Strain identifier

BacDive ID: 11045

Type strain: Yes

Species: Rhodococcus kyotonensis

Strain Designation: DS472

Strain history: CIP <- 2007, JCM <- 2007, IAM <- A. Yokota, Tokyo Univ., Tokyo, Japan: strain DS472

NCBI tax ID(s): 398843 (species)

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General

@ref: 15471

BacDive-ID: 11045

DSM-Number: 45159

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

description: Rhodococcus kyotonensis DS472 is an obligate aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil.

NCBI tax id

  • NCBI tax id: 398843
  • Matching level: species

strain history

@refhistory
15471<- JCM/RIKEN <- IAM <- A. Yokota; DS472
67770IAM 15415 <-- A. Yokota DS472.
120521CIP <- 2007, JCM <- 2007, IAM <- A. Yokota, Tokyo Univ., Tokyo, Japan: strain DS472

doi: 10.13145/bacdive11045.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus kyotonensis
  • full scientific name: Rhodococcus kyotonensis Li et al. 2007

  • synonyms

    • @ref: 20215
    • synonym: Rhodococcoides kyotonense

@ref: 15471

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus kyotonensis

full scientific name: Rhodococcus kyotonensis Li et al. 2007

strain designation: DS472

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
31989positiveno
69480positive100
120521positivenorod-shaped

pigmentation

  • @ref: 31989
  • production: yes

multimedia

  • @ref: 15471
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45159.jpg
  • caption: Medium 215 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15471BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
15471TRYPTICASE 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
37827MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
120521CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
15471positivegrowth28mesophilic
31989positivegrowth10-37
31989positiveoptimum28.5mesophilic
37827positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31989positivegrowth6.0-8.0
31989positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 120521
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
31989no
69481no100
69480no99.236

halophily

@refsaltgrowthtested relationconcentration
31989NaClpositivegrowth0-9 %
31989NaClpositiveoptimum4.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3198918403L-arabitol+carbon source
3198928757fructose+carbon source
3198928260galactose+carbon source
3198924265gluconate+carbon source
3198917234glucose+carbon source
3198917754glycerol+carbon source
3198929864mannitol+carbon source
3198917268myo-inositol+carbon source
3198926546rhamnose+carbon source
3198933942ribose+carbon source
3198930911sorbitol+carbon source
3198917992sucrose+carbon source
3198917151xylitol+carbon source
319894853esculin+hydrolysis
12052117632nitrate-reduction
12052116301nitrite-reduction

metabolite production

  • @ref: 120521
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31989acid phosphatase+3.1.3.2
31989catalase+1.11.1.6
31989urease+3.5.1.5
120521oxidase-
120521catalase+1.11.1.6
120521urease-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
120521-+++-++++-++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15471soilKyoto cityJapanJPNAsia
67770SoilKyoto CityJapanJPNAsia
120521Environment, SoilKyotoJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
154711Risk group (German classification)
1205211Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15471
  • description: Rhodococcus kyotonensis gene for 16S rRNA, partial sequence
  • accession: AB269261
  • length: 1420
  • database: ena
  • NCBI tax ID: 398843

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus kyotonensis strain JCM 23211398843.7wgspatric398843
66792Rhodococcus kyotonensis JCM 232112675903021draftimg398843
67770Rhodococcus kyotonensis JCM 23211GCA_900188125scaffoldncbi398843

GC content

@refGC-contentmethod
1547164.5
6777064.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes85.284yes
anaerobicno99.109no
halophileno90.46no
spore-formingno82.059yes
glucose-utilyes88.365yes
aerobicyes90.9no
flagellatedno97.969yes
thermophileno99.44yes
motileno91.437yes
glucose-fermentno89.672no

External links

@ref: 15471

culture collection no.: DSM 45159, CCTCC AB 206088, CIP 109729, IAM 15415, JCM 23211

straininfo link

  • @ref: 80297
  • straininfo: 309554

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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/urltitleID_cross_referencepubmedjournal
15471Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45159)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45159
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
31989Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2824328776041
37827Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7505
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
80297Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309554.1StrainInfo: A central database for resolving microbial strain identifiers
120521Curators of the CIPCollection of Institut Pasteur (CIP 109729)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109729