Strain identifier
BacDive ID: 159623
Type strain: 
Species: Pseudomonas saxonica
Strain Designation: WS 5072
Strain history: <- M. Wenning, BFLM, TU Munich, Freising-Weihenstephan, Germany; WS5072 <-
NCBI tax ID(s): 2600598 (species)
version 9.3 (current version)
General
@ref: 66458
BacDive-ID: 159623
DSM-Number: 108989
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile
description: Pseudomonas saxonica WS 5072 is an aerobe, mesophilic, motile bacterium that was isolated from skim milk concentrate.
NCBI tax id
- NCBI tax id: 2600598
- Matching level: species
strain history
- @ref: 66458
- history: <- M. Wenning, BFLM, TU Munich, Freising-Weihenstephan, Germany; WS5072 <-
doi: 10.13145/bacdive159623.20250331.9.3
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 saxonica
- full scientific name: Pseudomonas saxonica Hofmann et al. 2020
@ref: 66458
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas saxonica
full scientific name: Pseudomonas saxonica
strain designation: WS 5072
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 125438 | yes | 91.092 | |
| 125438 | 99 | negative | |
| 125439 | 97.4 | negative |
multimedia
- @ref: 66458
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_108989.jpg
- caption: DSM 108989 in DSMZ medium 535 at 28 °C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 66458 | 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 |
| 66458 | TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) | yes | https://mediadive.dsmz.de/medium/545 | Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water |
culture temp
- @ref: 66458
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 125438
- oxygen tolerance: aerobe
- confidence: 90.896
spore formation
- @ref: 125439
- spore formation: no
- confidence: 96
Isolation, sampling and environmental information
isolation
- @ref: 66458
- sample type: skim milk concentrate
- geographic location: Leppersdorf (48° 38' 48" N, 9° 25' 44.0" E)
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
- Cat1: #Engineered
- Cat2: #Food production
- Cat3: #Dairy product
Sequence information
16S sequences
- @ref: 66458
- description: Pseudomonas saxonica strain DSM 108989 RNA polymerase sigma factor RpoD (rpoD) gene, partial cds
- accession: MN068213
- length: 683
- database: nuccore
- NCBI tax ID: 2600598
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudomonas saxonica DSM 108989 | GCA_007858365 | contig | ncbi | 2600598 |
| 66792 | Pseudomonas sp. DSM 108989 | 2600598.3 | wgs | patric | 2600598 |
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 | 98.221 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.23 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 90.896 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 91.092 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 96 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 80.4 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 97.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 87.9 |
External links
@ref: 66458
culture collection no.: DSM 108989, LMG 31234
straininfo link
- @ref: 112097
- straininfo: 400476
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 31730030 | Pseudomonas saxonica sp. nov., isolated from raw milk and skimmed milk concentrate. | Hofmann K, Huptas C, Doll EV, Scherer S, Wenning M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003851 | 2020 | Animals, Bacterial Typing Techniques, Base Composition, Cattle, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, *Food Microbiology, Genes, Bacterial, Germany, Milk/*microbiology, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Biotechnology |
| Phylogeny | 34097596 | Pseudomonas paraversuta sp. nov. isolated from refrigerated dry-aged beef. | Lick S, Wibberg D, Winkler A, Blom J, Grimmler C, Goesmann A, Kalinowski J, Krockel L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004822 | 2021 | Animals, Bacterial Typing Techniques, Base Composition, Cattle, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Food Microbiology, Genes, Bacterial, Germany, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Red Meat/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Biotechnology |
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 | |
| 66458 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-108989 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108989) | |
| 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 | |
| 112097 | 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-ID400476.1 | |
| 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 |