Strain identifier

BacDive ID: 10908

Type strain: Yes

Species: Rhodococcus rhodochrous

Strain Designation: 372, KMRh

Strain history: CIP <- 1995, DSM <- NCTC, Mycobacterium rhodochrous <- R.E. Gordon: strain 372 <- R.S. Breed: strain KMRh, Rhodococcus rhodochrous <- Kràl Collection <- W. Migula <- Zopf

NCBI tax ID(s): 1219024 (strain), 1829 (species)

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General

@ref: 10897

BacDive-ID: 10908

DSM-Number: 43241

keywords: genome sequence, 16S sequence, aerobe, Gram-positive, oval-shaped, human pathogen

description: Rhodococcus rhodochrous 372 is an aerobe, Gram-positive, oval-shaped human pathogen.

NCBI tax id

NCBI tax idMatching level
1829species
1219024strain

strain history

@refhistory
10897<- NCTC (Mycobacterium rhodochrous) <- R.E. Gordon, 372 <- R.S. Breed, KMRh (Rhodococcus rhodochrous) <- Kral Collection <- W. Migula
67770KCC A-0202 <-- M. Goodfellow N54 <-- IMRU 732 <-- R. S. Breed KMRh <-- Král Collection <-- M. Migula.
122225CIP <- 1995, DSM <- NCTC, Mycobacterium rhodochrous <- R.E. Gordon: strain 372 <- R.S. Breed: strain KMRh, Rhodococcus rhodochrous <- Kràl Collection <- W. Migula <- Zopf

doi: 10.13145/bacdive10908.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus rhodochrous
  • full scientific name: Rhodococcus rhodochrous (Zopf 1891) Tsukamura 1974 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Staphylococcus rhodochrous
    20215Rhodococcus roseus

@ref: 10897

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus rhodochrous

full scientific name: Rhodococcus rhodochrous (Zopf 1891) Tsukamura 1974 emend. Nouioui et al. 2018

strain designation: 372, KMRh

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
122225positiveoval-shapedno
69480no92.5

colony morphology

@refcolony colorincubation periodmedium used
19560Orange red10-14 daysISP 2
19560Rose10-14 daysISP 3
19560Rose10-14 daysISP 4
19560Beige10-14 daysISP 5
19560Beige10-14 daysISP 6
19560Rose10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19560noISP 2
19560noISP 3
19560noISP 4
19560noISP 5
19560noISP 6
19560noISP 7

multimedia

  • @ref: 10897
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43241.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10897TRYPTICASE 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
10897GYM 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
19560ISP 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
19560ISP 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:
19560ISP 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
19560ISP 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
19560ISP 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
19560ISP 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
41148MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
122225CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperature
19560positiveoptimum30
10897positivegrowth28
41148positivegrowth30
57548positivegrowth20-30
67770positivegrowth28
122225positivegrowth25-45
122225nogrowth10

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57548aerobe
122225obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122225NaClpositivegrowth0-8 %
122225NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1956017234glucose+
1956022599arabinose-
1956017992sucrose-
1956018222xylose-
1956017268myo-inositol-
1956029864mannitol+
1956028757fructose+
1956026546rhamnose-
1956016634raffinose-
1956062968cellulose-
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836917306maltose-assimilation
6836916899D-mannitol+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
1222254853esculin-hydrolysis
12222517632nitrate+reduction
12222516301nitrite-reduction
12222517632nitrate-respiration
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12222535581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
6836815688acetoin-
6836835581indole-
12222515688acetoin-
12222517234glucose-

enzymes

@refvalueactivityec
68379catalase+1.11.1.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
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
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
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
122225oxidase-
122225beta-galactosidase-3.2.1.23
122225alcohol dehydrogenase-1.1.1.1
122225gelatinase-
122225amylase-
122225DNase-
122225caseinase-3.4.21.50
122225catalase+1.11.1.6
122225tween esterase-
122225gamma-glutamyltransferase-2.3.2.2
122225lecithinase-
122225lysine decarboxylase-4.1.1.18
122225ornithine decarboxylase-4.1.1.17
122225phenylalanine ammonia-lyase+4.3.1.24
122225tryptophan deaminase-
122225urease-3.5.1.5
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    57548C14:02.314
    57548C15:00.715
    57548C16:036.216
    57548C17:01.117
    57548C18:0218
    57548C19:00.719
    57548C20:01.320
    57548C16:0 10-methyl4.516.433
    57548C16:1 ω7c10.915.819
    57548C16:1 ω7c/C15:0 ISO 2OH14.215.85
    57548C16:1 ω9c0.415.774
    57548C17:0 10-methyl0.417.41
    57548C18:1 ω9c10.817.769
    57548C18:2 ω6,9c/C18:0 ANTE4.217.724
    57548TBSA 10Me18:010.218.392
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
57548+-----+-+-----------+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
57548--++++----++---++---
10897-+/--+-+----------+---
122225-+++++++++++----+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19560-----------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
10897+----+--++/-+/-++/--+/--++++/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122225++----------------+-------+------+--+-----------++------------+++-++-------+---++---------+------++

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_4519.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_14;97_14;98_16;99_4519&stattab=map
  • Last taxonomy: Rhodococcus
  • 16S sequence: X81936
  • Sequence Identity:
  • Total samples: 3510
  • soil counts: 1489
  • aquatic counts: 660
  • animal counts: 1166
  • plant counts: 195

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
10897yes, in single cases1Risk group (German classification)
195601Risk group (German classification)
1222251Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodococcus erythropolis strain ATCC 13808 16S ribosomal RNA gene, partial sequenceAY281106971nuccore1833
20218Rhodococcus rhodochrous strain ATCC 13808 16S ribosomal RNA gene, partial sequenceGQ871830609nuccore1829
20218Rhodococcus rhodochrous strain DSM 43241 16S ribosomal RNA gene, partial sequenceFJ4683421444nuccore1829
20218Rhodococcus rhodochrous strain DSM 43241 16S ribosomal RNA gene, partial sequenceKF4103661375nuccore1829
20218R.rhodochrous (DSM 43241) 16S rRNA geneX792881474nuccore1829
67770R.rhodochrous 16S rRNA gene (CIP 1759.88T)X819361320nuccore1829

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus rhodochrous NCTC10210GCA_900187265completencbi1829
66792Rhodococcus rhodochrous NBRC 160691219024.4wgspatric1219024
66792Rhodococcus rhodochrous strain DSM 432411829.21wgspatric1829
66792Rhodococcus rhodochrous strain NCTC102101829.30completepatric1829
66792Rhodococcus rhodochrous NBRC 160692630968521draftimg1219024
66792Rhodococcus rhodochrous NCTC 102102826464033completeimg1829
66792Rhodococcus rhodochrous DSM 432412744054617draftimg1829
67770Rhodococcus rhodochrous NBRC 16069GCA_001047055contigncbi1219024
67770Rhodococcus rhodochrous DSM 43241GCA_001646825scaffoldncbi1829

GC content

@refGC-contentmethod
6777069.5thermal denaturation, midpoint method (Tm)
6777062thermal denaturation, midpoint method (Tm)
6777068.2genome sequence analysis
6777068.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno87no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.892no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.969yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.485no
69480spore-formingspore-formingAbility to form endo- or exosporesno55.268no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.9no
69480flagellatedmotile2+Ability to perform flagellated movementno92.5no

External links

@ref: 10897

culture collection no.: DSM 43241, ATCC 13808, CIP 104376, IMET 7374, KCC A-0202, NCIB 11147, NCTC 10210, CCUG 47165, NRRL B-16536, JCM 3202, BCRC 16333, CECT 5749, CGMCC 1.2348, CGMCC 4.1815, HAMBI 1959, IAM 15167, IFM 0163, IFO 16069, KCTC 9086, LMG 5365, MTCC 265, NBRC 16069, NCIMB 11147, NRRL B-2149, VKM Ac-1227, VKM Ac-1338

straininfo link

  • @ref: 80162
  • straininfo: 4886

phages

  • @ref: 124042
  • name: Rhodococcus phage N18
  • strain number: DSM 43241
  • link: https://phagedive.dsmz.de/strain/733

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21642485Rhodococcus artemisiae sp. nov., an endophytic actinobacterium isolated from the pharmaceutical plant Artemisia annua L.Zhao GZ, Li J, Zhu WY, Tian SZ, Zhao LX, Yang LL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.031930-02011Artemisia annua/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology
Phylogeny26310241Rhodococcus lactis sp. nov., an actinobacterium isolated from sludge of a dairy waste treatment plant.Singh PK, Kumari A, Chawla N, Pinnaka AK, Korpole SInt J Syst Evol Microbiol10.1099/ijsem.0.0005652015Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, *Dairying, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
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
10897Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43241)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43241
19560Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43241.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
41148Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16277
57548Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47165)https://www.ccug.se/strain?id=47165
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
68369Automatically annotated from API 20NE
68379Automatically annotated from API Coryne
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
80162Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4886.1StrainInfo: A central database for resolving microbial strain identifiers
122225Curators of the CIPCollection of Institut Pasteur (CIP 104376)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104376
124042Dr. Johannes Wittmann, Dr. Clara Rolland, Dr. Lorenz Reimer, Joaquim Sardàhttps://phagedive.dsmz.de/PhageDive