Strain identifier

BacDive ID: 11042

Type strain: Yes

Species: Rhodococcus phenolicus

Strain Designation: G2P

Strain history: CIP <- 2006, DSMZ <- M. Rehfuss: strain G2P

NCBI tax ID(s): 1303680 (strain), 263849 (species)

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General

@ref: 12097

BacDive-ID: 11042

DSM-Number: 44812

keywords: genome sequence, 16S sequence, spore-forming, mesophilic

description: Rhodococcus phenolicus G2P is a spore-forming, mesophilic prokaryote that was isolated from biological wastewater processor.

NCBI tax id

NCBI tax idMatching level
263849species
1303680strain

strain history

@refhistory
12097<- M. Rehfuss; G2P <- J. Urban
67770DSM 44812 <-- M. Rehfuss G2P <-- J. Urban.
121795CIP <- 2006, DSMZ <- M. Rehfuss: strain G2P

doi: 10.13145/bacdive11042.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus phenolicus
  • full scientific name: Rhodococcus phenolicus Rehfuss and Urban 2006

@ref: 12097

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus phenolicus

full scientific name: Rhodococcus phenolicus Rehfuss and Urban 2006 emend. Nouioui et al. 2018

strain designation: G2P

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.117
6948099.999positive

multimedia

  • @ref: 12097
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44812.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12097TRYPTICASE 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
38383MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121795CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
12097positivegrowth28mesophilic
38383positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes91
69480no99.998

compound production

@refcompound
12097phenol
12097chlorobenzene
12097dichlorobenzenes

enzymes

@refvalueactivityec
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
121795-+++-+----+-----+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12097biological wastewater processorTexas, Johnson Space CenterUSAUSANorth America
67770Johnson Space Center graywater bioprocessorUSAUSANorth America
121795Environment, Johson Space Center graywater bioprocessorHouston, TexasUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Machines and devices
#Engineered#Waste#Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_5235.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_14;97_579;98_1052;99_5235&stattab=map
  • Last taxonomy: Rhodococcus
  • 16S sequence: AM933579
  • Sequence Identity:
  • Total samples: 900
  • soil counts: 259
  • aquatic counts: 349
  • animal counts: 272
  • plant counts: 20

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120971Risk group (German classification)
1217951Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodococcus phenolicus partial 16S rRNA gene, type strain DSM 44812TAM9335791511ena263849
20218Rhodococcus phenolicus strain DSM 44812 16S ribosomal RNA gene, partial sequenceKF4103541379ena263849
20218Rhodococcus phenolicus 16S ribosomal RNA gene, partial sequenceAY5332931395ena263849

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus phenolicus JCM 14914GCA_001313425contigncbi1303680
66792Rhodococcus phenolicus JCM 149141303680.3wgspatric1303680
66792Rhodococcus phenolicus strain DSM 44812263849.4wgspatric263849
66792Rhodococcus phenolicus DSM 448122744054614draftimg263849
66792Rhodococcus phenolicus JCM 149142675903364draftimg1303680
67770Rhodococcus phenolicus DSM 44812GCA_001646785scaffoldncbi263849

GC content

@refGC-contentmethod
1209766.7
6777066.7high performance liquid chromatography (HPLC)
6777068.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes91no
motileno91.389no
gram-positiveyes84.75no
anaerobicno98.047no
halophileno93.911no
spore-formingno90.865no
thermophileno99.644yes
glucose-utilyes84.716no
aerobicyes88.878no
flagellatedno98.452no
glucose-fermentno89.965no

External links

@ref: 12097

culture collection no.: DSM 44812, CIP 109148, JCM 14914, NRRL B-24323

straininfo link

  • @ref: 80294
  • straininfo: 291003

literature

  • topic: Phylogeny
  • Pubmed-ID: 16261859
  • title: Rhodococcus phenolicus sp. nov., a novel bioprocessor isolated actinomycete with the ability to degrade chlorobenzene, dichlorobenzene and phenol as sole carbon sources.
  • authors: Rehfuss M, Urban J
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2005.05.011
  • year: 2005
  • mesh: Bioreactors, Carbon/*metabolism, Chlorobenzenes/*metabolism, DNA, Bacterial/genetics, Molecular Sequence Data, Phenol/*metabolism, Phylogeny, Polymerase Chain Reaction, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/*metabolism, Sewage/*microbiology, Species Specificity
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12097Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44812)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44812
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
38383Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6857
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
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
80294Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID291003.1StrainInfo: A central database for resolving microbial strain identifiers
121795Curators of the CIPCollection of Institut Pasteur (CIP 109148)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109148