Strain identifier
BacDive ID: 132322
Type strain: 
Species: Oerskovia sp.
Strain Designation: Root918
Strain history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root918 <- Y. Bai
NCBI tax ID(s): 1915060 (species)
version 9.3 (current version)
General
@ref: 24111
BacDive-ID: 132322
DSM-Number: 102484
keywords: genome sequence, Bacteria, mesophilic
description: Oerskovia sp. Root918 is a mesophilic bacterium that was isolated from roots of Arabidopsis thaliana ecotype Shakdara .
NCBI tax id
- NCBI tax id: 1915060
- Matching level: species
strain history
- @ref: 24111
- history: <- P. Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Cologne, Germany; Root918 <- Y. Bai
doi: 10.13145/bacdive132322.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Promicromonosporaceae
- genus: Oerskovia
- species: Oerskovia sp.
- full scientific name: Oerskovia Prauser et al. 1970 (Approved Lists 1980)
@ref: 24111
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Promicromonosporaceae
genus: Oerskovia
species: Oerskovia sp.
full scientific name: Oerskovia sp.
strain designation: Root918
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence | motility |
|---|---|---|---|
| 125439 | positive | 98.1 | |
| 125438 | 93.5 | no | |
| 125438 | positive | 92.443 |
Culture and growth conditions
culture medium
- @ref: 24111
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: 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: 24111
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 97.7
Isolation, sampling and environmental information
isolation
- @ref: 24111
- sample type: roots of Arabidopsis thaliana ecotype Shakdara (Sha)
- host species: Arabidopsis thaliana
- geographic location: Cologne (50.958N 6.856E)
- country: Germany
- origin.country: DEU
- continent: Europe
- latitude: 50.958
- longitude: 6.856
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Oerskovia sp. Root918 | GCA_001428945 | scaffold | ncbi | 1736607 |
| 66792 | Oerskovia sp. Root918 | 1736607.3 | wgs | patric | 1736607 |
| 66792 | Oerskovia sp. Root918 | 2643221721 | draft | img | 1736607 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 92.443 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.936 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 76.076 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 50.344 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 97.5 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 93.5 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 51.9 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 71.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 98.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 97.7 |
External links
@ref: 24111
culture collection no.: DSM 102484
straininfo link
- @ref: 90669
- straininfo: 397317
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 | |
| 24111 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102484 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102484) | |
| 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 | |
| 90669 | 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-ID397317.1 | |
| 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 |