Strain identifier

BacDive ID: 2584

Type strain: No

Species: Clostridioides difficile

Strain Designation: A90

Strain history: <- F. Rieu-Lesme, A90

NCBI tax ID(s): 1496 (species)

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General

@ref: 4593

BacDive-ID: 2584

DSM-Number: 12057

keywords: Bacteria, anaerobe, spore-forming, mesophilic, rod-shaped, human pathogen

description: Clostridioides difficile A90 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: 4593
  • history: <- F. Rieu-Lesme, A90

doi: 10.13145/bacdive2584.20230509.8.1

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: 4593

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: A90

type strain: no

Morphology

cell morphology

@refcell shapegram stain
68367rod-shaped
68367positive

colony morphology

  • @ref: 4593
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4593CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: 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
4593FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)yeshttps://mediadive.dsmz.de/medium/1203Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water

culture temp

  • @ref: 4593
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 4593
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 68367
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
6836716024D-mannose+builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
6836730849L-arabinose-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol+builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
4593catalase+1.11.1.6
4593cytochrome-c oxidase-1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382alkaline phosphatase-3.1.3.1
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase-
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367catalase-1.11.1.6
68367beta-glucosidase+3.2.1.21
68367urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
4593--+/-+/--------+/---------

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECATSPORGRAMCOCC
4593--++----+-++-+++---+-
4593+/--++---+/-+/---+--++/----+/-++-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
4593----------------+/--++/----------

Isolation, sampling and environmental information

isolation

  • @ref: 4593
  • sample type: rumen of new-born lamb
  • country: France
  • origin.country: FRA
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Caprinae (Sheep/Goat)
#Host Body-Site#Organ#Rumen

Safety information

risk assessment

  • @ref: 4593
  • pathogenicity human: yes
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

GC content

  • @ref: 4593
  • GC-content: 29.3
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 4593

culture collection no.: DSM 12057

straininfo link

  • @ref: 72117
  • straininfo: 49232

Reference

@idauthorscataloguedoi/urltitle
4593Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12057)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12057
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
72117Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49232.1StrainInfo: A central database for resolving microbial strain identifiers