Strain identifier
BacDive ID: 130567
Type strain: 
Species: Pseudomonas putida
Strain Designation: SQ1
Strain history: <- D. Schleheck, Dept. Biol., Univ. Konstanz, Germany; SQ1 <- K. Denger and D. Schleheck
NCBI tax ID(s): 303 (species)
version 9.3 (current version)
General
@ref: 21480
BacDive-ID: 130567
DSM-Number: 100120
keywords: genome sequence, Bacteria, aerobe, mesophilic, Gram-negative, human pathogen
description: Pseudomonas putida SQ1 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from littoral sediment.
NCBI tax id
- NCBI tax id: 303
- Matching level: species
strain history
- @ref: 21480
- history: <- D. Schleheck, Dept. Biol., Univ. Konstanz, Germany; SQ1 <- K. Denger and D. Schleheck
doi: 10.13145/bacdive130567.20250331.9.3
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: 21480
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: SQ1
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 125438 | yes | 90.607 | |
| 125438 | 98.5 | negative | |
| 125439 | 98.3 | negative |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 21480 | REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) | yes | https://mediadive.dsmz.de/medium/1a | 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 |
| 21480 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
| 21480 | LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) | yes | https://mediadive.dsmz.de/medium/381 | Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water |
culture temp
- @ref: 21480
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 125438 | aerobe | 94.178 |
| 125439 | obligate aerobe | 95.4 |
spore formation
- @ref: 125439
- spore formation: no
- confidence: 98
Isolation, sampling and environmental information
isolation
- @ref: 21480
- sample type: littoral sediment
- geographic location: Lake Constance
- country: Germany
- origin.country: DEU
- continent: Europe
- latitude: 47.6958
- longitude: 9.193
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Sediment
Safety information
risk assessment
- @ref: 21480
- pathogenicity human: yes
- pathogenicity animal: yes
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudomonas putida SQ1 | GCA_000802565 | contig | ncbi | 303 |
| 66792 | Pseudomonas putida SQ1 | 303.141 | wgs | patric | 303 |
| 66792 | Pseudomonas putida SQ1 | 2524023231 | draft | img | 303 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.5 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 99.067 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.597 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 94.178 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98.486 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 90.607 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 83.1 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.3 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 95.4 |
External links
@ref: 21480
culture collection no.: DSM 100120
straininfo link
- @ref: 89086
- straininfo: 402100
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
| 21480 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100120 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100120) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 89086 | Reimer, 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 identifiers | 10.60712/SI-ID402100.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |