Strain identifier

BacDive ID: 2033

Type strain: Yes

Species: Cupriavidus necator

Strain Designation: N-1, Jr N-1

Strain history: CIP <- 1988, ATCC <- L.E. Casida: strain Jr N-1

NCBI tax ID(s): 106590 (species)

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General

@ref: 5069

BacDive-ID: 2033

DSM-Number: 13513

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

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

NCBI tax id

  • NCBI tax id: 106590
  • Matching level: species

strain history

@refhistory
5069<- ATCC <- L. E. Casida, Jr.
121251CIP <- 1988, ATCC <- L.E. Casida: strain Jr N-1

doi: 10.13145/bacdive2033.20230509.8.1

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: 5069

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: N-1, Jr N-1

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5069BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
5069NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37118MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121251CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
5069positivegrowth26mesophilic
37118positivegrowth30mesophilic
59481positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 59481
  • oxygen tolerance: aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5069+-------------++-+-++
5069+---+---------++-++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5069soilPensylvaniaUSAUSANorth America
59481SoilPA,University ParkUSAUSANorth America
121251Environment, SoilUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_662.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_409;97_464;98_534;99_662&stattab=map
  • Last taxonomy: Cupriavidus
  • 16S sequence: AF191737
  • Sequence Identity:
  • Total samples: 30560
  • soil counts: 15055
  • aquatic counts: 5686
  • animal counts: 7044
  • plant counts: 2775

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
50691Risk group (German classification)
1212511Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Cupriavidus necator 16S ribosomal RNA gene, partial sequence
  • accession: AF191737
  • length: 1356
  • database: ena
  • NCBI tax ID: 106590

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cupriavidus necator N-1GCA_000219215completencbi1042878
66792Cupriavidus necator N-11042878.50plasmidpatric1042878
66792Cupriavidus necator N-11042878.49plasmidpatric1042878
66792Cupriavidus necator N-11042878.5completepatric1042878
66792Cupriavidus necator N-1, ATCC 43291650716031completeimg1042878

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.259no
flagellatedno52.466no
gram-positiveno98.492no
anaerobicno98.868no
aerobicyes92.84yes
halophileno93.858no
spore-formingno94.23no
thermophileno98.817yes
glucose-utilno63.725yes
glucose-fermentno91.817yes

External links

@ref: 5069

culture collection no.: DSM 13513, ATCC 43291, CCUG 52238, CIP 103161, LMG 8453

straininfo link

  • @ref: 71680
  • straininfo: 2100

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology22342083Renewable 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 MABioresour Technol10.1016/j.biortech.2012.01.1192012Carbohydrates/chemistry/*isolation & purification, Eucalyptus/*chemistry, *FermentationPhylogeny
Metabolism23133311Factors 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 MAJ Biomed Biotechnol10.1155/2012/1258652012Ammonium Sulfate/pharmacology, Biomass, Bioreactors/microbiology, Cupriavidus necator/drug effects/growth & development/*metabolism, Hydrogen-Ion Concentration/drug effects, Hydroxybutyrates/*metabolism, Mechanical Phenomena/drug effects, Oxygen/pharmacology, Palm Oil, Plant Extracts/*metabolism, Plant Leaves/*metabolism, Plant Oils/*metabolism, Polyesters/*metabolism, Solubility, Temperature, Time FactorsPathogenicity
Phylogeny27001671Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge.Sun LN, Wang DS, Yang ED, Fang LC, Chen YF, Tang XY, Hua RMInt J Syst Evol Microbiol10.1099/ijsem.0.0010342016Bacterial Typing Techniques, Base Composition, China, Chlorpyrifos/*metabolism, Cupriavidus/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5069Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13513)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13513
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37118Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14928
59481Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52238)https://www.ccug.se/strain?id=52238
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68369Automatically annotated from API 20NE
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
71680Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2100.1StrainInfo: A central database for resolving microbial strain identifiers
121251Curators of the CIPCollection of Institut Pasteur (CIP 103161)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103161