Strain identifier

BacDive ID: 2043

Type strain: Yes

Species: Cupriavidus pauculus

Strain Designation: E6793

Strain history: CIP <- 1999, CCUG <- K. Kersters, LMG, Gent, Belgium <- R.E. Weaver, CDC: strain E6793

NCBI tax ID(s): 82633 (species)

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

@ref: 6891

BacDive-ID: 2043

DSM-Number: 17313

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Cupriavidus pauculus E6793 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from human endotrachea.

NCBI tax id

  • NCBI tax id: 82633
  • Matching level: species

strain history

@refhistory
6891<- CCUG <- K. Kersters, LMG Gent <-R. E. Weaver, CDC Atlanta
67770LMG 3244 <-- R. E. Weaver (CDC group IVc-2).
121637CIP <- 1999, CCUG <- K. Kersters, LMG, Gent, Belgium <- R.E. Weaver, CDC: strain E6793

doi: 10.13145/bacdive2043.20230509.8.1

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 pauculus
  • full scientific name: Cupriavidus pauculus (Vandamme et al. 1999) Vandamme and Coenye 2004
  • synonyms

    @refsynonym
    20215Ralstonia paucula
    20215Wautersia paucula

@ref: 6891

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Cupriavidus

species: Cupriavidus pauculus

full scientific name: Cupriavidus pauculus (Vandamme et al. 1999) Vandamme and Coenye 2004

strain designation: E6793

type strain: yes

Morphology

cell morphology

  • @ref: 121637
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6891CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
38594MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121637CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
6891positivegrowth37mesophilic
38594positivegrowth30mesophilic
67770positivegrowth30mesophilic
121637positivegrowth15-45
121637nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121637
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
121637NaClpositivegrowth0-2 %
121637NaClnogrowth4 %
121637NaClnogrowth6 %
121637NaClnogrowth8 %
121637NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68369malate+assimilation25115
68369adipate+assimilation17128
68369decanoate+assimilation27689
68369gluconate-assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin-hydrolysis5291
68369esculin-hydrolysis4853
68369urea+hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
121637citrate+carbon source16947
121637esculin-hydrolysis4853
121637hippurate+hydrolysis606565
121637nitrate-builds gas from17632
121637nitrate-reduction17632
121637nitrite-builds gas from16301
121637nitrite-reduction16301
121637malonate+assimilation15792
121637nitrate-respiration17632
68374ornithine-degradation18257
68374arginine-hydrolysis29016
68374lysine-degradation25094
68374urea+hydrolysis16199
68374L-arabitol-builds acid from18403
68374D-galacturonic acid-builds acid from18024
68374Potassium 5-ketogluconate-builds acid from
68374D-mannitol-builds acid from16899
68374maltose-builds acid from17306
68374ribitol-builds acid from15963
68374palatinose-builds acid from18394
68374malonate+assimilation15792
68374tryptophan-energy source27897
68374D-glucose-builds acid from17634
68374sucrose-builds acid from17992
68374L-arabinose-builds acid from30849
68374D-arabitol-builds acid from18333
68374trehalose-builds acid from27082
68374L-rhamnose-builds acid from62345
68374myo-inositol-builds acid from17268
68374cellobiose-builds acid from17057
68374sorbitol-builds acid from30911

antibiotic resistance

  • @ref: 121637
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836935581indoleno
12163735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole-
6836935581indole-
12163715688acetoin-
12163717234glucose-

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
68374L-aspartate arylamidase+3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase-3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase-3.2.1.23
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase-3.2.1.21
68374lipase-
68374urease+3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase-3.5.3.6
68374ornithine decarboxylase-4.1.1.17
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
121637oxidase+
121637beta-galactosidase-3.2.1.23
121637alcohol dehydrogenase-1.1.1.1
121637gelatinase-
121637amylase-
121637DNase-
121637caseinase-3.4.21.50
121637catalase+1.11.1.6
121637tween esterase+
121637gamma-glutamyltransferase-2.3.2.2
121637lecithinase+
121637lipase+
121637lysine decarboxylase-4.1.1.18
121637ornithine decarboxylase-4.1.1.17
121637phenylalanine ammonia-lyase-4.3.1.24
121637protease-
121637tryptophan deaminase-
121637urease+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
121637-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6891----+----------++++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121637-------------------------------------------------

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
45728---+----+------+---------------+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121637-------------------------------+-----------++--+++++++----+-++-------------++++++++----+++++-+-++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
6891human endotracheaUSAUSANorth America
45728Human respiratory tract (endotrachea)USAUSANorth AmericaOregon
67770Respiratory tract of human
121637Human, Respiratory tractUnited States of AmericaUSANorth AmericaOregon

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Trachea

taxonmaps

  • @ref: 69479
  • File name: preview.99_6931.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_409;97_464;98_1186;99_6931&stattab=map
  • Last taxonomy: Cupriavidus
  • 16S sequence: EU024165
  • Sequence Identity:
  • Total samples: 563
  • soil counts: 158
  • aquatic counts: 114
  • animal counts: 238
  • plant counts: 53

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
68912Risk group (German classification)
1216371Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Cupriavidus pauculus strain CIP 105943 16S ribosomal RNA gene, partial sequence
  • accession: EU024165
  • length: 1315
  • database: ena
  • NCBI tax ID: 82633

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cupriavidus pauculus strain CCUG 1250782633.14wgspatric82633
66792Cupriavidus pauculus strain FDAARGOS_147282633.20completepatric82633
67770Cupriavidus pauculus CCUG 12507GCA_008801835contigncbi82633
66792Cupriavidus pauculus strain FDAARGOS_147282633.27completepatric82633
66792Cupriavidus pauculus strain FDAARGOS_147282633.24completepatric82633
66792Cupriavidus pauculus strain FDAARGOS_147282633.22completepatric82633

GC content

  • @ref: 67770
  • GC-content: 67
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes85.908no
flagellatedno60.965no
gram-positiveno98.538no
anaerobicno98.533no
halophileno96.233no
spore-formingno94.657no
thermophileno99.255yes
glucose-utilno77.689yes
aerobicyes94.292no
glucose-fermentno89.799yes

External links

@ref: 6891

culture collection no.: DSM 17313, CCM 4867, CCUG 12507, CDC E6793, CIP 105943, LMG 3244, JCM 11286, ATCC 700817, BCRC 17496

straininfo link

  • @ref: 71690
  • straininfo: 1696

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319489Assignment of Centers for Disease Control group IVc-2 to the genus Ralstonia as Ralstonia paucula sp. nov.Vandamme P, Goris J, Coenye T, Hoste B, Janssens D, Kersters K, De Vos P, Falsen EInt J Syst Bacteriol10.1099/00207713-49-2-6631999Bacterial Proteins/chemistry, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Electrophoresis, Polyacrylamide Gel, Environmental Microbiology, Genes, rRNA, Gram-Negative Bacteria/*classification/genetics/isolation & purification/physiology, Gram-Negative Bacterial Infections/*microbiology, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6891Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17313)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17313
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
38594Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18018
45728Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12507)https://www.ccug.se/strain?id=12507
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68374Automatically annotated from API ID32E
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
71690Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1696.1StrainInfo: A central database for resolving microbial strain identifiers
121637Curators of the CIPCollection of Institut Pasteur (CIP 105943)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105943