Strain identifier
BacDive ID: 13104
Type strain: 
Species: Pseudomonas tremae
Strain history: <- CFBP <- ICMP
NCBI tax ID(s): 200454 (species)
version 8.1 (current version)
General
@ref: 6488
BacDive-ID: 13104
DSM-Number: 16744
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile, plant pathogen
description: Pseudomonas tremae DSM 16744 is a mesophilic, motile plant pathogen that was isolated from Trema orientalis.
NCBI tax id
- NCBI tax id: 200454
- Matching level: species
strain history
- @ref: 6488
- history: <- CFBP <- ICMP
doi: 10.13145/bacdive13104.20230509.8.1
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 tremae
- full scientific name: Pseudomonas tremae Gardan et al. 1999
@ref: 6488
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas tremae
full scientific name: Pseudomonas tremae Gardan et al. 1999
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 97.464 | |
| 69480 | 99.995 | negative |
Culture and growth conditions
culture medium
- @ref: 6488
- name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
- @ref: 6488
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.964 |
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 | cytochrome oxidase | - | 1.9.3.1 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 6488 | - | - | - | - | - | - | - | - | + | + | - | - | - | - | + | - | - | + | + | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 6488
- sample type: Trema orientalis
- host species: Trema orientalis
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Tree
taxonmaps
- @ref: 69479
- File name: preview.99_108.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_98;99_108&stattab=map
- Last taxonomy: Pseudomonas
- 16S sequence: AJ492826
- Sequence Identity:
- Total samples: 1469
- soil counts: 744
- aquatic counts: 346
- animal counts: 234
- plant counts: 145
Safety information
risk assessment
- @ref: 6488
- pathogenicity plant: yes
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6488
- description: Pseudomonas tremae partial 16S rRNA gene, type strain CFBP 6111T
- accession: AJ492826
- length: 1531
- database: ena
- NCBI tax ID: 200454
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudomonas tremae ICMP 9151 | GCA_001401155 | scaffold | ncbi | 200454 |
| 66792 | Pseudomonas tremae strain ICMP9151 | 200454.3 | wgs | patric | 200454 |
| 66792 | Pseudomonas tremae ICMP 9151 | 2713896868 | draft | img | 200454 |
GC content
- @ref: 6488
- GC-content: 60.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 70.606 | no |
| gram-positive | no | 98.183 | no |
| anaerobic | no | 97.963 | no |
| aerobic | yes | 94.819 | no |
| halophile | no | 93.463 | no |
| spore-forming | no | 94.01 | no |
| glucose-util | yes | 95.834 | no |
| thermophile | no | 99.705 | no |
| motile | yes | 90.767 | no |
| glucose-ferment | no | 88.986 | no |
External links
@ref: 6488
culture collection no.: DSM 16744, CFBP 6111, ICMP 9151, NCPPB 3465
straininfo link
- @ref: 82313
- straininfo: 41763
literature
- topic: Phylogeny
- Pubmed-ID: 33999789
- title: Pseudomonas quercus sp. nov, associated with leaf spot disease of Quercus mongolica.
- authors: Li Y, Wang S, Bian D, Sun S, Ma T
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.004800
- year: 2021
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Diseases/*microbiology, Pseudomonas/*classification/isolation & purification, Quercus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry
- topic2: Transcriptome
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 6488 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16744) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16744 | |
| 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 | |
| 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) | |
| 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 | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
| 82313 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID41763.1 | StrainInfo: A central database for resolving microbial strain identifiers |