Strain identifier

BacDive ID: 13181

Type strain: Yes

Species: Pseudomonas chlororaphis subsp. piscium

Strain Designation: JF3835

Strain history: CIP <- 2010, J. Frey, Bern Univ., Bern, Switzerland: strain JF3835

NCBI tax ID(s): 1513890 (subspecies)

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General

@ref: 15754

BacDive-ID: 13181

DSM-Number: 21509

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Pseudomonas chlororaphis subsp. piscium JF3835 is an obligate aerobe, mesophilic, motile bacterium that was isolated from distal intestine of a European perch .

NCBI tax id

  • NCBI tax id: 1513890
  • Matching level: subspecies

strain history

@refhistory
375872010, J. Frey, Bern Univ., Bern, Switzerland: strain JF3835
15754<- S. E. Burr, Univ. Bern, Switzerland; JF3835 <- E. Goldschmitt-Clermont
118244CIP <- 2010, J. Frey, Bern Univ., Bern, Switzerland: strain JF3835

doi: 10.13145/bacdive13181.20230509.8.1

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 chlororaphis subsp. piscium
  • full scientific name: Pseudomonas chlororaphis subsp. piscium Burr et al. 2010

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas piscium

@ref: 15754

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas chlororaphis subsp. piscium

full scientific name: Pseudomonas chlororaphis subsp. piscium Burr et al. 2010

strain designation: JF3835

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.566
6948099.997negative
118244yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15754TRYPTICASE 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
37587MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118244CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
15754positivegrowth28mesophilic
37587positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118244
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.991

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
11824417632nitrate+reduction
11824416301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11824435581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
118244oxidase+
118244catalase+1.11.1.6
118244urease-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
118244-+++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15754+--+--+-+-+++-++-++++

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
15754distal intestine of a European perch (Perca fluviatilis L.)Perca fluviatilisLake of NeuchatelSwitzerlandCHEEurope
118244European perch, distal intestine, Perca fluviatilisNeuchâtel lakeSwitzerlandCHEEurope2006

isolation source categories

Cat1Cat2
#Host#Fishes
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_287.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_98;99_287&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: FJ168539
  • Sequence Identity:
  • Total samples: 13
  • soil counts: 3
  • aquatic counts: 1
  • animal counts: 6
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
157541Risk group (German classification)
1182441Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15754
  • description: Pseudomonas chlororaphis subsp. piscium strain JF3835 16S ribosomal RNA gene, partial sequence
  • accession: FJ168539
  • length: 1239
  • database: ena
  • NCBI tax ID: 1513890

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas chlororaphis subsp. piscium DSM 21509GCA_003850345completencbi1513890
66792Pseudomonas chlororaphis DSM 21509GCA_900104995chromosomencbi587753
66792Pseudomonas chlororaphis strain DSM 21509587753.26completepatric587753
66792Pseudomonas chlororaphis subsp. piscium strain DSM 215091513890.3wgspatric1513890
66792Pseudomonas chlororaphis subsp. piscium strain DSM 215091513890.7completepatric1513890
66792Pseudomonas chlororaphis piscium DSM 215092667528180draftimg1513890
66792Pseudomonas chlororaphis piscium DSM 215092917178910draftimg1513890
66792Pseudomonas chlororaphis piscium DSM 215092917064153completeimg1513890
66792Pseudomonas chlororaphis subsp. piscium DSM 21509GCA_001269555contigncbi1513890
66792Pseudomonas chlororaphis DSM 21509GCA_028747385completencbi587753

GC content

  • @ref: 15754
  • GC-content: 62.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes91.909no
flagellatedyes79.628no
gram-positiveno98.187no
anaerobicno98.721no
aerobicyes94.9no
halophileno91.397no
spore-formingno94.455no
thermophileno99.861no
glucose-utilyes93.972no
glucose-fermentno88.586yes

External links

@ref: 15754

culture collection no.: DSM 21509, NCIMB 14478, CIP 110232

straininfo link

  • @ref: 82389
  • straininfo: 374143

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20061493Pseudomonas chlororaphis subsp. piscium subsp. nov., isolated from freshwater fish.Burr SE, Gobeli S, Kuhnert P, Goldschmidt-Clermont E, Frey JInt J Syst Evol Microbiol10.1099/ijs.0.011692-02010Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fishes/*microbiology, Fresh Water, Genes, Bacterial, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, SwitzerlandGenetics
Metabolism35365429Regulation of phenazine-1-carboxamide production by quorum sensing in type strains of Pseudomonas chlororaphis subsp. chlororaphis and Pseudomonas chlororaphis subsp. piscium.Morohoshi T, Yabe N, Yaguchi N, Xie X, Someya NJ Biosci Bioeng10.1016/j.jbiosc.2022.03.0042022Acyl-Butyrolactones, *Bacterial Proteins/genetics/metabolism, Phenazines/metabolism, Pseudomonas, *Quorum Sensing/physiologyBiotechnology

Reference

@idauthorscataloguedoi/urltitle
15754Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21509)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21509
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
37587Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8068
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
82389Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID374143.1StrainInfo: A central database for resolving microbial strain identifiers
118244Curators of the CIPCollection of Institut Pasteur (CIP 110232)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110232