Strain identifier

BacDive ID: 2060

Type strain: Yes

Species: Pandoraea pnomenusa

Strain Designation: R140

Strain history: CIP <- 2000, CCUG <- 1997, P. Vandamme, LMG, Gent, Belgium, Burkholderia cepacia: strain R140

NCBI tax ID(s): 93220 (species)

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

@ref: 6474

BacDive-ID: 2060

DSM-Number: 16536

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

description: Pandoraea pnomenusa R140 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from cystic fibrosis patient.

NCBI tax id

  • NCBI tax id: 93220
  • Matching level: species

strain history

@refhistory
6474<- CCM <- CCUG <- P. Vandamme
121915CIP <- 2000, CCUG <- 1997, P. Vandamme, LMG, Gent, Belgium, Burkholderia cepacia: strain R140

doi: 10.13145/bacdive2060.20230509.8.1

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 pnomenusa
  • full scientific name: Pandoraea pnomenusa Coenye et al. 2000

@ref: 6474

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Pandoraea

species: Pandoraea pnomenusa

full scientific name: Pandoraea pnomenusa Coenye et al. 2000

strain designation: R140

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilitycell shape
23367negative1.5-4.0 µm0.5-0.7 µmyes
121915negativeyesrod-shaped

pigmentation

  • @ref: 121915
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6474CASO 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
42009MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121915CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6474positivegrowth37mesophilic
23367positivegrowth30-37mesophilic
23367positivemaximum42thermophilic
42009positivegrowth37mesophilic
121915positivegrowth25-41
121915nogrowth5psychrophilic
121915nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121915
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 23367
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
23367NaClnogrowth3.0 %
23367NaClnogrowth4.5 %
121915NaClpositivegrowth0-4 %
121915NaClnogrowth6 %
121915NaClnogrowth8 %
121915NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2336727897tryptophan-energy source
2336717128adipate-growth
2336717634D-glucose-growth
2336717306maltose-growth
2336717992sucrose-growth
233674853esculin-hydrolysis
2336753426tween 80-hydrolysis
2336716301nitrite-reduction
2336727689decanoate+growth
2336716947citrate+growth
2336724996lactate+growth
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
12191516947citrate+carbon source
1219154853esculin-hydrolysis
12191517632nitrate+reduction
12191516301nitrite-reduction
12191517632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
2336735581indoleno
6836935581indoleno
12191535581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
2336735581indole-
6836935581indole-

enzymes

@refvalueactivityec
23367DNase-
23367tryptophan deaminase-4.1.99.1
23367urease+3.5.1.5
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
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121915oxidase+
121915beta-galactosidase-3.2.1.23
121915alcohol dehydrogenase-1.1.1.1
121915gelatinase-
121915amylase-
121915DNase-
121915caseinase-3.4.21.50
121915catalase+1.11.1.6
121915tween esterase-
121915lecithinase-
121915lipase-
121915lysine decarboxylase-4.1.1.18
121915ornithine decarboxylase-4.1.1.17
121915protease-
121915tryptophan deaminase-
121915urease+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
121915--++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6474+------------+++--++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121915+------------------------------+-----------++--+++++++++--+-++++-+++-+---+-++-+++++-----+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
6474cystic fibrosis patientUnited KingdomGBREurope
23367Edinburgh
54431Human,cystic fibrosis patientUnited KingdomGBREurope
121915Human, Cystic fibrosis patientUnited KingdomGBREuropeEdinburgh, Scotland

isolation source categories

Cat1Cat2Cat3
#Infection#Disease#Cystic fibrosis
#Infection#Patient

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: AY268170
  • Sequence Identity:
  • Total samples: 20583
  • soil counts: 6943
  • aquatic counts: 4192
  • animal counts: 3605
  • plant counts: 5843

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64742Risk group (German classification)
1219151Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pandoraea pnomenusa strain CCUG 38742 16S ribosomal RNA gene, partial sequenceAY2681701461ena93220
6474Pandoraea pnomenusa 16S ribosomal RNA gene, partial sequenceAF1391741474ena93220

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pandoraea pnomenusa DSM 16536GCA_000767615completencbi93220
66792Pandoraea pnomenusa strain DSM-1653693220.25completepatric93220

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes93.076yes
motileyes93.076yes
motileyes93.076yes
flagellatedno66.843no
flagellatedno66.843no
flagellatedno66.843no
gram-positiveno98.812no
gram-positiveno98.812no
gram-positiveno98.812no
anaerobicno99.232no
anaerobicno99.232no
anaerobicno99.232no
aerobicyes91.131no
aerobicyes91.131no
aerobicyes91.131no
halophileno93.153no
halophileno93.153no
halophileno93.153no
spore-formingno95.342yes
spore-formingno95.342yes
spore-formingno95.342yes
thermophileno98.889no
thermophileno98.889no
thermophileno98.889no
glucose-utilyes61.202yes
glucose-utilyes61.202yes
glucose-utilyes61.202yes
glucose-fermentno89.403yes
glucose-fermentno89.403yes
glucose-fermentno89.403yes

External links

@ref: 6474

culture collection no.: DSM 16536, CCM 4978, CCUG 38742, CIP 106626, LMG 18087

straininfo link

  • @ref: 71707
  • straininfo: 10798

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10758901Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb. nov.Coenye T, Falsen E, Hoste B, Ohlen M, Goris J, Govan JR, Gillis M, Vandamme PInt J Syst Evol Microbiol10.1099/00207713-50-2-8872000Base Composition, Betaproteobacteria/chemistry/*classification/genetics/physiology, Burkholderia/classification/genetics, Burkholderia Infections/microbiology, Cystic Fibrosis/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Electrophoresis, Polyacrylamide Gel, Fatty Acids/analysis, Genes, rRNA, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sputum/*microbiologyEnzymology
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
Phylogeny27267599Pandoraea terrae sp. nov., isolated from forest soil, and emended description of the genus Pandoraea Coenye et al. 2000.Jeong SE, Lee HJ, Jia B, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0012292016Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Islands, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Putrescine/analogs & derivatives/chemistry, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, UbiquinoneTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6474Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16536)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16536
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
23367T Coenye, E Falsen, B Hoste, M Ohlén, J Goris, J R Govan, M Gillis, P Vandamme10.1099/00207713-50-2-887Description of Pandoraea gen. nov. with Pandoraea apista sp. nov., Pandoraea pulmonicola sp. nov., Pandoraea pnomenusa sp. nov., Pandoraea sputorum sp. nov. and Pandoraea norimbergensis comb. nov.IJSEM 50: 887-899 200010758901
42009Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18777
54431Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38742)https://www.ccug.se/strain?id=38742
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
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
71707Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10798.1StrainInfo: A central database for resolving microbial strain identifiers
121915Curators of the CIPCollection of Institut Pasteur (CIP 106626)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106626