Strain identifier

BacDive ID: 23855

Type strain: No

Species: Clostridioides difficile

Strain Designation: 630 Delta erm

Strain history: <- R. Gerhard <- N. P. Minton <- H. A. Hussain; 630 Delta erm

NCBI tax ID(s): 1496 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 20944

BacDive-ID: 23855

DSM-Number: 28645

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

description: Clostridioides difficile 630 Delta erm is an anaerobe, spore-forming, mesophilic human pathogen of the family Peptostreptococcaceae.

NCBI tax id

  • NCBI tax id: 1496
  • Matching level: species

strain history

  • @ref: 20944
  • history: <- R. Gerhard <- N. P. Minton <- H. A. Hussain; 630 Delta erm

doi: 10.13145/bacdive23855.20230509.8.1

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: 20944

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 Delta erm

type strain: no

Morphology

cell morphology

@refcell shapegram stain
68367rod-shaped
68367positive

colony morphology

  • @ref: 20944
  • type of hemolysis: gamma
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20944FASTIDIOUS 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
20944CHOPPED 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: 20944
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 20944
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 68367
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose+builds acid from
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
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
20944cytochrome-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-
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
68367beta-glucosidase+3.2.1.21
68367gelatinase+
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECATSPORGRAMCOCC
20944--++---++-++-+/-++---++++-
20944--++---++-++-+++-+/--++/-++-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
20944----------+-------+----------
20944----------+-------++/--+/--------

Isolation, sampling and environmental information

isolation

  • @ref: 20944
  • country: United Kingdom
  • origin.country: GBR
  • continent: Europe

Safety information

risk assessment

  • @ref: 20944
  • 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 strain 630 delta erm1496.2352plasmidpatric1496
66792Clostridioides difficile strain 630 delta erm1496.2021completepatric1496

Genome-based predictions

predictions

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

External links

@ref: 20944

culture collection no.: DSM 28645

straininfo link

  • @ref: 87870
  • straininfo: 397186

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
Metabolism32302381Characterization of Clostridioides difficile DSM 101085 with A-B-CDT+ Phenotype from a Late Recurrent Colonization.Riedel T, Neumann-Schaal M, Wittmann J, Schober I, Hofmann JD, Lu CW, Dannheim A, Zimmermann O, Lochner M, Gross U, Overmann JGenome Biol Evol10.1093/gbe/evaa0722020ADP Ribose Transferases/*genetics/metabolism, Aged, Bacterial Proteins/*genetics/metabolism, Bacterial Toxins/*genetics/metabolism, Clostridioides/*genetics/metabolism/*pathogenicity, Enterotoxins/*genetics/metabolism, *Evolution, Molecular, Humans, Metabolome, *Phenotype, *VirulencePathogenicity

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
20944Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28645Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28645)
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
87870Reimer, 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-ID397186.1