Strain identifier

BacDive ID: 10836

Type strain: Yes

Species: Rhodococcus coprophilus

Strain Designation: N 744, A-0200, N744, 687

Strain history: CIP <- 1994, JCM <- KCC: strain A-0200 <- M. Goodfellow: strain N744 <- NCIB <- CUB: strain 687

NCBI tax ID(s): 1219011 (strain), 38310 (species)

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General

@ref: 10971

BacDive-ID: 10836

DSM-Number: 43347

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

description: Rhodococcus coprophilus N 744 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from lake mud.

NCBI tax id

NCBI tax idMatching level
38310species
1219011strain

strain history

@refhistory
10971<- M. Goodfellow, N 744 <- NCIB <- CUB
67770KCC A-0200 <-- M. Goodfellow N744 <-- NCIB 11211 <-- CUB 687.
118743CIP <- 1994, JCM <- KCC: strain A-0200 <- M. Goodfellow: strain N744 <- NCIB <- CUB: strain 687

doi: 10.13145/bacdive10836.20250331.9.3

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 coprophilus
  • full scientific name: Rhodococcus coprophilus Rowbotham and Cross 1979 (Approved Lists 1980)

@ref: 10971

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus coprophilus

full scientific name: Rhodococcus coprophilus Rowbotham and Cross 1979 emend. Nouioui et al. 2018

strain designation: N 744, A-0200, N744, 687

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
118743positiverod-shapedno
125438no91.5
125439positive98.9

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10971GYM 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
34042MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118743CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
18486positiveoptimum28
10971positivegrowth28
34042positivegrowth30
67770positivegrowth28
118743positivegrowth10-45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
118743obligate aerobe
125439obligate aerobe98.8

halophily

@refsaltgrowthtested relationconcentration
18486NaClpositivemaximum5 %
118743NaClpositivegrowth0-4 %
118743NaClnogrowth6 %
118743NaClnogrowth8 %
118743NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1848617234glucose+
1848622599arabinose+
1848617992sucrose+
1848618222xylose+
1848617268myo-inositol+
1848629864mannitol+
1848628757fructose+
1848626546rhamnose+
1848616634raffinose+
1848662968cellulose+
11874316947citrate-carbon source
1187434853esculin-hydrolysis
11874317234glucose-fermentation
118743606565hippurate-hydrolysis
11874317716lactose-fermentation
11874317632nitrate+reduction
11874316301nitrite-reduction
118743132112sodium thiosulfate-builds gas from
683714853esculin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-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
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837117716lactose+builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-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
6837117108D-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
11874335581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-testindole test
11874315688acetoin-
11874317234glucose-
6836815688acetoin-
6836835581indole-

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
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase-
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382esterase lipase (C 8)+
118743oxidase-
118743beta-galactosidase-3.2.1.23
118743alcohol dehydrogenase-1.1.1.1
118743amylase-
118743DNase-
118743catalase+1.11.1.6
118743gamma-glutamyltransferase-2.3.2.2
118743lecithinase-
118743lipase+
118743lysine decarboxylase-4.1.1.18
118743ornithine decarboxylase-4.1.1.17
118743phenylalanine ammonia-lyase+4.3.1.24
118743tryptophan deaminase-
118743urease-3.5.1.5
68382alpha-mannosidase-3.2.1.24
68382leucine arylamidase+3.4.11.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
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
18486--+-++---+----+----
118743+++++---------------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18486-----------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118743----------+++----------+/-----++/-++----------------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118743++---------------------------------------------------------------+++-----------------------------+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10971lake mud
67770Lake mudHawkworth Mere, West YorkshireUnited KingdomGBREurope
118743Environment, Lake mudHawkworth MereUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_838.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_14;97_579;98_666;99_838&stattab=map
  • Last taxonomy: Rhodococcus coprophilus subclade
  • 16S sequence: X80626
  • Sequence Identity:
  • Total samples: 2004
  • soil counts: 872
  • aquatic counts: 548
  • animal counts: 511
  • plant counts: 73

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
109711Risk group (German classification)
184861German classification
1187431Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218R.coprophilus 16S rRNA gene (ATCC 29080T)X819281321nuccore38310
20218Rhodococcus coprophilus strain DSM 43347 16S ribosomal RNA gene, partial sequenceKF4103481374nuccore38310
20218Rhodococcus coprophilus 16S rRNA gene, strain DSM43347TX806261481nuccore38310
20218Rhodococcus coprophilus strain JCM 3200 16S ribosomal RNA gene, partial sequenceU933401481nuccore38310

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus coprophilus NCTC10994GCA_900478115completencbi38310
66792Rhodococcus coprophilus NBRC 1006031219011.3wgspatric1219011
66792Rhodococcus coprophilus strain NCTC1099438310.3completepatric38310
66792Rhodococcus coprophilus NBRC 1006032903948744draftimg1219011
66792Rhodococcus coprophilus NCTC 109942808606534completeimg38310
67770Rhodococcus coprophilus NBRC 100603GCA_001895045contigncbi1219011

GC content

@refGC-contentmethod
6777060-64
6777069.3thermal denaturation, midpoint method (Tm)
6777066.9genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive98.9
125439BacteriaNetmotilityAbility to perform movementno89
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes60.5
125438gram-positivegram-positivePositive reaction to Gram-stainingyes89.753no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.921yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.304yes
125438spore-formingspore-formingAbility to form endo- or exosporesno58.64no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95yes
125438motile2+flagellatedAbility to perform flagellated movementno91.5no

External links

@ref: 10971

culture collection no.: DSM 43347, ATCC 29080, CUB 687, IMET 7375, JCM 3200, NCIB 11211, NCTC 10994, BCRC 13383, CBS 313.75, CCM 2723, CCUG 23572, CECT 5751, CGMCC 4.1813, CIP 104178, IFM 0143, IFM 0164, KCTC 9804, LMG 5357, NBRC 100603, NCIMB 11211, NRRL B-16537, PCM 2174, VKM Ac-571

straininfo link

  • @ref: 80096
  • straininfo: 92420

phages

  • @ref: 124042
  • name: Rhodococcus phage N36
  • strain number: DSM 43347
  • link: https://phagedive.dsmz.de/strain/736

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10971Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43347)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43347
18486Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43347.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
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
34042Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16058
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
80096Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92420.1StrainInfo: A central database for resolving microbial strain identifiers
118743Curators of the CIPCollection of Institut Pasteur (CIP 104178)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104178
124042Johannes Wittmann, Clara Rolland, Lorenz Reimer, Joaquim Sardàhttps://phagedive.dsmz.de/PhageDive
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