Strain identifier

BacDive ID: 134676

Type strain: No

Species: Clostridioides difficile

Strain Designation: CD196

Strain history: CIP <- 2003, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 196-84, Clostridium difficile

NCBI tax ID(s): 499176 (strain), 1496 (species)

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

@ref: 33182

BacDive-ID: 134676

keywords: genome sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive

description: Clostridioides difficile CD196 is an anaerobe, spore-forming, mesophilic bacterium of the family Peptostreptococcaceae.

NCBI tax id

NCBI tax idMatching level
499176strain
1496species

strain history

  • @ref: 33182
  • history: CIP <- 2003, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 196-84, Clostridium difficile

doi: 10.13145/bacdive134676.20230509.8.1

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: 33182

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Eubacteriales

family: Peptostreptococcaceae

genus: Clostridioides

species: Clostridioides difficile

strain designation: CD196

type strain: no

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
33182positiverod-shapedno

colony morphology

  • @ref: 33182

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33182MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
33182CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

  • @ref: 33182
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
69480anaerobe99.208
33182anaerobe

spore formation

@refspore formationconfidence
69481yes98
69480yes100
33182yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3318217108D-arabinose-degradation
3318215824D-fructose+degradation
3318217634D-glucose+degradation
3318265327D-xylose-degradation
3318217057cellobiose-degradation
3318217716lactose-degradation
3318217306maltose-degradation
3318217814salicin-degradation
3318217992sucrose-degradation
331824853esculin+hydrolysis
3318217632nitrate-reduction
3318216301nitrite-reduction
3318217632nitrate+respiration

metabolite production

  • @ref: 33182
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
33182oxidase-
33182beta-galactosidase+3.2.1.23
33182gelatinase-
33182amylase-
33182DNase-
33182caseinase-3.4.21.50
33182catalase-1.11.1.6
33182tween esterase-
33182lecithinase-
33182lipase-
33182protease-
33182urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
33182--------------------

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typeisolation date
33182ReimsFranceFRAEurope
33182ReimsFranceFRAEuropeHuman, Feces1984

Safety information

risk assessment

  • @ref: 33182
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridioides difficile CD196GCA_000085225completencbi645462
66792Clostridioides difficile CIP 107932GCA_000155045chromosomencbi499176
66792Clostridioides difficile CD196GCA_000449605contigncbi645462
66792Clostridium difficile CIP 107932499176.4wgspatric499176
66792Clostridioides difficile CIP 107932642791606draftimg499176
66792Clostridioides difficile CD1962541047488draftimg645462
66792Clostridioides difficile CD196646311914completeimg645462
66792Clostridioides difficile CD196GCA_021378415completencbi645462

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes98no
motileyes76.812no
flagellatedno66.247no
gram-positiveyes91.486no
anaerobicyes98.751no
aerobicno97.488no
halophileno93.847no
spore-formingyes94.392no
thermophileno91.456no
glucose-utilyes89.108no
glucose-fermentyes58.099no

