Strain identifier

BacDive ID: 2044

Type strain: Yes

Species: Cupriavidus taiwanensis

Strain Designation: R1

Strain history: CIP <- 2001, CCUG <- 2000, LMG

NCBI tax ID(s): 977880 (strain), 164546 (species)

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General

@ref: 6907

BacDive-ID: 2044

DSM-Number: 17343

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, human pathogen

description: Cupriavidus taiwanensis R1 is an aerobe, mesophilic, motile human pathogen that was isolated from root nodule of Mimosa pudica.

NCBI tax id

NCBI tax idMatching level
977880strain
164546species

strain history

@refhistory
6907<- CCUG <- LMG <- P. Vandamme, Ghent <- W.-M. Chen, Taiwan
123421CIP <- 2001, CCUG <- 2000, LMG

doi: 10.13145/bacdive2044.20230509.8.1

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 taiwanensis
  • full scientific name: Cupriavidus taiwanensis (Chen et al. 2001) Vandamme and Coenye 2004

  • synonyms

    @refsynonym
    20215Wautersia taiwanensis
    20215Ralstonia taiwanensis

@ref: 6907

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Cupriavidus

species: Cupriavidus taiwanensis

full scientific name: Cupriavidus taiwanensis (Chen et al. 2001) Vandamme and Coenye 2004

strain designation: R1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.428
6948099.997negative
123421yesnegativerod-shaped

colony morphology

  • @ref: 56268
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6907R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 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
34928MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123421CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6907positivegrowth28mesophilic
34928positivegrowth37mesophilic
56268positivegrowth28-42
123421positivegrowth25-41
123421nogrowth5psychrophilic
123421nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
56268aerobe
123421obligate aerobe

spore formation

@refspore formationconfidence
69481no94
69480no99.966

halophily

@refsaltgrowthtested relationconcentration
123421NaClpositivegrowth0-2 %
123421NaClnogrowth4 %
123421NaClnogrowth6 %
123421NaClnogrowth8 %
123421NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12342116947citrate-carbon source
1234214853esculin-hydrolysis
12342117632nitrate+reduction
12342116301nitrite+reduction
12342117632nitrate+respiration

antibiotic resistance

  • @ref: 123421
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12342135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123421oxidase+
123421beta-galactosidase-3.2.1.23
123421alcohol dehydrogenase-1.1.1.1
123421gelatinase-
123421amylase-
123421DNase-
123421caseinase-3.4.21.50
123421catalase+1.11.1.6
123421tween esterase+
123421lecithinase-
123421lysine decarboxylase-4.1.1.18
123421ornithine decarboxylase-4.1.1.17
123421protease-
123421tryptophan deaminase-
123421urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123421-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6907+--------------++++++
6907+-------------+++++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123421-------------------------------+-------------+-+++++++------+++--+-+-----+-+++-++++----++++++++-++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
6907root nodule of Mimosa pudicaMimosa pudicaPing-Tung CountryTaiwanTWNAsia
56268Root nodule of Mimosa pudicaTaiwanTWNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root nodule

taxonmaps

  • @ref: 69479
  • File name: preview.99_1912.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_409;97_464;98_534;99_1912&stattab=map
  • Last taxonomy: Cupriavidus
  • 16S sequence: AF300324
  • Sequence Identity:
  • Total samples: 2331
  • soil counts: 1401
  • aquatic counts: 297
  • animal counts: 341
  • plant counts: 292

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
6907yes, in single cases1Risk group (German classification)
1234211Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6907
  • description: Ralstonia taiwanensis strain LMG 19424 16S ribosomal RNA gene, partial sequence
  • accession: AF300324
  • length: 1542
  • database: ena
  • NCBI tax ID: 977880

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cupriavidus taiwanensis LMG 19424GCA_000069785chromosomencbi977880
66792Cupriavidus taiwanensis LMG 19424 strain LMG19424977880.27plasmidpatric977880
66792Cupriavidus taiwanensis strain LMG 19424164546.7completepatric164546
66792Cupriavidus taiwanensis LMG 19424644736347completeimg977880

GC content

  • @ref: 6907
  • GC-content: 67.3

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 94
  • training_data: no

External links

@ref: 6907

culture collection no.: DSM 17343, CCUG 44338, CIP 107717, LMG 19424, CIP 107171

straininfo link

  • @ref: 71691
  • straininfo: 13083

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11594603Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient.Chen WM, Laevens S, Lee TM, Coenye T, De Vos P, Mergeay M, Vandamme PInt J Syst Evol Microbiol10.1099/00207713-51-5-17292001Anti-Bacterial Agents/pharmacology, Bacterial Proteins/chemistry, Betaproteobacteria/*classification/enzymology/genetics/isolation & purification, Cystic Fibrosis/*microbiology, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Fabaceae/*microbiology, Gram-Negative Bacterial Infections/microbiology, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Restriction Mapping, Sequence Analysis, DNA, Sputum/*microbiologyEnzymology
Enzymology14651338Nodulation of Mimosa spp. by the beta-proteobacterium Ralstonia taiwanensis.Chen WM, James EK, Prescott AR, Kierans M, Sprent JIMol Plant Microbe Interact10.1094/MPMI.2003.16.12.10512003Blotting, Western, Electrophoresis, Polyacrylamide Gel, Green Fluorescent Proteins, Luminescent Proteins/genetics, Microscopy, Electron, Mimosa/microbiology/*physiology/ultrastructure, *Nitrogen Fixation, Ralstonia/genetics/*physiology, Transformation, Genetic
Phylogeny15545472Taxonomy of the genus Cupriavidus: a tale of lost and found.Vandamme P, Coenye TInt J Syst Evol Microbiol10.1099/ijs.0.63247-02004Bacterial Proteins/analysis/isolation & purification, Base Composition, Burkholderiaceae/*classification/genetics/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Proteome/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Phylogeny16269788Proof that Burkholderia strains form effective symbioses with legumes: a study of novel Mimosa-nodulating strains from South America.Chen WM, de Faria SM, Straliotto R, Pitard RM, Simoes-Araujo JL, Chou JH, Chou YJ, Barrios E, Prescott AR, Elliott GN, Sprent JI, Young JP, James EKAppl Environ Microbiol10.1128/AEM.71.11.7461-7471.20052005Acyltransferases/genetics, Bacterial Proteins/genetics, Base Sequence, Brazil, Burkholderia/*classification/growth & development, Mimosa/*microbiology, Molecular Sequence Data, *Nitrogen Fixation, Oxidoreductases/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Restriction Mapping, Sequence Analysis, DNA, South America, *Symbiosis, VenezuelaGenetics
Phylogeny17176403Burkholderia phymatum is a highly effective nitrogen-fixing symbiont of Mimosa spp. and fixes nitrogen ex planta.Elliott GN, Chen WM, Chou JH, Wang HC, Sheu SY, Perin L, Reis VM, Moulin L, Simon MF, Bontemps C, Sutherland JM, Bessi R, de Faria SM, Trinick MJ, Prescott AR, Sprent JI, James EKNew Phytol10.1111/j.1469-8137.2006.01894.x2007Bacterial Proteins/classification/genetics, Bacteriological Techniques, Burkholderia/genetics/isolation & purification/*metabolism, Cupriavidus/genetics/isolation & purification/metabolism, DNA, Ribosomal/chemistry/classification, Fabaceae/microbiology, Green Fluorescent Proteins/analysis, Mimosa/*microbiology, Nitrogenase/metabolism, Phylogeny, Root Nodules, Plant/growth & development/metabolism/microbiology, Species Specificity, *SymbiosisMetabolism
Genetics18490699Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia.Amadou C, Pascal G, Mangenot S, Glew M, Bontemps C, Capela D, Carrere S, Cruveiller S, Dossat C, Lajus A, Marchetti M, Poinsot V, Rouy Z, Servin B, Saad M, Schenowitz C, Barbe V, Batut J, Medigue C, Masson-Boivin CGenome Res10.1101/gr.076448.1082008Base Sequence, Cupriavidus/classification/*genetics, Fabaceae/microbiology, Genes, Bacterial, *Genome, Bacterial, Genomics, Molecular Sequence Data, Nitrogen Fixation/genetics, Phylogeny, Proteobacteria/genetics, Symbiosis/geneticsPhylogeny
Phylogeny19040456Burkholderia spp. are the most competitive symbionts of Mimosa, particularly under N-limited conditions.Elliott GN, Chou JH, Chen WM, Bloemberg GV, Bontemps C, Martinez-Romero E, Velazquez E, Young JP, Sprent JI, James EKEnviron Microbiol10.1111/j.1462-2920.2008.01799.x2008Alphaproteobacteria/classification/growth & development/*isolation & purification/*physiology, Betaproteobacteria/classification/growth & development/*isolation & purification/*physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Mexico, Mimosa/*microbiology, Nitrogen/*metabolism, Papua New Guinea, Phylogeny, Puerto Rico, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Symbiosis, TaiwanEnzymology
