Strain identifier

BacDive ID: 157669

Type strain: No

Species: Clostridioides difficile

Strain Designation: CD-16-113, D/6474/2015

Strain history: <- U. Nübel, Leibniz-Institut DSMZ GmbH, Braunschweig.; CD-16-113 <- U. Groß, Institut für Medizinische Mikrobiologie. Universitätsmedizin Göttingen.

NCBI tax ID(s): 1496 (species)

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General

@ref: 64238

BacDive-ID: 157669

DSM-Number: 102978

keywords: genome sequence, Bacteria, human pathogen

description: Clostridioides difficile CD-16-113 is a human pathogen that was isolated from Faeces from a symptomatic patient.

NCBI tax id

  • NCBI tax id: 1496
  • Matching level: species

strain history

  • @ref: 64238
  • history: <- U. Nübel, Leibniz-Institut DSMZ GmbH, Braunschweig.; CD-16-113 <- U. Groß, Institut für Medizinische Mikrobiologie. Universitätsmedizin Göttingen.

doi: 10.13145/bacdive157669.20250331.9.3

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
    20215Peptoclostridium difficile
    20215Bacillus difficilis
    20215Clostridium difficile

@ref: 64238

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: CD-16-113, D/6474/2015

type strain: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64238FASTIDIOUS 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
64238CHOPPED 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

culture temp

  • @ref: 64238
  • growth: positive
  • type: growth
  • temperature: 37

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: anaerobe
  • confidence: 99.8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838017632nitrate-reduction
6838027897tryptophan-energy source
6838029985L-glutamate-degradation
6838016634raffinose-fermentation
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016199urea-hydrolysis
6836727082trehalose-builds acid from
6836762345L-rhamnose-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

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
6836735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380tyrosine arylamidase-
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
68380alpha-fucosidase-3.2.1.51
68380tryptophan deaminase-4.1.99.1
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380alpha-arabinosidase-3.2.1.55
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
68380alanine arylamidase-3.4.11.2
68380pyrrolidonyl arylamidase-3.4.19.3
68380beta-glucuronidase-3.2.1.31
68380beta-glucosidase-3.2.1.21
68367catalase-1.11.1.6
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECAT
64238-----------------+/----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
64238------------------+----------

Isolation, sampling and environmental information

isolation

  • @ref: 64238
  • sample type: Faeces from a symptomatic patient
  • 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: 64238
  • 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 102978GCA_003457035completencbi1496
66792Clostridioides difficile strain DSM 1029781496.3068completepatric1496
66792Clostridioides difficile strain FDAARGOS_14691496.6351completepatric1496
66792Clostridioides difficile strain FDAARGOS_14691496.16088completepatric1496
66792Clostridioides difficile strain FDAARGOS_14691496.16110completepatric1496
66792Clostridioides difficile strain FDAARGOS_14691496.6374completepatric1496

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes58.898no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes88.344no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no98.577no
125438spore-formingspore-formingAbility to form endo- or exosporesyes64.744no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno90.757no
125438motile2+flagellatedAbility to perform flagellated movementyes73.733no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes79.3
125439BacteriaNetmotilityAbility to perform movementyes77.5
125439BacteriaNetgram_stainReaction to gram-stainingpositive78.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe99.8

External links

@ref: 64238

culture collection no.: DSM 102978

straininfo link

  • @ref: 110538
  • straininfo: 406209

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
64238Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102978Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102978)
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
110538Reimer, 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-ID406209.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG