Strain identifier
BacDive ID: 160415
Type strain: 
Species: Rhodococcus opacus
Strain Designation: 1CP
Strain history: <- D. Tischler, TU Bergakademie Freiberg, Germany; 1CP <- S.N. Gorlatov
NCBI tax ID(s): 37919 (species)
version 9.3 (current version)
General
@ref: 67321
BacDive-ID: 160415
DSM-Number: 46757
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Rhodococcus opacus 1CP is a mesophilic bacterium that was isolated from enrichment culture.
NCBI tax id
- NCBI tax id: 37919
- Matching level: species
strain history
- @ref: 67321
- history: <- D. Tischler, TU Bergakademie Freiberg, Germany; 1CP <- S.N. Gorlatov
doi: 10.13145/bacdive160415.20250331.9.3
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: 67321
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Mycobacteriales
family: Nocardiaceae
genus: Rhodococcus
species: Rhodococcus opacus
full scientific name: Rhodococcus opacus Klatte et al. 1995
strain designation: 1CP
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence | motility |
|---|---|---|---|
| 125439 | positive | 98.5 | |
| 125438 | 91.5 | no |
Culture and growth conditions
culture medium
- @ref: 67321
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
- @ref: 67321
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 97.8
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 24265 | gluconate | + | assimilation |
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 17128 | adipate | + | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | + | assimilation |
| 68369 | 16899 | D-mannitol | + | assimilation |
| 68369 | 17634 | D-glucose | + | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | - | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
| 68382 | alkaline phosphatase | + | 3.1.3.1 |
| 68382 | lipase (C 14) | - | |
| 68382 | leucine arylamidase | + | 3.4.11.1 |
| 68382 | valine arylamidase | + | |
| 68382 | trypsin | - | 3.4.21.4 |
| 68382 | alpha-chymotrypsin | - | 3.4.21.1 |
| 68382 | acid phosphatase | + | 3.1.3.2 |
| 68382 | beta-galactosidase | + | 3.2.1.23 |
| 68382 | beta-glucuronidase | - | 3.2.1.31 |
| 68382 | alpha-glucosidase | + | 3.2.1.20 |
| 68382 | beta-glucosidase | - | 3.2.1.21 |
| 68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
| 68382 | alpha-mannosidase | - | 3.2.1.24 |
| 68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
| @ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 67321 | - | + | +/- | +/- | - | + | + | +/- | - | - | + | +/- | +/- | + | - | + | - | - | - | - |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 67321 | + | - | - | - | - | - | - | + | + | +/- | +/- | + | + | +/- | + | - | + | + | + | + |
Isolation, sampling and environmental information
isolation
- @ref: 67321
- sample type: enrichment culture
- geographic location: Moscow Region
- country: Russia
- origin.country: RUS
- continent: Europe
taxonmaps
- @ref: 69479
- File name: preview.99_628.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_181;97_445;98_509;99_628&stattab=map
- Last taxonomy: Rhodococcus
- 16S sequence: Y11893
- Sequence Identity:
- Total samples: 806
- soil counts: 425
- aquatic counts: 116
- animal counts: 152
- plant counts: 113
Safety information
risk assessment
- @ref: 67321
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 67321
- description: R.opacus 16S rRNA gene, strain 1CP
- accession: Y11893
- length: 1485
- database: nuccore
- NCBI tax ID: 37919
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodococcus opacus 1CP | GCA_001685605 | complete | ncbi | 37919 |
| 66792 | Rhodococcus opacus 1CP | 2856586077 | complete | img | 37919 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 86.014 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.22 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 89.143 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 57.878 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.5 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 91.5 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 69.8 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 86.7 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 98.5 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 97.8 |
External links
@ref: 67321
culture collection no.: DSM 46757, VKM Ac-2638
straininfo link
- @ref: 112662
- straininfo: 396785
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 | |
| 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 | |
| 67321 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-46757 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46757) | |
| 68369 | Automatically annotated from API 20NE | |||
| 68382 | Automatically annotated from API zym | |||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 112662 | 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-ID396785.1 | |
| 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 |