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Taxonomy browser (Clostridioides difficile)

Clostridioides difficile

Taxonomy ID: 1496 (for references in articles please use NCBI:txid1496)
Scientific name: Clostridioides difficile (Hall and O'Toole 1935) Lawson et al. 2016
type strain of Clostridioides difficile: AS:1.2184
type strain of Clostridioides difficile: ATCC:9689
type strain of Clostridioides difficile: BCRC:10642
type strain of Clostridioides difficile: CCUG:4938
type strain of Clostridioides difficile: CIP:104282
type strain of Clostridioides difficile: DSM:1296
type strain of Clostridioides difficile: JCM:1296
type strain of Clostridioides difficile: BCCM/LMG:15861
type strain of Clostridioides difficile: NCIMB:10666
type strain of Clostridioides difficile: NCTC:11209
homotypic synonym: "Bacillus difficilis" Hall and O'Toole 1935, effective name 1)
homotypic synonym: "Peptoclostridium difficile" Yutin and Galperin 2013, effective name 1)
includes: Clostridium sp. HMSC19D05
equivalent: [Clostridium] difficile
homotypic genbank synonym: Clostridium difficile (Hall and O'Toole 1935) Prevot 1938 (Approved Lists 1980), nom. approb. 2)
homotypic genbank synonym: Clostridium difficle
Inherited blast name: firmicutes
Rank: species
Genetic code: Translation table 11 (Bacterial, Archaeal and Plant Plastid)
Lineage( full )
cellular organisms; Bacteria; Terrabacteria group; Firmicutes; Clostridia; Clostridiales; Peptostreptococcaceae; Clostridioides
   Entrez records   
Database name Subtree links Direct links
Nucleotide 1,286,591 1,196,365
Nucleotide GSS 103 103
Protein 3,175,740 2,293,630
Structure 144 41
Genome 1 1
Popset 109 109
Conserved Domains 5 2
GEO Datasets 529 401
PubMed Central 14,894 14,894
Gene 19,446 4,050
SRA Experiments 14,590 14,217
Protein Clusters 3,929 3,929
Identical Protein Groups 274,996 227,924
Bio Project 593 301
Bio Sample 16,003 15,524
Bio Systems 1,304 414
Assembly 1,634 1,203
Probe 15 15
PubChem BioAssay 717 685
Taxonomy 296 1

Notes:

Comments and References:

Hall IC & O'Toole E (1935)
Hall, I.C., and O'Toole, E. "Intestinal flora in newborn infants with a description of a new pathogenic anaerobe, Bacillus difficilis." Am. J. Dis. Child. (1935) 49:390-402. [No PubMed record available.]

Reference to PubMed documentLawson PA et al. (2016)
Lawson, P.A., Citron, D.M., Tyrrell, K.L., and Finegold, S.M. "Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O'Toole 1935) Prevot 1938." Anaerobe (2016) 40:95-99.

Prevot AR (1938b)
Prevot, A.R. "Etudes de systematique bacterienne. IV. Critique de la conception actuelle du genre Clostridium." Ann. Inst. Pasteur (Paris) (1938) 61:72-91. [No PubMed record available.]

Nota BeneSkerman VBD et al. (1980) (Clostridium difficile)
Skerman, V.B.D., McGowan, V., and Sneath, P.H.A. (editors). "Approved lists of bacterial names." Int. J. Syst. Bacteriol. (1980) 30:225-420.

Reference to PubMed documentVALIDATION LIST No. 171 (2016)
Validation List No. 171: "List of new names and new combinations previously effectively, but not validly, published." Int. J. Syst. Evol. Microbiol. (2016) 66:3761-3764.

Reference to PubMed documentYutin N & Galperin MY (2013)
Yutin, N., and Galperin, M.Y. "A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia." Environ. Microbiol. (2013) 15:2631-2641.


Genome Information

   Trace records (raw single-pass reads of DNA sequence)   
Sequencing Center Name
Record counts per type
454 PRIMERWALK ALL
SC - The Sanger Center
- 3 3
WUGSC - Washington University, Genome Sequencing Center
417,941 - 417,941
Totals per type
417,941 3 417,944

External Information Resources (NCBI LinkOut)

LinkOut Subject LinkOut Provider
Clostridioides difficile meta-databases BacDive
4 records from this provider organism-specific BioCyc
Clostridium difficile (Hall and O'Toole 1935) PrA%A9vot 1938 (Approved Lists 1980) taxonomy/phylogenetic Encyclopedia of life
30 records from this provider organism-specific Genomes On Line Database
Clostridium difficile culture/stock collections Global Catalogue of Microorganisms
Related Immune Epitope Information gene/protein/disease-specific Immune Epitope Database and Analysis Resource
31 records from this provider organism-specific Integrated Microbial Genomes
Clostridioides difficile taxonomy/phylogenetic Lifemap
Wikipedia taxonomy/phylogenetic iPhylo
Notes:
Groups interested in participating in the LinkOut program should visit the LinkOut home page.
A list of our current non-bibliographic LinkOut providers can be found here.

Information from sequence entries

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