Strain identifier

BacDive ID: 13131

Type strain: Yes

Species: Pseudomonas borbori

Strain Designation: R-20821

Strain history: CIP <- 2006, DSMZ <- B. Vanparys, Ghent Univ., Ghent, Belgium: strain R-20821

NCBI tax ID(s): 289003 (species)

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

@ref: 7205

BacDive-ID: 13131

DSM-Number: 17834

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

description: Pseudomonas borbori R-20821 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from nitrifying starting culture for the detoxification of aquaculture ponds and aquaria.

NCBI tax id

  • NCBI tax id: 289003
  • Matching level: species

strain history

@refhistory
7205<- B. Vanparys; R-20821
116841CIP <- 2006, DSMZ <- B. Vanparys, Ghent Univ., Ghent, Belgium: strain R-20821

doi: 10.13145/bacdive13131.20230509.8.1

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 borbori
  • full scientific name: Pseudomonas borbori Vanparys et al. 2006

@ref: 7205

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas borbori

full scientific name: Pseudomonas borbori Vanparys et al. 2006

strain designation: R-20821

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31765negative02-03 µm1 µmrod-shapedyes
69480yes98.273
69480negative99.995
116841negativerod-shapedyes

pigmentation

  • @ref: 31765
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7205REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37533MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
116841CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7205positivegrowth28mesophilic
31765positivegrowth22-28
31765positiveoptimum22-28
37533positivegrowth30mesophilic
60007positivegrowth30mesophilic

culture pH

@refabilitytypepH
31765positivegrowth7
31765positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31765aerobe
60007aerobe
116841obligate aerobe

spore formation

@refspore formationconfidence
31765no
69481no100
69480no99.993

observation

  • @ref: 31765
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3176524265gluconate+carbon source
3176517234glucose+carbon source
3176517306maltose+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
11684117632nitrate+reduction
11684116301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11684135581indoleno

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
116841oxidase+
116841catalase+1.11.1.6
116841urease-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
116841-+-+----------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7205+-------+----+++-++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7205nitrifying starting culture for the detoxification of aquaculture ponds and aquariaGentBelgiumBELEurope
60007A nitrifying inoculum
116841Nitrifying inoculumGhentBelgiumBELEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Aquaculture
#Engineered#Laboratory#Lab enrichment
#Environmental#Aquatic#Pond (small)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72051Risk group (German classification)
1168411Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7205
  • description: Pseudomonas borbori partial 16S rRNA gene, type strain R-20821T
  • accession: AM114527
  • length: 1494
  • database: ena
  • NCBI tax ID: 289003

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas borbori DSM 17834GCA_900115555scaffoldncbi289003
66792Pseudomonas borbori strain DSM 17834289003.4wgspatric289003
66792Pseudomonas borbori LMG 231992671180032draftimg289003

GC content

  • @ref: 31765
  • GC-content: 60.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.991yes
flagellatedyes81.167no
gram-positiveno98.705yes
anaerobicno98.186no
aerobicyes90.031no
halophileno63.103no
spore-formingno96.521no
glucose-fermentno91.475no
thermophileno99.564yes
glucose-utilyes88.078yes

External links

@ref: 7205

culture collection no.: CCUG 53773, DSM 17834, LMG 23199, CIP 109375

straininfo link

  • @ref: 82339
  • straininfo: 94088

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
Phylogeny18319482Pseudomonas marincola sp. nov., isolated from marine environments.Romanenko LA, Uchino M, Tebo BM, Tanaka N, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.65406-02008Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Echinodermata/*microbiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/genetics/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny21278410Pseudomonas composti sp. nov., isolated from compost samples.Gibello A, Vela AI, Martin M, Mengs G, Alonso PZ, Garbi C, Fernandez-Garayzabal JFInt J Syst Evol Microbiol10.1099/ijs.0.027086-02011DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny35396979Pseudomonas tumuqii sp. nov., isolated from greenhouse soil.Kong D, Li Q, Zhou Y, Wang Y, Jiang X, Wang Z, Ruan ZArch Microbiol10.1007/s00203-022-02869-y2022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, *Pseudomonas, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *SoilTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7205Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17834)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17834
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
37533Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7109
60007Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53773)https://www.ccug.se/strain?id=53773
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
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
82339Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID94088.1StrainInfo: A central database for resolving microbial strain identifiers
116841Curators of the CIPCollection of Institut Pasteur (CIP 109375)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109375