Strain identifier
BacDive ID: 10942
Type strain: 
Species: Rhodococcus ruber
Strain Designation: 219
Strain history: <- H. Diekmann, 219
NCBI tax ID(s): 1830 (species)
version 9.3 (current version)
General
@ref: 11588
BacDive-ID: 10942
DSM-Number: 44190
keywords: genome sequence, Bacteria, aerobe, mesophilic
description: Rhodococcus ruber 219 is an aerobe, mesophilic bacterium that was isolated from effluents of a chemical factory.
NCBI tax id
- NCBI tax id: 1830
- Matching level: species
strain history
- @ref: 11588
- history: <- H. Diekmann, 219
doi: 10.13145/bacdive10942.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Nocardiaceae
- genus: Rhodococcus
- species: Rhodococcus ruber
- full scientific name: Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Streptothrix rubra
@ref: 11588
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiaceae
genus: Rhodococcus
species: Rhodococcus ruber
full scientific name: Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 emend. Nouioui et al. 2018
strain designation: 219
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 125438 | no | 93 | |
| 125439 | 97.5 | positive |
multimedia
- @ref: 11588
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44190.jpg
- caption: Medium 215 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 11588 | 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 |
| 11588 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water |
culture temp
- @ref: 11588
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 125438
- oxygen tolerance: aerobe
- confidence: 92.034
Isolation, sampling and environmental information
isolation
- @ref: 11588
- sample type: effluents of a chemical factory
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Industrial | #Plant (Factory) |
| #Engineered | #Waste | #Industrial wastewater |
Safety information
risk assessment
- @ref: 11588
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
- @ref: 66792
- description: Rhodococcus ruber 219
- accession: GCA_021852985
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1830
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 87.975 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.359 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 92.034 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 62.207 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.9 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 93 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 56.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 84.5 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 97.5 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 77.8 |
External links
@ref: 11588
culture collection no.: DSM 44190
straininfo link
- @ref: 80196
- straininfo: 50518
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 11588 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44190) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44190 | |
| 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) | |
| 80196 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID50518.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |