Strain identifier

BacDive ID: 3009

Type strain: No

Species: Variovorax paradoxus

Strain Designation: 180, P2-106-S (3)

Strain history: IAM 12374 <-- ATCC 17549 <-- R. Y. Stanier 180 <-- E. Snell P2-106-S(3).

NCBI tax ID(s): 34073 (species)

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General

@ref: 9172

BacDive-ID: 3009

DSM-Number: 30162

keywords: 16S sequence, Bacteria

description: Variovorax paradoxus 180 is a bacterium that was isolated from soil by enrichment with pantothenate.

NCBI tax id

  • NCBI tax id: 34073
  • Matching level: species

strain history

@refhistory
9172<- ATCC <- R.Y. Stanier, 180 <- E.E. Snell, P2-106-S (3)
67770IAM 12374 <-- ATCC 17549 <-- R. Y. Stanier 180 <-- E. Snell P2-106-S(3).

doi: 10.13145/bacdive3009.20240510.9

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: 9172

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: 180, P2-106-S (3)

type strain: no

Culture and growth conditions

culture medium

  • @ref: 9172
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
9172positivegrowth30
67770positivegrowth25

Physiology and metabolism

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
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

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6837435581indole-
6836935581indole-

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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
44418-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
44418----+---++++-++++++++

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
44418-------++----------------------+

Isolation, sampling and environmental information

isolation

@refsample type
9172soil by enrichment with pantothenate
44418Soil by enrichment with pantothenate
67770Soil

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Environmental#Terrestrial#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: AB622223
  • Sequence Identity:
  • Total samples: 9717
  • soil counts: 3106
  • aquatic counts: 2157
  • animal counts: 2122
  • plant counts: 2332

Safety information

risk assessment

  • @ref: 9172
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Variovorax paradoxus gene for 16S rRNA, partial sequence, strain: DSM 30162AB6222231497nuccore34073
20218Variovorax paradoxus DNA, 16S-23S rRNA gene internal transcribed spacer, strain: DSM 30162AB622233584nuccore34073
20218Variovorax paradoxus gene for 16S rRNA, partial sequence, strain: NBRC 15150AB6807851460nuccore34073

GC content

  • @ref: 9172
  • GC-content: 67.1
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 9172

culture collection no.: CCUG 1778, LMG 1796, DSM 30162, ATCC 17549, DSM 67, IFO 15150, NBRC 15150, NCIB 11474, JCM 20527, IAM 12374, NCIMB 11474

straininfo link

  • @ref: 72531
  • straininfo: 5035

literature

  • topic: Enzymology
  • Pubmed-ID: 18838814
  • title: Gene cloning of alpha-methylserine aldolase from Variovorax paradoxus and purification and characterization of the recombinant enzyme.
  • authors: Nozaki H, Kuroda S, Watanabe K, Yokozeki K
  • journal: Biosci Biotechnol Biochem
  • DOI: 10.1271/bbb.80274
  • year: 2008
  • mesh: Amino 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, Temperature
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9172Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30162)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30162
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
44418Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 1778)https://www.ccug.se/strain?id=1778
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
72531Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5035.1StrainInfo: A central database for resolving microbial strain identifiers