Strain identifier
BacDive ID: 2583
Type strain:
Species: Clostridioides difficile
Strain Designation: AA1
Strain history: <- F. Rieu-Lesme, AA1
NCBI tax ID(s): 1496 (species)
General
@ref: 4592
BacDive-ID: 2583
DSM-Number: 12056
keywords: 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, rod-shaped, human pathogen
description: Clostridioides difficile AA1 is an anaerobe, spore-forming, mesophilic human pathogen that was isolated from rumen of new-born lamb.
NCBI tax id
- NCBI tax id: 1496
- Matching level: species
strain history
- @ref: 4592
- history: <- F. Rieu-Lesme, AA1
doi: 10.13145/bacdive2583.20230509.8.1
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: 4592
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: AA1
type strain: no
Morphology
cell morphology
@ref | cell shape | gram stain |
---|---|---|
68367 | rod-shaped | |
68367 | positive |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4592 | FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) | yes | https://mediadive.dsmz.de/medium/1203 | Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water |
4592 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: 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: 4592
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 4592
- oxygen tolerance: anaerobe
spore formation
- @ref: 68367
- spore formation: yes
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68367 | 27082 | trehalose | + | builds acid from |
68367 | 62345 | L-rhamnose | - | builds acid from |
68367 | 30911 | sorbitol | - | builds acid from |
68367 | 16634 | raffinose | - | builds acid from |
68367 | 6731 | melezitose | + | builds acid from |
68367 | 16024 | D-mannose | + | builds acid from |
68367 | 17754 | glycerol | - | builds acid from |
68367 | 4853 | esculin | + | hydrolysis |
68367 | 5291 | gelatin | + | hydrolysis |
68367 | 30849 | L-arabinose | - | builds acid from |
68367 | 17814 | salicin | - | builds acid from |
68367 | 17306 | maltose | - | builds acid from |
68367 | 17992 | sucrose | - | builds acid from |
68367 | 17716 | lactose | - | builds acid from |
68367 | 16899 | D-mannitol | + | builds acid from |
68367 | 17634 | D-glucose | + | builds acid from |
68367 | 16199 | urea | - | hydrolysis |
68367 | 27897 | tryptophan | - | energy source |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68367 | 35581 | indole | no |
68380 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test |
---|---|---|---|
68380 | 35581 | indole | - |
68367 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
4592 | catalase | + | 1.11.1.6 |
4592 | cytochrome-c oxidase | - | 1.9.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | proline-arylamidase | + | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | - | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | - | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
68367 | catalase | - | 1.11.1.6 |
68367 | beta-glucosidase | + | 3.2.1.21 |
68367 | gelatinase | + | |
68367 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
4592 | - | - | + | +/- | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - |
API 20A
@ref | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE | IND | CAT | SPOR | GRAM | COCC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
4592 | - | + | + | - | - | - | - | +/- | - | + | + | - | +/- | + | + | - | - | - | + | |||||
4592 | - | + | + | - | - | - | - | - | - | + | + | - | - | + | + | - | - | - | + | |||||
4592 | - | + | + | - | - | - | - | + | - | + | + | - | + | + | + | - | - | - | + | - | - | + | + | - |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
4592 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
4592 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | + | +/- | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 4592
- sample type: rumen of new-born lamb
- country: France
- origin.country: FRA
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Mammals | #Caprinae (Sheep/Goat) |
#Host Body-Site | #Organ | #Rumen |
taxonmaps
- @ref: 69479
- File name: preview.99_78.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2;96_63;97_66;98_71;99_78&stattab=map
- Last taxonomy: Clostridioides difficile
- 16S sequence: HM007570
- Sequence Identity:
- Total samples: 39293
- soil counts: 528
- aquatic counts: 1013
- animal counts: 37560
- plant counts: 192
Safety information
risk assessment
- @ref: 4592
- pathogenicity human: yes
- pathogenicity animal: yes
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Clostridium difficile strain DSM 12056 16S ribosomal RNA gene, partial sequence | HM007570 | 1303 | ena | 1496 |
4592 | Clostridium difficile strain DSM 12056 23S ribosomal RNA gene, partial sequence | HM007603 | 2509 | ena | 1496 |
GC content
- @ref: 4592
- GC-content: 31.3
- method: high performance liquid chromatography (HPLC)
External links
@ref: 4592
culture collection no.: DSM 12056
straininfo link
- @ref: 72116
- straininfo: 49231
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4592 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12056) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12056 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
68367 | Automatically annotated from API 20A | |||||
68380 | Automatically annotated from API rID32A | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
72116 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID49231.1 | StrainInfo: A central database for resolving microbial strain identifiers |