Strain identifier

BacDive ID: 2063

Type strain: Yes

Species: Pandoraea oxalativorans

Strain Designation: TA25

Strain history: <- N. Sahin, Mugla University, Kötekli, Turkey; TA25 <- A. Ü. Tamer, Celal Bayar University, Turkey

NCBI tax ID(s): 573737 (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: 17290

BacDive-ID: 2063

DSM-Number: 23570

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

description: Pandoraea oxalativorans TA25 is a mesophilic, Gram-negative, motile bacterium that was isolated from soil litter close to Oxalis sp..

NCBI tax id

  • NCBI tax id: 573737
  • Matching level: species

strain history

  • @ref: 17290
  • history: <- N. Sahin, Mugla University, Kötekli, Turkey; TA25 <- A. Ü. Tamer, Celal Bayar University, Turkey

doi: 10.13145/bacdive2063.20230509.8.1

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 oxalativorans
  • full scientific name: Pandoraea oxalativorans Sahin et al. 2011

@ref: 17290

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Pandoraea

species: Pandoraea oxalativorans

full scientific name: Pandoraea oxalativorans Sahin et al. 2011

strain designation: TA25

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23368negative2.3-2.8 µm0.7-0.9 µmrod-shapedyes
69480negative99.997

colony morphology

@refincubation periodcolony sizecolony colormedium used
172901-2 days
233682 days1-2 mmcreamTSA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17290TRYPTICASE 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
17290positivegrowth28mesophilic
23368positivegrowth30-37mesophilic
23368nogrowth42thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no96
69480no99.996

halophily

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2336817128adipate-carbon source
2336827689decanoate-carbon source
2336824265gluconate-carbon source
2336817057cellobiose-respiration
233688391D-gluconate-respiration
2336817784D-glucosaminic acid-respiration
2336814314D-glucose 6-phosphate-respiration
2336817992sucrose-respiration
2336828087glycogen-respiration
2336821217L-alaninamide-respiration
2336830849L-arabinose-respiration
2336841865sebacic acid-respiration
2336816947citrate+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
2336816383cis-aconitate+respiration
2336816947citrate+respiration
233688391D-gluconate+respiration
2336816523D-serine+respiration
2336815740formate+respiration
2336832323glucuronamide+respiration
2336817754glycerol+respiration
2336873804glycyl L-aspartic acid+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
2336815792malonate+respiration
2336851850methyl pyruvate+respiration
2336873784glycyl-l-glutamate+respiration
2336853426tween 80+respiration
2316373706bromosuccinate+respiration
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

antibiotic resistance

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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

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)+
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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
17290--------+/---------++++/-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
17290soil litter close to Oxalis sp.OxalisIzmirTurkeyTURAsia
23368soil litter close to oxalate-producing plants of the genera after enrichment with oxalate in mineral medium

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Engineered#Laboratory#Lab enrichment
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_842.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_494;97_563;98_648;99_842&stattab=map
  • Last taxonomy: Pandoraea
  • 16S sequence: AB469785
  • Sequence Identity:
  • Total samples: 5711
  • soil counts: 2081
  • aquatic counts: 1255
  • animal counts: 1218
  • plant counts: 1157

Safety information

risk assessment

  • @ref: 17290
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17290
  • description: Pandoraea oxalativorans gene for 16S rRNA, partial sequence, strain: TA25
  • accession: AB469785
  • length: 1375
  • database: ena
  • NCBI tax ID: 573737

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pandoraea oxalativorans DSM 23570GCA_000972785completencbi573737
66792Pandoraea oxalativorans strain DSM 23570573737.13plasmidpatric573737
66792Pandoraea oxalativorans strain DSM 23570573737.12plasmidpatric573737
66792Pandoraea oxalativorans strain DSM 23570573737.10plasmidpatric573737
66792Pandoraea oxalativorans strain DSM 23570573737.11plasmidpatric573737
66792Pandoraea oxalativorans strain DSM-23570573737.6completepatric573737

GC content

@refGC-contentmethod
1729062.1thermal denaturation, midpoint method (Tm)
2336862.1Thermal denaturation, fluorometry

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileyes89.413no
motileyes89.413no
motileyes89.413no
flagellatedno70.249no
flagellatedno70.249no
flagellatedno70.249no
gram-positiveno98.682yes
gram-positiveno98.682yes
gram-positiveno98.682yes
anaerobicno99.107no
anaerobicno99.107no
anaerobicno99.107no
aerobicyes91.752no
aerobicyes91.752no
aerobicyes91.752no
halophileno93.816no
halophileno93.816no
halophileno93.816no
spore-formingno94.855no
spore-formingno94.855no
spore-formingno94.855no
glucose-utilyes64.337yes
glucose-utilyes64.337yes
glucose-utilyes64.337yes
thermophileno99.063no
thermophileno99.063no
glucose-fermentno89.428yes
glucose-fermentno89.428yes
glucose-fermentno89.428yes
thermophileno99.063no

External links

@ref: 17290

culture collection no.: DSM 23570, CCM 7677, NBRC 106091, NEU 105

straininfo link

  • @ref: 71710
  • straininfo: 378119

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
Genetics26742625Complete genome sequence of Pandoraea oxalativorans DSM 23570(T), an oxalate metabolizing soil bacterium.Chan KG, Yong D, Ee R, Lim YL, Yu CY, Tee KK, Yin WF, Ang GYJ Biotechnol10.1016/j.jbiotec.2015.12.0372015Base Composition, Burkholderiaceae/*genetics/*isolation & purification, Genome Size, *Genome, Bacterial, Oxalates/metabolism, Sequence Analysis, DNA/methods, Soil MicrobiologyTranscriptome
27790203Characterization and Comparative Overview of Complete Sequences of the First Plasmids of Pandoraea across Clinical and Non-clinical Strains.Yong D, Tee KK, Yin WF, Chan KGFront Microbiol10.3389/fmicb.2016.016062016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17290Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23570)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23570
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
23163Martin W. Hahn, Elke Lang, Ulrike Brandt, Heinrich Lünsdorf, Qinglong L. Wu, Erko Stackebrandt10.1099/ijs.0.010595-0Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and riversIJSEM 60: 166-173 201019648339
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)
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
71710Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID378119.1StrainInfo: A central database for resolving microbial strain identifiers