Strain identifier

BacDive ID: 2563

Type strain: Yes

Species: Clostridium butyricum

Strain Designation: Rowett

Strain history: ATCC 19398 <-- NCTC 7423 <-- J. W. Howie strain Rowett.

NCBI tax ID(s): 1316931 (strain), 1492 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4045

BacDive-ID: 2563

DSM-Number: 10702

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

description: Clostridium butyricum Rowett is an anaerobe, mesophilic bacterium that was isolated from intestine of pig.

NCBI tax id

NCBI tax idMatching level
1316931strain
1492species

strain history

@refhistory
4045<- ATCC <- NCTC <- J. W. Howie, strain Rowett
67770ATCC 19398 <-- NCTC 7423 <-- J. W. Howie strain Rowett.

doi: 10.13145/bacdive2563.20230509.8.1

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 butyricum
  • full scientific name: Clostridium butyricum Prazmowski 1880 (Approved Lists 1980)

@ref: 4045

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium butyricum

full scientific name: Clostridium butyricum Prazmowski 1880

strain designation: Rowett

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4045RCM MEDIUM (DSMZ Medium 634)yeshttps://mediadive.dsmz.de/medium/634Name: RCM MEDIUM (DSMZ Medium 634) Composition: Sodium resazurin 0.0005 g/l dehydrated RCM medium
4045CHOPPED 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
4045PY + X MEDIUM (DSMZ Medium 104b)yeshttps://mediadive.dsmz.de/medium/104bName: PY + X MEDIUM (DSMZ Medium 104b) 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 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
33296MEDIUM 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)

culture temp

@refgrowthtypetemperaturerange
4045positivegrowth37mesophilic
33296positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 4045
  • oxygen tolerance: anaerobe

metabolite production

  • @ref: 67770
  • metabolite: butyricin 7423
  • production: yes

Isolation, sampling and environmental information

isolation

@refsample type
4045intestine of pig
67770Intestine of swine

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_535.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_149;97_160;98_434;99_535&stattab=map
  • Last taxonomy: Clostridium butyricum subclade
  • 16S sequence: AB595129
  • Sequence Identity:
  • Total samples: 143517
  • soil counts: 17569
  • aquatic counts: 19472
  • animal counts: 103476
  • plant counts: 3000

Safety information

risk assessment

  • @ref: 4045
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium butyricum gene for 16S rRNA, partial sequence, strain: ATCC 19398AB0757681451ena1492
20218Clostridium butyricum DNA, 16s-23s intergenic spacer region, clone: A1AB178153383ena1492
20218Clostridium butyricum DNA, 16s-23s intergenic spacer region, clone: A2AB178154470ena1492
20218Clostridium butyricum DNA, 16s-23s intergenic spacer region, clone: A3AB178155496ena1492
20218Clostridium butyricum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1391AB5951291474ena1492
20218Clostridium butyricum strain ATCC19398 16S ribosomal RNA gene, partial sequenceAF396963371ena1492
20218Clostridium butyricum 16S ribosomal RNAM590851516ena1492
4045Clostridium butyricum partial 16S rRNA gene, strain VPI3266AJ4584201425ena1492

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium butyricum DSM 10702GCA_014131795completencbi1492
66792Clostridium butyricum NBRC 13949GCA_006742065completencbi1492
66792Clostridium butyricum NBRC 13949GCA_007992895contigncbi1492
66792Clostridium butyricum DSM 107021316931.3wgspatric1316931
66792Clostridium butyricum strain DSM 107021492.204completepatric1492
66792Clostridium butyricum strain NBRC 139491492.174wgspatric1492
66792Clostridium butyricum strain NBRC 139491492.171wgspatric1492
66792Clostridium butyricum DSM 107022554235109draftimg1316931
67770Clostridium butyricum DSM 10702GCA_000409755contigncbi1316931

GC content

  • @ref: 4045
  • GC-content: 28
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes84.869no
flagellatedyes66.269no
gram-positiveyes73.809no
anaerobicyes96.975yes
aerobicno96.624yes
halophileno91.758no
spore-formingyes94.624no
glucose-utilyes89.786no
thermophileno97.369yes
glucose-fermentyes71.328no

