Strain identifier

BacDive ID: 2059

Type strain: Yes

Species: Pandoraea apista

Strain history: CIP <- 2000, CCUG <- 1997, P. Vandamme, LMG, Ghent, Belgium <- N. Höiby, Denmark

NCBI tax ID(s): 93218 (species)

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: 6473

BacDive-ID: 2059

DSM-Number: 16535

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

description: Pandoraea apista DSM 16535 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from sputum from cystic fibrosis patient.

NCBI tax id

  • NCBI tax id: 93218
  • Matching level: species

strain history

@refhistory
6473<- CCM <- CCUG <- P. Vandamme <- N. Hoiby
116422CIP <- 2000, CCUG <- 1997, P. Vandamme, LMG, Ghent, Belgium <- N. Höiby, Denmark

doi: 10.13145/bacdive2059.20230509.8.1

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

@ref: 6473

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Pandoraea

species: Pandoraea apista

full scientific name: Pandoraea apista Coenye et al. 2000

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidencecell shape
23367negative1.5-4.0 µm0.5-0.7 µmyes
69480yes92.695
69480negative99.988
116422negativeyesrod-shaped

pigmentation

  • @ref: 116422
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6473CASO 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
42011MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116422CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6473positivegrowth37mesophilic
23367positivegrowth30-37mesophilic
42011positivegrowth37mesophilic
116422positivegrowth25-41
116422nogrowth5psychrophilic
116422nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116422
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
23367no
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
116422NaClpositivegrowth0-4 %
116422NaClnogrowth6 %
116422NaClnogrowth8 %
116422NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2336727897tryptophan-energy source
2336717306maltose-growth
2336717992sucrose-growth
233674853esculin-hydrolysis
2336753426tween 80-hydrolysis
2336716301nitrite-reduction
2336727689decanoate+growth
2336716947citrate+growth
2336724996lactate+growth
6836925115malate+assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11642216947citrate+carbon source
1164224853esculin-hydrolysis
11642217632nitrate-reduction
11642216301nitrite-reduction
11642217632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
2336735581indoleno
6836935581indoleno
11642235581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
2336735581indole-
6836935581indole-

enzymes

@refvalueactivityec
23367amylase+
23367arginine dihydrolase+3.5.3.6
23367beta-galactosidase-3.2.1.23
23367catalase+1.11.1.6
23367DNase-
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
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
116422oxidase+
116422beta-galactosidase-3.2.1.23
116422alcohol dehydrogenase-1.1.1.1
116422gelatinase-
116422amylase-
116422DNase-
116422caseinase-3.4.21.50
116422catalase+1.11.1.6
116422tween esterase-
116422lecithinase-
116422lipase-
116422lysine decarboxylase-4.1.1.18
116422ornithine decarboxylase-4.1.1.17
116422protease-
116422tryptophan deaminase-
116422urease+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
116422-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6473--------++++++++++++-
6473--------------++-+++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116422+------------------------------+---------------+++++++++--+-++++-+++++-----++-+++++-----+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6473sputum from cystic fibrosis patientDenmarkDNKEurope
54244Human sputum,cystic fibrosisDenmarkDNKEurope
116422Human, SputumDenmarkDNKEurope

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: AY268172
  • 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
64732Risk group (German classification)
1164221Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pandoraea apista strain CCUG 38412 16S ribosomal RNA gene, partial sequenceAY2681721461ena93218
6473Pandoraea apista strain LMG 16407 16S ribosomal RNA gene, partial sequenceAF1391731485ena93218

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pandoraea apista DSM 16535GCA_001465595completencbi93218
66792Pandoraea apista LMG16407GCA_001049515contigncbi93218
66792Pandoraea apista strain DSM 1653593218.12completepatric93218
66792Pandoraea apista strain DSM 1653593218.21plasmidpatric93218
66792Pandoraea apista strain LMG1640793218.9wgspatric93218
66792Pandoraea apista LMG164072698536526draftimg93218
66792Pandoraea apista DSM 165352684623145completeimg93218

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno63.138no
flagellatedno63.138no
gram-positiveno98.924yes
gram-positiveno98.924yes
anaerobicno99.215no
anaerobicno99.215no
aerobicyes93.209no
aerobicyes93.209no
halophileno93.797no
halophileno93.797no
spore-formingno95.681yes
spore-formingno95.681yes
glucose-utilyes60.109no
glucose-utilyes60.109no
motileyes91.004yes
motileyes91.004yes
thermophileno99.086yes
thermophileno99.086yes
glucose-fermentno90.354yes
glucose-fermentno90.354yes

External links

@ref: 6473

culture collection no.: DSM 16535, CCM 4976, CCUG 38412, CIP 106627, LMG 16407

straininfo link

  • @ref: 71706
  • straininfo: 12489

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
Genetics26564037Draft Genome Sequence of the Pandoraea apista LMG 16407 Type Strain.Millard AD, Westblade LF, LiPuma JJ, Vavikolanu K, Read TD, Pallen MJ, Burd EM, Constantinidou CIGenome Announc10.1128/genomeA.01300-152015
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
6473Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16535)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16535
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
42011Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18779
54244Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38412)https://www.ccug.se/strain?id=38412
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
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
71706Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12489.1StrainInfo: A central database for resolving microbial strain identifiers
116422Curators of the CIPCollection of Institut Pasteur (CIP 106627)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106627