Strain identifier

BacDive ID: 23161

Type strain: Yes

Species: Rhodococcus cerastii

Strain Designation: C5, C5(2010)

Strain history: <- P. Kämpfer, Universität Giessen; C5 <- S.A. Wellner

NCBI tax ID(s): 908616 (species)

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General

@ref: 19257

BacDive-ID: 23161

DSM-Number: 45579

keywords: 16S sequence, aerobe, Gram-positive, rod-shaped

description: Rhodococcus cerastii C5 is an aerobe, Gram-positive, rod-shaped prokaryote that was isolated from leaf surface of Cerastium holosteoides.

NCBI tax id

  • NCBI tax id: 908616
  • Matching level: species

strain history

  • @ref: 19257
  • history: <- P. Kämpfer, Universität Giessen; C5 <- S.A. Wellner

doi: 10.13145/bacdive23161.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus cerastii
  • full scientific name: Rhodococcus cerastii Kämpfer et al. 2013

@ref: 19257

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus cerastii

full scientific name: Rhodococcus cerastii Kämpfer et al. 2013

strain designation: C5, C5(2010)

type strain: yes

Morphology

cell morphology

  • @ref: 30808
  • gram stain: positive
  • cell length: 2.5 µm
  • cell width: 0.9 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colormedium usedincubation period
69407Daffodil yellow (1007)suter with tyrosine
624152 days
69407Maize yellow (1006)ISP 2
69407Maize yellow (1006)ISP 5
69407Maize yellow (1006)ISP 7
69407Maize yellow (1006)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69407noAerial myceliumISP 2
69407noAerial myceliumISP 5
69407noAerial myceliumISP 7
69407noAerial myceliumsuter with tyrosine
69407noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
30808yes
69407noMelanin
69407nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
19257https://www.dsmz.de/microorganisms/photos/DSM_45579.jpgMedium 215 28°C© Leibniz-Institut DSMZ
69407DSM_45579_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69407DSM_45579_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

  • @ref: 19257
  • 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

@refgrowthtypetemperature
19257positivegrowth28
30808positivegrowth15-50
30808positiveoptimum30
62415positivegrowth30

culture pH

@refabilitytypepHPH range
30808positivegrowth6.5-10.5alkaliphile
30808positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30808aerobe
62415aerobe

spore formation

  • @ref: 30808
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30808NaClpositivegrowth01-06 %
30808NaClpositiveoptimum2.5 %
69407NaClpositivegrowth0-5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3080822599arabinose+carbon source
3080828260galactose+carbon source
3080825017leucine+carbon source
3080828053melibiose+carbon source
30808506227N-acetylglucosamine+carbon source
3080818401phenylacetate+carbon source
3080817148putrescine+carbon source
3080815361pyruvate+carbon source
3080833942ribose+carbon source
3080817814salicin+carbon source
3080830911sorbitol+carbon source
3080827082trehalose+carbon source
308084853esculin+hydrolysis
6940722599arabinose-growth
6940762968cellulose-growth
6940728757fructose-growth
6940717234glucose-growth
6940717268inositol-growth
6940737684mannose-growth
6940716634raffinose-growth
6940726546rhamnose-growth
6940717992sucrose-growth
6940718222xylose-growth
6837917632nitrate-reduction
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase-
68379urease+3.5.1.5
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
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382alpha-chymotrypsin-3.4.21.1
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69407-----++-+/-+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69407+/-+/-++/-+++/-+/--+/-+/-+++/-+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling date
19257leaf surface of Cerastium holosteoidesCerastium holosteoidesThuringia, Hainich-Dün regionGermanyDEUEurope
62415Leaf,Cerastium holosteoidesHainich-Dün (Thüringen)GermanyDEUEurope2008

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1120.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_181;97_197;98_220;99_1120&stattab=map
  • Last taxonomy: Rhodococcus
  • 16S sequence: FR714842
  • Sequence Identity:
  • Total samples: 3435
  • soil counts: 337
  • aquatic counts: 1392
  • animal counts: 1539
  • plant counts: 167

Safety information

risk assessment

  • @ref: 19257
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19257
  • description: Rhodococcus cerastii partial 16S rRNA gene, type strain C5T
  • accession: FR714842
  • length: 1337
  • database: nuccore
  • NCBI tax ID: 908616

External links

@ref: 19257

culture collection no.: DSM 45579, CCM 7906, LMG 26203, CCUG 60725

straininfo link

  • @ref: 87395
  • straininfo: 375955

literature

  • topic: Phylogeny
  • Pubmed-ID: 22685110
  • title: Rhodococcus cerastii sp. nov. and Rhodococcus trifolii sp. nov., two novel species isolated from leaf surfaces.
  • authors: Kampfer P, Wellner S, Lohse K, Lodders N, Martin K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.044958-0
  • year: 2012
  • mesh: Bacterial Typing Techniques, Caryophyllaceae/microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Germany, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Plant Leaves/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Trifolium/microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19257Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45579)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45579
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
30808Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2713928776041
62415Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60725)https://www.ccug.se/strain?id=60725
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69407Wink, J.https://cdn.dsmz.de/wink/DSM%2045579.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
87395Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID375955.1StrainInfo: A central database for resolving microbial strain identifiers