Strain identifier

BacDive ID: 3008

Type strain: Yes

Species: Variovorax paradoxus

Strain Designation: 351, B13-0-1 D, B13-0-1D

Strain history: CIP <- 1991, CCUG <- ATCC <- R.Y. Stanier, Inst. Pasteur, Paris, France: strain 351, Alcaligenes paradoxus biotype I <- D.H. Davis: strain B13-0-1D

NCBI tax ID(s): 1321610 (strain), 34073 (species)

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General

@ref: 9096

BacDive-ID: 3008

DSM-Number: 30034

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

description: Variovorax paradoxus 351 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
34073species
1321610strain

strain history

@refhistory
9096<- ATCC <- R.Y. Stanier, 351 <- D.H. Davis, B13-0-1 D
67770IAM 12373 <-- ATCC 17713 <-- R. Y. Stanier 351 <-- D. Davis 13-0-1D.
121552CIP <- 1991, CCUG <- ATCC <- R.Y. Stanier, Inst. Pasteur, Paris, France: strain 351, Alcaligenes paradoxus biotype I <- D.H. Davis: strain B13-0-1D

doi: 10.13145/bacdive3008.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Variovorax
  • species: Variovorax paradoxus
  • full scientific name: Variovorax paradoxus (Davis 1969) Willems et al. 1991

  • synonyms

    • @ref: 20215
    • synonym: Alcaligenes paradoxus

@ref: 9096

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Variovorax

species: Variovorax paradoxus

full scientific name: Variovorax paradoxus (Davis 1969) Willems et al. 1991

strain designation: 351, B13-0-1 D, B13-0-1D

type strain: yes

Morphology

cell morphology

  • @ref: 121552
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 121552

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
36606MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
9096MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)yesName: 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 waterhttps://mediadive.dsmz.de/medium/81
9096NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1
121552CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
36606positivegrowth25mesophilic
9096positivegrowth30mesophilic
44417positivegrowth30mesophilic
67770positivegrowth25mesophilic
121552positivegrowth15-37
121552nogrowth5psychrophilic
121552nogrowth41thermophilic
121552nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44417aerobe
121552obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
121552NaClpositivegrowth0-2 %
121552NaClnogrowth4 %
121552NaClnogrowth6 %
121552NaClnogrowth8 %
121552NaClnogrowth10 %

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
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12155216947citrate-carbon source
1215524853esculin-hydrolysis
121552606565hippurate-hydrolysis
12155217632nitrate-builds gas from
12155217632nitrate+reduction
12155216301nitrite-builds gas from
12155216301nitrite-reduction
12155215792malonate+assimilation
12155217632nitrate-respiration
6837418257ornithine-degradation
6837429016arginine-hydrolysis
6837425094lysine-degradation
6837416199urea-hydrolysis
6837418403L-arabitol-builds acid from
6837418024D-galacturonic acid-builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837416899D-mannitol-builds acid from
6837417306maltose-builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837415792malonate-assimilation
6837427897tryptophan-energy source
6837417634D-glucose-builds acid from
6837417992sucrose-builds acid from
6837430849L-arabinose-builds acid from
6837418333D-arabitol-builds acid from
6837427082trehalose-builds acid from
6837462345L-rhamnose-builds acid from
6837417268myo-inositol-builds acid from
6837417057cellobiose-builds acid from
6837430911sorbitol-builds acid from

antibiotic resistance

  • @ref: 121552
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836935581indoleno
12155235581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole-
6836935581indole-
12155215688acetoin-
12155217234glucose-

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
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
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
121552oxidase+
121552beta-galactosidase-3.2.1.23
121552alcohol dehydrogenase-1.1.1.1
121552gelatinase-
121552amylase-
121552DNase-
121552caseinase-3.4.21.50
121552catalase+1.11.1.6
121552tween esterase-
121552gamma-glutamyltransferase+2.3.2.2
121552lecithinase-
121552lipase-
121552lysine decarboxylase-4.1.1.18
121552ornithine decarboxylase-4.1.1.17
121552phenylalanine ammonia-lyase-4.3.1.24
121552protease-
121552tryptophan deaminase-
121552urease+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
44417-+++-+---------+----
121552-+++-+-----+--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
44417+----------+--+-++--+

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
44417--------+--------------+-------+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121552+++-+--------------+++--+-++---+-+--++--------+-++----+-+++-+-+++++--+---+-++-+++++----+++++-+++-+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
9096soil
44417Soil in mineral medium with an atmosphere of H2...USAUSANorth America
67770Soil
121552Environment, Soil enriched with pantothenate

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2305.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_308;97_342;98_387;99_2305&stattab=map
  • Last taxonomy: Variovorax
  • 16S sequence: D88006
  • Sequence Identity:
  • Total samples: 9717
  • soil counts: 3106
  • aquatic counts: 2157
  • animal counts: 2122
  • plant counts: 2332

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
90961Risk group (German classification)
1215521Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Variovorax paradoxus gene for 16S rRNA, partial sequence, strain: DSM 30034AB6222191483ena34073
20218Variovorax paradoxus DNA, 16S-23S rRNA gene internal transcribed spacer, strain: DSM 30034AB622229634ena34073
20218Variovorax paradoxus 16S rRNA gene, strain DSM 66AJ4203291483ena34073
20218Variovorax paradoxus gene for 16S ribosomal RNAD307931457ena34073
20218Variovorax paradoxus DNA for 16S ribosomal RNAD880061467ena34073
20218Variovorax paradoxus gene for 16S rRNA, partial sequence, strain: NBRC 15149AB6807841460ena1321610

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Variovorax paradoxus NBRC 151491321610.3wgspatric1321610
66792Variovorax paradoxus NBRC 151492731957648draftimg1321610
67770Variovorax paradoxus NBRC 15149GCA_001591365contigncbi1321610

GC content

@refGC-contentmethod
909667.0thermal denaturation, midpoint method (Tm)
909668.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes84.767no
gram-positiveno98.627no
anaerobicno98.094yes
halophileno95.905no
spore-formingno94.372no
glucose-utilyes65.199yes
flagellatedno53.019no
thermophileno98.76no
aerobicyes92.066yes
glucose-fermentno89.02no

External links

@ref: 9096

culture collection no.: DSM 30034, ATCC 17713, DSM 66, IFO 15149, NBRC 15149, CCUG 1777, LMG 1797, JCM 20526, IAM 12373, IAM 13535, ICPB 3985, JCM 20895, CIP 103459, NCIMB 11964

straininfo link

  • @ref: 72530
  • straininfo: 5036

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585700Variovorax dokdonensis sp. nov., isolated from soil.Yoon JH, Kang SJ, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64070-02006Comamonadaceae/*classification/genetics/growth & development/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny17158995Variovorax soli sp. nov., isolated from greenhouse soil.Kim BY, Weon HY, Yoo SH, Lee SY, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64390-02006Bacterial Typing Techniques, Comamonadaceae/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/analysis, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny18175723Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil.Miwa H, Ahmed I, Yoon J, Yokota A, Fujiwara TInt J Syst Evol Microbiol10.1099/ijs.0.65315-02008Bacterial Typing Techniques, Base Composition, Boron/*metabolism, Comamonadaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Enzymology18838814Gene cloning of alpha-methylserine aldolase from Variovorax paradoxus and purification and characterization of the recombinant enzyme.Nozaki H, Kuroda S, Watanabe K, Yokozeki KBiosci Biotechnol Biochem10.1271/bbb.802742008Amino Acid Sequence, Cloning, Molecular, Comamonadaceae/*enzymology/genetics, Conserved Sequence, Fructose-Bisphosphate Aldolase/chemistry/genetics/*isolation & purification/*metabolism, Gene Expression, Hydrogen-Ion Concentration, Molecular Sequence Data, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sequence Alignment, Serine/*analogs & derivatives/metabolism, Spectrophotometry, Substrate Specificity, TemperatureMetabolism
Phylogeny21948092Variovorax defluvii sp. nov., isolated from sewage.Jin L, Kim KK, Ahn CY, Oh HMInt J Syst Evol Microbiol10.1099/ijs.0.035295-02011Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/microbiology, Sequence Analysis, DNA, Sewage/*microbiologyGenetics
Phylogeny25504533Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere.Gao JL, Yuan M, Wang XM, Qiu TL, Li JW, Liu HC, Li XA, Chen J, Sun JGAntonie Van Leeuwenhoek10.1007/s10482-014-0304-32014Bacterial Typing Techniques, Base Composition, Carbon-Carbon Lyases/*metabolism, China, Cluster Analysis, Comamonadaceae/*classification/enzymology/genetics/*isolation & purification, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Musa, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyEnzymology
Phylogeny26341669Variovorax gossypii sp. nov., isolated from Gossypium hirsutum.Kampfer P, Busse HJ, McInroy JA, Glaeser SPInt J Syst Evol Microbiol10.1099/ijsem.0.0005812015Alabama, Bacterial Typing Techniques, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gossypium/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, Putrescine/analogs & derivatives/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny35791077Variovorax terrae sp. nov. Isolated from Soil with Potential Antioxidant Activity.Woo CY, Kim JJ Microbiol Biotechnol10.4014/jmb.2205.050182022Antioxidants/analysis, Bacterial Typing Techniques, *Comamonadaceae, DNA, Bacterial/genetics, Fatty Acids/analysis, *Phosphatidylethanolamines/analysis, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9096Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30034)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30034
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
36606Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15259
44417Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 1777)https://www.ccug.se/strain?id=1777
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
72530Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5036.1StrainInfo: A central database for resolving microbial strain identifiers
121552Curators of the CIPCollection of Institut Pasteur (CIP 103459)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103459