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Strain identifier

BacDive ID: 134676

Type strain: No

Species: Clostridioides difficile

Strain Designation: CD196

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, mesophilic

description: Clostridioides difficile CD196 is a mesophilic bacterium of the family Peptostreptococcaceae.

NCBI tax id

NCBI tax idMatching level
499176strain
1496species

doi: 10.13145/bacdive134676.20221219.7.1

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

  • @ref: 69480
  • gram stain: positive
  • confidence: 90.53

Culture and growth conditions

culture medium

  • @ref: 33182
  • name: MEDIUM 20 - for Anaerobic bacteria
  • growth: yes
  • composition: Agar (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)

culture temp

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

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: anaerobe
  • confidence: 98.853

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 92.281

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 95.323

Isolation, sampling and environmental information

isolation

  • @ref: 33182
  • geographic location: Reims
  • country: France
  • origin.country: FRA
  • continent: Europe

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridioides difficile CD196 CD196GCA_000085225completencbi645462
66792Clostridioides difficile CIP 107932 CIP 107932GCA_000155045chromosomencbi499176
66792Clostridioides difficile CD196 CD196GCA_000449605contigncbi645462
66792Clostridium difficile CIP 107932499176.4wgspatric499176
66792Clostridioides difficile CIP 107932642791606draftimg499176
66792Clostridioides difficile CD1962541047488draftimg645462
66792Clostridioides difficile CD196646311914completeimg645462
66792Clostridioides difficile CD196 CD196GCA_021378415completencbi645462
66792Lactiplantibacillus plantarum LP3GCA_002286275completepatric1590
66792Enterococcus casseliflavus 4928STDY7071761GCA_902163985scaffoldpatric37734

External links

@ref: 33182

culture collection no.: CIP 107932

straininfo link

@refpassport
20218http://www.straininfo.net/strains/840300
20218http://www.straininfo.net/strains/900918

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/urljournalpubmedcatalogue
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
33182Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5498 Collection 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
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