Strain identifier

BacDive ID: 2572

Type strain: Yes

Species: Clostridium cochlearium

Strain Designation: 1243, McClung, 1243, McClung, 10041

Strain history: CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10041 <- ATCC <- L.S. McClung: strain 1243

NCBI tax ID(s): 1494 (species)

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General

@ref: 605

BacDive-ID: 2572

DSM-Number: 1285

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, human pathogen

description: Clostridium cochlearium 1243 is an anaerobe, spore-forming, mesophilic human pathogen that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 1494
  • Matching level: species

strain history

@refhistory
605<- ATCC <- L. S. McClung, Indiana University, Bacteriological Laboratories, Bloomington, USA; 1243
67770ATCC 17787 <-- L. S. McClung 1243.
118322CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10041 <- ATCC <- L.S. McClung: strain 1243

doi: 10.13145/bacdive2572.20230509.8.1

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 cochlearium
  • full scientific name: Clostridium cochlearium (Douglas et al. 1919) Bergey et al. 1923 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Clostridium lentoputrescens
    20215Bacillus cochlearius

@ref: 605

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium cochlearium

full scientific name: Clostridium cochlearium (Douglas et al. 1919) Bergey et al. 1923

strain designation: 1243, McClung, 1243, McClung, 10041

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
605CHOPPED 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
37058MEDIUM 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)
118322CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
605positivegrowth37mesophilic
37058positivegrowth37mesophilic
50678positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
605anaerobe
50678anaerobe
69480anaerobe99.554

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 100

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_16844.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_643;97_746;98_865;99_16844&stattab=map
  • Last taxonomy: Clostridium cochlearium
  • 16S sequence: AB538429
  • Sequence Identity:
  • Total samples: 3721
  • soil counts: 855
  • aquatic counts: 733
  • animal counts: 1929
  • plant counts: 204

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
605yes, in single cases1Risk group (German classification)
1183222Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium cochlearium strain ATCC 17787 16S ribosomal RNA gene, partial sequenceDQ911265318ena1494
20218Clostridium cochlearium strain ATCC 17787 16S ribosomal RNA gene, partial sequenceM590931460ena1494
605Clostridium cochlearium gene for 16S ribosomal RNA, partial sequence, strain: JCM 1396AB5384291474ena1494

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium cochlearium NCTC13027GCA_900187165completencbi1494
66792Clostridium cochlearium strain NCTC130271494.5completepatric1494
66792Clostridium cochlearium NCTC 130272773857856completeimg1494
67770Clostridium cochlearium strain NCTC13027 genome assembly, chromosome: 1LT906477ncbi1494

GC content

@refGC-contentmethod
60528.0
6777028thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes88no
motileyes77.508no
flagellatedno58.695no
gram-positiveyes65.839no
anaerobicyes99.577yes
aerobicno97.849yes
halophileno86.437no
spore-formingyes96.828no
thermophileno86.576yes
glucose-utilyes81.992no
glucose-fermentyes59.992no

External links

@ref: 605

culture collection no.: DSM 1285, ATCC 17787, JCM 1396, NCIMB 10633, CCUG 31665, BCRC 14471, CIP 104319, NCTC 13027

straininfo link

  • @ref: 72105
  • straininfo: 36726

literature

  • topic: Genetics
  • Pubmed-ID: 32586862
  • title: Draft Genome Sequence of Clostridium cochlearium Strain AGROS13, Isolated from a Sheep Dairy Farm in New Zealand.
  • authors: Gupta TB, Maclean P, Jauregui R, Risson AN, Brightwell G
  • journal: Microbiol Resour Announc
  • DOI: 10.1128/MRA.00593-20
  • year: 2020
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
605Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1285)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1285
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
37058Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16215
50678Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 31665)https://www.ccug.se/strain?id=31665
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)
72105Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36726.1StrainInfo: A central database for resolving microbial strain identifiers
118322Curators of the CIPCollection of Institut Pasteur (CIP 104319)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104319