Strain identifier

BacDive ID: 3182

Type strain: Yes

Species: Corynebacterium singulare

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

NCBI tax ID(s): 161899 (species)

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General

@ref: 11701

BacDive-ID: 3182

DSM-Number: 44357

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

description: Corynebacterium singulare DSM 44357 is a facultative anaerobe, mesophilic, Gram-positive human pathogen that was isolated from human semen.

NCBI tax id

  • NCBI tax id: 161899
  • Matching level: species

strain history

@refhistory
11701<- CCUG <- P.Riegel, Univ. Louis Pasteur
67770CCUG 37330 <-- P. Riegel IBS B52218.
122632CIP <- 1998, CCUG <- P. Riegel, Louis Pasteur Univ., Strasbourg, France

doi: 10.13145/bacdive3182.20230509.8.1

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

@ref: 11701

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium singulare

full scientific name: Corynebacterium singulare Riegel et al. 1997 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
23180positiverod-shapedno
122632positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium usedtype of hemolysiscolony sizecolony shape
20050Ivory (1014)10-14 daysISP 2
20050Ivory (1014)10-14 daysISP 3
20050Ivory (1014)10-14 daysISP 4
20050Ivory (1014)10-14 daysISP 5
20050Ivory (1014)10-14 daysISP 6
20050Ivory (1014)10-14 daysISP 7
23180grayish1 daysheep blood agargamma1-2 mmcircular

multicellular morphology

@refforms multicellular complexmedium name
20050noISP 2
20050noISP 3
20050noISP 4
20050noISP 5
20050noISP 6
20050noISP 7

multimedia

  • @ref: 11701
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44357.jpg
  • caption: Medium 535a 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11701TRYPTICASE 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
11701TRYPTICASE 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
20050ISP 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
20050ISP 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:
20050ISP 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
20050ISP 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
20050ISP 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
20050ISP 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
23180sheep blood agaryes
34670MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
122632CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122632CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperaturerange
20050positiveoptimum37mesophilic
11701positivegrowth37mesophilic
23180positivegrowth37mesophilic
34670positivegrowth37mesophilic
53610positivegrowth37mesophilic
67770positivegrowth37mesophilic
122632positivegrowth25-41
122632nogrowth10psychrophilic
122632nogrowth15psychrophilic
122632nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23180facultative anaerobe
53610aerobe
122632facultative anaerobe

spore formation

@refspore formation
20050no
23180no

halophily

  • @ref: 122632
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2318065327D-xylose-builds acid from
2318028087glycogen-builds acid from
2318017716lactose-builds acid from
2318029864mannitol-builds acid from
2318033942ribose-builds acid from
2318027082trehalose-builds acid from
231808391D-gluconate-carbon source
2318016988D-ribose-carbon source
23180506227N-acetylglucosamine-carbon source
231804853esculin-hydrolysis
231805291gelatin-hydrolysis
2318017632nitrate-reduction
2318017234glucose+builds acid from
2318017306maltose+builds acid from
2318017992sucrose+builds acid from
23180370543-hydroxybutyrate+carbon source
2318025646octanoate+carbon source
2318015570D-alanine+carbon source
2318015824D-fructose+carbon source
2318017634D-glucose+carbon source
2318016024D-mannose+carbon source
2318032528turanose+carbon source
2318024996lactate+carbon source
2318029806fumarate+carbon source
2318017754glycerol+carbon source
2318029991L-aspartate+carbon source
2318029985L-glutamate+carbon source
2318015971L-histidine+carbon source
2318015589L-malate+carbon source
2318017115L-serine+carbon source
2318017895L-tyrosine+carbon source
2318017306maltose+carbon source
2318018401phenylacetate+carbon source
2318017272propionate+carbon source
2318017148putrescine+carbon source
2318030031succinate+carbon source
2318017992sucrose+carbon source
2318018186tyrosine+degradation
2318016199urea+degradation
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
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
1226324853esculin-hydrolysis
122632606565hippurate+hydrolysis
12263217632nitrate-reduction
12263216301nitrite-reduction
12263217632nitrate+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

antibiotic resistance

  • @ref: 122632
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122632
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12263215688acetoin+
12263217234glucose+

