Strain identifier

BacDive ID: 2710

Type strain: Yes

Species: Clostridium sporogenes

Strain Designation: McClung 2004, 388

Strain history: CIP <- 1999, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 10088 <- ATCC <- I.C. Hall <- E. Peterson

NCBI tax ID(s): 1509 (species)

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General

@ref: 452

BacDive-ID: 2710

DSM-Number: 795

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, rod-shaped

description: Clostridium sporogenes McClung 2004 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1509
  • Matching level: species

strain history

@refhistory
452<- ATCC; ATCC 3584 <- J.C. Hall; 388 <- E.C. Peterson;
67770ATCC 3584 <-- J. C. Hall 388 <-- E. C. Peterson (L. S. McClung 2004).
123271CIP <- 1999, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 10088 <- ATCC <- I.C. Hall <- E. Peterson

doi: 10.13145/bacdive2710.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: 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: 452

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: McClung 2004, 388

type strain: yes

Morphology

cell morphology

@refcell shapemotilityconfidencegram stain
68367rod-shaped
69480yes93.123
69480100positive
123271rod-shapednopositive

colony morphology

  • @ref: 123271
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
452COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
452CHOPPED 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
40299MEDIUM 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)
452FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1203a.pdf
123271CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
452positivegrowth37mesophilic
40299positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
452anaerobe
69480anaerobe99.999
123271anaerobe

spore formation

@refspore formationconfidence
69481yes91
69480yes100
123271yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose+builds acid from
6836762345L-rhamnose-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
1232714853esculin+hydrolysis
12327117632nitrate-reduction
12327116301nitrite+reduction
12327117632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
12327135581indoleno

metabolite tests

  • @ref: 68367
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

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
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
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 lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68367catalase-1.11.1.6
68367beta-glucosidase+3.2.1.21
68367gelatinase+
68367urease-3.5.1.5
123271oxidase-
123271beta-galactosidase-3.2.1.23
123271gelatinase+
123271amylase-
123271DNase+
123271caseinase+3.4.21.50
123271catalase-1.11.1.6
123271tween esterase-
123271lecithinase-
123271lipase+
123271protease-
123271urease-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
123271--++----+-++--------

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECATCOCC
452--+---+---++-----+/--+
452--+---+---++-------+--

Isolation, sampling and environmental information

isolation

@refsample type
452soil
67770Soil
123271Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_324.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_226;97_248;98_277;99_324&stattab=map
  • Last taxonomy: Clostridium
  • 16S sequence: AB595130
  • Sequence Identity:
  • Total samples: 41972
  • soil counts: 4923
  • aquatic counts: 3962
  • animal counts: 31978
  • plant counts: 1109

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
4522Risk group (German classification)
1232712Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium sporogenes strain ATCC 3584 16S ribosomal RNA gene, partial sequenceDQ911258318ena1509
20218Clostridium sporogenes 16S ribosomal RNAM591151463ena1509
452Clostridium sporogenes rrn gene for 16S RNAX681891510ena1509
67770Clostridium sporogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 1416AB5951301473ena1509

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium sporogenes DSM 795GCA_001020205completencbi1509
66792Clostridium sporogenes NCIMB 10696GCA_000973705completencbi1509
66792Clostridium sporogenes strain ATCC 35841509.66wgspatric1509
66792Clostridium sporogenes strain DSM 7951509.5wgspatric1509
66792Clostridium sporogenes strain DSM 7951509.39completepatric1509
66792Clostridium sporogenes strain NCIMB 106961509.28completepatric1509
66792Clostridium sporogenes strain NCTC130201509.100wgspatric1509
66792Clostridium sporogenes NCIMB 106962627853631completeimg1509
66792Clostridium sporogenes 388, DSM 7952562617037draftimg1509
66792Clostridium sporogenes DSM 7952636415665completeimg1509
67770Clostridium sporogenes DSM 795GCA_000685115contigncbi1509
67770Clostridium sporogenes ATCC 3584GCA_002008145contigncbi1509
67770Clostridium sporogenes NCTC13020GCA_900461305contigncbi1509

