Strain identifier

BacDive ID: 2713

Type strain: Yes

Species: Clostridium putrificum

Strain Designation: 2318, Prévot, 2318, Prévot, Prévot 2318

Strain history: CIP <- 1960, A.R. Prévot, Inst. Pasteur, Paris, France: strain 2318, Plectridium putrificum

NCBI tax ID(s): 1491 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 889

BacDive-ID: 2713

DSM-Number: 1734

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

description: Clostridium putrificum 2318 is an anaerobe, spore-forming, mesophilic bacterium of the family Clostridiaceae.

NCBI tax id

  • NCBI tax id: 1491
  • Matching level: species

strain history

@refhistory
889<- NCIB <- G. Hobbs
376061960, A.R. Prévot, Inst. Pasteur, Paris, France: strain 2318, Plectridium putrificum
67770ATCC 25784 <-- L. DS. Smith VPI 4440-1 <-- A. Prévot 2318.
122077CIP <- 1960, A.R. Prévot, Inst. Pasteur, Paris, France: strain 2318, Plectridium putrificum

doi: 10.13145/bacdive2713.20230509.8.1

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 putrificum
  • full scientific name: Clostridium putrificum (Trevisan 1889) Reddish and Rettger 1922 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Pacinia putrifica

@ref: 889

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium putrificum

full scientific name: Clostridium putrificum (Trevisan 1889) Reddish and Rettger 1922

strain designation: 2318, Prévot, 2318, Prévot, Prévot 2318

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes93.385
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
889CHOPPED 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
37606MEDIUM 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)
122077CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
889positivegrowth37mesophilic
37606positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
889anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481yes93
69480yes100

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typeisolation date
37606DakarSenegalSENAfrica
122077DakarSenegalSENAfricaHuman, Blood1960

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: AB558161
  • 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
8892Risk group (German classification)
1220772Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium botulinum strain ATCC 25784 16S ribosomal RNA gene, partial sequenceDQ911257318ena1491
889Clostridium botulinum 16S rRNA gene, strain DSM 1734X734421513ena1491
67770Clostridium sporogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 1410AB5581611473ena1509

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium botulinum strain NCTC130371491.1062wgspatric1491
66792Clostridium sporogenes strain FDAARGOS_15321509.235completepatric1509
66792Clostridium sporogenes strain FDAARGOS_15321509.218completepatric1509
66792Clostridium sporogenes strain FDAARGOS_15321509.227completepatric1509

GC content

@refGC-contentmethod
88927.0
6777027thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes93no
motileyes84.461no
gram-positiveyes90.88no
anaerobicyes97.413yes
aerobicno96.982no
halophileno78.898no
spore-formingyes93.349no
thermophileno97.11yes
glucose-utilyes85.49no
flagellatedyes51.416no
glucose-fermentyes64.072no

External links

@ref: 889

culture collection no.: DSM 1734, ATCC 25784, NCIB 10677, Prevot 2318, VPI 4440-1, CCUG 15942, JCM 1410, BCRC 14514, CIP 60.54, NCIMB 10677, NCTC 13037, VPI 4440

straininfo link

  • @ref: 72241
  • straininfo: 38669

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
889Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1734)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1734
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
37606Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/9871
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/
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
72241Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38669.1StrainInfo: A central database for resolving microbial strain identifiers
122077Curators of the CIPCollection of Institut Pasteur (CIP 60.54)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2060.54