Strain identifier
BacDive ID: 136650
Type strain:
Species: Rhodococcus opacus
Strain Designation: R7
Strain history: CIP <- 2002, G. Bestetti, Milano Univ., Milano, Italy: strain R7
NCBI tax ID(s): 37919 (species)
version 8.1 (current version)
General
@ref: 36128
BacDive-ID: 136650
keywords: genome sequence, obligate aerobe, mesophilic, Gram-positive, rod-shaped
description: Rhodococcus opacus R7 is an obligate aerobe, mesophilic, Gram-positive prokaryote.
NCBI tax id
- NCBI tax id: 37919
- Matching level: species
strain history
@ref | history |
---|---|
36128 | 2002, G. Bestetti, Degli Studi di Milano Univ., Milano, Italy: strain R7 |
36128 | CIP <- 2002, G. Bestetti, Milano Univ., Milano, Italy: strain R7 |
doi: 10.13145/bacdive136650.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- genus: Rhodococcus
- species: Rhodococcus opacus
- full scientific name: Rhodococcus opacus Klatte et al. 1995
synonyms
@ref synonym 20215 Rhodococcus imtechensis 20215 Rhodococcus percolatus
@ref: 36128
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Mycobacteriales
family: Nocardiaceae
genus: Rhodococcus
species: Rhodococcus opacus
strain designation: R7
type strain: no
Morphology
cell morphology
- @ref: 36128
- gram stain: positive
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 36128
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
36128 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
36128 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
36128 | positive | growth | 30 | mesophilic |
36128 | positive | growth | 10-30 | |
36128 | no | growth | 37 | mesophilic |
36128 | no | growth | 41 | thermophilic |
36128 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 36128
- oxygen tolerance: obligate aerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
36128 | NaCl | positive | growth | 0-6 % |
36128 | NaCl | no | growth | 8 % |
36128 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
36128 | 16947 | citrate | - | carbon source |
36128 | 4853 | esculin | - | hydrolysis |
36128 | 606565 | hippurate | + | hydrolysis |
36128 | 17632 | nitrate | - | reduction |
36128 | 16301 | nitrite | - | reduction |
36128 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 36128
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
- @ref: 36128
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
36128 | 15688 | acetoin | - | |
36128 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
36128 | oxidase | - | |
36128 | beta-galactosidase | - | 3.2.1.23 |
36128 | alcohol dehydrogenase | - | 1.1.1.1 |
36128 | gelatinase | - | |
36128 | amylase | - | |
36128 | DNase | - | |
36128 | caseinase | - | 3.4.21.50 |
36128 | catalase | + | 1.11.1.6 |
36128 | tween esterase | + | |
36128 | gamma-glutamyltransferase | - | 2.3.2.2 |
36128 | lecithinase | - | |
36128 | lipase | - | |
36128 | lysine decarboxylase | - | 4.1.1.18 |
36128 | ornithine decarboxylase | - | 4.1.1.17 |
36128 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
36128 | tryptophan deaminase | - | |
36128 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
36128 | - | - | + | + | - | + | + | + | - | - | + | + | - | - | - | + | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
36128 | + | + | - | + | - | - | - | + | - | + | + | - | - | - | - | - | - | - | + | + | - | - | + | + | - | + | + | - | - | - | - | - | + | + | + | + | + | - | - | - | - | - | - | + | - | + | - | + | - | + | + | + | - | + | - | - | + | + | - | + | + | + | + | + | + | + | + | + | + | + | - | + | + | + | + | + | - | - | - | + | + | + | - | + | + | - | + | + | + | + | - | + | + | - | - | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | geographic location | country | origin.country | continent | sample type | isolation date |
---|---|---|---|---|---|---|
36128 | Crespiatica Lodi | Italy | ITA | Europe | ||
36128 | Crespiatica Lodi | Italy | ITA | Europe | Environment, Contaminated soil | 2000 |
Safety information
risk assessment
- @ref: 36128
- biosafety level: 1
- biosafety level comment: Risk group (French classification)
Sequence information
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhodococcus opacus strain R7 | 37919.10 | complete | patric | 37919 |
66792 | Rhodococcus opacus strain R7 | 37919.22 | plasmid | patric | 37919 |
66792 | Rhodococcus opacus strain R7 | 37919.23 | plasmid | patric | 37919 |
66792 | Rhodococcus opacus strain R7 | 37919.21 | plasmid | patric | 37919 |
66792 | Rhodococcus opacus strain R7 | 37919.24 | plasmid | patric | 37919 |
66792 | Rhodococcus opacus strain R7 | 37919.20 | plasmid | patric | 37919 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | yes | 81.12 | no |
anaerobic | no | 98.837 | no |
halophile | no | 90.495 | no |
spore-forming | no | 57.846 | no |
glucose-util | yes | 92.234 | no |
aerobic | yes | 86.403 | no |
motile | no | 92.448 | no |
flagellated | no | 98.072 | no |
thermophile | no | 99.624 | yes |
glucose-ferment | no | 89.867 | no |
External links
@ref: 36128
culture collection no.: CIP 107348
straininfo link
- @ref: 93755
- straininfo: 362149
literature
- topic: Genetics
- Pubmed-ID: 25146139
- title: Genome Sequence of Rhodococcus opacus Strain R7, a Biodegrader of Mono- and Polycyclic Aromatic Hydrocarbons.
- authors: Di Gennaro P, Zampolli J, Presti I, Cappelletti M, D'Ursi P, Orro A, Mezzelani A, Milanesi L
- journal: Genome Announc
- DOI: 10.1128/genomeA.00827-14
- year: 2014
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 | |
36128 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107348 | Collection of Institut Pasteur (CIP 107348) | |
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 | |
68382 | Automatically annotated from API zym | |||
93755 | 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-ID362149.1 |