Strain identifier
BacDive ID: 134676
Type strain:
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)
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 id | Matching level |
---|---|
499176 | strain |
1496 | species |
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
@ref synonym 20215 Bacillus difficilis 20215 Peptoclostridium difficile 20215 Clostridium 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 | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | positive | 100 | ||
33182 | positive | rod-shaped | no |
colony morphology
- @ref: 33182
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
33182 | MEDIUM 20 - for Anaerobic bacteria | yes | 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) | |
33182 | CIP Medium 20 | yes | https://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
@ref | oxygen tolerance | confidence |
---|---|---|
69480 | anaerobe | 99.208 |
33182 | anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 98 |
69480 | yes | 100 |
33182 | yes |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
33182 | 17108 | D-arabinose | - | degradation |
33182 | 15824 | D-fructose | + | degradation |
33182 | 17634 | D-glucose | + | degradation |
33182 | 65327 | D-xylose | - | degradation |
33182 | 17057 | cellobiose | - | degradation |
33182 | 17716 | lactose | - | degradation |
33182 | 17306 | maltose | - | degradation |
33182 | 17814 | salicin | - | degradation |
33182 | 17992 | sucrose | - | degradation |
33182 | 4853 | esculin | + | hydrolysis |
33182 | 17632 | nitrate | - | reduction |
33182 | 16301 | nitrite | - | reduction |
33182 | 17632 | nitrate | + | respiration |
metabolite production
- @ref: 33182
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
33182 | oxidase | - | |
33182 | beta-galactosidase | + | 3.2.1.23 |
33182 | gelatinase | - | |
33182 | amylase | - | |
33182 | DNase | - | |
33182 | caseinase | - | 3.4.21.50 |
33182 | catalase | - | 1.11.1.6 |
33182 | tween esterase | - | |
33182 | lecithinase | - | |
33182 | lipase | - | |
33182 | protease | - | |
33182 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
33182 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | geographic location | country | origin.country | continent | sample type | isolation date |
---|---|---|---|---|---|---|
33182 | Reims | France | FRA | Europe | ||
33182 | Reims | France | FRA | Europe | Human, Feces | 1984 |
Safety information
risk assessment
- @ref: 33182
- biosafety level: 2
- biosafety level comment: Risk group (French classification)
Sequence information
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clostridioides difficile CD196 | GCA_000085225 | complete | ncbi | 645462 |
66792 | Clostridioides difficile CIP 107932 | GCA_000155045 | chromosome | ncbi | 499176 |
66792 | Clostridioides difficile CD196 | GCA_000449605 | contig | ncbi | 645462 |
66792 | Clostridium difficile CIP 107932 | 499176.4 | wgs | patric | 499176 |
66792 | Clostridioides difficile CIP 107932 | 642791606 | draft | img | 499176 |
66792 | Clostridioides difficile CD196 | 2541047488 | draft | img | 645462 |
66792 | Clostridioides difficile CD196 | 646311914 | complete | img | 645462 |
66792 | Clostridioides difficile CD196 | GCA_021378415 | complete | ncbi | 645462 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 98 | no |
motile | yes | 76.812 | no |
flagellated | no | 66.247 | no |
gram-positive | yes | 91.486 | no |
anaerobic | yes | 98.751 | no |
aerobic | no | 97.488 | no |
halophile | no | 93.847 | no |
spore-forming | yes | 94.392 | no |
thermophile | no | 91.456 | no |
glucose-util | yes | 89.108 | no |
glucose-ferment | yes | 58.099 | no |
External links
@ref: 33182
culture collection no.: CIP 107932
straininfo link
- @ref: 92157
- straininfo: 361807
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Pathogenicity | 3137166 | Actin-specific ADP-ribosyltransferase produced by a Clostridium difficile strain. | Popoff MR, Rubin EJ, Gill DM, Boquet P | Infect Immun | 10.1128/iai.56.9.2299-2306.1988 | 1988 | Actins/*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/toxicity | Cultivation |
Enzymology | 9119480 | Production of a complete binary toxin (actin-specific ADP-ribosyltransferase) by Clostridium difficile CD196. | Perelle S, Gibert M, Bourlioux P, Corthier G, Popoff MR | Infect Immun | 10.1128/iai.65.4.1402-1407.1997 | 1997 | Amino Acid Sequence, Bacterial Toxins/*biosynthesis/genetics, Base Sequence, Cloning, Molecular, Clostridioides difficile/genetics/*metabolism, *Genes, Bacterial, Molecular Sequence Data, Poly(ADP-ribose) Polymerases/*biosynthesis/genetics | Genetics |
Genetics | 11761709 | ADP-ribosylating binary toxin genes of Clostridium difficile strain CCUG 20309. | Chang SY, Song KP | DNA Seq | 10.3109/10425170109047564 | 2001 | ADP Ribose Transferases/*genetics, Amino Acid Sequence, Amino Acid Substitution/genetics, *Bacterial Proteins, Base Sequence, Clostridioides difficile/*genetics, Molecular Sequence Data | |
Pathogenicity | 18480332 | Assessing the role of p-cresol tolerance in Clostridium difficile. | Dawson LF, Stabler RA, Wren BW | J Med Microbiol | 10.1099/jmm.0.47744-0 | 2008 | Clostridioides difficile/classification/*drug effects/growth & development, Clostridium perfringens/drug effects, Clostridium sordellii/drug effects, Cresols/*pharmacology, Dose-Response Relationship, Drug, Drug Resistance, Bacterial/*physiology, Humans | Phylogeny |
Metabolism | 22398929 | Secretome analysis of Clostridium difficile strains. | Boetzkes A, Felkel KW, Zeiser J, Jochim N, Just I, Pich A | Arch Microbiol | 10.1007/s00203-012-0802-5 | 2012 | ADP Ribose Transferases/metabolism, Bacterial Proteins/*metabolism, Bacterial Toxins/metabolism, Chromatography, Liquid, Clostridioides difficile/genetics/*metabolism/pathogenicity, Mass Spectrometry, *Proteome, Species Specificity | Proteome |
Pathogenicity | 23208832 | Fidaxomicin inhibits toxin production in Clostridium difficile. | Babakhani F, Bouillaut L, Sears P, Sims C, Gomez A, Sonenshein AL | J Antimicrob Chemother | 10.1093/jac/dks450 | 2012 | Aminoglycosides/*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/metabolism | Metabolism |
Pathogenicity | 23415847 | Clostridium-DT(DB): a comprehensive database for potential drug targets of Clostridium difficile. | Jadhav A, Ezhilarasan V, Prakash Sharma O, Pan A | Comput Biol Med | 10.1016/j.compbiomed.2013.01.009 | 2013 | Anti-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 Interface | Genetics |
Metabolism | 23992299 | Analysis of metabolic evolution in bacteria using whole-genome metabolic models. | Bryant WA, Faruqi AA, Pinney JW | J Comput Biol | 10.1089/cmb.2013.0079 | 2013 | Adaptation, 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/genetics | Genetics |
Pathogenicity | 28279860 | Inhibition 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 CM | Anaerobe | 10.1016/j.anaerobe.2017.03.004 | 2017 | Animals, 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 & development | Metabolism |
29213333 | Comparative 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 JW | Gut Pathog | 10.1186/s13099-017-0219-4 | 2017 | |||
29928268 | A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile. | Thanissery R, Zeng D, Doyle RG, Theriot CM | Front Microbiol | 10.3389/fmicb.2018.01206 | 2018 | |||
Pathogenicity | 34908523 | Clostridioides difficile strain-dependent and strain-independent adaptations to a microaerobic environment. | Weiss A, Lopez CA, Beavers WN, Rodriguez J, Skaar EP | Microb Genom | 10.1099/mgen.0.000738 | 2021 | Animals, 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, RNA | Phylogeny |
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
33182 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107932 | Collection of Institut Pasteur (CIP 107932) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
68382 | Automatically annotated from API zym | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
92157 | Reimer, 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 identifiers | 10.60712/SI-ID361807.1 |