Strain identifier

BacDive ID: 23853

Type strain: No

Species: Clostridioides difficile

Strain Designation: 630

Strain history: <- P. Bracegirdle, NCTC <- P. Mullany <- H. Hächler <- J. Wüst; 630

NCBI tax ID(s): 1496 (species)

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General

@ref: 20942

BacDive-ID: 23853

DSM-Number: 27543

keywords: genome sequence, Bacteria, anaerobe, spore-forming, mesophilic, rod-shaped, human pathogen

description: Clostridioides difficile 630 is an anaerobe, spore-forming, mesophilic human pathogen that was isolated from clinical isolate.

NCBI tax id

  • NCBI tax id: 1496
  • Matching level: species

strain history

  • @ref: 20942
  • history: <- P. Bracegirdle, NCTC <- P. Mullany <- H. Hächler <- J. Wüst; 630

doi: 10.13145/bacdive23853.20230509.8.1

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: 20942

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: 630

type strain: no

Morphology

cell morphology

@refcell shapegram stainconfidence
68367rod-shaped
68367positive
69480positive100

colony morphology

  • @ref: 20942
  • type of hemolysis: gamma
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20942CHOPPED 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
20942FASTIDIOUS 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: 20942
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
20942anaerobe
69480anaerobe99.628

spore formation

@refspore formationconfidence
68367yes
69481yes100
69480yes99.728

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836762345L-rhamnose-builds acid from
6836716634raffinose-builds acid from
683676731melezitose+builds acid from
6836716024D-mannose+builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin+hydrolysis
6836730849L-arabinose-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
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
20942catalase+1.11.1.6
20942cytochrome-c oxidase-1.9.3.1
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
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
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380urease-3.5.1.5
68367catalase+1.11.1.6
68367beta-glucosidase+3.2.1.21
68367gelatinase+
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECATSPORGRAMCOCC
20942--++---++-++-+++-+/--+
20942--++---++-++--++-+/--+/-
20942--++---++-++-+/-++-+/---
20942--++---+/-+/--++--++----
20942--++---++-++-+/-++-+/--++++-
20942--++---++-++-+++-+-+/-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
20942-+----+/----+-------+----------
20942-+/-----+/----+-------+----------
20942------------------+----------
20942------+/------------+--+-------

Isolation, sampling and environmental information

isolation

  • @ref: 20942
  • sample type: clinical isolate
  • country: Switzerland
  • origin.country: CHE
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Infection#Medical environment#Clinic
#Infection#Patient
#Infection#Patient#Specimen

Safety information

risk assessment

  • @ref: 20942
  • 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 630GCA_000009205completencbi272563
66792Clostridioides difficile 630GCA_000932055completencbi272563
66792Clostridioides difficile 630272563.206plasmidpatric272563
66792Peptoclostridium difficile 630272563.120completepatric272563
66792Peptoclostridium difficile strain NCTC133071496.877completepatric1496
66792Clostridioides difficile NCTC133072663762959completeimg1496
66792Clostridioides difficile 6302634166508completeimg272563
66792Clostridioides difficile 630640069308completeimg272563
66792Clostridioides difficile 6302588253713draftimg272563

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes75.324no
motileyes75.324no
flagellatedno69.697no
flagellatedno69.697no
gram-positiveyes92.023yes
gram-positiveyes92.023yes
anaerobicyes98.664yes
anaerobicyes98.664yes
halophileno92.504no
halophileno92.504no
spore-formingyes94.993yes
spore-formingyes94.993yes
thermophileno93.381no
thermophileno93.381no
glucose-utilyes87.275no
glucose-utilyes87.275no
aerobicno97.893no
aerobicno97.893no
glucose-fermentyes56.74no
glucose-fermentyes56.74no

External links

@ref: 20942

culture collection no.: DSM 27543, ATCC BAA 1382, NCTC 13307

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics28357980Manual curation and reannotation of the genomes of Clostridium difficile 630Deltaerm and C. difficile 630.Dannheim H, Riedel T, Neumann-Schaal M, Bunk B, Schober I, Sproer C, Chibani CM, Gronow S, Liesegang H, Overmann J, Schomburg DJ Med Microbiol10.1099/jmm.0.0004272017Base Sequence, Bile Acids and Salts, Clostridioides difficile/*genetics/metabolism, DNA, Bacterial/genetics, Gas Chromatography-Mass Spectrometry, *Genome, Bacterial, High-Throughput Nucleotide Sequencing/methods, Humans, Molecular Sequence Annotation/*methods, Open Reading Frames, Oxidative Stress/genetics, Polymorphism, Single NucleotidePathogenicity
Cultivation31148548Generation of a fully erythromycin-sensitive strain of Clostridioides difficile using a novel CRISPR-Cas9 genome editing system.Ingle P, Groothuis D, Rowe P, Huang H, Cockayne A, Kuehne SA, Jiang W, Gu Y, Humphreys CM, Minton NPSci Rep10.1038/s41598-019-44458-y2019*CRISPR-Cas Systems, Clostridioides difficile/drug effects/*genetics, Codon, Initiator, Culture Media, Erythromycin/*pharmacology, Escherichia coli, Frameshift Mutation, Gene Deletion, *Gene Editing, Genetic Vectors, *Genome, Bacterial, Methyltransferases/genetics, Mutagenesis, Mutation, Phenotype, Plasmids/genetics, Polymerase Chain Reaction, Promoter Regions, GeneticGenetics
31921877In vitro Study of Lactobacillus paracasei CNCM I-1518 in Healthy and Clostridioides difficile Colonized Elderly Gut Microbiota.Fehlbaum S, Chassard C, Schwab C, Voolaid M, Fourmestraux C, Derrien M, Lacroix CFront Nutr10.3389/fnut.2019.001842019

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
20942Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27543Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27543)
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
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