Strain identifier

BacDive ID: 157663

Type strain: No

Species: Clostridioides difficile

Strain Designation: 4167/2013 2

Strain history: <- U. Groß, Universitätsmedizin Göttingen, Georg-August-Universität <- O. Zimmermann, Universitätsmedizin Göttingen, Georg-August-Universität; 4167/2013 2

NCBI tax ID(s): 1496 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 8.1 (current version)

General

@ref: 64232

BacDive-ID: 157663

DSM-Number: 27639

keywords: genome sequence, Bacteria, mesophilic, Gram-negative, human pathogen

description: Clostridioides difficile 4167/2013 2 is a mesophilic, Gram-negative human pathogen that was isolated from Faeces from a symptomatic patient .

NCBI tax id

  • NCBI tax id: 1496
  • Matching level: species

strain history

  • @ref: 64232
  • history: <- U. Groß, Universitätsmedizin Göttingen, Georg-August-Universität <- O. Zimmermann, Universitätsmedizin Göttingen, Georg-August-Universität; 4167/2013 2

doi: 10.13145/bacdive157663.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Peptostreptococcaceae
  • genus: Clostridioides
  • species: Clostridioides difficile
  • full scientific name: Clostridioides difficile (Hall and O'Toole 1935) Lawson et al. 2016

  • synonyms

    @refsynonym
    20215Bacillus difficilis
    20215Peptoclostridium difficile
    20215Clostridium difficile

@ref: 64232

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptostreptococcaceae

genus: Clostridioides

species: Clostridioides difficile

full scientific name: Clostridioides difficile (Hall and O'Toole 1935) Lawson et al. 2016

strain designation: 4167/2013 2

type strain: no

Morphology

cell morphology

  • @ref: 68367
  • gram stain: negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64232CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
64232FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)yeshttps://mediadive.dsmz.de/medium/1203Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water

culture temp

  • @ref: 64232
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

spore formation

  • @ref: 68367
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose-builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367catalase-1.11.1.6
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECATSPORGRAM
64232-----------------------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
64232------------------+--+-+/------

Isolation, sampling and environmental information

isolation

  • @ref: 64232
  • sample type: Faeces from a symptomatic patient (from the same patient are isolates DSM 27638 and DSM 27640)
  • geographic location: Göttingen
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Infection#Patient

Safety information

risk assessment

  • @ref: 64232
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridioides difficile DSM 27639GCA_003313565completencbi1496
66792Clostridioides difficile strain DSM 276391496.2747completepatric1496
66792Clostridioides difficile DSM 276392871965432completeimg1496

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes75.321no
flagellatedno71.41no
gram-positiveyes92.124no
anaerobicyes98.515no
aerobicno97.554no
halophileno92.985no
spore-formingyes94.673no
glucose-utilyes87.61no
thermophileno91.268yes
glucose-fermentyes56.69no

External links

@ref: 64232

culture collection no.: DSM 27639

straininfo link

  • @ref: 110532
  • straininfo: 400488

literature

  • topic: Phylogeny
  • Pubmed-ID: 29291715
  • title: Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile.
  • authors: Gross U, Brzuszkiewicz E, Gunka K, Starke J, Riedel T, Bunk B, Sproer C, Wetzel D, Poehlein A, Chibani C, Bohne W, Overmann J, Zimmermann O, Daniel R, Liesegang H
  • journal: BMC Genomics
  • DOI: 10.1186/s12864-017-4368-0
  • year: 2018
  • mesh: Clostridiales/classification/cytology/*genetics/isolation & purification, Flagella/genetics/ultrastructure, Gene Transfer, Horizontal, *Genome, Bacterial, Genomics, Gram-Positive Bacterial Infections/*microbiology, Humans, Phenotype, Phylogeny
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
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
64232Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27639Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27639)
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
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
110532Reimer, 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-ID400488.1