Strain identifier

BacDive ID: 10883

Type strain: Yes

Species: Rhodococcus fascians

Strain history: CIP <- 1996, DSM <- H. Seiler <- IFO <- ATCC <- W.H. Burkholder: strain CF 17, Corynebacterium fascians <- P. Tilford

NCBI tax ID(s): 1219015 (strain), 1828 (species)

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General

@ref: 8991

BacDive-ID: 10883

DSM-Number: 20669

keywords: genome sequence, 16S sequence, aerobe, mesophilic, plant pathogen

description: Rhodococcus fascians DSM 20669 is an aerobe, mesophilic plant pathogen that was isolated from Fasciation of sweet peas .

NCBI tax id

NCBI tax idMatching level
1828species
1219015strain

strain history

@refhistory
8991<- H. Seiler <- IFO <- ATCC <- P. Tilford
67770LMG 3623 <-- ATCC 12974 <-- W. H. Burkholder CF17 <-- P. Tilford.
119291CIP <- 1996, DSM <- H. Seiler <- IFO <- ATCC <- W.H. Burkholder: strain CF 17, Corynebacterium fascians <- P. Tilford

doi: 10.13145/bacdive10883.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus fascians
  • full scientific name: Rhodococcus fascians (Tilford 1936) Goodfellow 1984

  • synonyms

    @refsynonym
    20215Corynebacterium fascians
    20215Rhodococcoides fascians
    20215Phytomonas fascians
    20215Rhodococcus luteus

@ref: 8991

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus fascians

full scientific name: Rhodococcus fascians (Tilford 1936) Goodfellow 1984 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no97.41
69480100positive
119291nopositiveoval-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8991TRYPTICASE 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
8991GYM 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
37045MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119291CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
8991positivegrowth30mesophilic
37045positivegrowth30mesophilic
59099positivegrowth30mesophilic
67770positivegrowth28mesophilic
119291positivegrowth10-30
119291nogrowth37mesophilic
119291nogrowth41thermophilic
119291nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59099aerobe
119291obligate aerobe

spore formation

@refspore formationconfidence
69481no94
69480no99.978

compound production

@refcompound
89915' nucleotides
202165'-nucleotides

halophily

@refsaltgrowthtested relationconcentration
119291NaClpositivegrowth0-6 %
119291NaClnogrowth8 %
119291NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11929116947citrate+carbon source
1192914853esculin-hydrolysis
11929117632nitrate-reduction
11929116301nitrite-reduction
11929117632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 119291
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11929115688acetoin-
11929117234glucose-

enzymes

@refvalueactivityec
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrazinamidase+3.5.1.B15
119291oxidase-
119291beta-galactosidase+3.2.1.23
119291alcohol dehydrogenase-1.1.1.1
119291gelatinase-
119291amylase-
119291DNase-
119291caseinase-3.4.21.50
119291catalase+1.11.1.6
119291tween esterase-
119291gamma-glutamyltransferase-2.3.2.2
119291lecithinase-
119291lysine decarboxylase-4.1.1.18
119291ornithine decarboxylase-4.1.1.17
119291tryptophan deaminase-
119291urease+3.5.1.5
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382valine arylamidase-
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYG
8991-++/-+--+-------------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
8991---+-+/--+/---+/-----+/-----
119291-+++-+-++-+----+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119291-+--+--+------------+-----+----+-+--+--------+---+++-+---+---+-++----------+---++-------+----+-++++

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Fasciation of sweet peas (Lathyrus odoratus)
  • host species: Lathyrus odoratus

taxonmaps

  • @ref: 69479
  • File name: preview.99_2031.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_181;97_197;98_220;99_2031&stattab=map
  • Last taxonomy: Rhodococcus fascians
  • 16S sequence: X81930
  • Sequence Identity:
  • Total samples: 6997
  • soil counts: 894
  • aquatic counts: 1939
  • animal counts: 3728
  • plant counts: 436

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
8991yes1Risk group (German classification)
1192911Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218R.fascians 16S rRNA gene (ATCC 12974T)X819301314ena1828
20218R.fascians (DSM 20669) 16S rRNA geneX791861424ena1828

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus fascians NBRC 12155 = LMG 36231219015.3wgspatric1219015
66792Rhodococcus fascians NBRC 12155 = LMG 36231219015.4wgspatric1219015
66792Rhodococcus sp. AW25M091268303.4wgspatric1268303
66792Rhodococcus fascians NBRC 12155 = LMG 36232711768092draftimg1219015
67770Rhodococcus fascians NBRC 12155 = LMG 3623GCA_001894785contigncbi1219015
67770Rhodococcus fascians NBRC 12155 = LMG 3623GCA_000761055scaffoldncbi1219015

GC content

  • @ref: 67770
  • GC-content: 64.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno89.647no
gram-positiveyes87.075no
anaerobicno99.554yes
aerobicyes93.099no
halophileno83.461no
spore-formingno88.089no
thermophileno99.645yes
glucose-utilyes87.757no
flagellatedno98.023no
glucose-fermentno90.204yes

