Strain identifier

BacDive ID: 3233

Type strain: Yes

Species: Corynebacterium timonense

Strain Designation: 5401744

Strain history: CCUG 53856 <-- V. Roux; Timone Hosp., France; 5401744.

NCBI tax ID(s): 441500 (species)

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General

@ref: 16812

BacDive-ID: 3233

DSM-Number: 45434

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Corynebacterium timonense 5401744 is an aerobe, mesophilic bacterium that was isolated from human blood of a 56 year old man.

NCBI tax id

  • NCBI tax id: 441500
  • Matching level: species

strain history

@refhistory
16812<- CCUG; CCUG 53856 <- V. Roux, Timone Hospital, Marseille
67770CCUG 53856 <-- V. Roux; Timone Hosp., France; 5401744.

doi: 10.13145/bacdive3233.20230509.8.1

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 timonense
  • full scientific name: Corynebacterium timonense Merhej et al. 2009

@ref: 16812

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium timonense

full scientific name: Corynebacterium timonense Merhej et al. 2009 emend. Nouioui et al. 2018

strain designation: 5401744

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no97.537
69480100positive

colony morphology

  • @ref: 60037
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16812TRYPTICASE 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
16812COLUMBIA 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

culture temp

@refgrowthtypetemperaturerange
16812positivegrowth37mesophilic
60037positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 60037
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no95
69480no99.999

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16812human blood of a 56 year old manMarseille, Timone HospitalFranceFRAEurope
60037Human blood,56-yr-old manMarseille,Timone hospitalFranceFRAEurope2005-08-01
67770Blood of a 56-year-old patientMarseillesFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human#Male
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_5970.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2850;97_3504;98_4434;99_5970&stattab=map
  • Last taxonomy: Corynebacterium timonense subclade
  • 16S sequence: EF217055
  • Sequence Identity:
  • Total samples: 1297
  • soil counts: 34
  • aquatic counts: 130
  • animal counts: 1127
  • plant counts: 6

Safety information

risk assessment

  • @ref: 16812
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16812
  • description: Corynebacterium timonensis strain 5401744 16S ribosomal RNA gene, partial sequence
  • accession: EF217055
  • length: 1435
  • database: ena
  • NCBI tax ID: 441500

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium timonense DSM 45434GCA_900105305chromosomencbi441500
66792Corynebacterium timonense 54017441203190.3wgspatric1203190
66792Corynebacterium timonense strain DSM 45434441500.3completepatric441500
66792Corynebacterium timonense DSM 454342636416018draftimg441500
66792Corynebacterium timonense 54017442551306128draftimg1203190
67770Corynebacterium timonense 5401744GCA_000312345scaffoldncbi1203190

GC content

  • @ref: 67770
  • GC-content: 66.6
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
gram-positiveyes93.039no
anaerobicno98.524yes
halophileyes83.548no
spore-formingno91.62no
glucose-utilyes79.405no
aerobicno57.046yes
flagellatedno96.97no
thermophileno92.077no
motileno93.496no
glucose-fermentno65.629no

External links

@ref: 16812

culture collection no.: DSM 45434, CCUG 53856, CIP 109424, CSUR P20, JCM 32213

straininfo link

  • @ref: 72747
  • straininfo: 399253

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19567562Corynebacterium timonense sp. nov. and Corynebacterium massiliense sp. nov., isolated from human blood and human articular hip fluid.Merhej V, Falsen E, Raoult D, Roux VInt J Syst Evol Microbiol10.1099/ijs.0.005827-02009Anaerobiosis, Bacterial Typing Techniques, Blood/*microbiology, Cluster Analysis, Corynebacterium/*classification/genetics/*isolation & purification/physiology, Corynebacterium Infections/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hip Joint/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Genetics25197476Non-contiguous finished genome sequence of Corynebacterium timonense type strain 5401744(T.).Roux V, Robert C, Raoult DStand Genomic Sci10.4056/sigs.42779542014

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16812Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45434)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45434
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
60037Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53856)https://www.ccug.se/strain?id=53856
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/
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
72747Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399253.1StrainInfo: A central database for resolving microbial strain identifiers