Strain identifier

BacDive ID: 3084

Type strain: Yes

Species: Corynebacterium cystitidis

Strain Designation: 42 Fukuya

Strain history: CIP <- 1990, ATCC <- R. Yanagawa: strain 42 Fukuya <- K. Hirato

NCBI tax ID(s): 1121357 (strain), 35757 (species)

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General

@ref: 8892

BacDive-ID: 3084

DSM-Number: 20524

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic

description: Corynebacterium cystitidis 42 Fukuya is a facultative anaerobe, mesophilic bacterium that was isolated from urine of cow.

NCBI tax id

NCBI tax idMatching level
1121357strain
35757species

strain history

@refhistory
8892<- H. Seiler <- ATCC <- R. Yanagawa, 42 Fukuya <- K. Hirato
67770R. Yanagawa strain 42 Fukuya.
118835CIP <- 1990, ATCC <- R. Yanagawa: strain 42 Fukuya <- K. Hirato

doi: 10.13145/bacdive3084.20230509.8.1

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 cystitidis
  • full scientific name: Corynebacterium cystitidis Yanagawa and Honda 1978 (Approved Lists 1980)

@ref: 8892

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium cystitidis

full scientific name: Corynebacterium cystitidis Yanagawa and Honda 1978 emend. Nouioui et al. 2018

strain designation: 42 Fukuya

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no96.379
69480100positive
118835nopositiveflask-shaped

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
18445Saffron yellow (1017)10-14 daysISP 2
1188351

multicellular morphology

  • @ref: 18445
  • forms multicellular complex: no
  • medium name: ISP 2

multimedia

  • @ref: 8892
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_20524.jpg
  • caption: Medium 693 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18445ISP 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
8892COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yesName: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar basehttps://mediadive.dsmz.de/medium/693
40637MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118835CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18445positiveoptimum37mesophilic
8892positivegrowth37mesophilic
40637positivegrowth37mesophilic
67770positivegrowth37mesophilic
118835positivegrowth25-41
118835nogrowth10psychrophilic
118835nogrowth15psychrophilic
118835nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118835
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
18445NaClpositivemaximum5 %
118835NaClpositivegrowth0-6 %
118835NaClnogrowth8 %
118835NaClnogrowth10 %

murein

  • @ref: 8892
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1844517234glucose-
1844522599arabinose-
1844517992sucrose-
1844518222xylose-
1844517268myo-inositol-
1844529864mannitol-
1844528757fructose+/-
1844526546rhamnose+/-
1844516634raffinose-
1844562968cellulose-
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
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
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11883516947citrate-carbon source
1188354853esculin-hydrolysis
118835606565hippurate+hydrolysis
11883517632nitrate-reduction
11883516301nitrite-reduction
11883545285pyrazinamide-hydrolysis
11883517632nitrate+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

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11883535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11883515688acetoin+
11883517234glucose+

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+
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)+
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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
118835oxidase-
118835beta-galactosidase+3.2.1.23
118835alcohol dehydrogenase-1.1.1.1
118835gelatinase+
118835amylase-
118835DNase-
118835caseinase-3.4.21.50
118835catalase+1.11.1.6
118835tween esterase-
118835gamma-glutamyltransferase-2.3.2.2
118835lecithinase-
118835lipase-
118835lysine decarboxylase-4.1.1.18
118835ornithine decarboxylase-4.1.1.17
118835phenylalanine ammonia-lyase-4.3.1.24
118835protease-
118835tryptophan deaminase-
118835urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18445+---+----+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18445--+----+-++--+-----
118835-++-------+--+------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARA
18445------+--+----------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118835----++/-----++------------------------------------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8892urine of cow
49384Cow
67770Urine of cow
118835Animal, Bovine urine, pyelonephritisHokkaidoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Fluids#Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_17582.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_9006;97_10829;98_13296;99_17582&stattab=map
  • Last taxonomy: Corynebacterium cystitidis subclade
  • 16S sequence: X82058
  • Sequence Identity:
  • Total samples: 728
  • soil counts: 18
  • aquatic counts: 10
  • animal counts: 697
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level commentpathogenicity animal
184452German classification
88922Risk group (German classification)yes
1188352Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium cystitidis gene for 16S rRNAD379141438ena35757
20218C.cystitidis 16S ribosomal DNAX820581322ena35757
20218Corynebacterium cystitidis 16S rRNA gene, strain NCTC 11863X842521491ena35757

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium cystitidis NCTC11863GCA_900187295completencbi35757
66792Corynebacterium cystitidis DSM 205241121357.3wgspatric1121357
66792Corynebacterium cystitidis strain NCTC1186335757.3completepatric35757
66792Corynebacterium cystitidis DSM 205242599185266draftimg1121357
66792Corynebacterium cystitidis NCTC 118632773857908completeimg35757
67770Corynebacterium cystitidis DSM 20524GCA_900111265scaffoldncbi1121357

GC content

@refGC-contentmethod
889252.6
6777070.3thermal denaturation, midpoint method (Tm)
6777059.8
6777057genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.534no
gram-positiveyes90.263no
anaerobicno99.109no
aerobicno54.391no
halophileyes70.97no
spore-formingno92.751no
thermophileno97.482no
glucose-utilyes84.792no
motileno94.87no
glucose-fermentyes54.973yes

External links

@ref: 8892

culture collection no.: DSM 20524, ATCC 29593, CCUG 28794, JCM 3715, BCRC 12320, CCM 5742, CECT 4048, CGMCC 1.1932, CIP 103424, IFO 15284, KCTC 3433, LMG 19065, NBRC 15284, NCTC 11863

straininfo link

  • @ref: 72602
  • straininfo: 14085

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8892Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20524)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20524
18445Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20524.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
40637Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15220
49384Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28794)https://www.ccug.se/strain?id=28794
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/
68368Automatically annotated from API 20E
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
72602Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14085.1StrainInfo: A central database for resolving microbial strain identifiers
118835Curators of the CIPCollection of Institut Pasteur (CIP 103424)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103424