Strain identifier

BacDive ID: 3183

Type strain: Yes

Species: Corynebacterium confusum

Strain history: CIP <- 1999, CCUG <- 1998, G. Funke, Dep. Med. Microbiol., Zürich, Switzerland: strain DMMZ 2439

NCBI tax ID(s): 71254 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11505

BacDive-ID: 3183

DSM-Number: 44384

keywords: 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped

description: Corynebacterium confusum JCM 12102 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from human plantar abscess of 36-year-old male.

NCBI tax id

  • NCBI tax id: 71254
  • Matching level: species

strain history

@refhistory
11505<- CCUG <- G. Funke, DMMZ
67770CCUG 38267 <-- G. Funke DMMZ 2439.
118728CIP <- 1999, CCUG <- 1998, G. Funke, Dep. Med. Microbiol., Zürich, Switzerland: strain DMMZ 2439

doi: 10.13145/bacdive3183.20230509.8.1

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 confusum
  • full scientific name: Corynebacterium confusum Funke et al. 1998

@ref: 11505

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium confusum

full scientific name: Corynebacterium confusum Funke et al. 1998

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
23181positiverod-shapedno
118728positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium usedcolony size
19657Beige10-14 daysISP 2
19657Beige10-14 daysISP 3
19657Beige10-14 daysISP 4
23181whitish2 days1.5 mm
118728

multicellular morphology

@refforms multicellular complexmedium name
19657noISP 2
19657noISP 3
19657noISP 4
19657noISP 5
19657noISP 6
19657noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11505TRYPTICASE 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
11505COLUMBIA 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
19657ISP 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
19657ISP 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:
19657ISP 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
38547MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
118728CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
19657positiveoptimum37mesophilic
11505positivegrowth37mesophilic
38547positivegrowth37mesophilic
67770positivegrowth37mesophilic
118728positivegrowth25-37mesophilic
118728nogrowth10psychrophilic
118728nogrowth15psychrophilic
118728nogrowth41thermophilic
118728nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23181facultative anaerobe
54153microaerophile
118728facultative anaerobe

spore formation

  • @ref: 23181
  • spore formation: no

halophily

  • @ref: 118728
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23181168082-dehydro-D-gluconate-builds acid from
2318115963ribitol-builds acid from
2318127613amygdalin-builds acid from
2318122599arabinose-builds acid from
2318122605arabinitol-builds acid from
2318118305arbutin-builds acid from
2318117057cellobiose-builds acid from
2318162318D-lyxose-builds acid from
2318116634raffinose-builds acid from
2318132528turanose-builds acid from
2318165327D-xylose-builds acid from
2318116813galactitol-builds acid from
2318117113erythritol-builds acid from
2318133984fucose-builds acid from
2318128260galactose-builds acid from
2318124265gluconate-builds acid from
2318117754glycerol-builds acid from
2318128087glycogen-builds acid from
2318117268myo-inositol-builds acid from
2318115443inulin-builds acid from
2318117266L-sorbose-builds acid from
2318117716lactose-builds acid from
2318117306maltose-builds acid from
2318129864mannitol-builds acid from
231816731melezitose-builds acid from
2318128053melibiose-builds acid from
23181320061methyl alpha-D-glucopyranoside-builds acid from
2318143943methyl alpha-D-mannoside-builds acid from
2318174863methyl beta-D-xylopyranoside-builds acid from
23181506227N-acetylglucosamine-builds acid from
2318126546rhamnose-builds acid from
2318117814salicin-builds acid from
2318130911sorbitol-builds acid from
2318117992sucrose-builds acid from
2318127082trehalose-builds acid from
2318117151xylitol-builds acid from
231814853esculin-hydrolysis
2318118186tyrosine-hydrolysis
2318116199urea-hydrolysis
23181174265-dehydro-D-gluconate+builds acid from
2318115824D-fructose+builds acid from
2318117634D-glucose+builds acid from
2318133942ribose+builds acid from
2318133954tagatose+builds acid from
2318117632nitrate+reduction
2318128066gentiobiose+/-builds acid from
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-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
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
1187284853esculin-hydrolysis
118728606565hippurate-hydrolysis
11872817632nitrate+reduction
11872816301nitrite-reduction
11872817632nitrate+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

