Strain identifier
BacDive ID: 4365
Type strain:
Species: Enterobacter ludwigii
Strain Designation: EK4
Strain history: <- E. Katsivela; EK4
NCBI tax ID(s): 299767 (species)
General
@ref: 5760
BacDive-ID: 4365
DSM-Number: 15213
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Enterobacter ludwigii EK4 is a mesophilic, motile bacterium that was isolated from soil from a landfarm for treatment of refinery waste sludge.
NCBI tax id
- NCBI tax id: 299767
- Matching level: species
strain history
- @ref: 5760
- history: <- E. Katsivela; EK4
doi: 10.13145/bacdive4365.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Enterobacteriaceae
- genus: Enterobacter
- species: Enterobacter ludwigii
- full scientific name: Enterobacter ludwigii Hoffmann et al. 2005
@ref: 5760
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Enterobacteriaceae
genus: Enterobacter
species: Enterobacter ludwigii
full scientific name: Enterobacter ludwigii Hoffmann et al. 2005
strain designation: EK4
type strain: no
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 96.106 | |
69480 | 99.962 | negative |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5760 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
5760 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
culture temp
- @ref: 5760
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.972 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 30849 | L-arabinose | + | fermentation |
68368 | 27613 | amygdalin | + | fermentation |
68368 | 28053 | melibiose | + | fermentation |
68368 | 17992 | sucrose | + | fermentation |
68368 | 62345 | L-rhamnose | + | fermentation |
68368 | 30911 | sorbitol | + | fermentation |
68368 | 17268 | myo-inositol | + | fermentation |
68368 | 16899 | D-mannitol | + | fermentation |
68368 | 17634 | D-glucose | + | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | + | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | + | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | cytochrome oxidase | - | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | + | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | + | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
5760 | + | + | - | + | + | - | - | - | - | + | - | + | + | + | + | + | + | + | + | + | - |
Isolation, sampling and environmental information
isolation
- @ref: 5760
- sample type: soil from a landfarm for treatment of refinery waste sludge
- geographic location: Korinthos
- country: Greece
- origin.country: GRC
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | |
#Engineered | #Waste | |
#Environmental | #Terrestrial | #Mud (Sludge) |
#Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 5760
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5760
- description: Enterobacter sp. EK4 partial 16S rRNA gene, isolate EK4
- accession: AJ457062
- length: 481
- database: ena
- NCBI tax ID: 192167
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Enterobacter ludwigii strain FDAARGOS_1475 | 299767.207 | complete | patric | 299767 |
66792 | Enterobacter ludwigii strain FDAARGOS_1475 | 299767.225 | complete | patric | 299767 |
66792 | Enterobacter ludwigii strain FDAARGOS_1475 | 299767.235 | complete | patric | 299767 |
66792 | Enterobacter ludwigii strain FDAARGOS_1475 | 299767.215 | complete | patric | 299767 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 97.82 | no |
anaerobic | no | 96.483 | no |
halophile | no | 85.319 | no |
spore-forming | no | 93.756 | no |
glucose-util | yes | 95.383 | no |
motile | yes | 89.773 | no |
flagellated | no | 61.699 | no |
aerobic | yes | 82.449 | no |
thermophile | no | 99.318 | yes |
glucose-ferment | yes | 94.475 | yes |
External links
@ref: 5760
culture collection no.: DSM 15213
straininfo link
- @ref: 73856
- straininfo: 144473
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
5760 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15213) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15213 | |
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) | |
68368 | Automatically annotated from API 20E | |||
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 | |
73856 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID144473.1 | StrainInfo: A central database for resolving microbial strain identifiers |