Strain identifier

BacDive ID: 2783

Type strain: Yes

Species: Clostridium pascui

Strain Designation: Cm19, Cm 19

Strain history: CIP <- 1997, H. Hippe, Germany: strain Cm 19 <- N. Tosunoglu

NCBI tax ID(s): 46609 (species)

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

@ref: 3918

BacDive-ID: 2783

DSM-Number: 10365

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

description: Clostridium pascui Cm19 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from soil, donkey pasture.

NCBI tax id

  • NCBI tax id: 46609
  • Matching level: species

strain history

@refhistory
3918<- E. Wilde and H. Hippe; Cm19 <- N. Tosunoglu {1981}
121616CIP <- 1997, H. Hippe, Germany: strain Cm 19 <- N. Tosunoglu

doi: 10.13145/bacdive2783.20230509.8.1

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 pascui
  • full scientific name: Clostridium pascui Wilde et al. 1997

@ref: 3918

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium pascui

full scientific name: Clostridium pascui Wilde et al. 1997

strain designation: Cm19, Cm 19

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes91.303
69480100positive
121616nopositiverod-shaped

colony morphology

  • @ref: 121616

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3918WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)yeshttps://mediadive.dsmz.de/medium/339Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
3918CHOPPED 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
39214MEDIUM 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)
121616CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
3918positivegrowth37mesophilic
39214positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
3918anaerobe
69480anaerobe99.251

spore formation

@refspore formationconfidence
69481yes100
69480yes100
121616yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12161615824D-fructose-degradation
12161617634D-glucose-degradation
12161665327D-xylose-degradation
12161617057cellobiose-degradation
12161617716lactose-degradation
12161617306maltose-degradation
12161617814salicin-degradation
12161617992sucrose-degradation
1216164853esculin-hydrolysis
12161617632nitrate-reduction
12161616301nitrite-reduction
12161617632nitrate+respiration

metabolite production

  • @ref: 121616
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

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
121616oxidase-
121616beta-galactosidase+3.2.1.23
121616gelatinase-
121616catalase-1.11.1.6
121616urease-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
121616----------++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121616---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
3918soil, donkey pasturePakistanPAKAsia
121616Environment, Donkey, pasture soilPakistanPAKAsia1981

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Grassland
#Environmental#Terrestrial#Soil
#Host#Mammals#Equidae (Horse)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5428.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_2632;97_3224;98_4051;99_5428&stattab=map
  • Last taxonomy: Clostridium pascui
  • 16S sequence: NR_026322
  • Sequence Identity:
  • Total samples: 1907
  • soil counts: 839
  • aquatic counts: 543
  • animal counts: 469
  • plant counts: 56

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
39181Risk group (German classification)
1216162Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.pascui 16S rRNA geneX967361471ena46609
3918Clostridium pascui strain DSM 10365 16S ribosomal RNA, partial sequenceNR_0263221471nuccore46609

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium pascui DSM 10365GCA_016908015contigncbi46609
66792Clostridium pascui strain DSM 1036546609.3wgspatric46609
66792Clostridium pascui DSM 103652901044109draftimg46609

GC content

  • @ref: 3918
  • GC-content: 27
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveno52.644no
anaerobicyes98.892yes
halophileno94.092no
spore-formingyes94.428no
glucose-utilyes86.208no
aerobicno97.432no
flagellatedyes66.417no
thermophileno94.123no
motileyes84.984no
glucose-fermentyes52.814no

External links

@ref: 3918

culture collection no.: DSM 10365, CIP 105172, JCM 11012

straininfo link

  • @ref: 72310
  • straininfo: 48820

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism8995820Clostridium pascui sp. nov., a new glutamate-fermenting sporeformer from a pasture in Pakistan.Wilde E, Collins MD, Hippe HInt J Syst Bacteriol10.1099/00207713-47-1-1641997Acetates/metabolism, Bacterial Proteins/analysis, Bacteriological Techniques, Base Composition, Butyrates/metabolism, Carbon Dioxide/metabolism, Clostridium/chemistry/*classification/genetics/metabolism, Culture Media/metabolism, Ethanol/metabolism, Fatty Acids/analysis, Fermentation, Glutamates/metabolism, Histidine/metabolism, Hydrogen/metabolism, Indoles/metabolism, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, Pakistan, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Soil MicrobiologyPhylogeny
Phylogeny16514039Clostridium lundense sp. nov., a novel anaerobic lipolytic bacterium isolated from bovine rumen.Cirne DG, Delgado OD, Marichamy S, Mattiasson BInt J Syst Evol Microbiol10.1099/ijs.0.63730-02006Animals, Cattle/*microbiology, Clostridium/*classification/genetics/isolation & purification/physiology, DNA, Ribosomal/chemistry, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sequence Analysis, DNAPhenotype
Phylogeny16957104Gracilibacter thermotolerans gen. nov., sp. nov., an anaerobic, thermotolerant bacterium from a constructed wetland receiving acid sulfate water.Lee YJ, Romanek CS, Mills GL, Davis RC, Whitman WB, Wiegel JInt J Syst Evol Microbiol10.1099/ijs.0.64040-02006Bacteria, Anaerobic/classification/metabolism, Clostridium/classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, RNA, Ribosomal, 16S/analysis/genetics, Sulfates/*metabolism, Water MicrobiologyMetabolism
Phylogeny26597830Clostridium liquoris sp. nov., isolated from a fermentation pit used for the production of Chinese strong-flavoured liquor.Yin Q, Tao Y, Zhu X, Zhou Y, He X, Cheng L, Huang Y, Li DInt J Syst Evol Microbiol10.1099/ijsem.0.0007872015Biotechnology
Phylogeny31199222Clostridium prolinivorans sp. nov., a thermophilic bacterium isolated from an anaerobic reactor degrading propionate.Huang Y, Wei Z, Cong L, Qiu Z, Chen R, Deng Y, Zhang Y, Fan H, Ma SInt J Syst Evol Microbiol10.1099/ijsem.0.0035232019Anaerobiosis, Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Clostridium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Propionates/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3918Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10365)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10365
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
39214Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17162
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)
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
72310Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48820.1StrainInfo: A central database for resolving microbial strain identifiers
121616Curators of the CIPCollection of Institut Pasteur (CIP 105172)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105172