Strain identifier
BacDive ID: 11003
Type strain: 
Species: Rhodococcus opacus
Strain Designation: S676, 225
Strain history: KCC A-0009 <-- ATCC 4275 <-- H. J. Conn <-- P. H. H. Gray.
NCBI tax ID(s): 37919 (species)
version 9.3 (current version)
General
@ref: 10923
BacDive-ID: 11003
DSM-Number: 43280
keywords: genome sequence, Bacteria, mesophilic
description: Rhodococcus opacus S676 is a mesophilic bacterium of the family Nocardiaceae.
NCBI tax id
- NCBI tax id: 37919
- Matching level: species
strain history
| @ref | history |
|---|---|
| 10923 | <- K. Kieslich; Schering 225 (Nocardia convoluta) <- ATCC <- H.J. Conn (Mycobacterium convolutum) <- P. H. H. Gray |
| 67770 | KCC A-0009 <-- ATCC 4275 <-- H. J. Conn <-- P. H. H. Gray. |
doi: 10.13145/bacdive11003.20250331.9.3
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 opacus
- full scientific name: Rhodococcus opacus Klatte et al. 1995
synonyms
@ref synonym 20215 Rhodococcus percolatus 20215 Rhodococcus imtechensis
@ref: 10923
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiaceae
genus: Rhodococcus
species: Rhodococcus opacus
full scientific name: Rhodococcus opacus Klatte et al. 1995
strain designation: S676, 225
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 125438 | no | 94.5 | |
| 125439 | 98.5 | positive |
Culture and growth conditions
culture medium
- @ref: 10923
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: 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 | growth | type | temperature |
|---|---|---|---|
| 10923 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 99.5
compound production
- @ref: 67770
- compound: 3-Keto-δ-1,4 steroids (US Pat. 3,010,876)
Safety information
risk assessment
- @ref: 10923
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodococcus sp. JCM 3009 | GCA_001313505 | contig | ncbi | 1303684 |
| 66792 | Rhodococcus sp. JCM 3009 | 1303684.3 | wgs | patric | 1303684 |
| 66792 | Rhodococcus sp. JCM 3009 | 2734481949 | draft | img | 1303684 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 79.962 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.86 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 53.439 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 89.385 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.846 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 94.5 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 68.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 84.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 98.5 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 99.5 |
External links
@ref: 10923
culture collection no.: DSM 43280, ATCC 4275, IMET 7025, KCC A-0009, JCM 3009, IFM 0024
straininfo link
- @ref: 80257
- straininfo: 34702
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 10923 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43280) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43280 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 80257 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID34702.1 | 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 |