Archive BacDiveID:10.13145/bacdive2008.20230509.8.1

Strain identifier

BacDive ID: 2008

Type strain:

Species: Cupriavidus necator

Strain Designation: pHG1, H 16, H16

Strain history: IAM 12567 <-- NCIB 10442 <-- H. G. Schlegel H16.

NCBI tax ID(s): 381666 (strain), 106590 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 197

BacDive-ID: 2008

DSM-Number: 428

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Cupriavidus necator pHG1 is a mesophilic, motile bacterium that was isolated from sludge.

NCBI tax id

NCBI tax id	Matching level
381666	strain
106590	species

strain history

@ref	history
197	<- IMG (Alcaligenes eutrophus) <- E. Wilde, H 16
67770	IAM 12567 <-- NCIB 10442 <-- H. G. Schlegel H16.

doi: 10.13145/bacdive2008.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Cupriavidus
species: Cupriavidus necator
full scientific name: Cupriavidus necator Makkar and Casida 1987

@ref: 197

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Cupriavidus

species: Cupriavidus necator

full scientific name: Cupriavidus necator Makkar and Casida 1987

strain designation: pHG1, H 16, H16

type strain: no

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	yes	95.868
69480		99.996	negative

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
197	MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)	yes	https://mediadive.dsmz.de/medium/81	Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
197	NUTRIENT AGAR (DSMZ Medium 1)	yes	https://mediadive.dsmz.de/medium/1	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

culture temp

@ref	growth	type	temperature	range
197	positive	growth	30	mesophilic
67770	positive	growth	25	mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.949

compound production

@ref	compound
197	PHB
197	hydrogenase
197	phenylalanine, hydroxylation of
197	single cell protein

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
197	sludge	Göttingen, Weende-Quelle	Germany	DEU	Europe
67770	Sludge	Göttingen	Germany	DEU	Europe

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Mud (Sludge)

Safety information

risk assessment

@ref: 197
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 67770
description: Ralstonia eutropha DNA for 16S ribosomal RNA
accession: D88002
length: 1468
database: ena
NCBI tax ID: 106590

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Cupriavidus necator H16	GCA_004798725	complete	ncbi	381666
66792	Cupriavidus necator H16	GCA_000009285	complete	ncbi	381666
66792	Cupriavidus necator H16 strain DSM 428	381666.45	complete	patric	381666
66792	Ralstonia eutropha H16	381666.6	complete	patric	381666
66792	Ralstonia eutropha H16	381666.42	plasmid	patric	381666
66792	Cupriavidus necator H16	640427136	complete	img	381666
66792	Cupriavidus necator H16 DSM 428	2858669534	complete	img	381666

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	84.973	no
flagellated	no	53.301	no
gram-positive	no	98.409	no
anaerobic	no	99.009	no
aerobic	yes	93.48	no
halophile	no	95.064	no
spore-forming	no	94.059	no
glucose-util	no	67.858	no
thermophile	no	98.599	yes
glucose-ferment	no	90.494	no

External links

@ref: 197

culture collection no.: DSM 428, ATCC 17699, KCTC 22496, NCIB 10442, JCM 20644, ATCC 23440, IAM 12567, NCIMB 10442

straininfo link

@ref: 71655
straininfo: 13563

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Enzymology	4044	Aromatic amino acid biosynthesis in Alcaligenes eutrophus H 16 III. Properites and regulation of anthranilate synthase.	Friedrich CG, Friedrich B, Schlegel HG	Arch Microbiol	10.1007/BF00446831	1976	Alcaligenes/enzymology, Allosteric Regulation, Anthranilate Phosphoribosyltransferase, Anthranilate Synthase/analysis/antagonists & inhibitors/isolation & purification, Drug Stability, Hydrogen-Ion Concentration, Kinetics, Molecular Weight, Multienzyme Complexes, Temperature, Tryptophan/biosynthesis/pharmacology	Phylogeny
Metabolism	4432	Regulation of Chorismate mutase-prephenate dehydratase and prephenate dehydrogenase from alcaligenes eutrophus.	Friedrich CG, Friedrich B, Schlegel HG	J Bacteriol	10.1128/jb.126.2.723-732.1976	1976	Alcaligenes/enzymology/metabolism, Cell-Free System, Chorismate Mutase/antagonists & inhibitors/metabolism, Enzyme Activation, Feedback, Hydro-Lyases/metabolism, Hydrogen-Ion Concentration, Isomerases/metabolism, NAD/metabolism, Oxidoreductases/metabolism, Phenylalanine/analogs & derivatives/biosynthesis/pharmacology, Prephenate Dehydratase/antagonists & inhibitors/metabolism, Prephenate Dehydrogenase/antagonists & inhibitors/*metabolism, Pyruvates/metabolism, Temperature, Tryptophan/pharmacology, Tyrosine/biosynthesis/pharmacology	Enzymology
Enzymology	16576	Alpha-Isopropylmalate synthase from Alcaligenes eutrophus H 16 I. Purification and general properties.	Wiegel J, Schlegel HG	Arch Microbiol	10.1007/BF00413087	1977	2-Isopropylmalate Synthase/isolation & purification, Alcaligenes/enzymology/growth & development, Cold Temperature, Drug Stability, Electrophoresis, Polyacrylamide Gel, Enzyme Activation, Hydrogen-Ion Concentration, Kinetics, Molecular Weight, *Oxo-Acid-Lyases/isolation & purification	Phylogeny
Enzymology	20865	Alpha-isopropylmalate synthase from Alcaligenes eutrophus H 16. III. Endproduct inhibition and its relief by valine and isoleucine.	Wiegel J, Schlegel HG	Arch Microbiol	10.1007/BF00446863	1977	2-Isopropylmalate Synthase/antagonists & inhibitors/metabolism, Alcaligenes/enzymology, Caproates/pharmacology, Histidine/pharmacology, Hydrogen-Ion Concentration, Isoleucine/pharmacology, Keto Acids/pharmacology, Kinetics, Leucine/pharmacology, Oxo-Acid-Lyases/metabolism, Temperature, Valine/*pharmacology	Metabolism
Enzymology	186126	Purification and properties of soluble hydrogenase from Alcaligenes eutrophus H 16.	Schneider K, Schlegel HG	Biochim Biophys Acta	10.1016/0005-2744(76)90058-9	1976	Alcaligenes/enzymology, Hydrogen, Kinetics, Molecular Weight, NAD, Oxidation-Reduction, Oxidoreductases/isolation & purification/metabolism, Spectrometry, Fluorescence, Spectrophotometry, Spectrophotometry, Ultraviolet	Phylogeny
Enzymology	240336	Kinetics and properties of beta-ketothiolase from Clostridium pasteurianum.	Berndt H, Schlegel HG	Arch Microbiol	10.1007/BF00436325	1975	Acetoacetates, Acetyl-CoA C-Acyltransferase/antagonists & inhibitors/isolation & purification/metabolism, Acyltransferases/metabolism, Alcaligenes/enzymology, Clostridium/*enzymology, Coenzyme A/pharmacology, Electrophoresis, Polyacrylamide Gel, Hydrogen-Ion Concentration, Hydroxybutyrates/metabolism, Isoelectric Point, Isoenzymes/isolation & purification, Kinetics, Molecular Weight	Metabolism
Metabolism	678018	Mutants of Alcaligenes eutrophus defective in autotrophic metabolism.	Schink B, Schlegel HG	Arch Microbiol	10.1007/BF00402299	1978	Alcaligenes/genetics/metabolism, Carbon Dioxide/metabolism, Cell Membrane/enzymology, Cytoplasm/enzymology, Fructose/metabolism, Hydrogen/metabolism, Mutation, Oxidoreductases/genetics/metabolism, Pyruvates/metabolism	Enzymology
Phylogeny	722280	Isolation and characterization of polysheaths, phage tail-like defective bacteriophages of Alcaligenes eutrophus H 16.	Walther-Mauruschat A, Mayer F	J Gen Virol	10.1099/0022-1317-41-2-239	1978	Alcaligenes, Amino Acids/analysis, Bacteriophages/growth & development/ultrastructure, Defective Viruses/growth & development/ultrastructure, Models, Structural, Morphogenesis, Peptides/analysis, *Viral Proteins/analysis/isolation & purification	Enzymology
Metabolism	828363	[Adenosine-dependent death of Hydrogenomonas eutropha (Alcaligenes eutrophus) H 16 (author's transl)].	Kaltwasser H, Glaeser H	Zentralbl Bakteriol Parasitenkd Infektionskr Hyg	10.1016/s0044-4057(76)80055-x	1976	Adenosine/pharmacology, Bacterial Proteins/biosynthesis, Deoxyadenosines/pharmacology, Fructose/metabolism, Glutamates/metabolism, Nucleic Acids/biosynthesis, Nucleosides/metabolism, Peptones/metabolism, Pseudomonas/drug effects/growth & development/metabolism, Succinates/metabolism	Pathogenicity
Enzymology	871226	Localization and stability of hydrogenases from aerobic hydrogen bacteria.	Schneider K, Schlegel HG	Arch Microbiol	10.1007/BF00413086	1977	Aerobiosis, Alcaligenes/enzymology, Bacteria/enzymology, Corynebacterium/enzymology, Cytosol/enzymology, Drug Stability, Hydrogen, Oxidoreductases/analysis, Paracoccus denitrificans/enzymology, Pseudomonas/enzymology, Spirillum/enzymology, Subcellular Fractions/enzymology
Enzymology	871227	alpha-Isopropylmalate synthase from Alcaligenes eutrophus H 16. II. Substrate specificity and kinetics.	Wiegel J, Schlegel HG	Arch Microbiol	10.1007/BF00413088	1977	2-Isopropylmalate Synthase/metabolism, Alcaligenes/enzymology, Allosteric Regulation, Binding Sites, Coenzyme A/analogs & derivatives, Keto Acids, Kinetics, *Oxo-Acid-Lyases/metabolism	Metabolism
Metabolism	1156090	Aromatic amino acid biosynthesis in Alcaligenes eutrophus H16. II. The isolation and characterization of mutants auxotrophic for phenylalanine and tyrosine.	Friedrich B, Schlegel HG	Arch Microbiol	10.1007/BF00436341	1975	Alcaligenes/enzymology/isolation & purification/metabolism, Amino Acids/biosynthesis, Chorismic Acid/metabolism, Chromatography, DEAE-Cellulose, Culture Media, Cyclohexanecarboxylic Acids/metabolism, Mutagens, *Mutation, Phenylalanine/biosynthesis/deficiency, Prephenate Dehydratase/metabolism, Prephenate Dehydrogenase/metabolism, Pyruvates/metabolism, Tyrosine/biosynthesis/deficiency	Enzymology
Enzymology	1200735	Regulation of the pyruvate kinase from Alcaligenes eutrophus H 16 in vitro and in vivo.	Wilke D, Schlegel HG	Arch Microbiol	10.1007/BF00447123	1975	Acetates/metabolism, Adenosine Monophosphate/pharmacology, Adenosine Triphosphate/pharmacology, Alcaligenes/enzymology/growth & development, Allosteric Regulation, Enzyme Activation, Gluconates/metabolism, Glucosephosphates/pharmacology, Kinetics, Magnesium/pharmacology, Phosphates/pharmacology, Phosphoenolpyruvate, Pyruvate Kinase/antagonists & inhibitors/isolation & purification/metabolism, Ribosemonophosphates/pharmacology	Metabolism
Enzymology	7049889	Rhein as an electron acceptor for various flavoproteins and for electron transport particles.	Egerer P, Buhler M, Simon H	Hoppe Seylers Z Physiol Chem	10.1515/bchm2.1982.363.1.627	1982	Alcaligenes/enzymology, Animals, Anthraquinones/pharmacology, Cattle, Electron Transport, Flavoproteins/metabolism, Hydrogenase, Kinetics, Myocardium/metabolism, Oxidoreductases/metabolism, Saccharomyces cerevisiae/metabolism, Spectrophotometry	Metabolism
