Strain identifier

BacDive ID: 11024

Type strain: Yes

Species: Rhodococcus zopfii

Strain Designation: T-1

Strain history: CIP <- 1994, R. Ruimy, CNRS, Villefranche/Mer, France <- ATCC <- M.A. Stoecker: strain T-1 <- R.P. Herwig

NCBI tax ID(s): 1219030 (strain), 43772 (species)

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General

@ref: 11403

BacDive-ID: 11024

DSM-Number: 44108

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

description: Rhodococcus zopfii T-1 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from bioreactor.

NCBI tax id

NCBI tax idMatching level
43772species
1219030strain

strain history

@refhistory
11403<- J. T. Staley, T1
67770ATCC 51349 <-- M. A. Stoecker T1 <-- R. P. Herwig.
124038CIP <- 1994, R. Ruimy, CNRS, Villefranche/Mer, France <- ATCC <- M.A. Stoecker: strain T-1 <- R.P. Herwig

doi: 10.13145/bacdive11024.20250331.9.3

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 zopfii
  • full scientific name: Rhodococcus zopfii Stoecker et al. 1994

@ref: 11403

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus zopfii

full scientific name: Rhodococcus zopfii Stoecker et al. 1994 emend. Nouioui et al. 2018

strain designation: T-1

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
124038positiverod-shapedno
125438no92.5
125438positive91.466
125439no91.8
125439positive99.2

colony morphology

@refcolony colorincubation periodmedium used
19999Pastel orange (2003)10-14 daysISP 2
1999910-14 daysISP 3
1999910-14 daysISP 4
1999910-14 daysISP 5
1999910-14 daysISP 6
1999910-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19999noISP 2
19999noISP 3
19999noISP 4
19999noISP 5
19999noISP 6
19999noISP 7

multimedia

  • @ref: 11403
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44108.jpg
  • caption: Medium 215 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11403BHI 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
11403GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19999ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19999ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19999ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19999ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19999ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19999ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
41082MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
124038CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
19999positiveoptimum28
11403positivegrowth28
41082positivegrowth30
67770positivegrowth28
124038positivegrowth25-41
124038nogrowth10
124038nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
124038obligate aerobe
125439obligate aerobe99.2

spore formation

  • @ref: 19999
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
19999NaClpositivemaximum5 %
124038NaClpositivegrowth0-2 %
124038NaClnogrowth4 %
124038NaClnogrowth6 %
124038NaClnogrowth8 %
124038NaClnogrowth10 %

observation

  • @ref: 20216
  • observation: Degrades toluene and other benzene derivatives

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1999917234glucose+
1999922599arabinose+
1999917992sucrose+
1999918222xylose+
1999917268myo-inositol+
1999929864mannitol+
1999928757fructose+
1999926546rhamnose+
1999916634raffinose+
1999962968cellulose+
12403816947citrate-carbon source
1240384853esculin-hydrolysis
12403817234glucose-fermentation
124038606565hippurate-hydrolysis
12403817716lactose-fermentation
12403817632nitrate+reduction
12403816301nitrite-reduction
124038132112sodium thiosulfate-builds gas from
12403817632nitrate-respiration
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
12403835581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-testindole test
12403815688acetoin-
12403817234glucose-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-chymotrypsin-3.4.21.1
68382esterase lipase (C 8)+
124038oxidase-
124038beta-galactosidase-3.2.1.23
124038alcohol dehydrogenase-1.1.1.1
124038gelatinase-
124038amylase-
124038DNase-
124038caseinase-3.4.21.50
124038catalase+1.11.1.6
124038tween esterase-
124038gamma-glutamyltransferase-2.3.2.2
124038lecithinase-
124038lipase-
124038lysine decarboxylase-4.1.1.18
124038ornithine decarboxylase-4.1.1.17
124038phenylalanine ammonia-lyase+4.3.1.24
124038protease-
124038tryptophan deaminase-
124038urease+3.5.1.5
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68382lipase (C 14)-
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19999+-+-++++-+-----+---
124038-++------------+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19999+++-+-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
124038--+/--------++--+/-+/-+/-+/-+/--+/-+/---+----+/-+/-+/------+/------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
124038-+----------------+------------------------------------------+-++-++-------+-+-++--++---+-------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11403bioreactorUniversity Washington, Department of civil engeneeringUSAUSANorth America
67770Toluene-phenol bioreactor operated by the Department of Civil EngineeringUniversity of WashingtonUSAUSANorth America

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Bioreactor

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: X81934
  • 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
114031Risk group (German classification)
199991German classification
1240381Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodococcus zopfii 16S ribosomal RNA gene, partial sequenceAF1913431478nuccore43772
20218R.zopfii 16S rRNA gene (ATCC 51349T)X819341319nuccore43772
124043Rhodococcus zopfii strain DSM 44108 16S ribosomal RNA gene, partial sequence.KF4103501371nuccore43772

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus zopfii NBRC 100606 = JCM 9919GCA_001313705contigncbi1219030
66792Rhodococcus zopfii NBRC 100606 = JCM 99191219030.8wgspatric1219030
66792Rhodococcus zopfii NBRC 100606 = JCM 99191219030.9wgspatric1219030
66792Rhodococcus zopfii NBRC 100606, JCM 99192734481959draftimg1219030
66792Rhodococcus zopfii NBRC 1006062867071599draftimg1219030
67770Rhodococcus zopfii NBRC 100606 = JCM 9919GCA_001895025contigncbi1219030
66792Rhodococcus zopfii ATCC 51349GCA_022134735contigncbi43772

GC content

@refGC-contentmethod
1140370
6777070thermal denaturation, midpoint method (Tm)
6777068.2genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.2
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.2
125439BacteriaNetmotilityAbility to perform movementno91.8
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes69.9
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.466no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.526yes
125438spore-formingspore-formingAbility to form endo- or exosporesno63.513yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.251no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.5no
125438motile2+flagellatedAbility to perform flagellated movementno92.5no

External links

@ref: 11403

culture collection no.: DSM 44108, ATCC 51349, JCM 9919, CGMCC 4.1818, CIP 104275, KCTC 19218, KCTC 9812, MTCC 2572, NBRC 100606, NCIMB 13393, NRRL B-16942

straininfo link

  • @ref: 80278
  • straininfo: 42941

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16261859Rhodococcus phenolicus sp. nov., a novel bioprocessor isolated actinomycete with the ability to degrade chlorobenzene, dichlorobenzene and phenol as sole carbon sources.Rehfuss M, Urban JSyst Appl Microbiol10.1016/j.syapm.2005.05.0112005Bioreactors, 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 SpecificityMetabolism
Phylogeny35834390Rhodococcus yananensis sp. nov., a novel denitrification actinobacterium isolated from microbial fermentation bed material from a pig farm.Jiang Y, Zheng C, Yu T, Li J, Ai J, Li M, Liu X, Deng ZInt J Syst Evol Microbiol10.1099/ijsem.0.0054262022Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Denitrification, Farms, Fatty Acids/chemistry, Fermentation, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhodococcus, Sequence Analysis, DNA, SwineTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11403Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44108)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44108
19999Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44108.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
41082Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16165
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
80278Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42941.1StrainInfo: A central database for resolving microbial strain identifiers
124038Curators of the CIPCollection of Institut Pasteur (CIP 104275)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104275
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1