
#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 )
#37118	; Curators of the CIP;
#59481	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52238
#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 .
#121251	Collection of Institut Pasteur ; Curators of the CIP; CIP 103161
#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 necator (DSM 13513, ATCC 43291, CCUG 52238)

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_000219215

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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