Strain identifier

BacDive ID: 10865

Type strain: No

Species: Rhodococcus erythropolis

Strain Designation: No 52

Strain history: KCC A-0132 <-- Y. Okami <-- ATCC 11048 <-- NCTC 8036 <-- F. W. Moore.

NCBI tax ID(s): 1833 (species)

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General

@ref: 10724

BacDive-ID: 10865

DSM-Number: 43060

keywords: genome sequence, 16S sequence, microaerophile, mesophilic, human pathogen

description: Rhodococcus erythropolis No 52 is a microaerophile, mesophilic human pathogen that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1833
  • Matching level: species

strain history

@refhistory
10724<- CCM (Mycobacterium rhodochrous) <- M. Goodfellow, 52 <- NCIB
67770KCC A-0132 <-- Y. Okami <-- ATCC 11048 <-- NCTC 8036 <-- F. W. Moore.

doi: 10.13145/bacdive10865.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus erythropolis
  • full scientific name: Rhodococcus erythropolis (Gray and Thornton 1928) Goodfellow and Alderson 1979 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Mycobacterium erythropolis
    20215Rhodococcus qingshengii
    20215Rhodococcus baikonurensis
    20215Rhodococcus jialingiae
    20215Rhodococcus enclensis
    20215Rhodococcus degradans

@ref: 10724

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus erythropolis

full scientific name: Rhodococcus erythropolis (Gray and Thornton 1928) Goodfellow and Alderson 1979 emend. Nouioui et al. 2018

strain designation: No 52

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.047
69480100positive

Culture and growth conditions

culture medium

  • @ref: 10724
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
10724positivegrowth28mesophilic
45662positivegrowth22-37
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 45662
  • oxygen tolerance: microaerophile

spore formation

@refspore formationconfidence
69481no94
69480no98.805

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836817632nitrate-reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

  • @ref: 68368
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
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
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
10724-+/-+/-+/--++---+/-+/----++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARANO2N2
10724------+/---+/-------------

Isolation, sampling and environmental information

isolation

@refsample type
10724soil
67770Soil

isolation source categories

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

Safety information

risk assessment

  • @ref: 10724
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodococcus erythropolis partial 16S rRNA gene, strain CCM2595AJ620506881ena1833
20218Rhodococcus erythropolis DSM 43060 16S ribosomal RNA gene, partial sequenceAY017131625ena1833
20218Rhodococcus erythropolis strain ATCC 11048 16S ribosomal RNA gene, partial sequenceAY281107967ena1833

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus erythropolis CCM2595GCA_000454045completencbi1136179
66792Rhodococcus erythropolis CCM25951136179.20plasmidpatric1136179
66792Rhodococcus erythropolis CCM25951136179.4completepatric1136179
66792Rhodococcus erythropolis strain NCTC80361833.119wgspatric1833
66792Rhodococcus erythropolis NCTC 80362903984161draftimg1833
66792Rhodococcus erythropolis CCM25952561511168completeimg1136179
67770Rhodococcus erythropolis NCTC8036GCA_900455855contigncbi1833

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno92.921no
flagellatedno98.143no
gram-positiveyes85.095no
anaerobicno99.329yes
aerobicyes90.88yes
halophileno92.611no
spore-formingno72.127no
thermophileno99.199yes
glucose-utilyes90.797no
glucose-fermentno90.198yes

External links

@ref: 10724

culture collection no.: DSM 43060, ATCC 11048, CCM 2595, NCIB 8147, NCTC 8036, CCUG 12167, JCM 3132, CECT 3008, CGMCC 4.1491, IFO 13914, IMET 7462, NBRC 13914, NCIMB 8147, NRRL B-1574

straininfo link

  • @ref: 80121
  • straininfo: 297046

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology11748240Barbiturase, a novel zinc-containing amidohydrolase involved in oxidative pyrimidine metabolism.Soong CL, Ogawa J, Sakuradani E, Shimizu SJ Biol Chem10.1074/jbc.M1107842002001Amidohydrolases/chemistry/*physiology, Amino Acid Motifs, Amino Acid Sequence, Aminohydrolases/*metabolism, Base Sequence, Binding Sites, Binding, Competitive, Cloning, Molecular, Electrophoresis, Polyacrylamide Gel, Escherichia coli/enzymology, Hydrogen-Ion Concentration, Kinetics, Malonates/metabolism, Models, Chemical, Molecular Sequence Data, Oxygen/*metabolism, Peptides/chemistry, Phylogeny, Pyrimidines/*metabolism, Recombinant Proteins/chemistry, Rhodococcus/enzymology, Sequence Homology, Amino Acid, Spectrophotometry, Temperature, Triazines/*metabolism, Zinc/*chemistryMetabolism
Enzymology12764568Host-vector system for phenol-degrading Rhodococcus erythropolis based on Corynebacterium plasmids.Vesely M, Patek M, Nesvera J, Cejkova A, Masak J, Jirku VAppl Microbiol Biotechnol10.1007/s00253-003-1230-x2003Base Sequence, Biodegradation, Environmental, Chromosome Mapping, Cloning, Molecular, Corynebacterium/*genetics, DNA, Bacterial/genetics, Escherichia coli/genetics, Gene Expression, Genetic Vectors, Green Fluorescent Proteins, Luminescent Proteins/genetics, Phenol/*metabolism, Plasmids/genetics, Recombinant Proteins/genetics, Replicon/genetics, Rhodococcus/*genetics/*metabolism, Transformation, GeneticMetabolism
Metabolism17483937Analysis of catRABC operon for catechol degradation from phenol-degrading Rhodococcus erythropolis.Vesely M, Knoppova M, Nesvera J, Patek MAppl Microbiol Biotechnol10.1007/s00253-007-0997-62007Bacterial Proteins/*genetics/metabolism, Base Sequence, Carbon-Carbon Double Bond Isomerases/*genetics/metabolism, Catechol 1,2-Dioxygenase/*genetics/metabolism, Catechols/*metabolism, Cyclic AMP Receptor Protein/genetics, DNA, Intergenic/genetics, DNA-Binding Proteins/*genetics/metabolism, *Genes, Bacterial, Intramolecular Lyases/*genetics/metabolism, Molecular Sequence Data, Multigene Family/genetics, Operon/*genetics, Phenol/*metabolism, *Promoter Regions, Genetic, Repressor Proteins/genetics/metabolism, Rhodococcus/enzymology/*genetics, Sequence Alignment, Succinic Acid, Transcription Factors/*genetics/metabolism, *Transcription, GeneticGenetics
Phylogeny20138031RP-HPLC/MS-APCI analysis of odd-chain TAGs from Rhodococcus erythropolis including some regioisomers.Rezanka T, Schreiberova O, Krulikovska T, Masak J, Sigler KChem Phys Lipids10.1016/j.chemphyslip.2010.01.0072010Chromatography, Liquid/*methods, Isomerism, Rhodococcus/*classification/*metabolism, Species Specificity, Spectrometry, Mass, Electrospray Ionization/*methods, Triglycerides/analysis/*chemistryMetabolism
Metabolism22610598Structural analysis of mycolic acids from phenol-degrading strain of Rhodococcus erythropolis by liquid chromatography-tandem mass spectrometry.Kolouchova I, Schreiberova O, Masak J, Sigler K, Rezanka TFolia Microbiol (Praha)10.1007/s12223-012-0156-z2012Biotransformation, Carbon/metabolism, Chromatography, Liquid, Culture Media/chemistry, Humic Substances, Mycolic Acids/*chemistry/*metabolism, Phenol/*metabolism, Rhodococcus/*chemistry/*metabolism, Tandem Mass SpectrometryProteome
Genetics24652983Genome Sequence of Rhodococcus erythropolis Strain CCM2595, a Phenol Derivative-Degrading Bacterium.Strnad H, Patek M, Fousek J, Szokol J, Ulbrich P, Nesvera J, Paces V, Vlcek CGenome Announc10.1128/genomeA.00208-142014
Metabolism24781748Expression control of nitrile hydratase and amidase genes in Rhodococcus erythropolis and substrate specificities of the enzymes.Rucka L, Volkova O, Pavlik A, Kaplan O, Kracik M, Nesvera J, Martinkova L, Patek MAntonie Van Leeuwenhoek10.1007/s10482-014-0179-32014Amidohydrolases/*metabolism, DNA, Bacterial/chemistry/genetics, Gene Expression Profiling, *Gene Expression Regulation, Bacterial, Hydro-Lyases/*metabolism, Hydroxylamines/*metabolism, Multigene Family, Nitriles/*metabolism, Rhodococcus/*enzymology/genetics, Sequence Analysis, DNA, Substrate Specificity, Transcription, GeneticEnzymology
Metabolism24938209Induction and carbon catabolite repression of phenol degradation genes in Rhodococcus erythropolis and Rhodococcus jostii.Szokol J, Rucka L, Simcikova M, Halada P, Nesvera J, Patek MAppl Microbiol Biotechnol10.1007/s00253-014-5881-62014Bacterial Proteins/*genetics/metabolism, Biodegradation, Environmental, *Catabolite Repression, Gene Expression Regulation, Bacterial, Mixed Function Oxygenases/genetics/metabolism, Multigene Family, Phenol/*metabolism, Promoter Regions, Genetic, Rhodococcus/enzymology/genetics/*metabolismEnzymology
Genetics30923242Complete Genome Sequence of Rhodococcus erythropolis Phage Shuman.Ponce Reyes S, Park PJ, Kaluka D, Washington JMMicrobiol Resour Announc10.1128/MRA.00113-192019
Biotechnology32743216High Regioselectivity Production of 5-Cyanovaleramide from Adiponitrile by a Novel Nitrile Hydratase Derived from Rhodococcus erythropolis CCM2595.Wang L, Liu S, Du W, Dou T, Liang CACS Omega10.1021/acsomega.0c021882020
Enzymology34982253Identification of Rhodococcus erythropolis Promoters Controlled by Alternative Sigma Factors Using In Vivo and In Vitro Systems and Heterologous RNA Polymerase.Blumenstein J, Radisch R, Stepanek V, Grulich M, Dostalova H, Patek MCurr Microbiol10.1007/s00284-021-02747-82022Corynebacterium glutamicum/genetics, *DNA-Directed RNA Polymerases/genetics, *Promoter Regions, Genetic, *Rhodococcus/enzymology/genetics, *Sigma Factor/genetics
Metabolism35167670Sigma regulatory network in Rhodococcus erythropolis CCM2595.Stepanek V, Dostalova H, Busche T, Blumenstein J, Grulich M, Plasil L, Rucka L, Nesvera J, Patek MFEMS Microbiol Lett10.1093/femsle/fnac0142022*Bacterial Proteins/metabolism, *Gene Expression Regulation, Bacterial, Gene Regulatory Networks, Rhodococcus, Sigma Factor/metabolism, Transcription, Genetic
36456206Modification of nitrile hydratase from Rhodococcus erythropolis CCM2595 by semirational design to enhance its substrate affinity.Wang L, Cui B, Qiu K, Huang J, Liang CBiointerphases10.1116/6.00020612022*Hydro-Lyases/genetics, *Rhodococcus/genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10724Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43060)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43060
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
45662Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12167)https://www.ccug.se/strain?id=12167
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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80121Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297046.1StrainInfo: A central database for resolving microbial strain identifiers