Strain identifier

BacDive ID: 2820

Type strain: Yes

Species: Clostridium colicanis

Strain Designation: 3WC2

Strain history: CIP <- 2009, DSMZ <- H.L. Greetham: strain 3WC2

NCBI tax ID(s): 1121305 (strain), 179628 (species)

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General

@ref: 5026

BacDive-ID: 2820

DSM-Number: 13634

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

description: Clostridium colicanis 3WC2 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from canine individual .

NCBI tax id

NCBI tax idMatching level
1121305strain
179628species

strain history

@refhistory
5026<- H. L. Greetham, FMSU, Univ. Reading, Early Gate, United Kingdom; 3WC2 <- H. L. Greetham {2000}
118700CIP <- 2009, DSMZ <- H.L. Greetham: strain 3WC2

doi: 10.13145/bacdive2820.20230509.8.1

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 colicanis
  • full scientific name: Clostridium colicanis Greetham et al. 2003

@ref: 5026

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium colicanis

full scientific name: Clostridium colicanis Greetham et al. 2003

strain designation: 3WC2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes93.843
69480100positive
118700nopositiverod-shaped

colony morphology

  • @ref: 118700

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5026PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)yeshttps://mediadive.dsmz.de/medium/104cName: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l Na2CO3 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water
33889MEDIUM 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)
118700CIP Medium 137yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=137
118700CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
5026positivegrowth37mesophilic
33889positivegrowth37mesophilic
56376positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
5026anaerobe
56376anaerobe
69480anaerobe99.999
118700anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100
118700yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11870017108D-arabinose-degradation
11870015824D-fructose-degradation
11870017634D-glucose-degradation
11870065327D-xylose-degradation
11870017057cellobiose-degradation
11870017716lactose-degradation
11870017306maltose-degradation
11870017814salicin-degradation
11870017992sucrose-degradation
1187004853esculin-hydrolysis
11870017632nitrate+reduction
11870016301nitrite-reduction
11870017632nitrate+respiration

metabolite production

  • @ref: 118700
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
118700oxidase-
118700beta-galactosidase+3.2.1.23
118700gelatinase+/-
118700amylase-
118700DNase-
118700caseinase+3.4.21.50
118700catalase+1.11.1.6
118700tween esterase-
118700lecithinase-
118700lipase-
118700protease-
118700urease+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
118700----------++-++-----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5026canine individual (gut bacterial)United KingdomGBREurope
56376Canine,feces of a male Labrador
118700Animal, Canine individualUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Canidae (Dog)
#Host#Microbial#Bacteria
#Host Body-Site#Gastrointestinal tract#Stomach

taxonmaps

  • @ref: 69479
  • File name: preview.99_7500.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_3501;97_4291;98_5494;99_7500&stattab=map
  • Last taxonomy: Clostridium colicanis subclade
  • 16S sequence: AJ420008
  • Sequence Identity:
  • Total samples: 2088
  • soil counts: 83
  • aquatic counts: 103
  • animal counts: 1862
  • plant counts: 40

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
50261Risk group (German classification)
1187002Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5026
  • description: Clostridium colicanis 16S rRNA gene, strain 13634
  • accession: AJ420008
  • length: 1435
  • database: ena
  • NCBI tax ID: 179628

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium colicanis DSM 13634GCA_001593985contigncbi1121305
66792Clostridium colicanis DSM 136341121305.3wgspatric1121305
66792Clostridium colicanis 3WC22651869946draftimg179628
66792Clostridium colicanis DSM 136342724679202draftimg1121305

GC content

  • @ref: 5026
  • GC-content: 31.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes78.103no
flagellatedno58.471no
gram-positiveyes68.412no
anaerobicyes99.526yes
aerobicno98.755yes
halophileno78.529no
spore-formingyes86.185no
thermophileno51.475yes
glucose-utilyes84.598no
glucose-fermentyes55.716no

External links

@ref: 5026

culture collection no.: DSM 13634, CCUG 44556, CIP 108095, JCM 12244

straininfo link

  • @ref: 72344
  • straininfo: 100602

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656182Clostridium colicanis sp. nov., from canine faeces.Greetham HL, Gibson GR, Giffard C, Hippe H, Merkhoffer B, Steiner U, Falsen E, Collins MDInt J Syst Evol Microbiol10.1099/ijs.0.02260-02003Animals, Base Composition, Clostridium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Dogs, Feces/microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny27198021First Insights into the Draft Genome of Clostridium colicanis DSM 13634, Isolated from Canine Feces.Poehlein A, Schilling T, Bhaskar Sathya Narayanan U, Daniel RGenome Announc10.1128/genomeA.00385-162016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5026Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13634)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13634
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
33889Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5679
56376Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 44556)https://www.ccug.se/strain?id=44556
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
72344Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100602.1StrainInfo: A central database for resolving microbial strain identifiers
118700Curators of the CIPCollection of Institut Pasteur (CIP 108095)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108095