Strain identifier

BacDive ID: 13130

Type strain: Yes

Species: Pseudomonas peli

Strain Designation: R-20805

Strain history: CIP <- 2006, DSMZ

NCBI tax ID(s): 592361 (species)

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General

@ref: 7204

BacDive-ID: 13130

DSM-Number: 17833

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

description: Pseudomonas peli R-20805 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from nitrifying enrichment culture.

NCBI tax id

  • NCBI tax id: 592361
  • Matching level: species

strain history

@refhistory
7204<- B. Vanparys; R-20805
375322006, DSMZ
121654CIP <- 2006, DSMZ

doi: 10.13145/bacdive13130.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas peli
  • full scientific name: Pseudomonas peli Vanparys et al. 2006

@ref: 7204

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas peli

full scientific name: Pseudomonas peli Vanparys et al. 2006

strain designation: R-20805

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31765negative02-03 µm1 µmrod-shapedyes
69480yes97.997
69480negative100
121654negativerod-shapedyes

pigmentation

  • @ref: 31765
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7204NUTRIENT 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
7204TRYPTICASE 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
37532MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121654CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7204positivegrowth28mesophilic
31765positivegrowth28-37mesophilic
31765positiveoptimum30-37mesophilic
37532positivegrowth30mesophilic

culture pH

@refabilitytypepH
31765positivegrowth7
31765positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31765aerobe
121654obligate aerobe

spore formation

@refspore formationconfidence
31765no
69481no100
69480no99.991

observation

  • @ref: 31765
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3176525115malate+carbon source
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
12165417632nitrate+reduction
12165416301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12165435581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
31765catalase+1.11.1.6
31765cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121654oxidase+
121654catalase+1.11.1.6
121654urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121654-+-+------++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7204+--------------+-++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7204nitrifying enrichment cultureGentBelgiumBELEurope
60009A nitrifying inoculum
121654Nitrifying inoculumGhentBelgiumBELEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Laboratory
  • Cat3: #Lab enrichment

taxonmaps

  • @ref: 69479
  • File name: preview.99_8559.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_1186;98_6253;99_8559&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AM114534
  • Sequence Identity:
  • Total samples: 6438
  • soil counts: 958
  • aquatic counts: 4373
  • animal counts: 948
  • plant counts: 159

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72041Risk group (German classification)
1216541Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7204
  • description: Pseudomonas peli partial 16S rRNA gene, type strain R-20805T
  • accession: AM114534
  • length: 1497
  • database: ena
  • NCBI tax ID: 592361

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas peli DSM 17833GCA_900099645scaffoldncbi592361
66792Pseudomonas peli DSM 17833GCA_012986145contigncbi592361
66792Pseudomonas peli strain DSM 17833592361.12wgspatric592361
66792Pseudomonas peli strain DSM 17833592361.3wgspatric592361
66792Pseudomonas peli LMG 232012671180067draftimg592361

GC content

  • @ref: 31765
  • GC-content: 60.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.652yes
flagellatedyes90.207no
gram-positiveno98.754no
anaerobicno97.542yes
aerobicyes92.703no
halophileno69.417no
spore-formingno96.258yes
glucose-fermentno90.778yes
thermophileno99.814no
glucose-utilyes62.102yes

External links

@ref: 7204

culture collection no.: DSM 17833, CCM 7693, LMG 23201, CCUG 53775, CIP 109374

straininfo link

  • @ref: 82338
  • straininfo: 94072

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16902024Pseudomonas peli sp. nov. and Pseudomonas borbori sp. nov., isolated from a nitrifying inoculum.Vanparys B, Heylen K, Lebbe L, De Vos PInt J Syst Evol Microbiol10.1099/ijs.0.64224-02006*Aquaculture, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nitrites/*metabolism, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/chemistry/*classification/isolation & purification/physiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, *Water MicrobiologyGenetics
Phylogeny19502326Pseudomonas cuatrocienegasensis sp. nov., isolated from an evaporating lagoon in the Cuatro Cienegas valley in Coahuila, Mexico.Escalante AE, Caballero-Mellado J, Martinez-Aguilar L, Rodriguez-Verdugo A, Gonzalez-Gonzalez A, Toribio-Jimenez J, Souza VInt J Syst Evol Microbiol10.1099/ijs.0.006189-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genotype, Mexico, Molecular Sequence Data, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, Pseudomonas/*classification/genetics/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7204Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17833)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17833
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
31765Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2803828776041
37532Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7108
60009Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53775)https://www.ccug.se/strain?id=53775
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
82338Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID94072.1StrainInfo: A central database for resolving microbial strain identifiers
121654Curators of the CIPCollection of Institut Pasteur (CIP 109374)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109374