Enzymology	8020749	Stability and activity of hydrogenases of Methanobacterium thermoautotrophicum and Alcaligenes eutrophus in reversed micellar systems.	Hoppert M, Braks I, Mayer F	FEMS Microbiol Lett	10.1111/j.1574-6968.1994.tb06836.x	1994	Alcaligenes/enzymology, Alkanes, Emulsions, Enzyme Reactivators, Enzyme Stability, Hexoses, Methanobacterium/enzymology, Micelles, Models, Chemical, Oxidoreductases/*metabolism, Polysorbates	Metabolism
Metabolism	16821716	Identification of oxalotrophic bacteria by neural network analysis of numerical phenetic data.	Sahin N, Aydin S	Folia Microbiol (Praha)	10.1007/BF02932161	2006	Gram-Negative Aerobic Bacteria/classification/metabolism, Neural Networks, Computer, Oxalates/metabolism	Phylogeny
Metabolism	17318537	Biosynthesis of polyhydroxybutyrate (PHB) and extracellular polymeric substances (EPS) by Ralstonia eutropha ATCC 17699 in batch cultures.	Wang J, Yu HQ	Appl Microbiol Biotechnol	10.1007/s00253-007-0870-7	2007	Ammonium Sulfate/metabolism, Biomass, Biopolymers/metabolism, Bioreactors/microbiology, Culture Media/chemistry, Cupriavidus/growth & development/metabolism, Extracellular Space/metabolism, Glucose/metabolism, Hydroxybutyrates/*metabolism	Cultivation
Biotechnology	18266340	Monitoring poly(3-hydroxybutyrate) production in cupriavidus necator DSM 428 (H16) with raman spectroscopy.	Gelder JD, Willemse-Erix D, Scholtes MJ, Sanchez JI, Maquelin K, Vandenabeele P, Boever PD, Puppels GJ, Moens L, Vos PD	Anal Chem	10.1021/ac702185d	2008
Metabolism	20625719	Reaction engineering studies for the production of 2-hydroxyisobutyric acid with recombinant Cupriavidus necator H 16.	Hoefel T, Wittmann E, Reinecke L, Weuster-Botz D	Appl Microbiol Biotechnol	10.1007/s00253-010-2739-4	2010	Acyltransferases/genetics, Bioreactors, Culture Media, Cupriavidus necator/genetics/growth & development/metabolism, Fermentation, Gene Deletion, Genetic Engineering, Hydroxybutyrates/metabolism, Industrial Microbiology/methods, Intramolecular Transferases/genetics/metabolism, Vitamin B 12/metabolism	Biotechnology
Metabolism	21757489	Molecular genetics and biochemistry of N-acetyltaurine degradation by Cupriavidus necator H16.	Denger K, Lehmann S, Cook AM	Microbiology (Reading)	10.1099/mic.0.048462-0	2011	Amidohydrolases/chemistry/genetics/metabolism, Bacterial Proteins/chemistry/genetics/metabolism, Cupriavidus necator/enzymology/genetics/metabolism, Gene Expression Regulation, Bacterial, Kinetics, Membrane Transport Proteins/chemistry/genetics/metabolism, Metallochaperones/genetics/metabolism, Multigene Family, Taurine/analogs & derivatives/metabolism	Enzymology
Biotechnology	24594316	Production of polyhydroxyalkanoates from spent coffee grounds oil obtained by supercritical fluid extraction technology.	Cruz MV, Paiva A, Lisboa P, Freitas F, Alves VD, Simoes P, Barreiros S, Reis MA	Bioresour Technol	10.1016/j.biortech.2014.02.013	2014	Biomass, Chromatography, Supercritical Fluid/methods, Coffee/chemistry, Cupriavidus necator/growth & development/metabolism, Oils/chemistry, Polyhydroxyalkanoates/biosynthesis, Waste Products	Metabolism
