Strain identifier

BacDive ID: 10998

Type strain: Yes

Species: Rhodococcus opacus

Strain Designation: 1b, 18

Strain history: CIP <- 1995, DSM <- D. Claus, DSM 427 <- IMG: strain 1b <- D. Siebert: strain 18

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: 10865

BacDive-ID: 10998

DSM-Number: 43205

keywords: genome sequence, 16S sequence, obligate aerobe, mesophilic, Gram-positive

description: Rhodococcus opacus 1b is an obligate aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil.

NCBI tax id

  • NCBI tax id: 37919
  • Matching level: species

strain history

@refhistory
10865<- IMG, 1b (Nocardia opaca) <- D. Siebert, 1B
416302015, J. Kreit, Mohammed V Univ. Rabat, Morocco: strain GK3
67770DSM 43205 <-- IMG, 1b <-- D. Siebert 1B.
121422CIP <- 1995, DSM <- D. Claus, DSM 427 <- IMG: strain 1b <- D. Siebert: strain 18

doi: 10.13145/bacdive10998.20230509.8.1

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: 10865

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: 1b, 18

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
121422positiverod-shapedno

multimedia

  • @ref: 10865
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43205.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10865TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
10865GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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
35692MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
41630MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
121422CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
10865positivegrowth28mesophilic
35692positivegrowth30mesophilic
41630positivegrowth30mesophilic
67770positivegrowth28mesophilic
121422positivegrowth10-37
121422nogrowth41thermophilic
121422nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121422
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.368

halophily

@refsaltgrowthtested relationconcentration
18483NaClpositivemaximum7.5 %
121422NaClpositivegrowth0-6 %
121422NaClnogrowth8 %
121422NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis
1214224853esculin-hydrolysis
121422606565hippurate-hydrolysis
12142217632nitrate+reduction
12142216301nitrite-reduction
12142217632nitrate-respiration
683794853esculin-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-
12142215688acetoin-

enzymes

@refvalueactivityec
68379gelatinase-
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
121422oxidase-
121422beta-galactosidase+3.2.1.23
121422alcohol dehydrogenase-1.1.1.1
121422gelatinase-
121422amylase+
121422DNase-
121422catalase+1.11.1.6
121422tween esterase-
121422lecithinase-
121422lysine decarboxylase-4.1.1.18
121422ornithine decarboxylase-4.1.1.17
121422phenylalanine ammonia-lyase-4.3.1.24
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382alpha-chymotrypsin-3.4.21.1
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControl
18483-----++--+-------+-
10865+--+-+--------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18483----++++--+++-++---
10865+---++/----+/---+-+/------
121422-++-++---+-++-+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18483++-++-+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121422+++---++++-++++---+---+--++-----+++++----+-+-++--+++-+--++-+++++++++++-+++++---+++--+---++--++-++++

Isolation, sampling and environmental information

isolation

@refsample type
10865soil
67770Soil from the surroundings of a defective town gas pipe

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184831German classification
108651Risk group (German classification)
1214221Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodococcus opacus strain DSM 43205 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536493301ena37919
20218Rhodococcus opacus strain DSM 43205 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536494308ena37919
20218Rhodococcus opacus strain DSM 43205 note copy 3 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536495302ena37919
20218Rhodococcus opacus strain DSM 43205 16S ribosomal RNA gene, partial sequenceKF4103491481ena37919
20218Rhodococcus opacus 16S rRNA gene, strain DSM43205TX806301481ena37919
67770Rhodococcus opacus partial 16S rRNA gene, strain DSM 43205, isolate Clone 1LN8279181510ena37919
67770Rhodococcus opacus partial 16S rRNA gene, strain DSM 43205, isolate Clone 2LN8279191510ena37919
67770Rhodococcus opacus partial 16S rRNA gene, strain DSM 43205, isolate Clone 3LN8279201509ena37919

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus opacus strain ATCC 5188137919.38wgspatric37919
66792Rhodococcus opacus strain DSM 4320537919.12wgspatric37919
66792Rhodococcus opacus DSM 432052744054613draftimg37919
67770Rhodococcus opacus ATCC 51881GCA_012396235contigncbi37919
67770Rhodococcus opacus DSM 43205GCA_001646735contigncbi37919
66792Rhodococcus opacus DSM 43205GCA_910591545contigncbi37919

GC content

  • @ref: 67770
  • GC-content: 67.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes83no
gram-positiveyes81.053no
anaerobicno98.956no
halophileno85.91no
spore-formingno62.956no
glucose-utilyes89.686no
aerobicyes88.47no
motileno92.333no
flagellatedno97.941no
thermophileno99.488yes
glucose-fermentno89.538no

External links

@ref: 10865

culture collection no.: DSM 43205, ATCC 51881, CIP 104549, DSM 427, JCM 9703, CGMCC 4.1820, IFO 16217, KCTC 9811, LMG 18000, NBRC 100624, NBRC 16217, NCIMB 10810, NCIMB 13353

straininfo link

  • @ref: 80252
  • straininfo: 10716

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16902038Rhodococcus imtechensis sp. nov., a nitrophenol-degrading actinomycete.Ghosh A, Paul D, Prakash D, Mayilraj S, Jain RKInt J Syst Evol Microbiol10.1099/ijs.0.63939-02006Base Composition, Biodegradation, Environmental, DNA, Bacterial/chemistry/genetics, India, Molecular Sequence Data, Nitrophenols/*metabolism, Pesticides, Phylogeny, Rhodococcus/chemistry/*classification/genetics/metabolism, Sequence Homology, Nucleic Acid, Soil Pollutants, Species SpecificityGenetics
Biotechnology36281430Production of biopolymer precursors beta-alanine and L-lactic acid from CO(2) with metabolically versatile Rhodococcus opacus DSM 43205.Salusjarvi L, Ojala L, Peddinti G, Lienemann M, Jouhten P, Pitkanen JP, Toivari MFront Bioeng Biotechnol10.3389/fbioe.2022.9894812022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10865Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43205)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43205
18483Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43205.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
35692Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16470
41630Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/34481
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
80252Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10716.1StrainInfo: A central database for resolving microbial strain identifiers
121422Curators of the CIPCollection of Institut Pasteur (CIP 104549)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104549