Strain identifier

BacDive ID: 382

Type strain: Yes

Species: Bordetella petrii

Strain Designation: Se-1111R

Strain history: CIP <- 2001, CCUG <- F. von Wintzingerode, Techn. Univ. Berlin, Germany: strain Se-1111R

NCBI tax ID(s): 340100 (strain), 94624 (species)

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

@ref: 4829

BacDive-ID: 382

DSM-Number: 12804

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped, human pathogen

description: Bordetella petrii Se-1111R is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from bioreactor culture enriched from river sediment.

NCBI tax id

NCBI tax idMatching level
340100strain
94624species

strain history

@refhistory
4829<- F. von Wintzingerode, Techn. Univ. Berlin; Se-1111R
121788CIP <- 2001, CCUG <- F. von Wintzingerode, Techn. Univ. Berlin, Germany: strain Se-1111R

doi: 10.13145/bacdive382.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Bordetella
  • species: Bordetella petrii
  • full scientific name: Bordetella petrii Von Wintzingerode et al. 2001

@ref: 4829

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Bordetella

species: Bordetella petrii

full scientific name: Bordetella petrii von Wintzingerode et al. 2001

strain designation: Se-1111R

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23282negative1.0-2.8 µm0.4-0.7 µmrod-shapedno
69480negative99.981
121788negativerod-shapedno

colony morphology

@refincubation periodhemolysis ability
48291-2 days
1217881

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4829TRYPTICASE 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
4829CASO 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
4829NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
23282MacConkey agaryes
33725MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121788CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
4829positivegrowth30mesophilic
23282positivegrowth37mesophilic
23282positivegrowth30mesophilic
33725positivegrowth37mesophilic
55867positivegrowth37mesophilic
4829positivegrowth37mesophilic
121788positivegrowth25-45
121788nogrowth5psychrophilic
121788nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23282aerobe
23282anaerobe
55867aerobe
121788obligate aerobe

spore formation

@refspore formationconfidence
23282no
69481no100
69480no99.974

halophily

@refsaltgrowthtested relationconcentration
121788NaClpositivegrowth2-4 %
121788NaClnogrowth0 %
121788NaClnogrowth6 %
121788NaClnogrowth8 %
121788NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2328222599arabinose-anaerobic growth
2328217057cellobiose-anaerobic growth
2328217234glucose-anaerobic growth
2328217754glycerol-anaerobic growth
2328217716lactose-anaerobic growth
2328217306maltose-anaerobic growth
2328229864mannitol-anaerobic growth
2328237684mannose-anaerobic growth
232826731melezitose-anaerobic growth
2328217992sucrose-anaerobic growth
2328217814salicin-anaerobic growth
2328227082trehalose-anaerobic growth
2328218222xylose-anaerobic growth
2328215963ribitol-assimilation
2328227613amygdalin-assimilation
2328218305arbutin-assimilation
2328227689decanoate-assimilation
2328217057cellobiose-assimilation
2328217108D-arabinose-assimilation
2328217634D-glucose-assimilation
2328265327D-xylose-assimilation
2328217113erythritol-assimilation
2328228066gentiobiose-assimilation
2328217754glycerol-assimilation
2328228087glycogen-assimilation
2328217268myo-inositol-assimilation
2328215443inulin-assimilation
2328230849L-arabinose-assimilation
2328265328L-xylose-assimilation
2328217716lactose-assimilation
2328217306maltose-assimilation
2328229864mannitol-assimilation
2328237684mannose-assimilation
232826731melezitose-assimilation
2328228053melibiose-assimilation
23282320061methyl alpha-D-glucopyranoside-assimilation
2328274863methyl beta-D-xylopyranoside-assimilation
23282506227N-acetylglucosamine-assimilation
2328218401phenylacetate-assimilation
2328216634raffinose-assimilation
2328226546rhamnose-assimilation
2328233942ribose-assimilation
2328217992sucrose-assimilation
2328217814salicin-assimilation
2328230911sorbitol-assimilation
2328228017starch-assimilation
2328227082trehalose-assimilation
2328217151xylitol-assimilation
232824853esculin-hydrolysis
232825291gelatin-hydrolysis
2328217128adipate+assimilation
2328216947citrate+assimilation
232828391D-gluconate+assimilation
2328215589L-malate+assimilation
2328217632nitrate+degradation
2328278021tetrazolium+reduction
6836925115malate+assimilation
6836917128adipate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
12178816947citrate+carbon source
1217884853esculin-hydrolysis
121788606565hippurate+hydrolysis
12178817632nitrate+builds gas from
12178817632nitrate+reduction
12178816301nitrite+builds gas from
12178816301nitrite+reduction
12178815792malonate-assimilation
12178817632nitrate+respiration

antibiotic resistance

  • @ref: 121788
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
2328216301nitriteno
2328235581indoleno
2328215688acetoinno
6836935581indoleno
12178835581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12178815688acetoin-
12178817234glucose-

enzymes

@refvalueactivityec
4829catalase+1.11.1.6
4829cytochrome-c oxidase+1.9.3.1
23282catalase+1.11.1.6
23282cytochrome oxidase+1.9.3.1
23282urease-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
121788oxidase+
121788beta-galactosidase-3.2.1.23
121788alcohol dehydrogenase-1.1.1.1
121788gelatinase-
121788amylase-
121788DNase-
121788caseinase-3.4.21.50
121788catalase+1.11.1.6
121788tween esterase-
121788gamma-glutamyltransferase+2.3.2.2
121788lecithinase-
121788lipase-
121788lysine decarboxylase-4.1.1.18
121788ornithine decarboxylase-4.1.1.17
121788phenylalanine ammonia-lyase-4.3.1.24
121788tryptophan deaminase-
121788urease-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
121788-+++-+----++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4829--------------+-+++-
4829--------------++/-+++-
4829--------------++/-++++/-+
4829+----------+/---+-+++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121788-------------------------------------------+--+++++-++------+-+--+-+-------+---++++---+++++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
4829bioreactor culture enriched from river sedimentJena, SaaleGermanyDEUEurope
55867River sediment derived anaerobic bioreactorSaale near JenaGermanyDEUEurope1998
121788Environment, River sediment derived anaerobic bioreactorSwedenSWEEurope1996

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Environmental#Aquatic#River (Creek)
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
4829yes, in single cases1Risk group (German classification)
1217882Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Bordetella petrii 16S rRNA gene, strain DSM 12804
  • accession: AJ249861
  • length: 1496
  • database: ena
  • NCBI tax ID: 94624

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bordetella petrii DSM 12804GCA_000067205completencbi94624
66792Bordetella petrii DSM 12804340100.3completepatric340100
66792Bordetella petrii DSM 12804641228479completeimg340100

GC content

@refGC-contentmethod
482963.8
2328263.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.088yes
anaerobicno98.604no
halophileno87.179no
spore-formingno94.618yes
glucose-utilno77.736yes
motileyes85.235yes
flagellatedno66.267yes
thermophileno99.16yes
aerobicyes85.112no
glucose-fermentno91.872yes

External links

@ref: 4829

culture collection no.: DSM 12804, CCUG 43448, CIP 107267, ATCC BAA 461, CCM 7166

straininfo link

  • @ref: 70062
  • straininfo: 49365

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11491321Bordetella petrii sp. nov., isolated from an anaerobic bioreactor, and emended description of the genus Bordetella.von Wintzingerode F, Schattke A, Siddiqui RA, Rosick U, Gobel UB, Gross RInt J Syst Evol Microbiol10.1099/00207713-51-4-12572001Anaerobiosis, Base Composition, Base Sequence, Bioreactors, Bordetella/*classification/genetics/*isolation & purification/metabolism, Chlorobenzenes/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Genes, Bacterial, Geologic Sediments/microbiology, Microscopy, Electron, Molecular Sequence Data, Open Reading Frames, Phylogeny, Selenic Acid, Selenium Compounds/metabolism, Terminology as TopicMetabolism
Pathogenicity19390985New mobile genetic elements in Cupriavidus metallidurans CH34, their possible roles and occurrence in other bacteria.Van Houdt R, Monchy S, Leys N, Mergeay MAntonie Van Leeuwenhoek10.1007/s10482-009-9345-42009Betaproteobacteria/drug effects/*genetics, Bordetella/genetics, Burkholderia/genetics, Chemoautotrophic Growth, Cupriavidus/drug effects/*genetics/metabolism, *DNA Transposable Elements, Delftia/genetics, Drug Resistance, Bacterial, Gene Expression Regulation, Bacterial, Genomic Islands, *Genomics, Integrases, Metals, Heavy/pharmacology, Recombinases, Synteny, TyrosineGenetics
Metabolism26897378Successful expression of the Bordetella petrii nitrile hydratase activator P14K and the unnecessary role of Ser115.Sun W, Zhu L, Chen X, Chen P, Yang L, Ding W, Zhou Z, Liu YBMC Biotechnol10.1186/s12896-016-0252-22016Bacterial Proteins/chemistry/genetics/*metabolism, Bordetella/*enzymology/genetics, Enzyme Stability, Escherichia coli/genetics, Hydro-Lyases/chemistry/genetics/*metabolism, Models, Molecular, Recombinant Fusion Proteins/chemistry/genetics/*metabolism, Serine/*geneticsEnzymology
Enzymology27075457Activity Enhancement Based on the Chemical Equilibrium of Multiple-Subunit Nitrile Hydratase from Bordetella petrii.Liu Y, Liu P, Lin L, Zhao Y, Zhong W, Wu L, Zhou Z, Sun WAppl Biochem Biotechnol10.1007/s12010-016-2079-72016Bacterial Proteins/metabolism, Bordetella/*enzymology, Chromatography, Affinity, Electrophoresis, Polyacrylamide Gel, Hydro-Lyases/isolation & purification/*metabolism, Kinetics, Models, Biological, Plasmids/metabolism, Protein Subunits/*metabolism, Recombinant Proteins/isolation & purification/metabolismMetabolism
Phylogeny27902262Saccharedens versatilis gen. nov., sp. nov., a sugar-degrading member of the Burkholderiales isolated from Cephalotes rohweri ant guts.Lin JY, Hobson WJ, Wertz JTInt J Syst Evol Microbiol10.1099/ijsem.0.0016502017Alcaligenaceae/*classification/genetics/isolation & purification, Animals, Ants/*microbiology, Arizona, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Symbiosis, Ubiquinone/chemistryTranscriptome
Pathogenicity28154518Drug Target Identification and Elucidation of Natural Inhibitors for Bordetella petrii: An In Silico Study.Rath SN, Ray M, Pattnaik A, Pradhan SKGenomics Inform10.5808/GI.2016.14.4.2412016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4829Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12804)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12804
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
23282F von Wintzingerode, A Schattke, R A Siddiqui, U Rösick, U B Göbel, R Gross10.1099/00207713-51-4-1257Bordetella petrii sp. nov., isolated from an anaerobic bioreactor, and emended description of the genus Bordetella.IJSEM 51: 1257-1265 200111491321
33725Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4684
55867Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43448)https://www.ccug.se/strain?id=43448
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
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
70062Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49365.1StrainInfo: A central database for resolving microbial strain identifiers
121788Curators of the CIPCollection of Institut Pasteur (CIP 107267)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107267