Strain identifier
BacDive ID: 2949
Type strain: 
Species: Delftia sp.
Strain Designation: EK3
Strain history: <- E. Katsivela, GBF; EK3
NCBI tax ID(s): 2806556 (species)
version 8.1 (current version)
General
@ref: 4816
BacDive-ID: 2949
DSM-Number: 12781
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Delftia sp. EK3 is a mesophilic, motile bacterium that was isolated from water of river Elbe.
NCBI tax id
- NCBI tax id: 2806556
- Matching level: species
strain history
- @ref: 4816
- history: <- E. Katsivela, GBF; EK3
doi: 10.13145/bacdive2949.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Delftia
- species: Delftia sp.
- full scientific name: Delftia Wen et al. 1999
@ref: 4816
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Delftia
species: Delftia sp.
full scientific name: Delftia sp.
strain designation: EK3
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 97.426 | |
| 69480 | 99.986 | negative |
Culture and growth conditions
culture medium
- @ref: 4816
- name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)
- growth: yes
- link: https://mediadive.dsmz.de/medium/381
- composition: 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: 4816
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 96 |
| 69480 | no | 99.934 |
Isolation, sampling and environmental information
isolation
- @ref: 4816
- sample type: water of river Elbe
- geographic location: river Elbe
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #River (Creek)
taxonmaps
- @ref: 69479
- File name: preview.99_701.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_431;97_492;98_563;99_701&stattab=map
- Last taxonomy: Delftia
- 16S sequence: AJ237966
- Sequence Identity:
- Total samples: 58111
- soil counts: 6069
- aquatic counts: 15249
- animal counts: 31574
- plant counts: 5219
Sequence information
16S sequences
- @ref: 4816
- description: Delftia sp. EK3 16S rRNA gene, isolate EK3
- accession: AJ237966
- length: 1455
- database: ena
- NCBI tax ID: 91466
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Delftia sp. DSM 12781 | 2806556.3 | wgs | patric | 2806556 |
| 66792 | Delftia sp. DSM 12781 | 2901024625 | draft | img | 2806556 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 96 | no |
| motile | yes | 90.539 | no |
| gram-positive | no | 98.542 | no |
| anaerobic | no | 98.78 | no |
| halophile | no | 94.47 | no |
| spore-forming | no | 94.268 | no |
| glucose-util | no | 56.376 | no |
| flagellated | yes | 64.864 | no |
| aerobic | yes | 93.124 | no |
| thermophile | no | 99.598 | yes |
| glucose-ferment | no | 89.441 | no |
External links
@ref: 4816
culture collection no.: DSM 12781
straininfo link
- @ref: 72471
- straininfo: 49356
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 4816 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12781) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12781 | |
| 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) | |
| 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 | |
| 72471 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49356.1 | StrainInfo: A central database for resolving microbial strain identifiers |