Strain identifier

BacDive ID: 2058

Type strain: Yes

Species: Pandoraea pulmonicola

Strain Designation: FC 330, R-650

Strain history: CIP <- 2000, CCUG <- 1997, P. Vandamme, LMG, Ghent, Belgium: strain R-650 <- D.Speert

NCBI tax ID(s): 93221 (species)

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

@ref: 6516

BacDive-ID: 2058

DSM-Number: 16583

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

description: Pandoraea pulmonicola FC 330 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from sputum from cystic fibrosis patient.

NCBI tax id

  • NCBI tax id: 93221
  • Matching level: species

strain history

@refhistory
6516<- CCM <- CCUG <- P. Vandamme <- D. Speert
122046CIP <- 2000, CCUG <- 1997, P. Vandamme, LMG, Ghent, Belgium: strain R-650 <- D.Speert

doi: 10.13145/bacdive2058.20230509.8.1

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

@ref: 6516

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Pandoraea

species: Pandoraea pulmonicola

full scientific name: Pandoraea pulmonicola Coenye et al. 2000

strain designation: FC 330, R-650

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidencecell shape
23367negative1.5-4.0 µm0.5-0.7 µmyes
69480yes97.117
69480negative99.995
122046negativeyesrod-shaped

pigmentation

  • @ref: 122046
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6516CASO 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
42008MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122046CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6516positivegrowth37mesophilic
23367positivegrowth30-37mesophilic
23367positivemaximum42thermophilic
42008positivegrowth37mesophilic
122046positivegrowth25-41
122046nogrowth5psychrophilic
122046nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122046
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
23367no
69481no100
69480no99.913

halophily

@refsaltgrowthtested relationconcentration
23367NaClnogrowth>3.0 %
122046NaClpositivegrowth0-4 %
122046NaClnogrowth6 %
122046NaClnogrowth8 %
122046NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2336727897tryptophan-energy source
2336717128adipate-growth
2336717306maltose-growth
2336717992sucrose-growth
233674853esculin-hydrolysis
2336753426tween 80-hydrolysis
2336717632nitrate-reduction
2336716301nitrite-reduction
2336727689decanoate+growth
2336716947citrate+growth
2336717634D-glucose+growth
2336724996lactate+growth
12204616947citrate+carbon source
1220464853esculin-hydrolysis
12204617632nitrate-reduction
12204616301nitrite-reduction
12204617632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
2336735581indoleno
12204635581indoleno

metabolite tests

  • @ref: 23367
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
23367amylase-
23367arginine dihydrolase-3.5.3.6
23367cystine arylamidase-3.4.11.3
23367cytochrome oxidase+1.9.3.1
23367DNase-
23367esterase (C 4)-
23367esterase lipase (C 8)-
23367phosphoamidase+3.9.1.1
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
122046oxidase+
122046beta-galactosidase-3.2.1.23
122046alcohol dehydrogenase-1.1.1.1
122046gelatinase-
122046amylase-
122046caseinase-3.4.21.50
122046catalase+1.11.1.6
122046tween esterase-
122046lecithinase-
122046lipase-
122046lysine decarboxylase-4.1.1.18
122046ornithine decarboxylase-4.1.1.17
122046protease-
122046tryptophan deaminase-
122046urease-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
122046-++-------++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122046+------------------------------+-----------++--+++++-+++--+-++++-+++++---+-++-+++-+-----+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6516sputum from cystic fibrosis patientCanadaCANNorth America
54444Human sputum,cystic fibrosisCanadaCANNorth America
122046Human, SputumCanadaCANNorth America

isolation source categories

Cat1Cat2Cat3
#Infection#Disease#Cystic fibrosis
#Infection#Patient
#Host Body Product#Fluids#Sputum

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: AY268173
  • 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
65162Risk group (German classification)
1220461Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pandoraea pulmonicola strain CCUG 38759 16S ribosomal RNA gene, partial sequenceAY2681731461ena93221
23367Pandoraea pulmonicola 16S ribosomal RNA gene, partial sequenceAF1391751485nuccore93221

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pandoraea pulmonicola DSM 16583GCA_000815105completencbi93221
66792Pandoraea pulmonicola DSM 1658393221.4completepatric93221

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.357yes
motileyes89.357yes
flagellatedno62.423no
flagellatedno62.423no
gram-positiveno98.892yes
gram-positiveno98.892yes
anaerobicno99.28no
anaerobicno99.28no
aerobicyes90.401no
aerobicyes90.401no
halophileno94.204no
halophileno94.204no
spore-formingno95.239yes
spore-formingno95.239yes
glucose-utilyes69.505no
glucose-utilyes69.505no
thermophileno98.652no
thermophileno98.652no
glucose-fermentno86.708no
glucose-fermentno86.708no

External links

@ref: 6516

culture collection no.: DSM 16583, CCM 4979, CCUG 38759, CIP 106625, LMG 18106

straininfo link

  • @ref: 71705
  • straininfo: 10813

literature

  • topic: Phylogeny
  • Pubmed-ID: 10758901
  • title: Description 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.
  • authors: Coenye T, Falsen E, Hoste B, Ohlen M, Goris J, Govan JR, Gillis M, Vandamme P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-50-2-887
  • year: 2000
  • mesh: Base 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/*microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6516Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16583)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16583
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
42008Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18776
54444Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38759)https://www.ccug.se/strain?id=38759
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)
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
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
71705Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10813.1StrainInfo: A central database for resolving microbial strain identifiers
122046Curators of the CIPCollection of Institut Pasteur (CIP 106625)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106625