Strain identifier

BacDive ID: 3148

Type strain: Yes

Species: Corynebacterium urealyticum

Strain Designation: Armendariz, 1

Strain history: CIP <- 1992, NCTC <- 1988, ATCC <- F. Soriano, Spain: strain Armendariz, Corynebacterium group D2

NCBI tax ID(s): 504474 (strain), 43771 (species)

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General

@ref: 2986

BacDive-ID: 3148

DSM-Number: 7109

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, human pathogen

description: Corynebacterium urealyticum Armendariz is a microaerophile, mesophilic human pathogen that was isolated from bladder stone.

NCBI tax id

NCBI tax idMatching level
504474strain
43771species

strain history

@refhistory
2986<- ATCC <- F. Soriano, 1 (Corynebacterium group D2)
67770CIP 103524 <-- NCTC 12011 <-- ATCC 43042 <-- F. Soriano strain 1 (strain Armendariz).
123741CIP <- 1992, NCTC <- 1988, ATCC <- F. Soriano, Spain: strain Armendariz, Corynebacterium group D2

doi: 10.13145/bacdive3148.20230509.8.1

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 urealyticum
  • full scientific name: Corynebacterium urealyticum Pitcher et al. 1992

@ref: 2986

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium urealyticum

full scientific name: Corynebacterium urealyticum Pitcher et al. 1992 emend. Nouioui et al. 2018

strain designation: Armendariz, 1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.199
69480100positive
123741positiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19724Light ivory10-14 daysISP 2
19724Light ivory10-14 daysISP 3
19724Light ivory10-14 daysISP 4
19724Light ivory10-14 daysISP 5
19724Light ivory10-14 daysISP 6

multicellular morphology

@refforms multicellular complexmedium name
19724noISP 2
19724noISP 3
19724noISP 4
19724noISP 5
19724noISP 6

multimedia

  • @ref: 2986
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_7109.jpg
  • caption: Medium 693 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2986COLUMBIA 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
2986TRYPTICASE 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
19724ISP 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
19724ISP 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:
19724ISP 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
19724ISP 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
19724ISP 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
38133MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123741CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
123741CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
19724positiveoptimum37mesophilic
2986positivegrowth37mesophilic
38133positivegrowth37mesophilic
46774positivegrowth37mesophilic
67770positivegrowth37mesophilic
123741positivegrowth22-41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
46774microaerophile
123741facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.981

halophily

  • @ref: 19724
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 2986
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
123741esculin-hydrolysis4853
123741nitrate-reduction17632
123741nitrite-reduction16301
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea+hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

antibiotic resistance

  • @ref: 123741
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123741
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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)-
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
68379pyrrolidonyl arylamidase-3.4.19.3
123741oxidase-
123741beta-galactosidase-3.2.1.23
123741gelatinase-
123741amylase-
123741catalase+1.11.1.6
123741lipase-
123741urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
19724---------+---------
2986-+-+/------+----------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19724-++----------------
123741--------------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123741-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123741---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
2986bladder stone
46774Human bladder stoneMadridSpainESPEurope
67770Bladder stoneMadridSpainESPEurope
123741Human, Bladder stoneMadridSpainESPEurope1988

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body-Site#Urogenital tract#Bladder
#Host Body Product#Urogenital tract#Bladder stone

taxonmaps

  • @ref: 69479
  • File name: preview.99_354.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_139;97_269;98_299;99_354&stattab=map
  • Last taxonomy: Corynebacterium urealyticum subclade
  • 16S sequence: X81913
  • Sequence Identity:
  • Total samples: 9624
  • soil counts: 819
  • aquatic counts: 492
  • animal counts: 8209
  • plant counts: 104

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
2986yesyes2Risk group (German classification)
197242Risk group (German classification)
1237412Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.urealyticum 16S rRNA gene (ATCC 43042T)X819131401ena504474
20218Corynebacterium urealyticum partial 16S rRNA gene, strain DSM 7109X844391511ena504474

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium urealyticum NCTC12011GCA_900187235completencbi43771
66792Corynebacterium urealyticum DSM 7109GCA_000069945completencbi504474
66792Corynebacterium urealyticum DSM 7109504474.4completepatric504474
66792Corynebacterium urealyticum strain FDAARGOS_99443771.87completepatric43771
66792Corynebacterium urealyticum strain NCTC1201143771.9completepatric43771
66792Corynebacterium urealyticum NCTC 120112811995035completeimg43771
66792Corynebacterium urealyticum DSM 7109641522620completeimg504474

GC content

@refGC-contentmethod
298662.0thermal denaturation, midpoint method (Tm)
6777065high performance liquid chromatography (HPLC)
6777064.2genome sequence analysis
6777062thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.476no
flagellatedno98.101no
gram-positiveyes93.27no
anaerobicno99.015no
aerobicno78.963yes
halophileyes81.618no
spore-formingno89.764no
thermophileno91.558yes
glucose-utilyes85.666no
glucose-fermentno66.236no

External links

@ref: 2986

culture collection no.: DSM 7109, ATCC 43042, NCTC 12011, CCUG 18158, JCM 10395, CCM 3975, CECT 4142, CIP 103524, LMG 19041

straininfo link

  • @ref: 72664
  • straininfo: 13144

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1736965Classification of coryneform bacteria associated with human urinary tract infection (group D2) as Corynebacterium urealyticum sp. nov.Pitcher D, Soto A, Soriano F, Valero-Guillen PInt J Syst Bacteriol10.1099/00207713-42-1-1781992Base Composition, Corynebacterium/*classification/genetics/physiology, DNA, Bacterial/analysis, Humans, Urinary Tract Infections/*microbiologyPathogenicity
Genetics18367281The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing.Tauch A, Trost E, Tilker A, Ludewig U, Schneiker S, Goesmann A, Arnold W, Bekel T, Brinkrolf K, Brune I, Gotker S, Kalinowski J, Kamp PB, Lobo FP, Viehoever P, Weisshaar B, Soriano F, Droge M, Puhler AJ Biotechnol10.1016/j.jbiotec.2008.02.0092008Bacterial Proteins/*genetics, Base Sequence, Chromosome Mapping/*methods, Corynebacterium/*genetics, Genome, Bacterial/*genetics, Molecular Sequence Data, Open Reading Frames/*genetics, Sequence Analysis, DNA/*methodsTranscriptome
Genetics26041051Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology.Guimaraes L, Soares S, Trost E, Blom J, Ramos R, Silva A, Barh D, Azevedo VBMC Genomics10.1186/1471-2164-16-S5-S72015Comparative Genomic Hybridization/*methods, Computational Biology/*methods, Corynebacterium/classification/*genetics/pathogenicity, Corynebacterium Infections/drug therapy/microbiology, Drug Resistance, Multiple, Bacterial/genetics, Genome, Bacterial/*genetics, Genomics/methods, Humans, Virulence Factors/*geneticsPathogenicity
Metabolism29743008Identification and characterization of smallest pore-forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109.Abdali N, Younas F, Mafakheri S, Pothula KR, Kleinekathofer U, Tauch A, Benz RBMC Biochem10.1186/s12858-018-0093-92018Amino Acid Sequence, Anti-Bacterial Agents/pharmacology, Bacterial Proteins/chemistry/genetics/*metabolism, Cell Wall/*metabolism, Corynebacterium/*metabolism/pathogenicity, Electrophoresis, Polyacrylamide Gel, Humans, Hydrophobic and Hydrophilic Interactions, Lipid Bilayers, Molecular Dynamics Simulation, Porins/chemistry/genetics/*metabolism, Protein Structure, Secondary, Sequence Homology, Amino Acid, Urinary Tract Infections/drug therapy/microbiologyEnzymology
Phylogeny33427608Corynebacterium anserum sp. nov., isolated from the faeces of greater white-fronted geese (Anser albifrons) at Poyang Lake, PR China.Liu Q, Wu K, Fan G, Bai X, Yang X, Pan Y, Cao L, Song W, Chen S, Xiong Y, Chen HInt J Syst Evol Microbiol10.1099/ijsem.0.0046372021Animals, Bacterial Typing Techniques, Base Composition, China, Corynebacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Geese/*microbiology, Lakes, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2986Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7109)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7109
19724Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM7109.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
38133Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15331
46774Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 18158)https://www.ccug.se/strain?id=18158
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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)
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
72664Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13144.1StrainInfo: A central database for resolving microbial strain identifiers
123741Curators of the CIPCollection of Institut Pasteur (CIP 103524)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103524