Strain identifier

BacDive ID: 3116

Type strain: Yes

Species: Corynebacterium renale

Strain Designation: Charita a, Charita-a

Strain history: CIP <- 1990, ATCC <- NCTC <- 1948, B. Weitz: strain Charita-a

NCBI tax ID(s): 1724 (species)

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General

@ref: 9009

BacDive-ID: 3116

DSM-Number: 20688

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

description: Corynebacterium renale Charita a is a facultative anaerobe, mesophilic bacterium that was isolated from cow.

NCBI tax id

  • NCBI tax id: 1724
  • Matching level: species

strain history

@refhistory
9009<- NCTC <- B. Weitz, Charita a
67770NCTC 7448 <-- B. Weitz strain Charita a.
122155CIP <- 1990, ATCC <- NCTC <- 1948, B. Weitz: strain Charita-a

doi: 10.13145/bacdive3116.20230509.8.1

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 renale
  • full scientific name: Corynebacterium renale (Migula 1900) Ernst 1906 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacterium renale

@ref: 9009

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium renale

full scientific name: Corynebacterium renale (Migula 1900) Ernst 1906 emend. Nouioui et al. 2018

strain designation: Charita a, Charita-a

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no98.065
69480100positive
122155nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
18769Ivory10-14 daysISP 6
122155

multicellular morphology

  • @ref: 18769
  • forms multicellular complex: no
  • medium name: ISP 6

multimedia

  • @ref: 9009
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_20688.jpg
  • caption: Medium 535a 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18769ISP 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
9009TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a)yesName: 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 waterhttps://mediadive.dsmz.de/medium/535a
9009TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
40532MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122155CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18769positiveoptimum37mesophilic
9009positivegrowth37mesophilic
40532positivegrowth37mesophilic
67770positivegrowth37mesophilic
122155positivegrowth25-45
122155nogrowth10psychrophilic
122155nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122155
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no93
69480no99.913

halophily

@refsaltgrowthtested relationconcentration
18769NaClpositivemaximum7.5 %
122155NaClpositivegrowth2-10 %
122155NaClnogrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1876962968cellulose-
1876916634raffinose-
1876926546rhamnose-
1876928757fructose-
1876929864mannitol-
1876917268myo-inositol-
1876918222xylose-
1876917992sucrose+
1876922599arabinose+/-
1876917234glucose+
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
6837128053melibiose-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
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
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
12215516947citrate-carbon source
1221554853esculin-hydrolysis
122155606565hippurate+hydrolysis
12215517632nitrate+reduction
12215516301nitrite-reduction
12215545285pyrazinamide-hydrolysis
12215517632nitrate+respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837916988D-ribose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 122155
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12215535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12215515688acetoin+
12215517234glucose+

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)+
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
68379pyrrolidonyl arylamidase-3.4.19.3
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
122155oxidase-
122155beta-galactosidase-3.2.1.23
122155alcohol dehydrogenase-1.1.1.1
122155gelatinase-
122155amylase-
122155DNase-
122155caseinase+3.4.21.50
122155catalase+1.11.1.6
122155tween esterase+
122155gamma-glutamyltransferase-2.3.2.2
122155lecithinase+
122155lipase-
122155lysine decarboxylase-4.1.1.18
122155ornithine decarboxylase-4.1.1.17
122155phenylalanine ammonia-lyase-4.3.1.24
122155tryptophan deaminase-
122155urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
18769----+----+--+------
9009-+--+----+-++-------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18769--+-+--+-----+-----
122155-++-+--+-----+------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARA
18769---------+------+--+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122155----+----+/-+++--------------+/-+/--+/-------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122155++--+--------------+------------------+---------++----+----------+++-------+---++--------++-++-----

Isolation, sampling and environmental information

isolation

@refsample type
9009cow
48826Cow
67770Cow
122155Animal, Bovine

isolation source categories

  • Cat1: #Host
  • Cat2: #Mammals
  • Cat3: #Bovinae (Cow, Cattle)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6682.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_3166;97_3879;98_4928;99_6682&stattab=map
  • Last taxonomy: Corynebacterium renale subclade
  • 16S sequence: X81909
  • Sequence Identity:
  • Total samples: 2534
  • soil counts: 220
  • aquatic counts: 110
  • animal counts: 2185
  • plant counts: 19

Safety information

risk assessment

@refbiosafety levelbiosafety level commentpathogenicity animal
187692Risk group (German classification)
90092Risk group (German classification)yes
1221552Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.renale 16S ribosomal RNAM295531366ena1724
20218C.renale 16S rRNA gene (CIP 103421T)X819091395ena1724
20218Corynebacterium renale 16S rRNA gene, strain CIP 103421X842491447ena1724
20218Corynebacterium renale strain DSM 20688 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536498312ena1724
20218Corynebacterium renale strain DSM 20688 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536499312ena1724

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium renale NCTC7448GCA_900478035completencbi1724
66792Corynebacterium renale strain DSM 206881724.8wgspatric1724
66792Corynebacterium renale strain NCTC74481724.11completepatric1724
66792Corynebacterium renale DSM 206882627853607draftimg1724
66792Corynebacterium renale NCTC 74482808606807completeimg1724
67770Corynebacterium renale DSM 20688GCA_002563965contigncbi1724

GC content

@refGC-contentmethod
6777059.1genome sequence analysis
6777058.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno93no
flagellatedno97.661no
gram-positiveyes92.654no
anaerobicno98.6no
aerobicno76.779no
halophileyes83.524no
spore-formingno94.154no
thermophileno96.79yes
glucose-utilyes86.563no
motileno95.335no
glucose-fermentyes67.256no

External links

@ref: 9009

culture collection no.: DSM 20688, ATCC 19412, NCTC 7448, CCUG 27542, JCM 9391, BCRC 10657, CECT 4082, CIP 103421, HAMBI 2321, IFO 15290, NBRC 15290, PCM 2053

straininfo link

  • @ref: 72633
  • straininfo: 297047

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7548409Assignment of the bacterial agent of urinary calculus in young rats by the comparative sequence analysis of the 16S rRNA genes of corynebacteria.Takahashi T, Tsuji M, Kikuchi N, Ishihara C, Osanai T, Kasai N, Yanagawa R, Hiramune TJ Vet Med Sci10.1292/jvms.57.5151995Animals, Base Sequence, Biological Evolution, Corynebacterium/classification/genetics/*isolation & purification, Corynebacterium Infections/diagnosis/*veterinary, DNA Primers, Genes, Bacterial, Molecular Sequence Data, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/*genetics, Rats, Rats, Inbred Lew, *Rodent Diseases, Urinary Calculi/microbiology/*veterinaryGenetics
Pathogenicity10508100Toxigenic strains of Bacillus licheniformis related to food poisoning.Salkinoja-Salonen MS, Vuorio R, Andersson MA, Kampfer P, Andersson MC, Honkanen-Buzalski T, Scoging ACAppl Environ Microbiol10.1128/AEM.65.10.4637-4645.19991999Animals, Bacillus/classification/isolation & purification/*pathogenicity, Cattle, Female, Foodborne Diseases/*microbiology, Humans, Male, Sperm Motility/drug effects, SwinePhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9009Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20688)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20688
18769Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20688.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
40532Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15217
48826Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27542)https://www.ccug.se/strain?id=27542
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
72633Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297047.1StrainInfo: A central database for resolving microbial strain identifiers
122155Curators of the CIPCollection of Institut Pasteur (CIP 103421)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103421