Strain identifier

BacDive ID: 2057

Type strain: Yes

Species: Pandoraea sputorum

Strain history: CIP <- 2001, CCUG <- D. Janssens, LMG, Gent, Belgium <- T. Coenye, Gent, Belgium <- J. LiPuma, Philadelphia, USA

NCBI tax ID(s): 93222 (species)

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General

@ref: 15474

BacDive-ID: 2057

DSM-Number: 21091

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

description: Pandoraea sputorum ATCC BAA 64 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from human sputum, cystic fibrosis patient.

NCBI tax id

  • NCBI tax id: 93222
  • Matching level: species

strain history

@refhistory
15474<- CCUG {2007} <- D. Janssens, LMG <- J. J. LiPuma
123289CIP <- 2001, CCUG <- D. Janssens, LMG, Gent, Belgium <- T. Coenye, Gent, Belgium <- J. LiPuma, Philadelphia, USA

doi: 10.13145/bacdive2057.20230509.8.1

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

@ref: 15474

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Pandoraea

species: Pandoraea sputorum

full scientific name: Pandoraea sputorum Coenye et al. 2000

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidencecell shape
23367negative1.5-4.0 µm0.5-0.7 µmyes
69480yes97.651
69480negative99.97
123289negativeyesrod-shaped

pigmentation

  • @ref: 123289
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15474TRYPTICASE 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
42012MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123289CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
15474positivegrowth37mesophilic
23367positivegrowth30-37mesophilic
42012positivegrowth37mesophilic
56600positivegrowth37mesophilic
123289positivegrowth25-41
123289nogrowth5psychrophilic
123289nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
56600aerobe
123289obligate aerobe

spore formation

@refspore formationconfidence
23367no
69481no100
69480no99.953

halophily

@refsaltgrowthtested relationconcentration
123289NaClpositivegrowth0-2 %
123289NaClnogrowth4 %
123289NaClnogrowth6 %
123289NaClnogrowth8 %
123289NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2336727897tryptophan-energy source
2336717992sucrose-growth
233674853esculin-hydrolysis
2336753426tween 80-hydrolysis
2336716301nitrite-reduction
2336724996lactate+growth
2336717306maltose+growth
2336717632nitrate+reduction
6836925115malate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12328916947citrate+carbon source
1232894853esculin-hydrolysis
12328917632nitrate+reduction
12328916301nitrite-reduction
12328917632nitrate-respiration

antibiotic resistance

  • @ref: 123289
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
2336735581indoleno
6836935581indoleno
12328935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
2336735581indole-
6836935581indole-

enzymes

@refvalueactivityec
23367arginine dihydrolase-3.5.3.6
23367DNase-
23367esterase lipase (C 8)+
23367phosphoamidase+3.9.1.1
23367tryptophan deaminase-4.1.99.1
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
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123289oxidase-
123289beta-galactosidase+3.2.1.23
123289alcohol dehydrogenase-1.1.1.1
123289gelatinase-
123289amylase-
123289DNase+
123289caseinase-3.4.21.50
123289catalase+1.11.1.6
123289tween esterase+
123289lecithinase+
123289lipase-
123289lysine decarboxylase-4.1.1.18
123289ornithine decarboxylase-4.1.1.17
123289protease-
123289tryptophan deaminase-
123289urease-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
123289--++-+-----+---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15474--------------+--+++-
15474--------------+--++--
15474------+/--------+-+/-+++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123289+------------------------------+---------------++++++++-----++++-+++-+---------++++---+-+++++++-++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
15474human sputum, cystic fibrosis patientUSAUSANorth America
56600Human sputum,cystic fibrosisUSAUSANorth America
123289Human, Cystic fibrosis patientUnited States of AmericaUSANorth America

isolation source categories

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

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: AF139176
  • Sequence Identity:
  • Total samples: 5711
  • soil counts: 2081
  • aquatic counts: 1255
  • animal counts: 1218
  • plant counts: 1157

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
154742Risk group (German classification)
1232891Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15474
  • description: Pandoraea sputorum 16S ribosomal RNA gene, partial sequence
  • accession: AF139176
  • length: 1485
  • database: ena
  • NCBI tax ID: 93222

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pandoraea sputorum NCTC13161GCA_900187205completencbi93222
66792Pandoraea sputorum DSM 21091GCA_000814845completencbi93222
66792Pandoraea sputorum DSM 2109193222.6completepatric93222
66792Pandoraea sputorum strain NCTC1316193222.14completepatric93222
66792Pandoraea sputorum NCTC 131612840576683completeimg93222

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.735no
flagellatedno55.79no
gram-positiveno98.833yes
anaerobicno99.213yes
aerobicyes93.562yes
halophileno89.641no
spore-formingno94.574yes
thermophileno99.197yes
glucose-utilyes68.147no
glucose-fermentno86.748no

External links

@ref: 15474

culture collection no.: ATCC BAA 64, DSM 21091, CCUG 45026, CIP 107268, LMG 18819, NCTC 13161, CCUG 45206, CCUG 39682

straininfo link

  • @ref: 71704
  • straininfo: 14066

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
15474Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21091)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21091
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
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
42012Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4685
56600Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45026)https://www.ccug.se/strain?id=45026
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
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
71704Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14066.1StrainInfo: A central database for resolving microbial strain identifiers
123289Curators of the CIPCollection of Institut Pasteur (CIP 107268)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107268