Strain identifier

BacDive ID: 10572

Type strain: No

Species: Rhodococcus chubuensis

Strain Designation: E6324

Strain history: CIP <- 1994, JCM, Rhodococcus chubuensis <- M. Tsukamura: strain E6324

NCBI tax ID(s): 36823 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
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 8.1 (current version)

General

@ref: 11461

BacDive-ID: 10572

DSM-Number: 44019

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

description: Rhodococcus chubuensis E6324 is an obligate aerobe, mesophilic, Gram-positive prokaryote that was isolated from human sputum.

NCBI tax id

  • NCBI tax id: 36823
  • Matching level: species

strain history

@refhistory
11461<- ATCC <- M. Tsukamura, E 6324
67770M. Tsukamura E6324 (=61001).
123280CIP <- 1994, JCM, Rhodococcus chubuensis <- M. Tsukamura: strain E6324

doi: 10.13145/bacdive10572.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus chubuensis
  • full scientific name: Rhodococcus chubuensis Tsukamura 1983

@ref: 11461

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia sputi

full scientific name: Gordonia sputi (Tsukamura and Yano 1985) Stackebrandt et al. 1989 emend. Tsukamura 1991 emend. Riegel et al. 1994

strain designation: E6324

type strain: no

Morphology

cell morphology

  • @ref: 123280
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 123280

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11461TRYPTICASE 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
11461LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354)yeshttps://mediadive.dsmz.de/medium/354Name: LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354) Composition: Potato flour 18.6104 g/l L-Asparagin 2.23325 g/l KH2PO4 1.55087 g/l Mg-citrate 0.372208 g/l Malachite green 0.248139 g/l MgSO4 0.148883 g/l Glycerol Fresh egg mixture Distilled water
34521MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123280CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
11461positivegrowth37mesophilic
34521positivegrowth30mesophilic
67770positivegrowth28mesophilic
123280positivegrowth10-37
123280nogrowth41thermophilic
123280nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123280
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
123280NaClpositivegrowth0-8 %
123280NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
123280citrate-carbon source16947
123280esculin-hydrolysis4853
123280hippurate-hydrolysis606565
123280nitrate+reduction17632
123280nitrite-reduction16301
123280nitrate-respiration17632

antibiotic resistance

  • @ref: 123280
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123280
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12328015688acetoin-
12328017234glucose-

enzymes

@refvalueactivityec
123280oxidase-
123280beta-galactosidase-3.2.1.23
123280alcohol dehydrogenase-1.1.1.1
123280gelatinase-
123280amylase-
123280DNase-
123280caseinase-3.4.21.50
123280catalase+1.11.1.6
123280tween esterase-
123280gamma-glutamyltransferase-2.3.2.2
123280lecithinase-
123280lipase-
123280lysine decarboxylase-4.1.1.18
123280ornithine decarboxylase-4.1.1.17
123280phenylalanine ammonia-lyase+4.3.1.24
123280protease-
123280tryptophan deaminase-
123280urease+3.5.1.5
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
123280---+------+----++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123280+/----+/------+++/------------+/-+/-----+--------+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123280++-++--+------------------+----+-+-++----------------+---------++-------++++--------+---+--++---+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11461human sputum
67770Human sputa
123280Human, SputumJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_3430.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_2147;98_2632;99_3430&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: X80627
  • Sequence Identity:
  • Total samples: 5392
  • soil counts: 169
  • aquatic counts: 1283
  • animal counts: 3862
  • plant counts: 78

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
114612Risk group (German classification)
1232801Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gordonia sputi 16S rRNA gene, strain DSM44019TX806271484ena36823
67770G.sputi 16S rRNA gene (CIP 1781.88T)X819271320ena36823

External links

@ref: 11461

culture collection no.: DSM 44019, ATCC 33609, JCM 6047, CIP 104183, NCIMB 13125, NRRL B-16936

straininfo link

  • @ref: 79847
  • straininfo: 40586

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11461Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44019)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44019
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
34521Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16063
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
79847Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40586.1StrainInfo: A central database for resolving microbial strain identifiers
123280Curators of the CIPCollection of Institut Pasteur (CIP 104183)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104183