Strain identifier

BacDive ID: 10885

Type strain: No

Species: Rhodococcus fascians

Strain history: CIP <- 1994, JCM, Rhodococcus luteus <- VKM <- N. Agre: strain IMV 385 <- O.A. Nesterenko

NCBI tax ID(s): 1828 (species)

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General

@ref: 11236

BacDive-ID: 10885

DSM-Number: 43673

keywords: genome sequence, 16S sequence, obligate aerobe, mesophilic, Gram-positive, rod-shaped, plant pathogen

description: Rhodococcus fascians DSM 43673 is an obligate aerobe, mesophilic, Gram-positive plant pathogen that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1828
  • Matching level: species

strain history

@refhistory
11236<- N. Agre, IMV 385
67770VKM Ac-594 <-- IMV 385.
119288CIP <- 1994, JCM, Rhodococcus luteus <- VKM <- N. Agre: strain IMV 385 <- O.A. Nesterenko

doi: 10.13145/bacdive10885.20230509.8.1

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: 11236

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: no

Morphology

cell morphology

  • @ref: 119288
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11236GYM 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
35632MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119288CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
11236positivegrowth28mesophilic
35632positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119288
  • oxygen tolerance: obligate aerobe

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11928817632nitrate-reduction
11928816301nitrite-reduction

metabolite production

  • @ref: 119288
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119288oxidase-
119288catalase+1.11.1.6
119288urease+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
119288-+-+-++++-++---+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11236soil
67770Soil
119288Environment, SoilUkraineUKREurope

isolation source categories

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

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: X79187
  • 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
11236yes1Risk group (German classification)
1192881Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218R.luteus (DSM 43673) 16S rRNA geneX791871467ena1828
20218R.fascians 16S rRNA gene (ATCC 35014T)X819321316ena1828

Genome sequences

  • @ref: 66792
  • description: Rhodococcus luteus DSM 43673
  • accession: 2926799693
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1828

GC content

  • @ref: 67770
  • GC-content: 64.1
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 11236

culture collection no.: DSM 43673, ATCC 35014, AUCNM A-594, JCM 6162, VKM Ac-594, IMV 385, CIP 104187, IFO 15528, LMG 5360, NBRC 15528, NCIMB 11743, NRRL B-16939

straininfo link

  • @ref: 80140
  • straininfo: 4880

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11236Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43673)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43673
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
35632Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16068
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/
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
80140Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4880.1StrainInfo: A central database for resolving microbial strain identifiers
119288Curators of the CIPCollection of Institut Pasteur (CIP 104187)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104187