Strain identifier

BacDive ID: 12922

Type strain: No

Species: Pseudomonas putida

Strain Designation: 53-2

Strain history: M. Tsuda <-- K. Furukawa <-- A. M. Chakrabarty <-- I. C. Gunsalus G7 <-- W. R. Sistrom 53-2.

NCBI tax ID(s): 1295132 (strain), 303 (species)

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General

@ref: 12676

BacDive-ID: 12922

DSM-Number: 50208

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile, human pathogen

description: Pseudomonas putida 53-2 is a mesophilic, motile human pathogen that was isolated from soil, enrichment with naphthalene.

NCBI tax id

NCBI tax idMatching level
1295132strain
303species

strain history

@refhistory
12676<- ICPB <- W.R. Sistrom; 53-2
67770M. Tsuda <-- K. Furukawa <-- A. M. Chakrabarty <-- I. C. Gunsalus G7 <-- W. R. Sistrom 53-2.

doi: 10.13145/bacdive12922.20230509.8.1

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 putida
  • full scientific name: Pseudomonas putida (Trevisan 1889) Migula 1895 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Bacillus putidus
    20215Arthrobacter siderocapsulatus

@ref: 12676

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas putida

full scientific name: Pseudomonas putida (Trevisan 1889) Migula 1895

strain designation: 53-2

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes92.816
6948099.998negative

Culture and growth conditions

culture medium

  • @ref: 12676
  • name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1a
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
12676positivegrowth26mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.924

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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
12676---+----+-----++-++-+

Isolation, sampling and environmental information

isolation

@refsample type
12676soil, enrichment with naphthalene
67770Soil with naphthalene enrichment

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_863.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_203;99_863&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AF094739
  • Sequence Identity:
  • Total samples: 1972
  • soil counts: 444
  • aquatic counts: 421
  • animal counts: 802
  • plant counts: 305

Safety information

risk assessment

  • @ref: 12676
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas putida strain ATCC 17485 16S ribosomal RNA gene, partial sequenceAF0947391449ena303
20218Pseudomonas putida 16S ribosomal RNA gene, strain: ATCC 17485, partial sequenceD859941329ena303

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas putida JCM 18452GCA_001312165contigncbi1295132
66792Pseudomonas putida JCM 184521295132.3wgspatric1295132
66792Pseudomonas putida JCM 184522728369712draftimg1295132

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.941no
gram-positiveno97.95no
anaerobicno97.922no
aerobicyes95.13no
halophileno87.406no
spore-formingno94.756no
glucose-utilyes92.615yes
flagellatedyes79.005no
thermophileno99.811yes
glucose-fermentno90.093yes

External links

@ref: 12676

culture collection no.: DSM 50208, ATCC 17485, ICPB 2789-111, JCM 18452, BCRC 10461, JCM 6158, KCTC 1642, NCIMB 12092

straininfo link

  • @ref: 82135
  • straininfo: 36668

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12676Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 50208)https://www.dsmz.de/collection/catalogue/details/culture/DSM-50208
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
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
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
82135Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36668.1StrainInfo: A central database for resolving microbial strain identifiers