Strain identifier

BacDive ID: 2041

Type strain: Yes

Species: Cupriavidus gilardii

Strain Designation: 4325

Strain history: CIP <- 1999, CCUG <- P. Vandamme, LMG, Gent, Belgium, Alcaligenes faecalis subsp. faecalis <- D. Monget, API, France: strain API141-2-84, Alcaligenes faecalis <- G.L. Gilardi, USA: strain 4325

NCBI tax ID(s): 82541 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 6877

BacDive-ID: 2041

DSM-Number: 17292

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

description: Cupriavidus gilardii 4325 is an obligate aerobe, mesophilic, Gram-negative human pathogen that was isolated from whirlpool.

NCBI tax id

  • NCBI tax id: 82541
  • Matching level: species

strain history

@refhistory
6877<- CCUG <- P. Vandamme, LMG, Gent <- D. Monget, Api, France (Alcaligenes faecalis) <- G. L. Gilardi, USA
67770LMG 5886 <-- D. Monget API 141-2-84 <-- G. Gilandi 4325.
119616CIP <- 1999, CCUG <- P. Vandamme, LMG, Gent, Belgium, Alcaligenes faecalis subsp. faecalis <- D. Monget, API, France: strain API141-2-84, Alcaligenes faecalis <- G.L. Gilardi, USA: strain 4325

doi: 10.13145/bacdive2041.20230509.8.1

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

  • synonyms

    @refsynonym
    20215Wautersia gilardii
    20215Ralstonia gilardii

@ref: 6877

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Cupriavidus

species: Cupriavidus gilardii

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

strain designation: 4325

type strain: yes

Morphology

cell morphology

  • @ref: 119616
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6877CASO 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
40276MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119616CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119616CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
6877positivegrowth37mesophilic
40276positivegrowth30mesophilic
67770positivegrowth30mesophilic
119616positivegrowth25-41
119616nogrowth5psychrophilic
119616nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119616
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
119616NaClpositivegrowth0-4 %
119616NaClnogrowth6 %
119616NaClnogrowth8 %
119616NaClnogrowth10 %

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
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
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
119616citrate-carbon source16947
119616esculin-hydrolysis4853
119616nitrate-reduction17632
119616nitrite-reduction16301
119616phenol-degradation15882
119616nitrate-respiration17632

antibiotic resistance

  • @ref: 119616
  • 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
11961635581indoleno

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
119616oxidase+
119616beta-galactosidase-3.2.1.23
119616alcohol dehydrogenase-1.1.1.1
119616gelatinase-
119616amylase-
119616DNase-
119616caseinase+3.4.21.50
119616catalase+1.11.1.6
119616tween esterase-
119616gamma-glutamyltransferase-2.3.2.2
119616lecithinase-
119616lipase-
119616lysine decarboxylase-4.1.1.18
119616ornithine decarboxylase-4.1.1.17
119616protease-
119616tryptophan deaminase-
119616urease-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
119616-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6877--------------++++--+
6877--------------++++-++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119616----+-----+++--------++/-++++/-+---+---++------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119616-------------------------------+-----------++--+-+--------+-+------------+-++++++++----++++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6877whirlpoolUSAUSANorth America
54234Whirl pool
67770Whirl pool
119616Environment, Whirl pool

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Built environment
  • Cat3: #Water reservoir (Aquarium/pool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2523.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_409;97_464;98_1186;99_2523&stattab=map
  • Last taxonomy: Cupriavidus
  • 16S sequence: EU024163
  • Sequence Identity:
  • Total samples: 1710
  • soil counts: 301
  • aquatic counts: 204
  • animal counts: 739
  • plant counts: 466

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
6877yes, in single cases1Risk group (German classification)
1196161Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Cupriavidus gilardii strain CIP 105966 16S ribosomal RNA gene, partial sequenceEU0241631315ena82541
6877Ralstonia gilardii 16S ribosomal RNA gene, complete sequenceAF0766451451ena82541

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cupriavidus gilardii strain ATCC 70081582541.17wgspatric82541
66792Cupriavidus gilardii strain CCUG 3840182541.14wgspatric82541
67770Cupriavidus gilardii ATCC 700815GCA_013004615contigncbi82541
67770Cupriavidus gilardii CCUG 38401GCA_008801915contigncbi82541

GC content

@refGC-contentmethod
687768-69
6777068.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.019no
flagellatedyes51.367no
gram-positiveno98.819no
anaerobicno99.032no
halophileno94.915no
spore-formingno94.425no
thermophileno98.596yes
glucose-utilno72.611yes
aerobicyes93.519no
glucose-fermentno91.669yes

External links

@ref: 6877

culture collection no.: LMG 5886, CCM 4866, DSM 17292, ATCC 700815, CCUG 38401, CIP 105966, JCM 11283, BCRC 17471

straininfo link

  • @ref: 71688
  • straininfo: 765

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319461Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov.Coenye T, Falsen E, Vancanneyt M, Hoste B, Govan JR, Kersters K, Vandamme PInt J Syst Bacteriol10.1099/00207713-49-2-4051999Bacterial Proteins/chemistry, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Electrophoresis, Polyacrylamide Gel, Environmental Microbiology, Fatty Acids/analysis, Gram-Negative Aerobic Rods and Cocci/chemistry/*classification/genetics/isolation & purification, Gram-Negative Bacterial Infections/*microbiology, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, 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
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
Phylogeny33847555Cupriavidus cauae sp. nov., isolated from blood of an immunocompromised patient.Kweon OJ, Ruan W, Khan SA, Lim YK, Kim HR, Jeon CO, Lee MKInt J Syst Evol Microbiol10.1099/ijsem.0.0047592021Adult, Bacterial Typing Techniques, Base Composition, Blood/*microbiology, Cupriavidus/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Humans, *Immunocompromised Host, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6877Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17292)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17292
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
40276Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18043
54234Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38401)https://www.ccug.se/strain?id=38401
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
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
71688Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID765.1StrainInfo: A central database for resolving microbial strain identifiers
119616Curators of the CIPCollection of Institut Pasteur (CIP 105966)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105966