Strain identifier

BacDive ID: 136650

Type strain: No

Species: Rhodococcus opacus

Strain Designation: R7

Strain history: CIP <- 2002, G. Bestetti, Milano Univ., Milano, Italy: strain R7

NCBI tax ID(s): 37919 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
361282002, G. Bestetti, Degli Studi di Milano Univ., Milano, Italy: strain R7
36128CIP <- 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

    @refsynonym
    20215Rhodococcus imtechensis
    20215Rhodococcus 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

@refnamegrowthcompositionlink
36128MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
36128CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
36128positivegrowth30mesophilic
36128positivegrowth10-30
36128nogrowth37mesophilic
36128nogrowth41thermophilic
36128nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 36128
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
36128NaClpositivegrowth0-6 %
36128NaClnogrowth8 %
36128NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3612816947citrate-carbon source
361284853esculin-hydrolysis
36128606565hippurate+hydrolysis
3612817632nitrate-reduction
3612816301nitrite-reduction
3612817632nitrate-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

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
3612815688acetoin-
3612817234glucose-

enzymes

@refvalueactivityec
36128oxidase-
36128beta-galactosidase-3.2.1.23
36128alcohol dehydrogenase-1.1.1.1
36128gelatinase-
36128amylase-
36128DNase-
36128caseinase-3.4.21.50
36128catalase+1.11.1.6
36128tween esterase+
36128gamma-glutamyltransferase-2.3.2.2
36128lecithinase-
36128lipase-
36128lysine decarboxylase-4.1.1.18
36128ornithine decarboxylase-4.1.1.17
36128phenylalanine ammonia-lyase-4.3.1.24
36128tryptophan deaminase-
36128urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
36128--++-+++--++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
36128++-+---+-++-------++--++-++-----+++++------+-+-+-+++-+--++-+++++++++++-+++++---+++-++-++++-++--++++

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typeisolation date
36128Crespiatica LodiItalyITAEurope
36128Crespiatica LodiItalyITAEuropeEnvironment, Contaminated soil2000

Safety information

risk assessment

  • @ref: 36128
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus opacus strain R737919.10completepatric37919
66792Rhodococcus opacus strain R737919.22plasmidpatric37919
66792Rhodococcus opacus strain R737919.23plasmidpatric37919
66792Rhodococcus opacus strain R737919.21plasmidpatric37919
66792Rhodococcus opacus strain R737919.24plasmidpatric37919
66792Rhodococcus opacus strain R737919.20plasmidpatric37919

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes81.12no
anaerobicno98.837no
halophileno90.495no
spore-formingno57.846no
glucose-utilyes92.234no
aerobicyes86.403no
motileno92.448no
flagellatedno98.072no
thermophileno99.624yes
glucose-fermentno89.867no

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

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
36128Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107348Collection of Institut Pasteur (CIP 107348)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68382Automatically annotated from API zym
93755Reimer, 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 identifiers10.60712/SI-ID362149.1