Strain identifier

BacDive ID: 2056

Type strain: Yes

Species: Pandoraea norimbergensis

Strain Designation: R2, UBM 101

Strain history: CIP <- 1998, R. Wittke, Bayreuth Univ., Bayreuth, Germany: strain R2

NCBI tax ID(s): 93219 (species)

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General

@ref: 4429

BacDive-ID: 2056

DSM-Number: 11628

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

description: Pandoraea norimbergensis R2 is an obligate aerobe, mesophilic, Gram-negative human pathogen that was isolated from oxic water above sulfide containing lake sediment.

NCBI tax id

  • NCBI tax id: 93219
  • Matching level: species

strain history

@refhistory
4429<- D. Kleiner, Univ. Bayreuth; R2
420071998, R. Wittke, Lehrstuhl Mikrobiol. Univ., Bayreuth, Germany: strain R2
67770LMG 18379 <-- DSM 11628 <-- D. Kleiner R2.
121350CIP <- 1998, R. Wittke, Bayreuth Univ., Bayreuth, Germany: strain R2

doi: 10.13145/bacdive2056.20230509.8.1

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 norimbergensis
  • full scientific name: Pandoraea norimbergensis (Wittke et al. 1998) Coenye et al. 2000

  • synonyms

    • @ref: 20215
    • synonym: Burkholderia norimbergensis

@ref: 4429

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Pandoraea

species: Pandoraea norimbergensis

full scientific name: Pandoraea norimbergensis (Wittke et al. 1998) Coenye et al. 2000

strain designation: R2, UBM 101

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidencecell shape
23367negative1.5-4.0 µm0.5-0.7 µmyes
69480yes92.821
69480negative99.99
121350negativeyesrod-shaped

pigmentation

  • @ref: 121350
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4429NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
42007MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121350CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4429positivegrowth28mesophilic
23367positivegrowth30-37mesophilic
23367nogrowth42thermophilic
42007positivegrowth30mesophilic
67770positivegrowth28mesophilic
121350positivegrowth25-37mesophilic
121350nogrowth5psychrophilic
121350nogrowth10psychrophilic
121350nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121350
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
23367no
69481no100
69480no99.984

halophily

@refsaltgrowthtested relationconcentration
23367NaClnogrowth4.5 %
121350NaClpositivegrowth0-4 %
121350NaClnogrowth6 %
121350NaClnogrowth8 %
121350NaClnogrowth10 %

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
2336716947citrate+growth
2336717634D-glucose+growth
2336718132phosphocholine+growth
68371Potassium 5-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
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
12135016947citrate+carbon source
1213504853esculin-hydrolysis
12135017632nitrate-reduction
12135016301nitrite-reduction
12135017632nitrate-respiration

antibiotic resistance

  • @ref: 121350
  • 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
12135035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
2336735581indole-
6836935581indole-

enzymes

@refvalueactivityec
23367arginine dihydrolase+3.5.3.6
23367cystine arylamidase-3.4.11.3
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
121350oxidase+
121350beta-galactosidase-3.2.1.23
121350alcohol dehydrogenase-1.1.1.1
121350gelatinase-
121350amylase-
121350DNase-
121350caseinase-3.4.21.50
121350catalase+1.11.1.6
121350tween esterase-
121350lecithinase-
121350lipase-
121350lysine decarboxylase-4.1.1.18
121350ornithine decarboxylase-4.1.1.17
121350tryptophan deaminase-
121350urease-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
121350-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4429--------+-----+--++++

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
4429-+---------+-------------------+/----------------++/--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121350+------------------------------+---------------+++++-+++--+-++++-+++----------++++------+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4429oxic water above sulfide containing lake sedimentNürnberg, SilberseeGermanyDEUEurope
54694Oxic water layer above a sulfide containing sedim.Nürnberg,SilberseeGermanyDEUEurope
67770Oxic water column (pH 8.4) overlaying the sulfide-bearing sediment of lake SilberseeNurnbergGermanyDEUEurope
121350Environment, Water Column, overlaying sedimentGermanyDEUEurope1991

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment
#Condition#Sulfuric

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
4429yes, in single cases1Risk group (German classification)
1213501Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia norimbergensis 16S rRNA geneY098791504ena93219
20218Pandoraea norimbergensis strain CCUG 39188 16S ribosomal RNA gene, partial sequenceAY2681741461ena93219
67770Pandoraea norimbergensis 16S ribosomal RNA gene, partial sequenceAF1391711485ena93219

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pandoraea norimbergensis DSM 11628GCA_001465545completencbi93219
66792Pandoraea norimbergensis strain DSM 1162893219.4completepatric93219
66792Pandoraea norimbergensis DSM 116282684623126completeimg93219

GC content

@refGC-contentmethod
6777063.2high performance liquid chromatography (HPLC)
6777064thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno64.353no
flagellatedno64.353no
flagellatedno64.353no
gram-positiveno98.667yes
gram-positiveno98.667yes
gram-positiveno98.667yes
anaerobicno99.288no
anaerobicno99.288no
anaerobicno99.288no
aerobicyes93.864no
aerobicyes93.864no
aerobicyes93.864no
halophileno90.442no
halophileno90.442no
halophileno90.442no
spore-formingno95.229yes
spore-formingno95.229yes
spore-formingno95.229yes
glucose-utilyes64.298yes
glucose-utilyes64.298yes
glucose-utilyes64.298yes
motileyes90.428no
motileyes90.428no
motileyes90.428no
thermophileno99.333no
thermophileno99.333no
thermophileno99.333no
glucose-fermentno87.184no
glucose-fermentno87.184no
glucose-fermentno87.184no

External links

@ref: 4429

culture collection no.: DSM 11628, CCUG 39188, LMG 18379, CIP 39188, JCM 10565, ATCC BAA 65, CIP 105463

straininfo link

  • @ref: 71703
  • straininfo: 7306

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
4429Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11628)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11628
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
42007Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17485
54694Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39188)https://www.ccug.se/strain?id=39188
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
71703Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7306.1StrainInfo: A central database for resolving microbial strain identifiers
121350Curators of the CIPCollection of Institut Pasteur (CIP 105463)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105463