enzymes

@refvalueactivityec
23180alkaline phosphatase+3.1.3.1
23180alpha-glucosidase-3.2.1.20
23180beta-galactosidase-3.2.1.23
23180beta-glucuronidase-3.2.1.31
23180catalase+1.11.1.6
23180cytochrome oxidase-1.9.3.1
23180N-acetyl-beta-glucosaminidase-3.2.1.52
23180pyrazinamidase+3.5.1.B15
23180pyrrolidonyl 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
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
122632oxidase-
122632beta-galactosidase-3.2.1.23
122632alcohol dehydrogenase-1.1.1.1
122632gelatinase-
122632amylase+
122632DNase-
122632caseinase-3.4.21.50
122632catalase+1.11.1.6
122632tween esterase+
122632gamma-glutamyltransferase+2.3.2.2
122632lecithinase-
122632lipase-
122632lysine decarboxylase-4.1.1.18
122632ornithine decarboxylase-4.1.1.17
122632phenylalanine ammonia-lyase-4.3.1.24
122632tryptophan deaminase-
122632urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20050+--------+-+-------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20050-++-+--+-++--------
122632+++-+----++---------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122632+/----+/------+++--------+/---------+------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122632++--+--+-----------+-----------+-----------------+----------------------++-+--+++--+--+--++-+++-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11701human semenStrasbourgFranceFRAEurope
53610Human semenStrasbourgFranceFRAEurope
67770Human semen specimenStrasbourgFranceFRAEurope
122632Human, SemenStrasbourgFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Urogenital tract#Semen
#Host#Human
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_3289.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_322;97_835;98_971;99_3289&stattab=map
  • Last taxonomy: Corynebacterium
  • 16S sequence: Y10999
  • Sequence Identity:
  • Total samples: 22059
  • soil counts: 1440
  • aquatic counts: 1218
  • animal counts: 18979
  • plant counts: 422

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11701yes, in single cases1Risk group (German classification)
200501German classification
1226322Risk group (French classification)

Sequence information

16S sequences

  • @ref: 23180
  • description: Corynebacterium singulare 16S rRNA gene, strain IBS B52218; CCUG 37330
  • accession: Y10999
  • length: 1323
  • database: nuccore
  • NCBI tax ID: 161899

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium singulare IBS B52218161899.3completepatric161899
67770Corynebacterium singulare IBS B52218GCA_000833575completencbi161899

GC content

@refGC-contentmethod
1170162
2318062.0high performance liquid chromatography (HPLC)
6777062capillary zone electrophoresis (CZE)
6777060.12genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.625no
gram-positiveyes94.611yes
anaerobicno99.054yes
aerobicno66.706no
halophileyes74.954no
spore-formingno94.265yes
thermophileno98.519yes
glucose-utilyes82.568yes
flagellatedno95.686yes
glucose-fermentyes72.97yes

External links

@ref: 11701

culture collection no.: DSM 44357, CCUG 37330, CIP 105491, IBS B52218, IFO 16162, NBRC 16162, LMG 19056, CCM 4729, JCM 10385

straininfo link

  • @ref: 72698
  • straininfo: 264413

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9336912Corynebacterium singulare sp. nov., a new species for urease-positive strains related to Corynebacterium minutissimum.Riegel P, Ruimy R, Renaud FN, Freney J, Prevost G, Jehl F, Christen R, Monteil HInt J Syst Bacteriol10.1099/00207713-47-4-10921997Base Composition, Cell Wall/chemistry, Corynebacterium/chemistry/*classification/genetics/physiology, Culture Media/metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Urease/analysisGenetics
Genetics25814602Complete Genome Sequence and Annotation of Corynebacterium singulare DSM 44357, Isolated from a Human Semen Specimen.Merten M, Brinkrolf K, Albersmeier A, Kutter Y, Ruckert C, Tauch AGenome Announc10.1128/genomeA.00183-152015Phylogeny
Phylogeny26243302Corynebacterium tapiri sp. nov. and Corynebacterium nasicanis sp. nov., isolated from a tapir and a dog, respectively.Baumgardt S, Loncaric I, Kampfer P, Busse HJInt J Syst Evol Microbiol10.1099/ijsem.0.0005102015Animals, Bacterial Typing Techniques, Corynebacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Dogs/*microbiology, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nose/microbiology, Nucleic Acid Hybridization, Palatine Tonsil/microbiology, Peptidoglycan/chemistry, Perissodactyla/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11701Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44357)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44357
20050Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44357.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
23180Philippe Riegel, Raymond Ruimy, Francois N. R. Renaud, Jean Freney, Gilles Prevost, Francois Jehl, Richard Christen, Henri Monteil10.1099/00207713-47-4-1092Corynebacterium singulare sp. nov., a New Species for Urease-Positive Strains Related to Corynebacterium minutissimumIJSEM 47: 1092-1096 19979336912
34670Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17516
53610Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37330)https://www.ccug.se/strain?id=37330
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
72698Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264413.1StrainInfo: A central database for resolving microbial strain identifiers
122632Curators of the CIPCollection of Institut Pasteur (CIP 105491)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105491