Strain identifier

BacDive ID: 131922

Type strain: No

Species: Rhodococcus sp.

Strain Designation: Leaf233

Strain history: <- J. A. Vorholt, Institute of Microbiology, ETH Zurich, Switzerland; Leaf233 <- D. B. Müller, E. Potthoff and M. Remus-Emsermann

NCBI tax ID(s): 194249 (species)

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General

@ref: 23714

BacDive-ID: 131922

DSM-Number: 102718

keywords: genome sequence, Bacteria, mesophilic, Gram-positive

description: Rhodococcus sp. Leaf233 is a mesophilic, Gram-positive bacterium that was isolated from leaf of Arabidopsis thaliana, wild-type genotype.

NCBI tax id

  • NCBI tax id: 194249
  • Matching level: species

strain history

  • @ref: 23714
  • history: <- J. A. Vorholt, Institute of Microbiology, ETH Zurich, Switzerland; Leaf233 <- D. B. Müller, E. Potthoff and M. Remus-Emsermann

doi: 10.13145/bacdive131922.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Rhodococcus
  • species: Rhodococcus sp.
  • full scientific name: Rhodococcus Zopf 1891 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Rhodococcoides
    20215Prescottella
    20215Prescottia

@ref: 23714

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus sp.

full scientific name: Rhodococcus sp.

strain designation: Leaf233

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
125438no93
12543891.234positive
12543992.2positive

multimedia

  • @ref: 23714
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_102718.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 23714
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

  • @ref: 23714
  • growth: positive
  • type: growth
  • temperature: 28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 97.9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase-3.2.1.23
68382alpha-chymotrypsin-3.4.21.1
68382alpha-galactosidase-3.2.1.22
68382valine arylamidase+
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382alpha-mannosidase-3.2.1.24
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
68369gelatinase-
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
23714--+/-+-+++/---+/-+/----+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
23714----+/-+/----+-+--+--+++

Isolation, sampling and environmental information

isolation

  • @ref: 23714
  • sample type: leaf of Arabidopsis thaliana, wild-type genotype
  • host species: Arabidopsis thaliana
  • geographic location: Hoengg (47.4090306N 8.470169444E)
  • country: Switzerland
  • origin.country: CHE
  • continent: Europe
  • latitude: 47.409
  • longitude: 8.4702

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus sp. Leaf233GCA_001426165contigncbi1736302
66792Rhodococcus sp. Leaf2331736302.3wgspatric1736302
66792Rhodococcus sp. Leaf2332643221954draftimg1736302

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.234no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.98no
125438spore-formingspore-formingAbility to form endo- or exosporesno59.121no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.978no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.5no
125438motile2+flagellatedAbility to perform flagellated movementno93no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno59.9
125439BacteriaNetmotilityAbility to perform movementno66.4
125439BacteriaNetgram_stainReaction to gram-stainingpositive92.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.9

External links

@ref: 23714

culture collection no.: DSM 102718

straininfo link

  • @ref: 90309
  • straininfo: 402568

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
23714Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102718Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102718)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
90309Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID402568.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG