Strain identifier

BacDive ID: 3190

Type strain: Yes

Species: Corynebacterium freneyi

Strain Designation: 6695110

Strain history: CIP <- 2000, F. Renaud, ISPB, Lyon: strain 6695110

NCBI tax ID(s): 134034 (species)

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General

@ref: 11830

BacDive-ID: 3190

DSM-Number: 44506

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

description: Corynebacterium freneyi 6695110 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from pus of a toe.

NCBI tax id

  • NCBI tax id: 134034
  • Matching level: species

strain history

@refhistory
11830<- F. Renaud, ISPB, Lyon; 6695110
386472000, F. Renaud, ISPB, Lyon: strain 6695110
67770CCUG 45704 <-- P. Riegel ISPB 6695110.
119452CIP <- 2000, F. Renaud, ISPB, Lyon: strain 6695110

doi: 10.13145/bacdive3190.20230509.8.1

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 freneyi
  • full scientific name: Corynebacterium freneyi Renaud et al. 2001

@ref: 11830

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium freneyi

full scientific name: Corynebacterium freneyi Renaud et al. 2001 emend. Funke and Frodl 2008

strain designation: 6695110

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23184positiverod-shapedno
69480no93.269
69480positive100
119452positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium usedcolony sizecolony shape
20067Sand yellow (1002)10-14 daysISP 2
20067Sand yellow (1002)10-14 daysISP 3
20067Sand yellow (1002)10-14 daysISP 4
20067Sand yellow (1002)10-14 daysISP 5
20067Sand yellow (1002)10-14 daysISP 6
20067Sand yellow (1002)10-14 daysISP 7
23184white2 daysblood-enriched medium0.5-1.0 mmirregular
119452

multicellular morphology

@refforms multicellular complexmedium name
20067noISP 2
20067noISP 3
20067noISP 4
20067noISP 5
20067noISP 6
20067noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11830COLUMBIA 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
11830TRYPTICASE 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
20067ISP 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
20067ISP 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:
20067ISP 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
20067ISP 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
20067ISP 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
20067ISP 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
23184blood-enriched mediumyes
38647MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
119452CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
20067positiveoptimum37mesophilic
11830positivegrowth37mesophilic
23184positivegrowth20psychrophilic
38647positivegrowth37mesophilic
56889positivegrowth37mesophilic
67770positivegrowth37mesophilic
119452positivegrowth25-41
119452nogrowth10psychrophilic
119452nogrowth15psychrophilic
119452nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
56889aerobe
119452obligate aerobe

spore formation

@refspore formationconfidence
23184no
69480no99.982

halophily

@refsaltgrowthtested relationconcentration
119452NaClpositivegrowth2-10 %
119452NaClnogrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2318429991L-aspartate-carbon source
2318415971L-histidine-carbon source
2318417716lactose-carbon source
2318428087glycogen-fermentation
2318417716lactose-fermentation
2318429864mannitol-fermentation
2318418222xylose-fermentation
231844853esculin-hydrolysis
231845291gelatin-hydrolysis
2318416199urea-hydrolysis
2318417234glucose+builds acid from
2318417306maltose+builds acid from
2318433942ribose+builds acid from
2318417992sucrose+builds acid from
2318432528turanose+carbon source
2318430031succinate+carbon source
2318417234glucose+fermentation
2318417632nitrate+/-reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-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
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
1194524853esculin-hydrolysis
119452606565hippurate-hydrolysis
11945217632nitrate+reduction
11945216301nitrite-reduction
11945217632nitrate-respiration
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 119452
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11945215688acetoin+
11945217234glucose+

enzymes

@refvalueactivityec
231846-phospho-beta-galactosidase-3.2.1.85
23184alkaline phosphatase+3.1.3.1
23184alpha-glucosidase+3.2.1.20
23184beta-glucuronidase-3.2.1.31
23184catalase+1.11.1.6
23184N-acetyl-beta-glucosaminidase-3.2.1.52
23184pyrazinamidase+3.5.1.B15
23184pyrrolidonyl arylamidase-3.4.19.3
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
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
119452oxidase-
119452beta-galactosidase-3.2.1.23
119452alcohol dehydrogenase-1.1.1.1
119452gelatinase-
119452amylase+
119452DNase-
119452caseinase-3.4.21.50
119452catalase+1.11.1.6
119452tween esterase+
119452lecithinase-
119452lipase+
119452lysine decarboxylase-4.1.1.18
119452ornithine decarboxylase-4.1.1.17
119452phenylalanine ammonia-lyase-4.3.1.24
119452tryptophan deaminase-
119452urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
20067+--+--+----+-----+-
11830++-+--+----++--+-+--+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20067+++-+----++---+----
119452+++-+----++---+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119452----+----++++--------------+--++-------+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119452+--+---+-++------------------------+-------------+----------+--------------+---++-------+-+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11830pus of a toeLyonFranceFRAEurope
56889Human wound,toeLyon,E.Herriot HospitalFranceFRAEurope
67770Pus from a toeLyonFranceFRAEurope
119452Human, Toe pusLyonFranceFRAEurope1988

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Limb#Foot
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_3865.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1038;97_1212;98_1453;99_3865&stattab=map
  • Last taxonomy: Corynebacterium
  • 16S sequence: AJ292762
  • Sequence Identity:
  • Total samples: 3366
  • soil counts: 269
  • aquatic counts: 247
  • animal counts: 2814
  • plant counts: 36

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118302Risk group (German classification)
200672German classification
1194522Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium freneyi partial 16S rRNA gene, strain 20695110AJ2927621365ena134034
20218Corynebacterium freneyi 16S ribosomal RNA gene, partial sequenceAY438056418ena134034

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium freneyi DSM 44506GCA_017876455contigncbi134034
66792Corynebacterium freneyi strain DSM 44506134034.4wgspatric134034
66792Corynebacterium freneyi strain FDAARGOS 1426134034.5completepatric134034
66792Corynebacterium freneyi DSM 445062918343737draftimg134034

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno63no
motileno93.402yes
gram-positiveyes92.079yes
anaerobicno98.148yes
halophileyes53.054no
spore-formingno88.967no
glucose-utilyes88.248no
aerobicno51.56yes
flagellatedno96.767no
thermophileno90.939no
glucose-fermentno51.308yes

External links

@ref: 11830

culture collection no.: CCUG 45704, CIP 106767, JCM 45704, DSM 44506, JCM 12104

straininfo link

  • @ref: 72706
  • straininfo: 50662

literature

  • topic: Phylogeny
  • Pubmed-ID: 11594602
  • title: Corynebacterium freneyi sp. nov., alpha-glucosidase-positive strains related to Corynebacterium xerosis.
  • authors: Renaud FN, Aubel D, Riegel P, Meugnier H, Bollet C
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-5-1723
  • year: 2001
  • mesh: Anti-Bacterial Agents/pharmacology, Corynebacterium/chemistry/*classification/drug effects/*enzymology/genetics, Corynebacterium Infections/*microbiology, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, DNA, Ribosomal Spacer/genetics, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, alpha-Glucosidases/*metabolism
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11830Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44506)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44506
20067Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44506.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
23184F N Renaud, D Aubel, P Riegel, H Meugnier, C Bollet10.1099/00207713-51-5-1723Corynebacterium freneyi sp. nov., alpha-glucosidase-positive strains related to Corynebacterium xerosis.IJSEM 51: 1723-1728 200111594602
38647Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18934
56889Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45704)https://www.ccug.se/strain?id=45704
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/
68371Automatically annotated from API 50CH acid
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)
72706Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50662.1StrainInfo: A central database for resolving microbial strain identifiers
119452Curators of the CIPCollection of Institut Pasteur (CIP 106767)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106767