GC content

@refGC-contentmethod
45226.0
6777026thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes91no
motileyes82.447no
flagellatedyes51.208no
gram-positiveyes91.068no
anaerobicyes97.551no
aerobicno97.126yes
halophileno79.655no
spore-formingyes93.373no
thermophileno98.071yes
glucose-utilyes85.039no
glucose-fermentyes64.373no

External links

@ref: 452

culture collection no.: DSM 795, ATCC 3584, IFO 13950, NBRC 13950, NCIB 10696, JCM 1416, BCRC 11259, CCUG 15941, CECT 892, CIP 106155, LMG 8421, NCIMB 10696, NCTC 13020, AIP 10088

straininfo link

  • @ref: 72238
  • straininfo: 13623

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Biotechnology8486848Growth of Listeria monocytogenes and Clostridium sporogenes in cottage cheese in modified atmosphere packaging.Chen JH, Hotchkiss JHJ Dairy Sci10.3168/jds.S0022-0302(93)77424-X1993Carbon Dioxide, Cheese/*microbiology, Clostridium/*growth & development, *Food Handling, *Food Microbiology, Listeria monocytogenes/*growth & development, Time Factors
9281845Exosporial membrane plasticity of Clostridium sporogenes and Clostridium difficile.Panessa-Warren BJ, Tortora GT, Warren JBTissue Cell10.1016/s0040-8166(97)80031-61997Bacterial Adhesion, Cell Membrane/*ultrastructure, Clostridioides difficile/*cytology, Clostridium/*cytology, Microscopy, Electron, Scanning, Spores, Bacterial/cytology
Metabolism20453132Regulation of neurotoxin production and sporulation by a Putative agrBD signaling system in proteolytic Clostridium botulinum.Cooksley CM, Davis IJ, Winzer K, Chan WC, Peck MW, Minton NPAppl Environ Microbiol10.1128/AEM.03038-092010*Bacterial Proteins/genetics/metabolism, Bacterial Toxins/biosynthesis, Clostridium/genetics/metabolism/physiology, *Clostridium botulinum/genetics/metabolism/physiology, *Gene Expression Regulation, Bacterial, Molecular Sequence Data, Neurotoxins/*biosynthesis, Quorum Sensing, Sequence Analysis, DNA, *Signal Transduction, Spores, Bacterial/*physiologyPathogenicity
Pathogenicity21470574Antimicrobial properties of stem bark extracts from Phyllanthus muellerianus (Kuntze) Excell.Brusotti G, Cesari I, Frassa G, Grisoli P, Dacarro C, Caccialanza GJ Ethnopharmacol10.1016/j.jep.2011.03.0422011Anti-Infective Agents/*pharmacology, Blacks, Clostridium/*drug effects, Humans, Medicine, Traditional, Microbial Sensitivity Tests, *Phyllanthus, Phytotherapy, Plant Bark, Plant Extracts/*pharmacology, Plant Stems, Streptococcus/*drug effects, Tetanus
Pathogenicity21569941Reduction of Clostridium sporogenes spore outgrowth in natural sausage casings using nisin.Wijnker JJ, Weerts EA, Breukink EJ, Houben JH, Lipman LJFood Microbiol10.1016/j.fm.2011.01.0092011Clostridium/*drug effects/growth & development, Food Preservation/*methods, Food Preservatives/*pharmacology, Nisin/*pharmacology, Spores, Bacterial/drug effects/*growth & development
Pathogenicity22683494Chemical composition and antimicrobial activity of Phyllanthus muellerianus (Kuntze) Excel essential oil.Brusotti G, Cesari I, Gilardoni G, Tosi S, Grisoli P, Picco AM, Caccialanza GJ Ethnopharmacol10.1016/j.jep.2012.05.0322012*Anti-Infective Agents/chemistry/pharmacology, Candida albicans/drug effects, Clostridium/drug effects, Escherichia coli/drug effects, Microbial Sensitivity Tests, Microsporum/drug effects, *Oils, Volatile/chemistry/pharmacology, *Phyllanthus, Plant Bark/chemistry, Streptococcus/drug effects, Trichophyton/drug effects
