Strain identifier

BacDive ID: 2061

Type strain: Yes

Species: Pandoraea thiooxydans

Strain Designation: ATSB16

Strain history: CIP <- 2010, KACC <- D. M. Sa, Nat. Chungbuk. Univ., Cheongju, Korea: strain ATSB16

NCBI tax ID(s): 445709 (species)

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General

@ref: 18000

BacDive-ID: 2061

DSM-Number: 25325

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

description: Pandoraea thiooxydans ATSB16 is an aerobe, chemolithoautotroph, mesophilic bacterium that was isolated from rhizosphere soils of sesame Sesamum indicum L..

NCBI tax id

  • NCBI tax id: 445709
  • Matching level: species

strain history

@refhistory
18000<- LMG <- T.-M. Sa; ATSB16
123526CIP <- 2010, KACC <- D. M. Sa, Nat. Chungbuk. Univ., Cheongju, Korea: strain ATSB16

doi: 10.13145/bacdive2061.20230509.8.1

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 thiooxydans
  • full scientific name: Pandoraea thiooxydans Anandham et al. 2010

@ref: 18000

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Pandoraea

species: Pandoraea thiooxydans

full scientific name: Pandoraea thiooxydans Anandham et al. 2010

strain designation: ATSB16

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23162negative1.2-4.5 µm0.5-0.7 µmrod-shapedyes
69480yes94.673
69480negative99.978
123526negativerod-shapedyes

colony morphology

@refincubation periodcolony colorcolony shapemedium used
180001-2 days
231622 dayswhitecircularR2A

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18000CASO 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
23162Reasoner's 2A agar (R2A)yes
42013MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123526CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123526CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
18000positivegrowth30mesophilic
23162positivegrowth4-42
23162positiveoptimum30mesophilic
42013positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
23162positivegrowth4.0-10.0alkaliphile
23162positiveoptimum7.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23162aerobe
123526obligate aerobe

nutrition type

  • @ref: 23162
  • type: chemolithoautotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.988

halophily

  • @ref: 23162
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23162168082-dehydro-D-gluconate-assimilation
23162161933-hydroxybenzoate-assimilation
23162178794-hydroxybenzoate-assimilation
23162174265-dehydro-D-gluconate-assimilation
2316227689decanoate-assimilation
2316216988D-ribose-assimilation
2316217268myo-inositol-assimilation
2316217240itaconate-assimilation
2316230849L-arabinose-assimilation
2316228053melibiose-assimilation
23162506227N-acetylglucosamine-assimilation
2316217814salicin-assimilation
2316217992sucrose-assimilation
2316227897tryptophan-energy source
231624853esculin-hydrolysis
231625291gelatin-hydrolysis
23162yeast extract-required for growth
23162370543-hydroxybutyrate+assimilation
2316217128adipate+assimilation
2316227442beta-D-fucose+assimilation
2316217634D-glucose+assimilation
2316216899D-mannitol+assimilation
2316216024D-mannose+assimilation
2316217924D-sorbitol+assimilation
2316228087glycogen+assimilation
2316216977L-alanine+assimilation
2316218287L-fucose+assimilation
2316217203L-proline+assimilation
2316262345L-rhamnose+assimilation
2316217115L-serine+assimilation
2316224996lactate+assimilation
2316225115malate+assimilation
2316217306maltose+assimilation
2316230860methylmalonic acid+assimilation
2316218401phenylacetate+assimilation
2316232032potassium gluconate+assimilation
2316217272propionate+assimilation
2316232954sodium acetate+assimilation
231629300suberic acid+assimilation
2316231011valerate+assimilation
2316217234glucose+fermentation
2316253426tween 80+hydrolysis
2316217632nitrate+reduction
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
12352617632nitrate+reduction
12352616301nitrite-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
23162100147nalidixic acidyesyes
2316228971ampicillinyesyes
2316217698chloramphenicolyesyes
231626104kanamycinyesyes
2316245924trimethoprimyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2316235581indoleno
6836935581indoleno
12352635581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
2316235581indole-
6836935581indole-

enzymes

@refvalueactivityec
23162acid phosphatase-3.1.3.2
23162alkaline phosphatase-3.1.3.1
23162alpha-chymotrypsin-3.4.21.1
23162alpha-fucosidase-3.2.1.51
23162alpha-galactosidase-3.2.1.22
23162alpha-glucosidase-3.2.1.20
23162alpha-mannosidase-3.2.1.24
23162arginine dihydrolase-3.5.3.6
23162beta-galactosidase-3.2.1.23
23162beta-glucosidase-3.2.1.21
23162beta-glucuronidase-3.2.1.31
23162catalase-1.11.1.6
23162cystine arylamidase-3.4.11.3
23162cytochrome oxidase+1.9.3.1
23162esterase (C 4)+
23162esterase lipase (C 8)-
23162leucine arylamidase+3.4.11.1
23162lipase (C 14)-
23162N-acetyl-beta-glucosaminidase-3.2.1.52
23162naphthol-AS-BI-phosphohydrolase+
23162trypsin-3.4.21.4
23162tryptophan deaminase-4.1.99.1
23162urease+3.5.1.5
23162valine arylamidase-
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123526oxidase+
123526catalase-1.11.1.6
123526urease-3.5.1.5

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
18000+------------------+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
18000rhizosphere soils of sesame Sesamum indicum L.Sesamum indicumJung ha-dongRepublic of KoreaKORAsia
123526Environment, Sesam, rhizosphere soilsJung ha dongRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_7855.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_494;97_4473;98_5739;99_7855&stattab=map
  • Last taxonomy: Pandoraea thiooxydans subclade
  • 16S sequence: EF397578
  • Sequence Identity:
  • Total samples: 2826
  • soil counts: 299
  • aquatic counts: 210
  • animal counts: 166
  • plant counts: 2151

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
180001Risk group (German classification)
1235261Risk group (French classification)

Sequence information

16S sequences

  • @ref: 18000
  • description: Pandoraea thiooxydans strain ATSB16 16S ribosomal RNA gene, partial sequence
  • accession: EF397578
  • length: 1410
  • database: ena
  • NCBI tax ID: 445709

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pandoraea thiooxydans DSM 25325GCA_001017775completencbi445709
66792Pandoraea thiooxydans ATSB16GCA_001931675completencbi445709
66792Pandoraea thiooxydans strain ATSB16445709.9completepatric445709
66792Pandoraea thiooxydans strain DSM 25325445709.3completepatric445709
66792Pandoraea thiooxydans ATSB162721755763completeimg445709
66792Pandoraea thiooxydans DSM 253252648501246completeimg445709

GC content

@refGC-contentmethod
1800064.0
2316264.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes84.895yes
motileyes84.895yes
motileyes84.895yes
flagellatedno72.498no
flagellatedno72.498no
flagellatedno72.498no
gram-positiveno98.575yes
gram-positiveno98.575yes
gram-positiveno98.575yes
anaerobicno97.787yes
anaerobicno97.787yes
anaerobicno97.787yes
aerobicyes84.537yes
aerobicyes84.537yes
aerobicyes84.537yes
halophileno91.351no
halophileno91.351no
halophileno91.351no
spore-formingno95.659no
spore-formingno95.659no
spore-formingno95.659no
thermophileno98.034no
thermophileno98.034no
thermophileno98.034no
glucose-utilno51.362no
glucose-utilno51.362no
glucose-utilno51.362no
glucose-fermentno90.586no
glucose-fermentno90.586no
glucose-fermentno90.586no

External links

@ref: 18000

culture collection no.: DSM 25325, KACC 12757, LMG 24779, CIP 110207

straininfo link

  • @ref: 71708
  • straininfo: 356279

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19643869Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.).Anandham R, Indiragandhi P, Kwon SW, Sa TM, Jeon CO, Kim YK, Jee HJInt J Syst Evol Microbiol10.1099/ijs.0.012823-02009Burkholderiaceae/classification/genetics/*isolation & purification/*metabolism, Chemoautotrophic Growth, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sesamum/*microbiology, *Soil Microbiology, Thiosulfates/*metabolismMetabolism
Genetics26603120Complete genome sequence of Pandoraea thiooxydans DSM 25325(T), a thiosulfate-oxidizing bacterium.Yong D, Ee R, Lim YL, Yu CY, Ang GY, How KY, Tee KK, Yin WF, Chan KGJ Biotechnol10.1016/j.jbiotec.2015.11.0092015*Base Sequence, Biodegradation, Environmental, Burkholderiaceae/enzymology/*genetics/metabolism, DNA, Bacterial/genetics, Genome, Bacterial, Molecular Sequence Data, Oxidation-Reduction, Oxidoreductases/genetics/metabolism, Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, Thiosulfates/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18000Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25325)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25325
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
23162Rangasamy Anandham, Pandiyan Indiragandhi, Soon Wo Kwon, Tong Min Sa, Che Ok Jeon, Yong Ki Kim, Hyeong Jin Jee10.1099/ijs.0.012823-0Pandoraea thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sesame (Sesamum indicum L.)IJSEM 60: 21-26 201019643869
42013Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8041
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
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
71708Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID356279.1StrainInfo: A central database for resolving microbial strain identifiers
123526Curators of the CIPCollection of Institut Pasteur (CIP 110207)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110207