External links

@ref: 4045

culture collection no.: DSM 10702, ATCC 19398, IAM 14194, IFO 13949, JCM 1391, NBRC 13949, NCIMB 7423, NCTC 7423, VPI 3266, BCRC 11665, CCUG 4217, CECT 361, CIP 103309, CIP 109397, HAMBI 482, KCTC 1786, KCTC 1871, LMG 1217, NCFB 1713, VTT E-97426

straininfo link

  • @ref: 72096
  • straininfo: 92601

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism4020299Phosphatidylserine decarboxylase from Clostridium butyricum.Verma JN, Goldfine HJ Lipid ResS0022-2275(20)34348-01985Carboxy-Lyases/antagonists & inhibitors/*metabolism, Chromatography, Thin Layer, Clostridium/*enzymology/growth & development, Decarboxylation, Detergents/pharmacology, Phosphatidylserines/metabolism, Plasmalogens/metabolism, Protoplasts/enzymologyEnzymology
Enzymology9353929Molecular analysis of a Clostridium butyricum NCIMB 7423 gene encoding 4-alpha-glucanotransferase and characterization of the recombinant enzyme produced in Escherichia coli.Goda SK, Eissa O, Akhtar M, Minton NPMicrobiology (Reading)10.1099/00221287-143-10-32871997Amino Acid Sequence, Amylose/metabolism, Base Sequence, Cloning, Molecular, Clostridium/*enzymology/*genetics, DNA, Bacterial/genetics, Escherichia coli/enzymology/genetics, *Genes, Bacterial, Glucosyltransferases/genetics, Glycogen Debranching Enzyme System/biosynthesis/*genetics/metabolism, Molecular Sequence Data, Molecular Weight, Open Reading Frames, Recombinant Proteins/biosynthesis/genetics, Sequence Homology, Amino AcidMetabolism
Enzymology9711857Molecular analysis of the malR gene of Clostridium butyricum NCIMB 7423, a member of the LacI-GalR family of repressor proteins.Goda SK, Eisa O, Akhter M, Minton NPFEMS Microbiol Lett10.1111/j.1574-6968.1998.tb13146.x1998Amino Acid Sequence, Bacillus subtilis/genetics, Bacterial Proteins/analysis, Cloning, Molecular, Clostridium/enzymology/*genetics, Escherichia coli/genetics, Genes, Regulator/*genetics, Glycogen Debranching Enzyme System/analysis/genetics/metabolism, Molecular Sequence Data, Open Reading Frames/genetics, Repressor Proteins/chemistry/*genetics, Sequence Homology, Amino Acid, Streptomyces/genetics, Transformation, BacterialGenetics
Metabolism11160107Regulation of carbon and electron flow in Clostridium butyricum VPI 3266 grown on glucose-glycerol mixtures.Saint-Amans S, Girbal L, Andrade J, Ahrens K, Soucaille PJ Bacteriol10.1128/JB.183.5.1748-1754.20012001Carbon/*metabolism, Clostridium/enzymology/*growth & development, Culture Media, Electron Transport, Electrons, *Gene Expression Regulation, Bacterial, Glucose/*metabolism, Glycerol/*metabolism, Hydrogen-Ion Concentration, Phosphates/metabolism, Propylene Glycols/metabolism, Proton-Motive ForceCultivation
Metabolism15378388Production of 1,3-propanediol by Clostridium butyricum VPI 3266 using a synthetic medium and raw glycerol.Gonzalez-Pajuelo M, Andrade JC, Vasconcelos IJ Ind Microbiol Biotechnol10.1007/s10295-004-0168-z2004Clostridium butyricum/drug effects/growth & development/*metabolism, Culture Media/*metabolism/pharmacology, Fermentation, Glycerol/*metabolism/pharmacology, Propylene Glycols/*metabolismBiotechnology
Biotechnology16044292Production of 1,3-Propanediol by Clostridium butyricum VPI 3266 in continuous cultures with high yield and productivity.Gonzalez-Pajuelo M, Andrade JC, Vasconcelos IJ Ind Microbiol Biotechnol10.1007/s10295-005-0012-02005Acetates/analysis, Aldehydes/analysis, Biomass, Butyrates/analysis, Clostridium butyricum/growth & development/*metabolism, Culture Media/chemistry, Fermentation, Glyceraldehyde/analogs & derivatives/analysis, Glycerol/metabolism, Industrial Microbiology, Propane/analysis, Propylene Glycols/*metabolismMetabolism
Metabolism16095939Metabolic engineering of Clostridium acetobutylicum for the industrial production of 1,3-propanediol from glycerol.Gonzalez-Pajuelo M, Meynial-Salles I, Mendes F, Andrade JC, Vasconcelos I, Soucaille PMetab Eng10.1016/j.ymben.2005.06.0012005Cell Culture Techniques/methods, Clostridium acetobutylicum/*genetics/*metabolism, Escherichia coli/*genetics/metabolism, Genetic Enhancement/*methods, Glycerol/*metabolism, Industrial Microbiology/*methods, Propylene Glycols/*metabolismBiotechnology
