Strain identifier

BacDive ID: 2754

Type strain: Yes

Species: Clostridium colinum

Strain Designation: 72042

Strain history: ATCC 27770 <-- G. A. Berkhoff 72042.

NCBI tax ID(s): 36835 (species)

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General

@ref: 2418

BacDive-ID: 2754

DSM-Number: 6011

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, animal pathogen

description: Clostridium colinum 72042 is an anaerobe, mesophilic animal pathogen that was isolated from chicken with ulcerative enteritis.

NCBI tax id

  • NCBI tax id: 36835
  • Matching level: species

strain history

@refhistory
2418<- ATCC <- G.A. Berkhoff, 72042
67770ATCC 27770 <-- G. A. Berkhoff 72042.

doi: 10.13145/bacdive2754.20230509.8.1

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 colinum
  • full scientific name: Clostridium colinum (ex Berkhoff et al. 1974) Berkhoff 1985

  • synonyms

    • @ref: 20215
    • synonym: Tyzzerella colina

@ref: 2418

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium colinum

full scientific name: Clostridium colinum (ex Berkhoff et al. 1974) Berkhoff 1985

strain designation: 72042

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 2418
  • name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/110
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
2418positivegrowth35mesophilic
47519positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2418anaerobe
47519anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase+3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    47519C10:026.610
    47519C12:05.912
    47519C14:03.214
    47519C18:0818
    47519C20:045.220
    47519C18:1 ω9c2.217.769
    47519C18:2 ω6,9c/C18:0 ANTE3.217.724
    47519C20:1 ω9c2.719.77
    47519C20:2 ω6,9c0.919.735
    47519Unidentified2
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
2418-----++-+-++-----------------

Isolation, sampling and environmental information

isolation

@refsample type
2418chicken with ulcerative enteritis
47519Chicken with ulcerative enteritis
67770Chicken with ulcerative enteritis

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Birds#Chicken
#Host#Microbial#Bacteria

taxonmaps

  • @ref: 69479
  • File name: preview.99_58195.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1060;96_5187;97_32331;98_41439;99_58195&stattab=map
  • Last taxonomy: [Clostridium] colinum subclade
  • 16S sequence: X76748
  • Sequence Identity:
  • Total samples: 906
  • soil counts: 4
  • aquatic counts: 8
  • animal counts: 890
  • plant counts: 4

Safety information

risk assessment

  • @ref: 2418
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium colinum strain DSM 6011 16S ribosomal RNA gene, partial sequenceHM245938842ena36835
2418Clostridium colinum 16S rRNA gene, type strain DSM 6011TX767481473ena36835
67770[Clostridium] colinum gene for 16S ribosomal RNA, partial sequence, strain: JCM 5831LC0110401481ena36835

Genome sequences

  • @ref: 66792
  • description: [Clostridium] colinum DSM 6011
  • accession: GCA_940677205
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 36835

GC content

@refGC-contentmethod
241843.0
6777043thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
aerobicno98.803yes
flagellatedno84.617no
gram-positiveyes89.69no
anaerobicyes98.705yes
halophileno75.434no
spore-formingno68.848no
thermophileno88.109yes
glucose-utilyes84.719no
motileyes76.381no
glucose-fermentyes77.071no

External links

@ref: 2418

culture collection no.: DSM 6011, ATCC 27770, JCM 5831, CCUG 21927, CCM 3932

straininfo link

  • @ref: 72284
  • straininfo: 39168

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2418Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6011)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6011
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
47519Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 21927)https://www.ccug.se/strain?id=21927
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/
68380Automatically annotated from API rID32A
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
72284Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39168.1StrainInfo: A central database for resolving microbial strain identifiers