Strain identifier

BacDive ID: 139735

Type strain: Yes

Species: Corynebacterium gottingense

Strain Designation: 99221/2016

Strain history: CIP <- 2017, DSMZ <- O. Zimmermann, Göttingen Univ., Göttingen, Germany: strain 99221/2016

NCBI tax ID(s): 2041036 (species)

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General

@ref: 42346

BacDive-ID: 139735

DSM-Number: 103494

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive, rod-shaped, colony-forming, human pathogen

description: Corynebacterium gottingense 99221/2016 is a mesophilic, Gram-positive, rod-shaped human pathogen that forms circular colonies and was isolated from blood of a clinical patient.

NCBI tax id

  • NCBI tax id: 2041036
  • Matching level: species

strain history

@refhistory
42346<- O. Zimmerman, Institut für Medizinische Mikrobiologie. Universitätsmedizin Göttingen.; 99221/2016
67770U. Groß; Univ. Med. Göttingen, Germany; 99221/2016.
119716CIP <- 2017, DSMZ <- O. Zimmermann, Göttingen Univ., Göttingen, Germany: strain 99221/2016

doi: 10.13145/bacdive139735.20230509.8.1

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 gottingense
  • full scientific name: Corynebacterium gottingense Atasayar et al. 2017

  • synonyms

    @refsynonym
    20215Corynebacterium godavarianum
    20215Corynebacterium hadale

@ref: 42346

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium gottingense

full scientific name: Corynebacterium gottingense Atasayar et al. 2017

strain designation: 99221/2016

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
65271positiverod-shaped
69480no98.264
69480positive100
119716positiverod-shapedno

colony morphology

  • @ref: 65271
  • colony color: white-cream
  • colony shape: circular

multimedia

  • @ref: 42346
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_103494.jpg
  • caption: Medium 693 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
42346TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
42346COLUMBIA 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
119716CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
42346positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
65271no
69481no100
69480no99.987

observation

@refobservation
65271non-lipophilic
65271Grows at 37 C aerobically and microaerophilically on Columbia blood agar after 1 day of incubation and as facultative anaerobe after 2 days of incubation.
65271CAMP test is negative.
67770quinones: MK-8(H2), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
652714853esculin-hydrolysis
652715291gelatin-hydrolysis
6527117234glucose+builds acid from
6527128087glycogen-builds acid from
6527117716lactose-builds acid from
6527117306maltose+builds acid from
6527129864mannitol-builds acid from
6527117632nitrate-reduction
6527133942ribose+builds acid from
6527117992sucrose-builds acid from
6527116199urea-hydrolysis
6527118222xylose-builds acid from
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
65271catalase+1.11.1.6
65271cytochrome oxidase-1.9.3.1
65271pyrazinamidase+3.5.1.B15
65271pyrrolidonyl arylamidase+3.4.19.3
65271alkaline phosphatase+3.1.3.1
65271alpha-glucosidase+3.2.1.20
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
42346---+--------++--+---+
42346---+--------++--+/----+
42346---+--------++/---+/-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation date
42346blood of a clinical patientGöttingen, Institut für Medizinische Mikrobiologie, University of GöttingenGermanyDEUEurope
65271blood sample of a clinical patient with bacteraemia of unknown originInstitute of Medical Microbiology, University of GöttingenGermanyDEUEuropeColumbia blood agar1 day37
67770Blood of a patient with bacteraemia at the Institute of Medical MicrobiologyGöttingenGermanyDEUEurope
119716Human, BloodGöttingenGermanyDEUEurope2016-05-11

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Blood
#Infection#Medical environment#Clinic
#Infection#Patient

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
42346yes, in single cases1Risk group (German classification)
1197162Risk group (French classification)

Sequence information

16S sequences

  • @ref: 42346
  • description: Corynebacterium gottingense strain 99221/2016 16S ribosomal RNA gene, partial sequence
  • accession: KY593177
  • length: 1492
  • database: ena
  • NCBI tax ID: 2041036

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium gottingense strain DSM 1034942041036.3wgspatric2041036
66792Corynebacterium gottingense DSM 1034942862065897draftimg2041036
67770Corynebacterium gottingense DSM 103494GCA_003693265contigncbi2041036

GC content

  • @ref: 42346
  • GC-content: 69.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.758no
gram-positiveyes93.988yes
anaerobicno99.11no
aerobicyes57.248no
halophileyes60.567no
spore-formingno94.019yes
glucose-utilyes83.07no
flagellatedno96.812no
thermophileno96.817no
glucose-fermentyes57.064yes

External links

@ref: 42346

culture collection no.: DSM 103494, CIP 111599, JCM 31931

straininfo link

  • @ref: 96187
  • straininfo: 402618

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28950931Corynebacterium gottingense sp. nov., isolated from a clinical patient.Atasayar E, Zimmermann O, Sproer C, Schumann P, Gross UInt J Syst Evol Microbiol10.1099/ijsem.0.0023222017Bacterial Typing Techniques, Base Composition, Blood/*microbiology, Corynebacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Germany, Humans, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny32375937Corynebacterium godavarianum Jani et al. 2018 and Corynebacterium hadale Wei et al. 2018 are both later heterotypic synonyms of Corynebacterium gottingense Atasayar et al. 2017, proposal of an emended description of Corynebacterium gottingense Atasayar et al. 2017.Bernard KA, Pacheco AL, Burdz T, Wiebe D, Bernier AMInt J Syst Evol Microbiol10.1099/ijsem.0.0041532020Bacterial Typing Techniques, Base Composition, Canada, Corynebacterium/*classification, DNA, Bacterial/genetics, Genes, Bacterial, Humans, India, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
42346Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103494Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103494)
65271Ewelina Atasayar, Ortrud Zimmermann, Cathrin Spröer, Peter Schumann, Uwe GroßCorynebacterium gottingense sp. nov., isolated from a clinical patient10.1099/ijsem.0.002322IJSEM 67: 4494-4499 201728950931
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
96187Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID402618.1
119716Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111599Collection of Institut Pasteur (CIP 111599)