Strain identifier

BacDive ID: 2583

Type strain: No

Species: Clostridioides difficile

Strain Designation: AA1

Strain history: <- F. Rieu-Lesme, AA1

NCBI tax ID(s): 1496 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

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

    @refsynonym
    20215Bacillus difficilis
    20215Peptoclostridium difficile
    20215Clostridium 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

@refcell shapegram stain
68367rod-shaped
68367positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4592FASTIDIOUS 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
4592CHOPPED 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

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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose+builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose+builds acid from
6836716024D-mannose+builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin+hydrolysis
6836730849L-arabinose-builds acid from
6836717814salicin-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
6836727897tryptophan-energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
4592catalase+1.11.1.6
4592cytochrome-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)-
68382esterase (C 4)+
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
68367gelatinase+
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
4592--++/--------+/---------

API 20A

@refUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATREINDCATSPORGRAMCOCC
4592-++----+/--++-+/-++---+
4592-++------++--++---+
4592-++----+-++-+++---+--++-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
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

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium difficile strain DSM 12056 16S ribosomal RNA gene, partial sequenceHM0075701303ena1496
4592Clostridium difficile strain DSM 12056 23S ribosomal RNA gene, partial sequenceHM0076032509ena1496

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

@idauthorscataloguedoi/urltitlejournalpubmed
4592Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12056)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12056
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
69479João 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
72116Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49231.1StrainInfo: A central database for resolving microbial strain identifiers