Strain identifier

BacDive ID: 130925

Type strain: No

Species: Clostridium perfringens

Strain Designation: D10

Strain history: CIP <- 2016, CCUG <- 2015, NCTC, Julie Russell

NCBI tax ID(s): 1502 (species)

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General

@ref: 22217

BacDive-ID: 130925

DSM-Number: 100947

keywords: genome sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, rod-shaped, human pathogen

description: Clostridium perfringens D10 is an anaerobe, spore-forming, mesophilic human pathogen that was isolated from patient/food.

NCBI tax id

  • NCBI tax id: 1502
  • Matching level: species

strain history

@refhistory
22217<- S. Alexander, NCTC; NCTC 13170 <- K.A. Mooijman, RIVM;
121679CIP <- 2016, CCUG <- 2015, NCTC, Julie Russell

doi: 10.13145/bacdive130925.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Clostridium
  • species: Clostridium perfringens
  • full scientific name: Clostridium perfringens (Veillon and Zuber 1898) Hauduroy et al. 1937 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Bacillus perfringens
    20215Clostridioides perfringens

@ref: 22217

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium perfringens

full scientific name: Clostridium perfringens (Veillon and Zuber 1898) Hauduroy et al. 1937

strain designation: D10

type strain: no

Morphology

cell morphology

  • @ref: 121679
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22217FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1203a.pdf
22217COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
22217CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
121679CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

  • @ref: 22217
  • growth: positive
  • type: growth
  • temperature: 37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
22217anaerobe
125439anaerobe99.1

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan-energy source
6838029985L-glutamate-degradation
6838017632nitrate+reduction
6838016024D-mannose+fermentation
6838029016arginine-hydrolysis
6838016199urea-hydrolysis
6838016634raffinose+fermentation

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
68380tyrosine arylamidase-
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380glutamate decarboxylase-4.1.1.15
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380beta-Galactosidase 6-phosphate-
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380pyrrolidonyl arylamidase+3.4.19.3
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase+3.2.1.51
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
22217--+--+/----+++-++-+-----+------

Isolation, sampling and environmental information

isolation

@refsample type
22217patient/food
121679Human, Food

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Food
#Infection#Patient

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
22217yesyes2Risk group (German classification)
1216792Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium perfringens NCTC13170GCA_900475545completencbi1502
66792Clostridium perfringens strain NCTC131701502.467completepatric1502
66792Clostridium perfringens NCTC 131702875113875completeimg1502

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes73.253no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes85.433yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no91.457yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes76.431no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.376yes
125438motile2+flagellatedAbility to perform flagellated movementno67.205no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes89.5
125439BacteriaNetmotilityAbility to perform movementyes83.6
125439BacteriaNetgram_stainReaction to gram-stainingpositive77.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe99.1

External links

@ref: 22217

culture collection no.: DSM 100947, NCTC 13170, WDCM 00201, CIP 111239, CCUG 67301

straininfo link

  • @ref: 89405
  • straininfo: 400302

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
22217Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100947Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100947)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68380Automatically annotated from API rID32A
89405Reimer, 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 identifiers10.60712/SI-ID400302.1
121679Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111239Collection of Institut Pasteur (CIP 111239)
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG