Strain identifier

BacDive ID: 3245

Type strain: Yes

Species: Corynebacterium otitidis

Strain Designation: GF 234/92

Strain history: CIP <- 1994, G. Funke, Inst. Med. Mikrobiol., Zürich, Switzerland: strain GF 234/92

NCBI tax ID(s): 883169 (strain), 29321 (species)

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General

@ref: 3416

BacDive-ID: 3245

DSM-Number: 8821

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive

description: Corynebacterium otitidis GF 234/92 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from middle ear fluid from otitis media patient.

NCBI tax id

NCBI tax idMatching level
29321species
883169strain

strain history

@refhistory
3416<- G. Funke, GF 234/92
363961994, G. Funke, Inst. Med. Mikrobiol., Zürich, Switzerland: strain GF 234/92
67770LMG 19071 <-- CIP 104075 <-- G. Funke 234/92.
121468CIP <- 1994, G. Funke, Inst. Med. Mikrobiol., Zürich, Switzerland: strain GF 234/92

doi: 10.13145/bacdive3245.20230509.8.1

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 otitidis
  • full scientific name: Corynebacterium otitidis (Funke et al. 1994) Baek et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Turicella otitidis

@ref: 3416

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium otitidis

full scientific name: Corynebacterium otitidis (Funke et al. 1994) Baek et al. 2018

strain designation: GF 234/92

type strain: yes

Morphology

cell morphology

@refgram stainmotilitycell shape
23103positiveno
121468positivenorod-shaped

colony morphology

@refcolony colorincubation periodmedium usedcolony sizecolony shape
20211Ivory (1014)10-14 daysISP 2
20211Ivory (1014)10-14 daysISP 3
2021110-14 daysISP 4
2021110-14 daysISP 5
2021110-14 daysISP 6
2021110-14 daysISP 7
23103creamy2 dayssheep blood agar1.0-2.0 mmcircular
509333 days
121468

multicellular morphology

@refforms multicellular complexmedium name
20211noISP 2
20211noISP 3
20211noISP 4
20211noISP 5
20211noISP 6
20211noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3416BHI/1 MEDIUM (DSMZ Medium 216)yeshttps://mediadive.dsmz.de/medium/216Name: BHI/1 MEDIUM (DSMZ Medium 216) Composition: Brain heart infusion 37.0 g/l Yeast extract 2.0 g/l Distilled water
20211ISP 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
20211ISP 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:
20211ISP 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
20211ISP 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
20211ISP 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
20211ISP 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
23103Columbia agar base (Becton Dickinson, Cockeysville, Md.)yessupplemented with 5% sheep blood
23103sheep blood agaryes
36396MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
3416COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
3416TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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 water
121468CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
20211positiveoptimum37mesophilic
3416positivegrowth37mesophilic
36396positivegrowth37mesophilic
50933positivegrowth37mesophilic
67770positivegrowth37mesophilic
121468positivegrowth37mesophilic
121468nogrowth10psychrophilic
121468nogrowth15psychrophilic
121468nogrowth30mesophilic
121468nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
50933microaerophile
121468obligate aerobe

spore formation

  • @ref: 23103
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
20211NaClpositivemaximum7.5 %
23103NaClpositivegrowth6.5 %
121468NaClnogrowth0 %
121468NaClnogrowth2 %
121468NaClnogrowth4 %
121468NaClnogrowth6 %
121468NaClnogrowth8 %

murein

  • @ref: 3416
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2021117234glucose-
2021122599arabinose-
2021117992sucrose-
2021118222xylose-
2021117268myo-inositol-
2021129864mannitol-
2021128757fructose-
2021126546rhamnose-
2021116634raffinose-
2021162968cellulose-
2310317634D-glucose-builds acid from
231034853esculin-hydrolysis
2310316199urea-hydrolysis
2310317632nitrate-reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12146816947citrate-carbon source
1214684853esculin-hydrolysis
121468606565hippurate+hydrolysis
12146817632nitrate-reduction
12146816301nitrite-reduction
12146817632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation
6838129016arginine-hydrolysis
6838116988D-ribose-builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose-builds acid from
6838127082trehalose-builds acid from
6838116634raffinose-builds acid from
6838117992sucrose-builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin-builds acid from
68381606565hippurate+hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose-builds acid from
6838128053melibiose-builds acid from
683816731melezitose-builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose-builds acid from
6838116199urea+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2310335581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12146835581indoleno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6838115688acetoin-
6836815688acetoin-
6836835581indole-
12146815688acetoin-
12146817234glucose-

enzymes

@refvalueactivityec
23103acid phosphatase+3.1.3.2
23103alkaline phosphatase+3.1.3.1
23103catalase+1.11.1.6
23103cytochrome oxidase-1.9.3.1
23103leucine arylamidase+3.4.11.1
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+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68381urease+3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase+
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase-3.2.1.21
68381arginine dihydrolase-3.5.3.6
68379catalase+1.11.1.6
68379gelatinase-
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
121468oxidase-
121468beta-galactosidase-3.2.1.23
121468alcohol dehydrogenase-1.1.1.1
121468gelatinase-
121468amylase-
121468DNase-
121468caseinase-3.4.21.50
121468catalase+1.11.1.6
121468tween esterase-
121468gamma-glutamyltransferase-2.3.2.2
121468lecithinase+/-
121468lipase-
121468lysine decarboxylase-4.1.1.18
121468ornithine decarboxylase-4.1.1.17
121468phenylalanine ammonia-lyase-4.3.1.24
121468protease-
121468tryptophan deaminase-
121468urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
20211---+-----+-------+-
3416---+----------------+
50933---+----------------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20211+++-+++--++--------
50933+-+-+-+---+---------
121468+++-+----++---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARA
20211-++++-+-------------

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
50933-----------------+---++--------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
3416middle ear fluid from otitis media patientZürichSwitzerlandCHEEurope47.36878.5392
50933Human otitis mediaZürichSwitzerlandCHEEurope
67770Middle ear fluid from a patient with otitis media treatedZurichSwitzerlandCHEEurope
121468Human, Middle ear effusionZurichSwitzerlandCHEEurope1992

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Infection#Patient
#Host Body-Site#Organ#Ear
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_6414.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_571;96_3039;97_3734;98_4736;99_6414&stattab=map
  • Last taxonomy: Corynebacterium otitidis subclade
  • 16S sequence: X73976
  • Sequence Identity:
  • Total samples: 12900
  • soil counts: 786
  • aquatic counts: 1368
  • animal counts: 10139
  • plant counts: 607

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
34162Risk group (German classification)
202112German classification
1214682Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: C.otitidis gene for 16S rRNA
  • accession: X73976
  • length: 1461
  • database: ena
  • NCBI tax ID: 29321

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium otitidis ATCC 51513883169.8wgspatric883169
66792Turicella otitidis ATCC 51513883169.3wgspatric883169
66792Corynebacterium otitidis ATCC 515132537561797draftimg883169
66792Corynebacterium otitidis DSM 8821 Genome sequencing2623620536completeimg29321
66792Corynebacterium otitidis ATCC 515132600255151draftimg883169
67770Corynebacterium otitidis ATCC 51513GCA_000296405scaffoldncbi883169
67770Corynebacterium otitidis ATCC 51513GCA_000297795scaffoldncbi883169

GC content

@refGC-contentmethod
341665thermal denaturation, midpoint method (Tm)
2310365.0

External links

@ref: 3416

culture collection no.: CCUG 32254, DSM 8821, ATCC 51513, JCM 12146, CCM 4568, CIP 104075, IFM 10650, LMG 19071, NBRC 106139

straininfo link

  • @ref: 72758
  • straininfo: 13111

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8186090Turicella otitidis gen. nov., sp. nov., a coryneform bacterium isolated from patients with otitis media.Funke G, Stubbs S, Altwegg M, Carlotti A, Collins MDInt J Syst Bacteriol10.1099/00207713-44-2-2701994Actinomycetales/*classification/genetics, Bacterial Typing Techniques, Base Sequence, Child, Preschool, DNA, Ribosomal/genetics, Humans, Infant, Molecular Sequence Data, Otitis Media/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K/analysisPathogenicity
Genetics23045487Draft genome sequence of Turicella otitidis ATCC 51513, isolated from middle ear fluid from a child with otitis media.Brinkrolf K, Schneider J, Knecht M, Ruckert C, Tauch AJ Bacteriol10.1128/JB.01412-122012Actinobacteria/*genetics/isolation & purification/metabolism/pathogenicity, Child, DNA, Bacterial/*chemistry/*genetics, Ear, Middle/microbiology, Exudates and Transudates/microbiology, *Genome, Bacterial, Humans, Metabolic Networks and Pathways/genetics, Molecular Sequence Data, Otitis Media/microbiology, *Sequence Analysis, DNA, Virulence, Virulence Factors/geneticsPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3416Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8821)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8821
20211Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM8821.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
23103Guido Funke,Simon Stubbs,Martin Altwegg,Arnaud Carlotti,Matthew D. Collins10.1099/00207713-44-2-270Turicella otitidis gen. nov., sp. nov., a Coryneform Bacterium Isolated from Patients with Otitis MediaIJSEM 44: 270-273 19948186090
36396Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15942
50933Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32254)https://www.ccug.se/strain?id=32254
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
68379Automatically annotated from API Coryne
68381Automatically annotated from API rID32STR
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
72758Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13111.1StrainInfo: A central database for resolving microbial strain identifiers
121468Curators of the CIPCollection of Institut Pasteur (CIP 104075)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104075