Strain identifier

BacDive ID: 3107

Type strain: Yes

Species: Corynebacterium mycetoides

Strain history: CIP <- 1955, A. Castellani, Lisbon, Micrococcus mycetoides

NCBI tax ID(s): 38302 (species)

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General

@ref: 8978

BacDive-ID: 3107

DSM-Number: 20632

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Corynebacterium mycetoides DSM 20632 is an aerobe, mesophilic bacterium that was isolated from tropicaloid ulcer.

NCBI tax id

  • NCBI tax id: 38302
  • Matching level: species

strain history

@refhistory
8978<- NCTC <- A. Castellani
399241955, A. Castellani, Lisbon, Micrococcus mycetoides
67770NCTC 9864 <-- A. Castellani.
121208CIP <- 1955, A. Castellani, Lisbon, Micrococcus mycetoides

doi: 10.13145/bacdive3107.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Corynebacteriaceae
  • genus: Corynebacterium
  • species: Corynebacterium mycetoides
  • full scientific name: Corynebacterium mycetoides (ex Castellani 1942) Collins 1983

@ref: 8978

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium mycetoides

full scientific name: Corynebacterium mycetoides (ex Castellani 1942) Collins 1983 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no96.719
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
18765Golden yellow10-14 daysISP 2
1876510-14 daysISP 4
18765Oyster white10-14 daysISP 5
1876510-14 daysISP 6
18765Ivory10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18765noISP 2
18765noISP 4
18765noISP 5
18765noISP 6
18765noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18765ISP 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
18765ISP 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
18765ISP 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
18765ISP 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
18765ISP 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
8978TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/92
39924MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121208CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18765positiveoptimum37mesophilic
8978positivegrowth37mesophilic
39924positivegrowth37mesophilic
48822positivegrowth30-42
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 48822
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

  • @ref: 18765
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 8978
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1876562968cellulose-
1876516634raffinose+/-
1876526546rhamnose+/-
1876528757fructose+
1876529864mannitol+/-
1876517268myo-inositol+/-
1876518222xylose+/-
1876517992sucrose+/-
1876522599arabinose+/-
1876517234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
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
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
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
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
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
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    48822C16:02016
    48822C17:08.317
    48822C18:06.818
    48822C16:1 ω9c3.215.774
    48822C17:1 ω8c5.516.792
    48822C18:1 ω9c56.117.769
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18765---+---------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18765+-+-+--+-+---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18765---------+-

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
8978tropicaloid ulcer
67770Tropicaloid ulcer
121208Human, Tropicaloid ulcer1942

isolation source categories

Cat1Cat2
#Infection#Inflammation
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_17581.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_944;97_1098;98_13295;99_17581&stattab=map
  • Last taxonomy: Corynebacterium mycetoides subclade
  • 16S sequence: X82066
  • Sequence Identity:
  • Total samples: 1319
  • soil counts: 20
  • aquatic counts: 128
  • animal counts: 1156
  • plant counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
187652Risk group (German classification)
89782Risk group (German classification)
1212082Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.mycetoides 16S ribosomal DNAX820661396ena38302
20218Corynebacterium mycetoides gene for 16S rRNA, partial sequenceD63355504ena38302
20218Corynebacterium mycetoides 16S rRNA gene, strain NCTC 9864X842411477ena38302

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium mycetoides DSM 20632GCA_900103625chromosomencbi38302
66792Corynebacterium mycetoides strain DSM 2063238302.4completepatric38302
66792Corynebacterium mycetoides DSM 206322634166344draftimg38302

GC content

@refGC-contentmethod
897859.0
6777065.3thermal denaturation, midpoint method (Tm)
6777059thermal denaturation, midpoint method (Tm)
6777068high performance liquid chromatography (HPLC)
6777066.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes94.966no
anaerobicno98.965no
halophileyes81.086no
spore-formingno94.164no
glucose-utilyes85.179yes
aerobicno53.419no
flagellatedno96.872no
motileno91.685no
thermophileno92.754yes
glucose-fermentno76.188yes

External links

@ref: 8978

culture collection no.: DSM 20632, ATCC 43995, NCTC 9864, CCUG 27538, JCM 9388, BCRC 14871, CIP 55.51, IFO 15289, IMSNU 21213, NBRC 15289

straininfo link

  • @ref: 72625
  • straininfo: 42165

literature

  • topic: Phylogeny
  • Pubmed-ID: 33974533
  • title: Corynebacterium lizhenjunii sp. nov., isolated from the respiratory tract of Marmota himalayana, and Corynebacterium qintianiae sp. nov., isolated from the lung tissue of Pseudois nayaur.
  • authors: Zhou J, Xu M, Guo W, Yang J, Pu J, Lai XH, Jin D, Lu S, Zhang S, Huang Y, Zhu W, Huang Y, Zheng H, Xu J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.004803
  • year: 2021
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, China, Corynebacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lung/*microbiology, Marmota/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Respiratory System/*microbiology, Sequence Analysis, DNA, Sheep/*microbiology, Vitamin K 2/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8978Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20632)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20632
18765Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20632.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
39924Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5127
48822Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27538)https://www.ccug.se/strain?id=27538
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
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
72625Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42165.1StrainInfo: A central database for resolving microbial strain identifiers
121208Curators of the CIPCollection of Institut Pasteur (CIP 55.51)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2055.51