Metabolism25163827Clostridium sporogenes delivers interleukin-12 to hypoxic tumours, producing antitumour activity without significant toxicity.Zhang YL, Lu R, Chang ZS, Zhang WQ, Wang QB, Ding SY, Zhao WLett Appl Microbiol10.1111/lam.123222014Animals, Cell Hypoxia, Clostridium/*genetics/growth & development/metabolism, Female, Genetic Therapy, Genetic Vectors, Interferon-gamma/biosynthesis/blood, Interleukin-12/genetics/*metabolism, Mammary Neoplasms, Experimental/immunology/*microbiology/*therapy, Mice, Inbred BALB C, Recombinant Proteins/metabolism
Pathogenicity26185111The differential effects of heat-shocking on the viability of spores from Bacillus anthracis, Bacillus subtilis, and Clostridium sporogenes after treatment with peracetic acid- and glutaraldehyde-based disinfectants.March JK, Pratt MD, Lowe CW, Cohen MN, Satterfield BA, Schaalje B, O'Neill KL, Robison RAMicrobiologyopen10.1002/mbo3.2772015Colony Count, Microbial, Disinfectants/*toxicity, Glutaral/*toxicity, Gram-Positive Bacteria/drug effects/*radiation effects, *Hot Temperature, Microbial Viability/drug effects/*radiation effects, Peracetic Acid/*toxicity, Spores, Bacterial/drug effects/*radiation effectsStress
Genetics26221421Genome sequence of Clostridium sporogenes DSM 795(T), an amino acid-degrading, nontoxic surrogate of neurotoxin-producing Clostridium botulinum.Poehlein A, Riegel K, Konig SM, Leimbach A, Daniel R, Durre PStand Genomic Sci10.1186/s40793-015-0016-y2015
Genetics26227598First Complete Genome Sequence of Clostridium sporogenes DSM 795T, a Nontoxigenic Surrogate for Clostridium botulinum, Determined Using PacBio Single-Molecule Real-Time Technology.Nakano K, Terabayashi Y, Shiroma A, Shimoji M, Tamotsu H, Ashimine N, Ohki S, Shinzato M, Teruya K, Satou K, Hirano TGenome Announc10.1128/genomeA.00832-152015
Genetics26294634Complete Genome Sequence of the Nonpathogenic Soil-Dwelling Bacterium Clostridium sporogenes Strain NCIMB 10696.Kubiak AM, Poehlein A, Budd P, Kuehne SA, Winzer K, Theys J, Lambin P, Daniel R, Minton NPGenome Announc10.1128/genomeA.00942-152015
Enzymology29111967Recombinant expression and characterisation of the oxygen-sensitive 2-enoate reductase from Clostridium sporogenes.Mordaka PM, Hall SJ, Minton N, Stephens GMicrobiology (Reading)10.1099/mic.0.0005682017*Anaerobiosis, Bacterial Proteins/biosynthesis/*genetics/*metabolism, Biocatalysis, Cloning, Molecular, Clostridium/*enzymology/genetics, Escherichia coli/enzymology/genetics, Gene Expression, Genes, Bacterial/genetics, Oxidation-Reduction, Oxidoreductases Acting on CH-CH Group Donors/biosynthesis/*genetics/*metabolism, Recombinant Proteins/biosynthesis/genetics/metabolismMetabolism
Metabolism36265075Heterologous Gene Regulation in Clostridia: Rationally Designed Gene Regulation for Industrial and Medical Applications.Zhang Y, Bailey TS, Kubiak AM, Lambin P, Theys JACS Synth Biol10.1021/acssynbio.2c004012022*Escherichia coli/genetics/metabolism, Codon, Initiator/metabolism, *Escherichia coli K12/genetics, Clostridium/genetics, Promoter Regions, Genetic/genetics, 5' Untranslated RegionsGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
452Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 795)https://www.dsmz.de/collection/catalogue/details/culture/DSM-795
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
40299Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18254
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72238Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13623.1StrainInfo: A central database for resolving microbial strain identifiers
123271Curators of the CIPCollection of Institut Pasteur (CIP 106155)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106155