Metabolism22556357Biosynthesis of branched-chain amino acids is essential for effective symbioses between betarhizobia and Mimosa pudica.Chen WM, Prell J, James EK, Sheu DS, Sheu SYMicrobiology (Reading)10.1099/mic.0.058370-02012Amino Acids, Branched-Chain/*biosynthesis, Burkholderia/genetics/growth & development/metabolism/*physiology, Culture Media/chemistry, Cupriavidus/genetics/growth & development/metabolism/*physiology, DNA Transposable Elements, Gene Deletion, Genes, Bacterial, Genetic Complementation Test, Mimosa/*microbiology/*physiology, Mutagenesis, Insertional, *SymbiosisCultivation
Metabolism22865066The type 3 protein secretion system of Cupriavidus taiwanensis strain LMG19424 compromises symbiosis with Leucaena leucocephala.Saad MM, Crevecoeur M, Masson-Boivin C, Perret XAppl Environ Microbiol10.1128/AEM.01691-122012*Bacterial Secretion Systems, Cupriavidus/metabolism/*physiology, Fabaceae/*microbiology, Gene Knockout Techniques, Glutamates/metabolism, Proteins, *Symbiosis, Transcription, Genetic, Transcriptional Activation
Genetics22972004Genomics-driven discovery of taiwachelin, a lipopeptide siderophore from Cupriavidus taiwanensis.Kreutzer MF, Nett MOrg Biomol Chem10.1039/c2ob26296g2012Computational Biology, Cupriavidus/*chemistry/*genetics, *Genomics, Lipopeptides/*chemistry, Magnetic Resonance Spectroscopy, Siderophores/*chemistry, Spectroscopy, Fourier Transform Infrared
Metabolism24012541Exploration and prediction of interactions between methanotrophs and heterotrophs.Stock M, Hoefman S, Kerckhof FM, Boon N, De Vos P, De Baets B, Heylen K, Waegeman WRes Microbiol10.1016/j.resmic.2013.08.0062013Bacteria/*growth & development/*metabolism, Carbon/metabolism, Energy Metabolism, *Heterotrophic Processes, Methane/*metabolism, *Microbial Interactions, Nitrogen/metabolism
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
Metabolism29378510Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history.Klonowska A, Melkonian R, Miche L, Tisseyre P, Moulin LBMC Genomics10.1186/s12864-018-4487-22018Burkholderia/*genetics/metabolism, Cupriavidus/*genetics/metabolism, Gene Expression Profiling, Genome, Bacterial, Microbial Interactions, Mimosa/*microbiology, Plant Root Nodulation/*genetics, Plant Roots/physiology, Rhizobium/*genetics/metabolism, Symbiosis/geneticsGenetics
Phylogeny31617792noeM, a New Nodulation Gene Involved in the Biosynthesis of Nod Factors with an Open-Chain Oxidized Terminal Residue and in the Symbiosis with Mimosa pudica.Daubech B, Poinsot V, Klonowska A, Capela D, Chaintreuil C, Moulin L, Marchetti M, Masson-Boivin CMol Plant Microbe Interact10.1094/MPMI-06-19-0168-R2019*Cupriavidus/classification/genetics, Genes, Bacterial/genetics, *Mimosa/microbiology, Phylogeny, Plasmids/genetics, *Rhizobium, Symbiosis/genetics
Phylogeny32143559Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil.Klonowska A, Moulin L, Ardley JK, Braun F, Gollagher MM, Zandberg JD, Marinova DV, Huntemann M, Reddy TBK, Varghese NJ, Woyke T, Ivanova N, Seshadri R, Kyrpides N, Reeve WGBMC Genomics10.1186/s12864-020-6623-z2020Cadmium/metabolism, Cupriavidus/*drug effects/*genetics, Metals, Heavy/*toxicity, Mimosa/*microbiology, Multigene Family, Nickel/toxicity, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/drug effects/genetics, Soil, Soil Microbiology, Symbiosis, Synteny/genetics, Zinc/toxicityPathogenicity
Metabolism32484353A Unique Combination of Two Different Quorum Sensing Systems in the beta-Rhizobium Cupriavidus taiwanensis.Wakimoto T, Nakagishi S, Matsukawa N, Tani S, Kai KJ Nat Prod10.1021/acs.jnatprod.0c000542020Biofilms, Chromatography, Gas, Coproporphyrins/metabolism, Cupriavidus/*genetics, Escherichia coli/metabolism, Gene Deletion, Genes, Bacterial/genetics, Mimosa/chemistry, Mutation/genetics, Quorum Sensing/*genetics, Ralstonia/drug effects, Ralstonia solanacearum, Rhizobium/*genetics, Spectrometry, Mass, Electrospray Ionization, Vibrio cholerae/drug effectsPathogenicity

Reference

@idauthorscataloguedoi/urltitle
6907Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17343)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17343
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
34928Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4577
56268Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 44338)https://www.ccug.se/strain?id=44338
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
68382Automatically annotated from API zym
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71691Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13083.1StrainInfo: A central database for resolving microbial strain identifiers
123421Curators of the CIPCollection of Institut Pasteur (CIP 107171)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107171