Strain identifier

BacDive ID: 2712

Type strain: No

Species: Clostridium sporogenes

Strain Designation: SR 5, SR5

Strain history: CIP <- 1979, ATCC <- NCTC 532 <- 1920, M. Robertson, Lister Inst., London, UK: strain SR5

NCBI tax ID(s): 1509 (species)

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General

@ref: 845

BacDive-ID: 2712

DSM-Number: 1664

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

description: Clostridium sporogenes SR 5 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from gas gangrene.

NCBI tax id

  • NCBI tax id: 1509
  • Matching level: species

strain history

@refhistory
845<- ATCC; ATCC 19404 <- NCTC; NCTC 532 <- M. Robertson; SR 5
123273CIP <- 1979, ATCC <- NCTC 532 <- 1920, M. Robertson, Lister Inst., London, UK: strain SR5

doi: 10.13145/bacdive2712.20250331.9.3

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 sporogenes
  • full scientific name: Clostridium sporogenes (Metchnikoff 1908) Bergey et al. 1923 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacillus sporogenes

@ref: 845

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium sporogenes

full scientific name: Clostridium sporogenes (Metchnikoff 1908) Bergey et al. 1923

strain designation: SR 5, SR5

type strain: no

Morphology

cell morphology

  • @ref: 123273
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 123273
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
845CHOPPED 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
845FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://mediadive.dsmz.de/medium/1203aName: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water
36205MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
845COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
123273CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperature
845positivegrowth37
36205positivegrowth37
123273positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
845anaerobe
123273anaerobe
125439anaerobe99.1

spore formation

  • @ref: 123273
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838017632nitrate-reduction
6838029985L-glutamate-degradation
6838016634raffinose-fermentation
6838016024D-mannose-fermentation
6838029016arginine+hydrolysis
1232734853esculin+hydrolysis
12327317632nitrate-reduction
12327316301nitrite+reduction
6838027897tryptophan-energy source
6838016199urea-hydrolysis
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
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin+hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-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

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
12327335581indoleno
6836735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
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
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
123273oxidase-
123273alcohol dehydrogenase+1.1.1.1
123273catalase-1.11.1.6
123273lysine decarboxylase-4.1.1.18
123273ornithine decarboxylase-4.1.1.17
123273urease-3.5.1.5
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380leucine arylamidase-3.4.11.1
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380urease-3.5.1.5
68367urease-3.5.1.5
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380phenylalanine arylamidase-
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-Galactosidase 6-phosphate-
68380arginine dihydrolase+3.5.3.6
68367beta-glucosidase+3.2.1.21
68367gelatinase+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123273--++-+--+------+----

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
845--+---+---++-------+

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
845-+---+/-+/------------+---+------
845-+----+/------------+----------

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
845gas gangrene
123273Gas gangrene1920

isolation source categories

  • Cat1: #Infection
  • Cat2: #Disease

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
8452Risk group (German classification)
1232732Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium sporogenes ATCC 19404GCA_001573855contigncbi1509
66792Clostridium sporogenes NCTC 532GCA_011019475contigncbi1509
66792Clostridium sporogenes strain ATCC 194041509.40wgspatric1509
66792Clostridium sporogenes strain FDAARGOS_14701509.207completepatric1509
66792Clostridium sporogenes strain NCTC 5321509.155wgspatric1509
66792Clostridium sporogenes ATCC 194042724679562draftimg1509
66792Clostridium sporogenes strain FDAARGOS_14701509.232completepatric1509
66792Clostridium sporogenes strain FDAARGOS_14701509.224completepatric1509
66792Clostridium sporogenes strain FDAARGOS_14701509.215completepatric1509

GC content

  • @ref: 845
  • GC-content: 27.0

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes63.228no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes83.249yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes71.328no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.665no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.616no
125438motile2+flagellatedAbility to perform flagellated movementyes80.28no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes79.4
125439BacteriaNetmotilityAbility to perform movementyes75.9
125439BacteriaNetgram_stainReaction to gram-stainingpositive84.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe99.1

External links

@ref: 845

culture collection no.: DSM 1664, ATCC 19404, CIP 79.3, NCIB 532, NCTC 532, WDCM 00008, NCIMB 532, LMG 10143, CCM 4409, CECT 485, CMCC (B) 64941

straininfo link

  • @ref: 72240
  • straininfo: 1974

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2
Pathogenicity1146437Induction of chain formation in Clostridium sporogenes by suramin.Rafi Shaikh M, Lominski IZentralbl Bakteriol Orig A1975Cell Division/drug effects, Cell Wall/enzymology/ultrastructure, Clostridium/*drug effects/ultrastructure, Muramidase/antagonists & inhibitors, Suramin/*pharmacologyEnzymology
Enzymology1179871Feathery outbrusts of the colonies of Clostridium sporogenes containing chain forming mutants after ultraviolet irradiation.Shaikh MR, Lominski IZentralbl Bakteriol Orig A1975Cell Adhesion, Clostridium/enzymology/*radiation effects, Genetics, Microbial, Mutation/*radiation effects, *Radiation Genetics, *Ultraviolet Rays

Reference

@idauthorscataloguedoi/urltitle
845Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1664)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1664
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
36205Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11025
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
72240Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1974.1StrainInfo: A central database for resolving microbial strain identifiers
123273Curators of the CIPCollection of Institut Pasteur (CIP 79.3)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2079.3
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1