Strain identifier

BacDive ID: 3144

Type strain: Yes

Species: Corynebacterium pseudodiphtheriticum

Strain Designation: 153

Strain history: CIP <- 1990, ATCC <- J.M. Coffey: strain 153

NCBI tax ID(s): 1121368 (strain), 37637 (species)

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General

@ref: 11534

BacDive-ID: 3144

DSM-Number: 44287

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

description: Corynebacterium pseudodiphtheriticum 153 is a microaerophile, Gram-positive bacterium that was isolated from human throat.

NCBI tax id

NCBI tax idMatching level
37637species
1121368strain

strain history

@refhistory
11534<- CCUG <- NCTC <- ATCC <- J. M. Coffey, 153
67770CECT 755 <-- NCTC 11136 <-- ATCC 10700 <-- J. M. Coffey 153.
121985CIP <- 1990, ATCC <- J.M. Coffey: strain 153

doi: 10.13145/bacdive3144.20240916.9.1

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 pseudodiphtheriticum
  • full scientific name: Corynebacterium pseudodiphtheriticum Lehmann and Neumann 1896 (Approved Lists 1980)

@ref: 11534

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium pseudodiphtheriticum

full scientific name: Corynebacterium pseudodiphtheriticum Lehmann and Neumann 1896 emend. Nouioui et al. 2018

strain designation: 153

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121985positiverod-shapedno
69480no94

colony morphology

@refcolony colorincubation periodmedium used
19645Beige10-14 daysISP 2
19645Beige10-14 daysISP 3
19645Beige10-14 daysISP 4
19645Beige10-14 daysISP 5
19645Beige10-14 daysISP 6
19645Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19645noISP 2
19645noISP 3
19645noISP 4
19645noISP 5
19645noISP 6
19645noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11534BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
11534COLUMBIA 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
19645ISP 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
19645ISP 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:
19645ISP 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
19645ISP 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
19645ISP 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
19645ISP 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
41653MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121985CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121985CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
19645positiveoptimum37
11534positivegrowth37
41653positivegrowth30
48823positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 48823
  • oxygen tolerance: microaerophile

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation

enzymes

@refvalueactivityec
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
19645---------+-------++
11534+++------+----------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19645-++-+----++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11534human throatNew YorkUSAUSANorth America
48823Human throatNew YorkUSAUSANorth America
67770Human throatNew YorkUSAUSANorth America
121985Human, ThroatNew YorkUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Throat

taxonmaps

  • @ref: 69479
  • File name: preview.99_2125.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1164;97_1368;98_1659;99_2125&stattab=map
  • Last taxonomy: Corynebacterium pseudodiphtheriticum
  • 16S sequence: X81918
  • Sequence Identity:
  • Total samples: 20952
  • soil counts: 674
  • aquatic counts: 814
  • animal counts: 19306
  • plant counts: 158

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115342Risk group (German classification)
196452Risk group (German classification)
1219852Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium pseudodiphthericum partial 16S rRNA gene, strain CIP103420TAJ4393431503nuccore37637
20218C.pseudodiphtheriticum 16S rRNA gene (CIP 103420T)X819181396nuccore37637
20218Corynebacterium pseudodiphtheriticum gene for 16S rRNA, partial sequenceAB470617542nuccore37637
20218Corynebacterium pseudodiphtheriticum 16S rRNA gene, strain NCTC 11136X842581483nuccore37637
124043Corynebacterium pseudodiphtheriticum CIP 103420 gene for 16S rRNA, partial sequence.LC7523351503nuccore37637
124043Corynebacterium pseudodiphtheriticum CIP 103420 gene for 16S rRNA, partial sequence.LC752453374nuccore37637
124043Corynebacterium pseudodiphtheriticum NCTC 11136 gene for 16S rRNA, partial sequence.LC752456569nuccore37637

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium pseudodiphtheriticum DSM 442871121368.3wgspatric1121368
66792Corynebacterium pseudodiphtheriticum DSM 442872556921672draftimg1121368
67770Corynebacterium pseudodiphtheriticum DSM 44287GCA_000688415contigncbi1121368

GC content

@refGC-contentmethod
6777055.3genome sequence analysis
6777054.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes84.717no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.341yes
69480spore-formingspore-formingAbility to form endo- or exosporesno81.29no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes67.852no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.467yes
69480flagellatedmotile2+Ability to perform flagellated movementno94no

External links

@ref: 11534

culture collection no.: DSM 44287, ATCC 10700, ATCC 7091, CCUG 27539, IFO 15362, NBRC 15362, NCTC 11136, JCM 11665, BCRC 10656, CCM 2821, CECT 755, CIP 103420, LMG 19053, PCM 2051

straininfo link

  • @ref: 72661
  • straininfo: 12979

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity22666859Aggregative adherent strains of Corynebacterium pseudodiphtheriticum enter and survive within HEp-2 epithelial cells.Souza MC, Santos LS, Gomes DL, Sabbadini PS, Santos CS, Camello TC, Asad LM, Rosa AC, Nagao PE, Hirata Junior R, Guaraldi ALMem Inst Oswaldo Cruz10.1590/s0074-027620120004000082012Bacterial Adhesion/*physiology, Corynebacterium/*pathogenicity/physiology, Epithelial Cells/*microbiology, Hep G2 Cells, Humans, Virulence
Metabolism25828766Biofilm formation and fibrinogen and fibronectin binding activities by Corynebacterium pseudodiphtheriticum invasive strains.Souza MC, dos Santos LS, Sousa LP, Faria YV, Ramos JN, Sabbadini PS, da Santos CS, Nagao PE, Vieira VV, Gomes DL, Hirata Junior R, Mattos-Guaraldi ALAntonie Van Leeuwenhoek10.1007/s10482-015-0433-32015Adhesins, Bacterial/metabolism, Bacteremia/microbiology, *Bacterial Adhesion, Bacteriological Techniques, Biofilms/*growth & development, Corynebacterium/growth & development/isolation & purification/*physiology, Corynebacterium Infections/microbiology, *Environmental Microbiology, Fibrinogen/*metabolism, Fibronectins/*metabolism, Glass, Humans, Microscopy, Pharyngitis/microbiology, PlasticsPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11534Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44287)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44287
19645Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44287.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
41653Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15216
48823Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27539)https://www.ccug.se/strain?id=27539
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/
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72661Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12979.1StrainInfo: A central database for resolving microbial strain identifiers
121985Curators of the CIPCollection of Institut Pasteur (CIP 103420)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103420
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy