Strain identifier

BacDive ID: 10832

Type strain: Yes

Species: Rhodococcus corynebacterioides

Strain history: CIP <- 1995, IFO <- ATCC, Rhodococcus globerulus <- A.J. Crowle, Corynebacterium rubrum

NCBI tax ID(s): 1219012 (strain), 53972 (species)

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General

@ref: 8575

BacDive-ID: 10832

DSM-Number: 20151

keywords: genome sequence, 16S sequence, obligate aerobe, mesophilic

description: Rhodococcus corynebacterioides DSM 20151 is an obligate aerobe, mesophilic prokaryote that was isolated from air contaminant of culture medium.

NCBI tax id

NCBI tax idMatching level
53972species
1219012strain

strain history

@refhistory
8575<- ATCC <- A.J. Crowle (Corynebacterium rubrum)
67770IFM 0238 <-- IFO 14404 <-- ATCC 14898 <-- A. J. Crowle.
118759CIP <- 1995, IFO <- ATCC, Rhodococcus globerulus <- A.J. Crowle, Corynebacterium rubrum

doi: 10.13145/bacdive10832.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus corynebacterioides
  • full scientific name: Rhodococcus corynebacterioides (Serrano et al. 1972) Yassin and Schaal 2005

  • synonyms

    @refsynonym
    20215Rhodococcoides corynebacterioides
    20215Nocardia corynebacterioides

@ref: 8575

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus corynebacterioides

full scientific name: Rhodococcus corynebacterioides (Serrano et al. 1972) Yassin and Schaal 2005 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.166
69480100positive
118759nopositiverod-shaped

multimedia

@refmultimedia contentintellectual property rightscaption
8575https://www.dsmz.de/microorganisms/photos/DSM_20151-1.jpg© Leibniz-Institut DSMZ
8575https://www.dsmz.de/microorganisms/photos/DSM_20151.jpg© Leibniz-Institut DSMZMedium 535 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8575TRYPTICASE 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
41205MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118759CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
8575positivegrowth28mesophilic
41205positivegrowth30mesophilic
67770positivegrowth28mesophilic
118759positivegrowth10-37
118759nogrowth41thermophilic
118759nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118759
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.825

halophily

@refsaltgrowthtested relationconcentration
118759NaClpositivegrowth0-8 %
118759NaClnogrowth10 %

murein

  • @ref: 8575
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371gentiobiose-builds acid from28066
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
118759citrate-carbon source16947
118759esculin-hydrolysis4853
118759hippurate+hydrolysis606565
118759nitrate-reduction17632
118759nitrite-reduction16301
118759nitrate-respiration17632

metabolite production

  • @ref: 118759
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11875915688acetoin-
11875917234glucose-

enzymes

@refvalueactivityec
118759oxidase-
118759beta-galactosidase-3.2.1.23
118759alcohol dehydrogenase-1.1.1.1
118759gelatinase-
118759amylase+
118759DNase-
118759caseinase-3.4.21.50
118759catalase+1.11.1.6
118759tween esterase+
118759gamma-glutamyltransferase-2.3.2.2
118759lecithinase-
118759lipase-
118759lysine decarboxylase-4.1.1.18
118759ornithine decarboxylase-4.1.1.17
118759phenylalanine ammonia-lyase-4.3.1.24
118759protease-
118759tryptophan deaminase-
118759urease-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
118759-++++++---++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118759+/----------+/-+/-+/-----+/-+/------------+/-+/------+/--+/-----+/-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118759++-++--+------------------+----+-+--+------------+++-+-----+-------+-------+---++---+---+-------+--

Isolation, sampling and environmental information

isolation

@refsample typesampling date
8575air contaminant of culture medium
53925Air contaminant of culture medium1959
67770Air contaminant of culture medium
118759Environment, Air contaminant of culture medium

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Contaminant
#Engineered#Laboratory#Lab enrichment
#Environmental#Air