Metabolism	24751509	Recovery of amorphous polyhydroxybutyrate granules from Cupriavidus necator cells grown on used cooking oil.	Martino L, Cruz MV, Scoma A, Freitas F, Bertin L, Scandola M, Reis MA	Int J Biol Macromol	10.1016/j.ijbiomac.2014.04.016	2014	Biomass, Biopolymers/chemistry/metabolism, Bioreactors, Cooking, Cupriavidus necator/metabolism, Fermentation, Hydroxybutyrates/chemistry/isolation & purification/metabolism, Liquid-Liquid Extraction, Plant Oils/*chemistry, Thermogravimetry	Enzymology
Pathogenicity	25738966	Sophorolipid biosurfactants: Possible uses as antibacterial and antibiofilm agent.	Diaz De Rienzo MA, Banat IM, Dolman B, Winterburn J, Martin PJ	N Biotechnol	10.1016/j.nbt.2015.02.009	2015	Anti-Bacterial Agents/chemistry/pharmacology, Bacterial Physiological Phenomena/drug effects, Biofilms/drug effects/growth & development, Cell Adhesion/drug effects/physiology, Cell Survival/drug effects, Glycolipids/chemistry/pharmacology, Surface-Active Agents/chemistry/pharmacology
Metabolism	26206741	Characterization of poly-3-hydroxybutyrate (PHB) produced from Ralstonia eutropha using an alkali-pretreated biomass feedstock.	Saratale GD, Oh MK	Int J Biol Macromol	10.1016/j.ijbiomac.2015.07.034	2015	Alkalies/pharmacology, Biomass, Carbohydrate Metabolism/drug effects, Cupriavidus necator/drug effects/growth & development/metabolism, Hydrolysis, Hydroxybutyrates/chemistry/metabolism, Polyesters/chemistry/metabolism, Spectrum Analysis, Raman, Thermogravimetry	Pathogenicity
Genetics	31515345	Complete Genome Sequence of Cupriavidus necator H16 (DSM 428).	Little GT, Ehsaan M, Arenas-Lopez C, Jawed K, Winzer K, Kovacs K, Minton NP	Microbiol Resour Announc	10.1128/MRA.00814-19	2019
Metabolism	31917558	Characterization of an l-Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations.	Stack TMM, Morrison KN, Dettmer TM, Wille B, Kim C, Joyce R, Jermain M, Naing YT, Bhatti K, Francisco BS, Carter MS, Gerlt JA	J Am Chem Soc	10.1021/jacs.9b09863	2020	Ascorbic Acid/metabolism, Bacterial Proteins/metabolism, Cupriavidus necator/enzymology/genetics/metabolism, Enzymes/metabolism, Genes, Bacterial, Oxidation-Reduction	Enzymology
	32260526	Preparation and Characterization of Films Based on a Natural P(3HB)/mcl-PHA Blend Obtained through the Co-culture of Cupriavidus Necator and Pseudomonas Citronellolis in Apple Pulp Waste.	Rebocho AT, Pereira JR, Neves LA, Alves VD, Sevrin C, Grandfils C, Freitas F, Reis MAM	Bioengineering (Basel)	10.3390/bioengineering7020034	2020
Biotechnology	32751380	Utilization of Noxious Weed Water Hyacinth Biomass as a Potential Feedstock for Biopolymers Production: A Novel Approach.	Saratale RG, Cho SK, Ghodake GS, Shin HS, Saratale GD, Park Y, Lee HS, Bharagava RN, Kim DS	Polymers (Basel)	10.3390/polym12081704	2020
	34771249	Upcycling Biodegradable PVA/Starch Film to a Bacterial Biopigment and Biopolymer.	Pantelic B, Ponjavic M, Jankovic V, Aleksic I, Stevanovic S, Murray J, Fournet MB, Nikodinovic-Runic J	Polymers (Basel)	10.3390/polym13213692	2021
Biotechnology	35215639	Developing Microbial Co-Culture System for Enhanced Polyhydroxyalkanoates (PHA) Production Using Acid Pretreated Lignocellulosic Biomass.	Saratale RG, Cho SK, Kadam AA, Ghodake GS, Kumar M, Bharagava RN, Varjani S, Nair S, Kim DS, Shin HS, Saratale GD	Polymers (Basel)	10.3390/polym14040726	2022

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
197	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 428)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-428
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
71655	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID13563.1	StrainInfo: A central database for resolving microbial strain identifiers