Strain identifier
BacDive ID: 12922
Type strain: 
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)
version 9.3 (current version)
General
@ref: 12676
BacDive-ID: 12922
DSM-Number: 50208
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, human pathogen
description: Pseudomonas putida 53-2 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from soil, enrichment with naphthalene.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1295132 | strain |
| 303 | species |
strain history
| @ref | history |
|---|---|
| 12676 | <- ICPB <- W.R. Sistrom; 53-2 |
| 67770 | M. Tsuda <-- K. Furukawa <-- A. M. Chakrabarty <-- I. C. Gunsalus G7 <-- W. R. Sistrom 53-2. |
doi: 10.13145/bacdive12922.20250331.9.3
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
@ref synonym 20215 Arthrobacter siderocapsulatus 20215 Bacillus putidus
@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
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 98.4 |
| 125438 | negative | 99 |
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
| @ref | growth | type | temperature |
|---|---|---|---|
| 12676 | positive | growth | 26 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 125438
- oxygen tolerance: aerobe
- confidence: 91.028
spore formation
- @ref: 125439
- spore formation: no
- confidence: 98.2
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | + | assimilation |
| 68369 | 24265 | gluconate | + | assimilation |
| 68369 | 17306 | maltose | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | - | assimilation |
| 68369 | 16899 | D-mannitol | - | assimilation |
| 68369 | 16024 | D-mannose | - | assimilation |
| 68369 | 30849 | L-arabinose | - | assimilation |
| 68369 | 17634 | D-glucose | + | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | - | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | + | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68369 | gelatinase | - | |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | cytochrome oxidase | + | 1.9.3.1 |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 68369 | arginine dihydrolase | + | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 12676 | - | - | - | + | - | - | - | - | + | - | - | - | - | - | + | + | - | + | + | - | + |
Isolation, sampling and environmental information
isolation
| @ref | sample type |
|---|---|
| 12676 | soil, enrichment with naphthalene |
| 67770 | Soil 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
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Pseudomonas putida strain ATCC 17485 16S ribosomal RNA gene, partial sequence | AF094739 | 1449 | nuccore | 303 |
| 20218 | Pseudomonas putida 16S ribosomal RNA gene, strain: ATCC 17485, partial sequence | D85994 | 1329 | nuccore | 303 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudomonas putida JCM 18452 | GCA_001312165 | contig | ncbi | 1295132 |
| 66792 | Pseudomonas putida JCM 18452 | 1295132.3 | wgs | patric | 1295132 |
| 66792 | Pseudomonas putida JCM 18452 | 2728369712 | draft | img | 1295132 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.72 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 84.765 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 91.028 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 97.986 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 84.919 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 85.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 85 |
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
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 12676 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 50208) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-50208 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 68369 | Automatically annotated from API 20NE | |||||
| 69479 | João 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 | |||
| 82135 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID36668.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |