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)

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General

@ref: 36128

BacDive-ID: 136650

keywords: genome sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, rod-shaped

description: Rhodococcus opacus R7 is an obligate aerobe, mesophilic, Gram-positive bacterium of the family Nocardiaceae.

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/bacdive136650.20250331.9.3

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

    @refsynonym
    20215Rhodococcus percolatus
    20215Rhodococcus imtechensis

@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

@refgram stainconfidencecell shapemotility
125439positive94
36128positiverod-shapedno

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

@refgrowthtypetemperature
36128positivegrowth30
36128positivegrowth10-30
36128nogrowth37
36128nogrowth41
36128nogrowth45

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
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
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

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes84.087no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.719yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes59.068no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.831yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98yes
125438motile2+flagellatedAbility to perform flagellated movementno89no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes58.2
125439BacteriaNetmotilityAbility to perform movementno74
125439BacteriaNetgram_stainReaction to gram-stainingpositive94
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe79.8

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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG