Strain identifier

BacDive ID: 2066

Type strain: Yes

Species: Pandoraea vervacti

Strain Designation: 561, NS15

Strain history: <- N. Sahin, Mugla University, Kötekli, Turkey; NS15

NCBI tax ID(s): 656178 (species)

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

@ref: 17291

BacDive-ID: 2066

DSM-Number: 23571

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

description: Pandoraea vervacti 561 is a mesophilic, Gram-negative, motile bacterium that was isolated from uncultivated field soil.

NCBI tax id

  • NCBI tax id: 656178
  • Matching level: species

strain history

  • @ref: 17291
  • history: <- N. Sahin, Mugla University, Kötekli, Turkey; NS15

doi: 10.13145/bacdive2066.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Pandoraea
  • species: Pandoraea vervacti
  • full scientific name: Pandoraea vervacti Sahin et al. 2011

@ref: 17291

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Pandoraea

species: Pandoraea vervacti

full scientific name: Pandoraea vervacti Sahin et al. 2011

strain designation: 561, NS15

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23368negative2.8 µm0.9 µmrod-shapedyes
69480yes95.793
69480negative99.982

colony morphology

@refincubation periodcolony sizecolony colormedium used
172911-2 days
233682 days1-2 mmcreamTSA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17291TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
23368Trypticase Soy Agar (TSA)yes

culture temp

@refgrowthtypetemperaturerange
17291positivegrowth28mesophilic
23368positivegrowth30-42

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.963

halophily

@refsaltgrowthtested relationconcentration
23368NaClpositivegrowth3 %(w/v)
23368NaClnogrowth4.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2336817128adipate-carbon source
2336817057cellobiose-respiration
2336814314D-glucose 6-phosphate-respiration
2336817992sucrose-respiration
2336816523D-serine-respiration
2336832323glucuronamide-respiration
2336828087glycogen-respiration
2336873804glycyl L-aspartic acid-respiration
2336830849L-arabinose-respiration
2336815792malonate-respiration
2336873784glycyl-l-glutamate-respiration
2336841865sebacic acid-respiration
2336827689decanoate+carbon source
2336816947citrate+carbon source
2336824265gluconate+carbon source
2336817234glucose+carbon source
2336825115malate+carbon source
2336818401phenylacetate+carbon source
23368645522-hydroxybutyrate+respiration
23368167632-oxobutanoate+respiration
23368286442-oxopentanoate+respiration
23368370543-hydroxybutyrate+respiration
23368167244-hydroxybutyrate+respiration
2336830089acetate+respiration
2336817925alpha-D-glucose+respiration
2336873706bromosuccinate+respiration
2336816383cis-aconitate+respiration
2336816947citrate+respiration
233688391D-gluconate+respiration
2336817784D-glucosaminic acid+respiration
2336815740formate+respiration
2336817754glycerol+respiration
2336821217L-alaninamide+respiration
2336873786L-alanylglycine+respiration
2336817196L-asparagine+respiration
2336829985L-glutamate+respiration
2336815971L-histidine+respiration
2336815603L-leucine+respiration
2336817295L-phenylalanine+respiration
2336817203L-proline+respiration
2336818183L-pyroglutamic acid+respiration
2336817115L-serine+respiration
2336816857L-threonine+respiration
2336824996lactate+respiration
2336851850methyl pyruvate+respiration
2336853426tween 80+respiration
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
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

antibiotic resistance

  • @ref: 23368
  • ChEBI: 27902
  • metabolite: tetracycline
  • is antibiotic: yes
  • is resistant: no
  • resistance conc.: 30 µg

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
23368acid phosphatase+3.1.3.2
23368alkaline phosphatase+3.1.3.1
23368catalase+1.11.1.6
23368cystine arylamidase-3.4.11.3
23368cytochrome oxidase+1.9.3.1
23368esterase (C 4)+
23368esterase lipase (C 8)-
23368esterase lipase (C 8)+
23368leucine arylamidase+3.4.11.1
23368naphthol-AS-BI-phosphohydrolase+
23368nitrate reductase-1.7.99.4
23368urease+3.5.1.5
23368valine arylamidase-
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
17291----+-+-------------+/-

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
17291----+---+-----++-++++/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17291uncultivated field soilMuglaTurkeyTURAsia
23368field soil after enrichment with oxalate in mineral medium

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_814.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_494;97_563;98_648;99_814&stattab=map
  • Last taxonomy: Pandoraea
  • 16S sequence: AB510956
  • Sequence Identity:
  • Total samples: 20583
  • soil counts: 6943
  • aquatic counts: 4192
  • animal counts: 3605
  • plant counts: 5843

Safety information

risk assessment

  • @ref: 17291
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17291
  • description: Pandoraea vervacti gene for 16S rRNA, partial sequence, strain: NS15
  • accession: AB510956
  • length: 1378
  • database: ena
  • NCBI tax ID: 656178

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pandoraea vervacti NS15GCA_000934605completencbi656178
66792Pandoraea vervacti strain NS15656178.9plasmidpatric656178
66792Pandoraea vervacti strain NS15656178.5completepatric656178
66792Pandoraea vervacti NS152927181219completeimg656178

GC content

@refGC-contentmethod
1729165.8thermal denaturation, midpoint method (Tm)
2336865.8Thermal denaturation, fluorometry

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.68no
motileyes88.68no
flagellatedno58.531no
flagellatedno58.531no
gram-positiveno98.717no
gram-positiveno98.717no
anaerobicno98.81no
anaerobicno98.81no
aerobicyes90.975no
aerobicyes90.975no
halophileno94.024no
halophileno94.024no
spore-formingno94.044no
spore-formingno94.044no
glucose-utilyes64.918yes
glucose-utilyes64.918yes
thermophileno98.902yes
thermophileno98.902yes
glucose-fermentno89.565yes
glucose-fermentno89.565yes

External links

@ref: 17291

culture collection no.: DSM 23571, CCM 7667, NBRC 106088

straininfo link

  • @ref: 71713
  • straininfo: 378120

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20952546Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture.Sahin N, Tani A, Kotan R, Sedlacek I, Kimbara K, Tamer AUInt J Syst Evol Microbiol10.1099/ijs.0.026138-02010Aerobiosis, Bacterial Typing Techniques, Burkholderiaceae/*classification/genetics/*isolation & purification/metabolism, Cluster Analysis, Culture Media/chemistry, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalates/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Genetics25848988Complete genome sequence of oxalate-degrading bacterium Pandoraea vervacti DSM 23571(T).Ee R, Yong D, Lim YL, Yin WF, Chan KGJ Biotechnol10.1016/j.jbiotec.2015.03.0202015Base Composition, Base Sequence, Burkholderiaceae/*genetics/metabolism, Gene Components, Genome, Bacterial/*genetics, Industrial Microbiology, Metabolic Networks and Pathways/genetics, Molecular Sequence Data, Oxalates/metabolism, Sequence Analysis, DNA, *Soil Microbiology, TurkeyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17291Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23571)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23571
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
23368Nurettin Sahin, Akio Tani, Recep Kotan, Ivo Sedlácek, Kazuhide Kimbara, Abdurrahman U. Tamer10.1099/ijs.0.026138-0Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched cultureIJSEM 61: 2247-2253 201120952546
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)
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
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
71713Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID378120.1StrainInfo: A central database for resolving microbial strain identifiers