Strain identifier

BacDive ID: 23160

Type strain: Yes

Species: Rhodococcus trifolii

Strain Designation: T8

Strain history: <- P. Kämpfer, Universität Giessen; T8 <- S.A. Wellner

NCBI tax ID(s): 908250 (species)

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General

@ref: 19256

BacDive-ID: 23160

DSM-Number: 45580

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

description: Rhodococcus trifolii T8 is an aerobe, mesophilic prokaryote that builds an aerial mycelium and was isolated from leaf surface of Trifolium repens.

NCBI tax id

  • NCBI tax id: 908250
  • Matching level: species

strain history

  • @ref: 19256
  • history: <- P. Kämpfer, Universität Giessen; T8 <- S.A. Wellner

doi: 10.13145/bacdive23160.20230509.8.1

Name and taxonomic classification

LPSN

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

  • synonyms

    • @ref: 20215
    • synonym: Rhodococcoides trifolii

@ref: 19256

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus trifolii

full scientific name: Rhodococcus trifolii Kämpfer et al. 2013

strain designation: T8

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.1
69480100positive

colony morphology

@refcolony colormedium usedincubation period
69408Bright red orange (2008)ISP 5
624142 days
69408Red orange (2001)ISP 2
69408Red orange (2001), salmon orange (2012)suter with tyrosine
69408Salmon orange (2012)ISP 3
69408Salmon orange (2012)ISP 4
69408Salmon orange (2012)ISP 6
69408Salmon orange (2012), red orange (2001)ISP 7
69408Yellow orange (2000)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69408noAerial myceliumISP 2
69408noAerial myceliumISP 3
69408noAerial myceliumISP 4
69408noAerial myceliumISP 5
69408noAerial myceliumISP 6
69408yesAerial myceliumISP 7
69408noAerial myceliumsuter with tyrosine
69408noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69408noMelanin
69408nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69408DSM_45580_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69408DSM_45580_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

  • @ref: 19256
  • 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

@refgrowthtypetemperaturerange
19256positivegrowth28mesophilic
62414positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 62414
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.971

halophily

  • @ref: 69408
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6940822599arabinose+/-growth
6940862968cellulose-growth
6940828757fructose+growth
6940817234glucose+growth
6940817268inositol+growth
6940837684mannose+growth
6940816634raffinose-growth
6940826546rhamnose+growth
6940817992sucrose+/-growth
6940818222xylose-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
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382acid phosphatase+3.1.3.2
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69408---+----+/-+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69408++/-++++++/-+/-++/----++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling date
19256leaf surface of Trifolium repensTrifolium repensThuringia, Hainich-Dün regionGermanyDEUEurope
62414Leaf surface,Trifolium repensThüringen,Hainich-DünGermanyDEUEurope2008

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5123.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2217;97_2684;98_3331;99_5123&stattab=map
  • Last taxonomy: Rhodococcus
  • 16S sequence: FR714843
  • Sequence Identity:
  • Total samples: 9339
  • soil counts: 1910
  • aquatic counts: 1647
  • animal counts: 3413
  • plant counts: 2369

Safety information

risk assessment

  • @ref: 19256
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19256
  • description: Rhodococcus trifolii partial 16S rRNA gene, type strain T8T
  • accession: FR714843
  • length: 1364
  • database: ena
  • NCBI tax ID: 908250

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus trifolii CCM 7905GCA_014635345contigncbi908250
66792Rhodococcus trifolii strain CCM 7905908250.3wgspatric908250

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno85no
motileno90.604no
flagellatedno97.892no
gram-positiveyes88.66no
anaerobicno99.235no
halophileno91.372no
spore-formingno83.053no
thermophileno99.488yes
glucose-utilyes88.041yes
aerobicyes89.047yes
glucose-fermentno89.238yes

External links

@ref: 19256

culture collection no.: DSM 45580, CCM 7905, LMG 26204, CCUG 60724

straininfo link

  • @ref: 87394
  • straininfo: 375956

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/urltitle
19256Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45580)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45580
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
62414Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60724)https://www.ccug.se/strain?id=60724
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)
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69408Wink, J.https://cdn.dsmz.de/wink/DSM%2045580.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
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)
87394Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID375956.1StrainInfo: A central database for resolving microbial strain identifiers