Strain identifier

BacDive ID: 10893

Type strain: Yes

Species: Rhodococcus rhodnii

Strain Designation: B/O, N 445, A-0203, N445

Strain history: CIP <- 1994, JCM <- KCC: strain A-0203 <- M. Goodfellow: strain N445 <- P. Hill: strain B/O, Nocardia rhodnii

NCBI tax ID(s): 1219023 (strain), 38312 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.1 (current version)

General

@ref: 10962

BacDive-ID: 10893

DSM-Number: 43336

keywords: genome sequence, 16S sequence, obligate aerobe, spore-forming, Gram-positive

description: Rhodococcus rhodnii B/O is an obligate aerobe, spore-forming, Gram-positive prokaryote that was isolated from reduviid bug.

NCBI tax id

NCBI tax idMatching level
1219023strain
38312species

strain history

@refhistory
10962<- M. Goodfellow, N 445 <- P. Hill, B/O (Nocardia rhodnii)
67770KCC A-0203 <-- M. Goodfellow N445 <-- P. Hill B/O.
122220CIP <- 1994, JCM <- KCC: strain A-0203 <- M. Goodfellow: strain N445 <- P. Hill: strain B/O, Nocardia rhodnii

doi: 10.13145/bacdive10893.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus rhodnii
  • full scientific name: Rhodococcus rhodnii Goodfellow and Alderson 1979 (Approved Lists 1980)

@ref: 10962

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus rhodnii

full scientific name: Rhodococcus rhodnii Goodfellow and Alderson 1979 emend. Nouioui et al. 2018

strain designation: B/O, N 445, A-0203, N445

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
122220positiverod-shapedno
69480no92.5
69480positive90.541

colony morphology

@refincubation periodmedium used
1956710-14 daysISP 2
1956710-14 daysISP 3
1956710-14 daysISP 4
1956710-14 daysISP 5
1956710-14 daysISP 6
1956710-14 daysISP 7
122220

multicellular morphology

@refforms multicellular complexmedium name
19567noISP 2
19567noISP 3
19567noISP 4
19567noISP 5
19567noISP 6
19567noISP 7

multimedia

  • @ref: 10962
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43336.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10962GYM 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
19567ISP 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
19567ISP 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:
19567ISP 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
19567ISP 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
19567ISP 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
19567ISP 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
41037MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122220CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
19567positiveoptimum28
10962positivegrowth28
41037positivegrowth30
67770positivegrowth28
122220positivegrowth25-37
122220nogrowth10
122220nogrowth41
122220nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
122220obligate aerobe
69480aerobe90.261

spore formation

@refspore descriptiontype of sporespore formationconfidence
19567Formation of spores, spore surface smooth, fragmentationsporeyes
122220no
69481no94

halophily

@refsaltgrowthtested relationconcentration
19567NaClpositivemaximum5 %
122220NaClpositivegrowth0-8 %
122220NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1956717234glucose-
1956722599arabinose-
1956717992sucrose-
1956718222xylose-
1956717268myo-inositol-
1956729864mannitol-
1956728757fructose-
1956726546rhamnose-
1956716634raffinose-
1956762968cellulose-
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-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
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-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
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-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
12222016947citrate-carbon source
1222204853esculin-hydrolysis
122220606565hippurate-hydrolysis
12222017632nitrate+reduction
12222016301nitrite-reduction
12222017632nitrate-respiration

antibiotic resistance

  • @ref: 122220
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12222035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12222015688acetoin-
12222017234glucose-

enzymes

@refvalueactivityec
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
122220oxidase+
122220beta-galactosidase-3.2.1.23
122220alcohol dehydrogenase-1.1.1.1
122220gelatinase-
122220amylase+
122220DNase-
122220caseinase-3.4.21.50
122220catalase+1.11.1.6
122220tween esterase-
122220gamma-glutamyltransferase-2.3.2.2
122220lecithinase-
122220lipase-
122220lysine decarboxylase-4.1.1.18
122220ornithine decarboxylase-4.1.1.17
122220phenylalanine ammonia-lyase-4.3.1.24
122220tryptophan deaminase-
122220urease+3.5.1.5
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
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

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19567++++++--++---------
122220-+++++---+----------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19567-+++--+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122220----+/-+/-----+/-+/-+/-+/---------------------------+/----+/-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122220++------------------------+-+----+--+------------+----------++-------------+---++-------+-------++-

Isolation, sampling and environmental information

isolation

@refsample typehost species
10962reduviid bug
67770Reduviid bug (Rhodnius prolixus)Rhodnius prolixus
122220Reduviid bug, Rhodnius prolixus

isolation source categories

  • Cat1: #Host
  • Cat2: #Arthropoda
  • Cat3: #Insecta

taxonmaps

  • @ref: 69479
  • File name: preview.99_4925.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_14;97_1541;98_3688;99_4925&stattab=map
  • Last taxonomy: Rhodococcus rhodnii subclade
  • 16S sequence: X80621
  • Sequence Identity:
  • Total samples: 381
  • soil counts: 172
  • aquatic counts: 89
  • animal counts: 101
  • plant counts: 19

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
109621Risk group (German classification)
195671Risk group (German classification)
1222201Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218R.rhodnii 16S rRNA gene (ATCC 35071T)X819351369nuccore38312
20218Rhodococcus rhodnii strain DSM 43336 16S ribosomal RNA gene, partial sequenceKF4103521360nuccore38312
20218Rhodococcus rhodnii 16S rRNA gene, strain DSM43336TX806211476nuccore38312

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus rhodnii NBRC 1006041219023.3wgspatric1219023
66792Rhodococcus rhodnii strain ATCC 3507138312.5wgspatric38312
67770Rhodococcus rhodnii NBRC 100604GCA_001894925contigncbi1219023
67770Rhodococcus rhodnii NRRL B-16535GCA_000720375contigncbi38312
67770Rhodococcus rhodnii ATCC 35071GCA_008011915scaffoldncbi38312

GC content

@refGC-contentmethod
6777069.7genome sequence analysis
6777070.2high performance liquid chromatography (HPLC)
6777072.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno94no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.541no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.188yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes58.335yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.261no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno92.5no

External links

@ref: 10962

culture collection no.: DSM 43336, ATCC 35071, KCC A-0203, NCIB 11279, JCM 3203, BCRC 13390, CCUG 23604, CECT 5750, CGMCC 4.1816, CIP 104181, IFM 0149, IMSNU 21249, KCTC 9805, LMG 5363, NBRC 100604, NCIMB 11279, NRRL B-16535, PCM 2157, RIA 1613, VKM Ac-1187

straininfo link

  • @ref: 80148
  • straininfo: 13835

literature

  • topic: Phylogeny
  • Pubmed-ID: 8946691
  • title: A chemotaxonomic study of the lipoglycans of Rhodococcus rhodnii N445 (NCIMB 11279).
  • authors: Flaherty C, Minnikin DE, Sutcliffe IC
  • journal: Zentralbl Bakteriol
  • DOI: 10.1016/s0934-8840(96)80017-x
  • year: 1996
  • mesh: Lipopolysaccharides/*chemistry/*classification/isolation & purification, Rhodococcus/isolation & purification/*metabolism
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10962Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43336)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43336
19567Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43336.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
41037Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16061
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
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
80148Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13835.1StrainInfo: A central database for resolving microbial strain identifiers
122220Curators of the CIPCollection of Institut Pasteur (CIP 104181)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104181