  • @ref: 118728
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11872815688acetoin-
11872817234glucose-

enzymes

@refvalueactivityec
23181alkaline phosphatase+3.1.3.1
23181alpha-fucosidase-3.2.1.51
23181alpha-galactosidase-3.2.1.22
23181alpha-glucosidase-3.2.1.20
23181alpha-mannosidase-3.2.1.24
23181beta-galactosidase-3.2.1.23
23181beta-glucosidase-3.2.1.21
23181beta-glucuronidase-3.2.1.31
23181catalase+1.11.1.6
23181chymotrypsin-3.4.4.5
23181esterase (C 4)+
23181esterase lipase (C 8)+
23181leucine arylamidase+/-3.4.11.1
23181N-acetyl-beta-glucosaminidase-3.2.1.52
23181phosphoamidase+/-3.9.1.1
23181pyrazinamidase+3.5.1.B15
23181pyrrolidonyl arylamidase-3.4.19.3
23181trypsin-3.4.21.4
23181valine arylamidase-
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
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
118728oxidase-
118728beta-galactosidase-3.2.1.23
118728alcohol dehydrogenase-1.1.1.1
118728gelatinase-
118728amylase-
118728caseinase-3.4.21.50
118728catalase+1.11.1.6
118728tween esterase+
118728gamma-glutamyltransferase-2.3.2.2
118728lecithinase-
118728lipase-
118728lysine decarboxylase-4.1.1.18
118728ornithine decarboxylase-4.1.1.17
118728tryptophan deaminase-
118728urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19657---------+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19657-++-+----+---------
118728-++-+-----+---------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118728----+/-----+/-+/-+/-+/---------------+------------------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118728+++++----------+---+-----------------------------+---+------+--------------+--+++--------++-+++-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
11505human plantar abscess of 36-year-old maleZürichSwitzerlandCHEEurope
54153Human plantar abscess,36-year-old maleZürichSwitzerlandCHEEurope1997
67770Plantar abscess
118728Human, Plantar abscessSwitzerlandCHEEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human#Male
#Host Body-Site#Other#Abscess
#Host Body-Site#Limb#Foot

taxonmaps

  • @ref: 69479
  • File name: preview.99_5712.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2743;97_3374;98_4255;99_5712&stattab=map
  • Last taxonomy: Corynebacterium confusum subclade
  • 16S sequence: Y15886
  • Sequence Identity:
  • Total samples: 18390
  • soil counts: 1249
  • aquatic counts: 768
  • animal counts: 16131
  • plant counts: 242

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115052Risk group (German classification)
196572Risk group (German classification)
1187282Risk group (French classification)

Sequence information

16S sequences

  • @ref: 23181
  • description: Corynebacterium confusum 16S rRNA gene, strain DMMZ 2439
  • accession: Y15886
  • length: 1404
  • database: nuccore
  • NCBI tax ID: 71254

External links

@ref: 11505

culture collection no.: JCM 12102, DSM 44384, CCUG 38267, DMMZ 2439, CIP 105403, LMG 19073

straininfo link

  • @ref: 72699
  • straininfo: 13115

literature

  • topic: Phylogeny
  • Pubmed-ID: 9828429
  • title: Corynebacterium confusum sp. nov., isolated from human clinical specimens.
  • authors: Funke G, Osorio CR, Frei R, Riegel P, Collins MD
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-48-4-1291
  • year: 1998
  • mesh: Abscess/microbiology, Adult, Anti-Bacterial Agents/pharmacology, Bacteremia/microbiology, Corynebacterium/*classification/drug effects/*isolation & purification/physiology, Corynebacterium Infections/*microbiology, Foot Diseases/microbiology, Genes, rRNA, Humans, Male, Microbial Sensitivity Tests, Molecular Sequence Data, Osteomyelitis/microbiology, Phenotype, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Terminology as Topic
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11505Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44384)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44384
19657Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44384.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
23181GUIDO FUNKE, CARLOS R. OSORIO, RENO FREI, PHILIPPE RIEGEL, MATTHEW D. COLLINS10.1099/00207713-48-4-1291Corynebacterium confusum sp. nov., isolated from human clinical specimensIJSEM 48: 1291-1296 19989828429
38547Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17418
54153Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38267)https://www.ccug.se/strain?id=38267
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
72699Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13115.1StrainInfo: A central database for resolving microbial strain identifiers
118728Curators of the CIPCollection of Institut Pasteur (CIP 105403)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105403