External links

@ref: 8991

culture collection no.: DSM 20669, ATCC 12974, CIP 104713, IFO 12155, JCM 1316, NBRC 12155, NCPPB 3067, CCUG 51073, JCM 10002, BCRC 13609, CFBP 2401, CGMCC 4.1817, CNCTC Cor 66/77, ICMP 5833, ICPB CF122, KCTC 9813, LMG 3623, MTCC 1531, NBRC 100625, NCIMB 13432, NRRL B-16937, VKM Ac-1462, IAM 12427, ICPB CF 122

straininfo link

  • @ref: 80138
  • straininfo: 92423

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology3162908Conjugative transfer of cadmium resistance plasmids in Rhodococcus fascians strains.Desomer J, Dhaese P, Van Montagu MJ Bacteriol10.1128/jb.170.5.2401-2405.19881988Cadmium/*pharmacology, *Conjugation, Genetic, DNA, Bacterial/genetics, Drug Resistance, Microbial, Genetic Markers, Kinetics, Mutation, Nucleic Acid Hybridization, *R Factors, Rhodococcus/drug effects/*geneticsPhylogeny
Enzymology9541568Pulsed-field gel electrophoresis analysis of the genome of Rhodococcus fascians: genome size and linear and circular replicon composition in virulent and avirulent strains.Pisabarro A, Correia A, Martin JFCurr Microbiol10.1007/s0028499003141998DNA, Circular, Deoxyribonucleases, Type II Site-Specific, Electrophoresis, Gel, Pulsed-Field, Genetic Code, *Genome, Bacterial, Markov Chains, Nucleic Acid Conformation, *Replicon, Restriction Mapping, Rhodococcus/classification/*genetics/pathogenicity, Species SpecificityPhylogeny
Enzymology9546162Characterization of the rrnB operon of the plant pathogen Rhodococcus fascians and targeted integrations of exogenous genes at rrn loci.Pisabarro A, Correia A, Martin JFAppl Environ Microbiol10.1128/AEM.64.4.1276-1282.19981998Base Sequence, Cloning, Molecular, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gene Targeting, *Genes, Bacterial, Genetic Vectors, Molecular Sequence Data, Operon, Plants/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, RNA, Ribosomal, 5S/genetics, Restriction Mapping, Rhodococcus/*genetics/*pathogenicity, Sequence Homology, Nucleic Acid, Virulence/geneticsGenetics
Metabolism10423744Characterization of antarctic hydrocarbon-degrading bacteria capable of producing bioemulsifiers.Yakimov MM, Giuliano L, Bruni V, Scarfi S, Golyshin PNNew Microbiol1999Alkanes/metabolism, Antarctic Regions, Biodegradation, Environmental, Biphenyl Compounds/metabolism, Burkholderia cepacia/drug effects, DNA, Ribosomal/genetics, Glycolipids/*biosynthesis/pharmacology, Hydrocarbons/*metabolism, Marine Biology, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodococcus/classification/genetics/*isolation & purification/metabolism, Spectrometry, Mass, Fast Atom Bombardment, Surface-Active Agents/*metabolism/pharmacology, Trehalose, Water MicrobiologyPhylogeny
Phylogeny15879245Rhodococcus yunnanensis sp. nov., a mesophilic actinobacterium isolated from forest soil.Zhang YQ, Li WJ, Kroppenstedt RM, Kim CJ, Chen GZ, Park DJ, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63390-02005Aerobiosis, Base Composition, Carbohydrates/analysis/isolation & purification, China, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Peptidoglycan/chemistry/isolation & purification, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/cytology/*isolation & purification/physiology, Sequence Analysis, DNA, *Soil Microbiology, Temperature, Trees, Vitamin K 2/analysis/isolation & purificationEnzymology
Phylogeny17766854Rhodococcus kyotonensis sp. nov., a novel actinomycete isolated from soil.Li B, Furihata K, Ding LX, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.64770-02007Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Japan, Molecular Sequence Data, Mycolic Acids/analysis, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodococcus/chemistry/*classification/genetics/*isolation & purification, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Terminology as TopicGenetics
Phylogeny18485653Rhodococcus cercidiphylli sp. nov., a new endophytic actinobacterium isolated from a Cercidiphyllum japonicum leaf.Li J, Zhao GZ, Chen HH, Qin S, Xu LH, Jiang CL, Li WJSyst Appl Microbiol10.1016/j.syapm.2008.03.0042008Bacterial Typing Techniques, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Magnoliopsida/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Leaves/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/*isolation & purification/metabolism, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny27902266Rhodococcus sovatensis sp. nov., an actinomycete isolated from the hypersaline and heliothermal Lake Ursu.Tancsics A, Mathe I, Benedek T, Toth EM, Atasayar E, Sproer C, Marialigeti K, Felfoldi T, Kriszt BInt J Syst Evol Microbiol10.1099/ijsem.0.0015142017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Mycolic Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/isolation & purification, Romania, *Salinity, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8991Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20669)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20669
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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
37045Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16652
59099Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51073)https://www.ccug.se/strain?id=51073
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
80138Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92423.1StrainInfo: A central database for resolving microbial strain identifiers
119291Curators of the CIPCollection of Institut Pasteur (CIP 104713)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104713