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, Gram-positive, rod-shaped, human pathogen

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

NCBI tax id

NCBI tax idMatching level
43771species
504474strain

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/bacdive3148.20250331.9.3

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

@refgram staincell shapemotilityconfidence
123741positiverod-shaped
125438no92
125438positive91.805
125439positive98.2
125439no96.7

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

@refgrowthtypetemperature
19724positiveoptimum37
2986positivegrowth37
38133positivegrowth37
46774positivegrowth37
67770positivegrowth37
123741positivegrowth22-41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
46774microaerophile
123741facultative anaerobe
125439anaerobe96.6

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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917716lactose-fermentation
6837917306maltose-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin-hydrolysis
6837916199urea+hydrolysis
683794853esculin-hydrolysis
6837917632nitrate-reduction
1237414853esculin-hydrolysis
12374117632nitrate-reduction
12374116301nitrite-reduction
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837112936D-galactose-builds acid from
6837916899D-mannitol-fermentation
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
6837159640N-acetylglucosamine-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
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

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
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
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
68382alkaline phosphatase-3.1.3.1
68382lipase (C 14)-
123741oxidase-
123741beta-galactosidase-3.2.1.23
123741gelatinase-
123741amylase-
123741catalase+1.11.1.6
123741lipase-
123741urease+3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68382acid phosphatase-3.1.3.2
68379catalase+1.11.1.6
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase-3.4.19.3

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)X819131401nuccore504474
20218Corynebacterium urealyticum partial 16S rRNA gene, strain DSM 7109X844391511nuccore504474
124043Corynebacterium urealyticum gene for 16S rRNA, partial sequence.AB470616543nuccore43771

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.805no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.419no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes55.812yes
125438spore-formingspore-formingAbility to form endo- or exosporesno80.557no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.857yes
125438motile2+flagellatedAbility to perform flagellated movementno92no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno84.4
125439BacteriaNetmotilityAbility to perform movementno96.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive98.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe96.6

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
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
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1