Strain identifier

BacDive ID: 3181

Type strain: Yes

Species: Corynebacterium durum

Strain history: CIP <- 1998, CCUG <- P. Riegel, Louis Pasteur Univ., Strasbourg, France

NCBI tax ID(s): 61592 (species)

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General

@ref: 16295

BacDive-ID: 3181

DSM-Number: 45333

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

description: Corynebacterium durum IFO 16161 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from human sputum.

NCBI tax id

  • NCBI tax id: 61592
  • Matching level: species

strain history

@refhistory
16295<- CCUG; CCUG 37331 <- P. Riegel, Univ. Loius Pasteur, Strasbourg, France
67770CIP 105490 <-- CCUG 37331 <-- P. Riegel IBS G15036.
118983CIP <- 1998, CCUG <- P. Riegel, Louis Pasteur Univ., Strasbourg, France

doi: 10.13145/bacdive3181.20230509.8.1

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 durum
  • full scientific name: Corynebacterium durum Riegel et al. 1997

@ref: 16295

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium durum

full scientific name: Corynebacterium durum Riegel et al. 1997

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
23179positiverod-shapedno
118983positiverod-shapedno

colony morphology

  • @ref: 23179
  • colony size: 0.5-1.0 mm
  • colony color: beige
  • incubation period: 3 days

multimedia

  • @ref: 16295
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45333.jpg
  • caption: Medium 535 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16295TRYPTICASE 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
16295TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a)yeshttps://mediadive.dsmz.de/medium/535aName: TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) Composition: None 50.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
34040MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
118983CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
16295positivegrowth37mesophilic
23179positivegrowth37mesophilic
34040positivegrowth37mesophilic
53611positivegrowth37mesophilic
67770positivegrowth37mesophilic
118983positivegrowth25-41
118983nogrowth10psychrophilic
118983nogrowth15psychrophilic
118983nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23179aerobe
53611aerobe
118983facultative anaerobe

spore formation

  • @ref: 23179
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
118983NaClpositivegrowth0-4 %
118983NaClnogrowth6 %
118983NaClnogrowth8 %
118983NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2317928087glycogen-builds acid from
2317917716lactose-builds acid from
2317933942ribose-builds acid from
2317927082trehalose-builds acid from
2317918222xylose-builds acid from
231795291gelatin-degradation
2317918186tyrosine-degradation
2317928757fructose+builds acid from
2317928260galactose+builds acid from
2317917234glucose+builds acid from
2317917306maltose+builds acid from
2317929864mannitol+builds acid from
2317917992sucrose+builds acid from
2317916199urea+degradation
2317917632nitrate+reduction
231794853esculin+/-hydrolysis
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
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
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11898316947citrate-carbon source
1189834853esculin-hydrolysis
118983606565hippurate+hydrolysis
11898317632nitrate+reduction
11898316301nitrite-reduction
11898317632nitrate+respiration
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 118983
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118983
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11898315688acetoin+
11898317234glucose+

enzymes

@refvalueactivityec
231796-phospho-beta-galactosidase-3.2.1.85
23179alkaline phosphatase-3.1.3.1
23179alpha-glucosidase-3.2.1.20
23179beta-glucuronidase-3.2.1.31
23179N-acetyl-beta-glucosaminidase-3.2.1.52
23179pyrazinamidase+3.5.1.B15
23179pyrrolidonyl 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
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)-
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
118983oxidase-
118983beta-galactosidase+3.2.1.23
118983alcohol dehydrogenase-1.1.1.1
118983gelatinase-
118983amylase+
118983DNase-
118983caseinase-3.4.21.50
118983catalase+1.11.1.6
118983tween esterase-
118983gamma-glutamyltransferase+2.3.2.2
118983lecithinase-
118983lipase-
118983lysine decarboxylase-4.1.1.18
118983ornithine decarboxylase-4.1.1.17
118983phenylalanine ammonia-lyase-4.3.1.24
118983tryptophan deaminase-
118983urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYG
16295+-------+---+/------+/--

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
16295--------------------
118983--++-------+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118983----+/-----++++----+-----+/-+--+--+-----------------+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118983+++-+--+-++------+-+-------------+-----------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16295human sputumStrasbourgFranceFRAEurope
53611Human sputumStrasbourgFranceFRAEurope
67770Sputum of a patientNew CaledoniaFrench OverseasFRA
118983Human, SputumStrasbourgFranceFRAEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5795.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2775;97_3413;98_4310;99_5795&stattab=map
  • Last taxonomy: Corynebacterium durum subclade
  • 16S sequence: Z97069
  • Sequence Identity:
  • Total samples: 61569
  • soil counts: 865
  • aquatic counts: 1504
  • animal counts: 58839
  • plant counts: 361

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
16295yes, in single cases1Risk group (German classification)
1189832Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium durum 16S ribosomal RNA gene, partial sequenceAY438053419ena61592
23179Corynebacterium durum 16S ribosomal RNAZ970691423nuccore61592

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium durum strain DSM 4533361592.134wgspatric61592
66792Corynebacterium durum DSM 45333 Genome sequencing2623620526completeimg61592
66792Corynebacterium durum DSM 453332856490523draftimg61592
67770Corynebacterium durum DSM 45333GCA_013410305contigncbi61592

GC content

@refGC-contentmethod
2317955.0high performance liquid chromatography (HPLC)
6777055.4capillary zone electrophoresis (CZE)

External links

@ref: 16295

culture collection no.: IFO 16161, LMG 19045, CIP 105490, CCM 4727, DSM 45333, CCUG 37331, DSM 44351, JCM 11948, NBRC 16161

straininfo link

  • @ref: 72697
  • straininfo: 12971

literature

  • topic: Phylogeny
  • Pubmed-ID: 9336915
  • title: Corynebacterium durum sp. nov., from human clinical specimens.
  • authors: Riegel P, Heller R, Prevost G, Jehl F, Monteil H
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-47-4-1107
  • year: 1997
  • mesh: Base Composition, Cell Wall/physiology, Corynebacterium/chemistry/*classification/genetics/growth & development/physiology, Culture Media, DNA, Bacterial/analysis, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/analysis, Respiratory Tract Infections/microbiology
  • topic2: Cultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16295Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45333)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45333
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
23179Philippe Riegel, Remy Heller, Gilles Prevost, Francois Jehl, Henri Monteil10.1099/00207713-47-4-1107Corynebacterium durum sp. nov., from Human Clinical SpecimensIJSEM 47: 1107-1111 19979336915
34040Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17515
53611Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37331)https://www.ccug.se/strain?id=37331
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
72697Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12971.1StrainInfo: A central database for resolving microbial strain identifiers
118983Curators of the CIPCollection of Institut Pasteur (CIP 105490)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105490