Strain identifier

BacDive ID: 24384

Type strain: No

Species: Pseudomonas putida

Strain Designation: S16

Strain history: <- P. Xu, Shanghai Jiao Tong Univ., China; S16

NCBI tax ID(s): 303 (species)

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General

@ref: 20319

BacDive-ID: 24384

DSM-Number: 28022

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, human pathogen

description: Pseudomonas putida S16 is a Gram-negative human pathogen that was isolated from soil.

NCBI tax id

  • NCBI tax id: 303
  • Matching level: species

strain history

  • @ref: 20319
  • history: <- P. Xu, Shanghai Jiao Tong Univ., China; S16

doi: 10.13145/bacdive24384.20240916.9.1

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: 20319

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: S16

type strain: no

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.5

multimedia

  • @ref: 20319
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_28022.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20319MINERAL MEDIUM PH 7.25 (DSMZ Medium 465)yeshttps://mediadive.dsmz.de/medium/465Name: MINERAL MEDIUM PH 7.25 (DSMZ Medium 465; with strain-specific modifications) Composition: Na2HPO4 x 2 H2O 3.5 g/l None 2.0 g/l KH2PO4 1.0 g/l MgCl2 x 6 H2O 0.1 g/l None 0.05 g/l Calcium Chloride 0.05 g/l Na2-EDTA 0.0005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l FeSO4 x 7 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
20319NUTRIENT 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
20319PSEUDOMONAS AGAR F (DSMZ Medium 907)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium907.pdf

culture temp

  • @ref: 20319
  • growth: positive
  • type: growth
  • temperature: 28

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: aerobe
  • confidence: 93.482

Isolation, sampling and environmental information

isolation

  • @ref: 20319
  • sample type: soil
  • geographic location: Shandong Province, Jinan
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_239.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_203;99_239&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AY574282
  • Sequence Identity:
  • Total samples: 2133
  • soil counts: 368
  • aquatic counts: 543
  • animal counts: 799
  • plant counts: 423

Safety information

risk assessment

  • @ref: 20319
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20319
  • description: Pseudomonas putida strain S16 16S ribosomal RNA gene, partial sequence
  • accession: AY574282
  • length: 1453
  • database: nuccore
  • NCBI tax ID: 1042876

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas putida S16GCA_000219705completencbi1042876
66792Pseudomonas putida S161042876.5completepatric1042876
66792Pseudomonas putida S16650716076completeimg1042876

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no99.658no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes93.482no
69480spore-formingspore-formingAbility to form endo- or exosporesno87.316no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.986yes
69480flagellatedmotile2+Ability to perform flagellated movementyes88.171no

External links

@ref: 20319

culture collection no.: DSM 28022

straininfo link

  • @ref: 88294
  • straininfo: 403568

literature

  • topic: Metabolism
  • Pubmed-ID: 32873764
  • title: Molecular Deceleration Regulates Toxicant Release to Prevent Cell Damage in Pseudomonas putida S16 (DSM 28022).
  • authors: Tang H, Zhang K, Hu H, Wu G, Wang W, Zhu X, Liu G, Xu P
  • journal: mBio
  • DOI: 10.1128/mBio.02012-20
  • year: 2020
  • mesh: Bacterial Proteins/*genetics/metabolism, Nicotine/metabolism, Oxidoreductases/genetics/*metabolism, Pseudomonas putida/*enzymology/*genetics, Sequence Homology, Amino Acid
  • topic2: Enzymology

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20319Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28022Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28022)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
88294Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID403568.1