Metabolism16321068Hydrogen production from glucose by anaerobes.Ogino H, Miura T, Ishimi K, Seki M, Yoshida HBiotechnol Prog10.1021/bp050224r2005Bacteria, Anaerobic/*metabolism, Biotechnology, Carbohydrate Metabolism, Clostridium acetobutylicum/metabolism, Clostridium butyricum/metabolism, Culture Media, Enterobacter aerogenes/metabolism, Glucose/*metabolism, Hydrogen/*metabolism, Reducing AgentsBiotechnology
Metabolism16391030Microbial conversion of glycerol to 1,3-propanediol: physiological comparison of a natural producer, Clostridium butyricum VPI 3266, and an engineered strain, Clostridium acetobutylicum DG1(pSPD5).Gonzalez-Pajuelo M, Meynial-Salles I, Mendes F, Soucaille P, Vasconcelos IAppl Environ Microbiol10.1128/AEM.72.1.96-101.20062006Clostridium acetobutylicum/*enzymology/*genetics/growth & development/metabolism, Clostridium butyricum/*enzymology/genetics/growth & development/metabolism, Culture Media, Gene Expression Regulation, Bacterial, Genetic Engineering/*methods, Glycerol/*metabolism, NAD/metabolism, Plasmids, Propylene Glycols/*metabolismEnzymology
Genetics23908293Genome Sequence of Clostridium butyricum Strain DSM 10702, a Promising Producer of Biofuels and Biochemicals.Xin B, Tao F, Wang Y, Gao C, Ma C, Xu PGenome Announc10.1128/genomeA.00563-132013
25401066Reduced catabolic protein expression in Clostridium butyricum DSM 10702 correlate with reduced 1,3-propanediol synthesis at high glycerol loading.Gungormusler-Yilmaz M, Shamshurin D, Grigoryan M, Taillefer M, Spicer V, Krokhin OV, Sparling R, Levin DBAMB Express10.1186/s13568-014-0063-62014
Phylogeny28754474Description of Absiella argi gen. nov., sp. nov., and transfer of Eubacterium dolichum and Eubacterium tortuosum to the genus Absiella as Absiella dolichum comb. nov. and Absiella tortuosum comb. nov.Paek J, Shin Y, Kim JS, Kim H, Kook JK, Paek WK, Chang YHAnaerobe10.1016/j.anaerobe.2017.07.0062017Animals, Bacterial Typing Techniques/*veterinary, Base Composition/genetics, Clostridium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Dogs, Eubacterium/*classification/genetics/isolation & purification, Fatty Acids/analysis, Firmicutes/*classification/genetics/isolation & purification, Intestines/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Metabolism29580783Enhancement of fermentative hydrogen production from Spirogyra sp. by increased carbohydrate accumulation and selection of the biomass pretreatment under a biorefinery model.Pinto T, Gouveia L, Ortigueira J, Saratale GD, Moura PJ Biosci Bioeng10.1016/j.jbiosc.2018.02.0172018Biodegradation, Environmental, Biofuels, *Biomass, *Bioreactors/microbiology, Biotechnology/economics/*methods/standards, Carbohydrate Metabolism/*physiology, Carbohydrates, *Fermentation, Green Chemistry Technology/economics/methods/standards, Hydrogen/*metabolism, Hydrolysis, Microalgae/metabolism, Models, Theoretical, Nitrogen/metabolism, Spirogyra/*metabolismBiotechnology
Pathogenicity32066216Effect of Probiotic Clostridium butyricum NCTC 7423 Supernatant on Biofilm Formation and Gene Expression of Bacteroides fragilis.Shin DS, Rhee KJ, Eom YBJ Microbiol Biotechnol10.4014/jmb.2001.010272020Anti-Bacterial Agents/pharmacology, Bacteroides fragilis/drug effects/*physiology, *Biofilms, *Clostridium butyricum, Gene Expression, Gene Expression Regulation, Bacterial/*drug effects, Probiotics/*pharmacology
Phylogeny33555251Clostridium vitabionis sp. nov., isolated from the large intestine of a mini-pig.Shin Y, Paek J, Kim H, Kook JK, Chang YHInt J Syst Evol Microbiol10.1099/ijsem.0.0046942021
Metabolism36265075Heterologous Gene Regulation in Clostridia: Rationally Designed Gene Regulation for Industrial and Medical Applications.Zhang Y, Bailey TS, Kubiak AM, Lambin P, Theys JACS Synth Biol10.1021/acssynbio.2c004012022*Escherichia coli/genetics/metabolism, Codon, Initiator/metabolism, *Escherichia coli K12/genetics, Clostridium/genetics, Promoter Regions, Genetic/genetics, 5' Untranslated RegionsGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4045Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10702)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10702
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
33296Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7134
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
72096Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92601.1StrainInfo: A central database for resolving microbial strain identifiers