External links

@ref: 33182

culture collection no.: CIP 107932

straininfo link

  • @ref: 92157
  • straininfo: 361807

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity3137166Actin-specific ADP-ribosyltransferase produced by a Clostridium difficile strain.Popoff MR, Rubin EJ, Gill DM, Boquet PInfect Immun10.1128/iai.56.9.2299-2306.19881988Actins/*physiology, Adult, Animals, Antibodies, Bacterial/physiology, Cells, Cultured, Clostridium/*enzymology, Culture Media, Cytotoxins/toxicity, Enterotoxins/pharmacology, Female, Humans, Lethal Dose 50, Mice, Molecular Weight, Poly(ADP-ribose) Polymerases/*biosynthesis/immunology/toxicityCultivation
Enzymology9119480Production of a complete binary toxin (actin-specific ADP-ribosyltransferase) by Clostridium difficile CD196.Perelle S, Gibert M, Bourlioux P, Corthier G, Popoff MRInfect Immun10.1128/iai.65.4.1402-1407.19971997Amino Acid Sequence, Bacterial Toxins/*biosynthesis/genetics, Base Sequence, Cloning, Molecular, Clostridioides difficile/genetics/*metabolism, *Genes, Bacterial, Molecular Sequence Data, Poly(ADP-ribose) Polymerases/*biosynthesis/geneticsGenetics
Genetics11761709ADP-ribosylating binary toxin genes of Clostridium difficile strain CCUG 20309.Chang SY, Song KPDNA Seq10.3109/104251701090475642001ADP Ribose Transferases/*genetics, Amino Acid Sequence, Amino Acid Substitution/genetics, *Bacterial Proteins, Base Sequence, Clostridioides difficile/*genetics, Molecular Sequence Data
Pathogenicity18480332Assessing the role of p-cresol tolerance in Clostridium difficile.Dawson LF, Stabler RA, Wren BWJ Med Microbiol10.1099/jmm.0.47744-02008Clostridioides difficile/classification/*drug effects/growth & development, Clostridium perfringens/drug effects, Clostridium sordellii/drug effects, Cresols/*pharmacology, Dose-Response Relationship, Drug, Drug Resistance, Bacterial/*physiology, HumansPhylogeny
Metabolism22398929Secretome analysis of Clostridium difficile strains.Boetzkes A, Felkel KW, Zeiser J, Jochim N, Just I, Pich AArch Microbiol10.1007/s00203-012-0802-52012ADP Ribose Transferases/metabolism, Bacterial Proteins/*metabolism, Bacterial Toxins/metabolism, Chromatography, Liquid, Clostridioides difficile/genetics/*metabolism/pathogenicity, Mass Spectrometry, *Proteome, Species SpecificityProteome
Pathogenicity23208832Fidaxomicin inhibits toxin production in Clostridium difficile.Babakhani F, Bouillaut L, Sears P, Sims C, Gomez A, Sonenshein ALJ Antimicrob Chemother10.1093/jac/dks4502012Aminoglycosides/*metabolism, Anti-Bacterial Agents/*metabolism, Bacterial Proteins/*antagonists & inhibitors/biosynthesis, Bacterial Toxins/*antagonists & inhibitors/biosynthesis, Clostridioides difficile/*drug effects, Culture Media/chemistry, Enterotoxins/*antagonists & inhibitors/biosynthesis, Enzyme-Linked Immunosorbent Assay, Fidaxomicin, Gene Expression/drug effects, Gene Expression Profiling, Humans, Metronidazole/metabolism, Vancomycin/metabolismMetabolism
Pathogenicity23415847Clostridium-DT(DB): a comprehensive database for potential drug targets of Clostridium difficile.Jadhav A, Ezhilarasan V, Prakash Sharma O, Pan AComput Biol Med10.1016/j.compbiomed.2013.01.0092013Anti-Bacterial Agents/*pharmacology, Clostridioides difficile/*drug effects/*genetics, Clostridium Infections/drug therapy, Computational Biology/methods, *Databases, Factual, Drug Resistance, Multiple, Bacterial/*genetics, Genes, Bacterial, Genomics/methods, Internet, Intestines/microbiology, Technology, Pharmaceutical/methods, User-Computer InterfaceGenetics
Metabolism23992299Analysis of metabolic evolution in bacteria using whole-genome metabolic models.Bryant WA, Faruqi AA, Pinney JWJ Comput Biol10.1089/cmb.2013.00792013Adaptation, Biological/genetics, Clostridioides difficile/*genetics/metabolism, Evolution, Molecular, *Genome, Bacterial, Humans, Metabolic Networks and Pathways/*genetics, Models, Genetic, Phylogeny, Phytoplasma/*genetics/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 23S/geneticsGenetics
Pathogenicity28279860Inhibition of spore germination, growth, and toxin activity of clinically relevant C. difficile strains by gut microbiota derived secondary bile acids.Thanissery R, Winston JA, Theriot CMAnaerobe10.1016/j.anaerobe.2017.03.0042017Animals, Anti-Bacterial Agents/*metabolism, Antibiosis, Bacterial Toxins/*metabolism, Bile Acids and Salts/*metabolism, Clostridioides difficile/*drug effects/growth & development, Gastrointestinal Microbiome, Gastrointestinal Tract/*microbiology, Humans, Mice, Spores, Bacterial/*drug effects/growth & developmentMetabolism
29213333Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan.Suzuki H, Tomita M, Tsai PJ, Ko WC, Hung YP, Huang IH, Chen JWGut Pathog10.1186/s13099-017-0219-42017
29928268A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile.Thanissery R, Zeng D, Doyle RG, Theriot CMFront Microbiol10.3389/fmicb.2018.012062018
Pathogenicity34908523Clostridioides difficile strain-dependent and strain-independent adaptations to a microaerobic environment.Weiss A, Lopez CA, Beavers WN, Rodriguez J, Skaar EPMicrob Genom10.1099/mgen.0.0007382021Animals, Anti-Bacterial Agents/pharmacology, Bacterial Proteins/*genetics, Carbohydrate Metabolism, Clostridioides difficile/*classification/drug effects/genetics/isolation & purification, Disease Models, Animal, Gastrointestinal Tract/*microbiology, Gene Expression Profiling/*methods, Gene Expression Regulation, Bacterial/drug effects, Humans, Oxidative Stress, Oxygen/*pharmacology, Sequence Analysis, RNAPhylogeny

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
33182Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107932Collection of Institut Pasteur (CIP 107932)
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
68382Automatically annotated from API zym
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
92157Reimer, 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-ID361807.1