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
85751Risk group (German classification)
1187592Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodococcus corynebacterioides gene for 16S ribosomal RNA, partial sequence, strain: DSM 20151AB915624941ena53972
20218Rhodococcus corynebacterioides gene for 16S ribosomal RNA, partial sequence, strain: DSM 20151, clone: NTS9AB9205661443ena53972
20218Nocardia corynebacterioides strain DSM 20151 16S ribosomal RNA gene, complete sequenceAF4300661494ena53972
20218Rhodococcus corynebacterioides strain DSM 20151 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536414365ena53972
20218Rhodococcus corynebacterioides strain DSM 20151 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536415332ena53972
20218Rhodococcus corynebacterioides strain DSM 20151 note copy 3 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536416346ena53972
20218Rhodococcus corynebacterioides strain DSM 20151 note copy 4 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536417362ena53972
20218Rhodococcus corynebacterioides strain DSM 20151 16S ribosomal RNA gene, partial sequenceKF4103451367ena53972
20218Rhodococcus corynebacterioides 16S rRNA gene, type strain DSM 20151TX806151477ena53972

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus corynebacterioides NBRC 144041219012.3wgspatric1219012
66792Rhodococcus corynebacterioides strain DSM 2015153972.3wgspatric53972
66792Rhodococcus corynebacterioides DSM 201512744054539draftimg53972
67770Rhodococcus corynebacterioides NBRC 14404GCA_001894765contigncbi1219012
67770Rhodococcus corynebacterioides DSM 20151GCA_001646675contigncbi53972

GC content

  • @ref: 67770
  • GC-content: 70.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno93.388no
gram-positiveyes87.557no
anaerobicno99.49no
aerobicyes92.213no
halophileno89.804no
spore-formingno90.943no
thermophileno98.695yes
glucose-utilyes87.148no
flagellatedno98.16no
glucose-fermentno89.043no

External links

@ref: 8575

culture collection no.: DSM 20151, ATCC 14898, CIP 104510, NCIB 9433, NCTC 10391, NRRL B-24037, CCUG 37877, IFM 0238, IFO 14404, IMET 7767, JCM 3376, BCRC 13739, CECT 420, JCM 3391, KCTC 9613, KCTC 9820, MTCC 699, NBRC 14404, NCIMB 9433, VKM Ac-870

straininfo link

  • @ref: 80093
  • straininfo: 45572

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879280Reclassification of Nocardia corynebacterioides Serrano et al. 1972 (Approved Lists 1980) as Rhodococcus corynebacterioides comb. nov.Yassin AF, Schaal KPInt J Syst Evol Microbiol10.1099/ijs.0.63529-02005Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Molecular Sequence Data, Nocardia/*classification/cytology/*genetics/physiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/cytology/*genetics/physiology, Sequence Analysis, DNA, Vitamin K 2/analysis/isolation & purificationEnzymology
Phylogeny16627641Rhodococcus kroppenstedtii sp. nov., a novel actinobacterium isolated from a cold desert of the Himalayas, India.Mayilraj S, Krishnamurthi S, Saha P, Saini HSInt J Syst Evol Microbiol10.1099/ijs.0.63831-02006Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Desert Climate, Genes, rRNA/genetics, India, Molecular Sequence Data, Nocardia/genetics, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/*isolation & purification/physiology, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny24854006Rhodococcus enclensis sp. nov., a novel member of the genus Rhodococcus.Dastager SG, Mawlankar R, Tang SK, Krishnamurthi S, Ramana VV, Joseph N, Shouche YSInt J Syst Evol Microbiol10.1099/ijs.0.061390-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8575Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20151)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20151
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
41205Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16427
53925Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37877)https://www.ccug.se/strain?id=37877
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/
68371Automatically annotated from API 50CH acid
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
80093Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45572.1StrainInfo: A central database for resolving microbial strain identifiers
118759Curators of the CIPCollection of Institut Pasteur (CIP 104510)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104510