Strain identifier
BacDive ID: 2563
Type strain:
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)
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 id | Matching level |
---|---|
1316931 | strain |
1492 | species |
strain history
@ref | history |
---|---|
4045 | <- ATCC <- NCTC <- J. W. Howie, strain Rowett |
67770 | ATCC 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
@ref | name | growth | link | composition |
---|---|---|---|---|
4045 | RCM MEDIUM (DSMZ Medium 634) | yes | https://mediadive.dsmz.de/medium/634 | Name: RCM MEDIUM (DSMZ Medium 634) Composition: Sodium resazurin 0.0005 g/l dehydrated RCM medium |
4045 | CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) | yes | https://mediadive.dsmz.de/medium/110 | 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 |
4045 | PY + X MEDIUM (DSMZ Medium 104b) | yes | https://mediadive.dsmz.de/medium/104b | Name: 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 |
33296 | MEDIUM 20 - for Anaerobic bacteria | yes | Agar (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
@ref | growth | type | temperature | range |
---|---|---|---|---|
4045 | positive | growth | 37 | mesophilic |
33296 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
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
@ref | sample type |
---|---|
4045 | intestine of pig |
67770 | Intestine of swine |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Clostridium butyricum gene for 16S rRNA, partial sequence, strain: ATCC 19398 | AB075768 | 1451 | ena | 1492 |
20218 | Clostridium butyricum DNA, 16s-23s intergenic spacer region, clone: A1 | AB178153 | 383 | ena | 1492 |
20218 | Clostridium butyricum DNA, 16s-23s intergenic spacer region, clone: A2 | AB178154 | 470 | ena | 1492 |
20218 | Clostridium butyricum DNA, 16s-23s intergenic spacer region, clone: A3 | AB178155 | 496 | ena | 1492 |
20218 | Clostridium butyricum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1391 | AB595129 | 1474 | ena | 1492 |
20218 | Clostridium butyricum strain ATCC19398 16S ribosomal RNA gene, partial sequence | AF396963 | 371 | ena | 1492 |
20218 | Clostridium butyricum 16S ribosomal RNA | M59085 | 1516 | ena | 1492 |
4045 | Clostridium butyricum partial 16S rRNA gene, strain VPI3266 | AJ458420 | 1425 | ena | 1492 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clostridium butyricum DSM 10702 | GCA_014131795 | complete | ncbi | 1492 |
66792 | Clostridium butyricum NBRC 13949 | GCA_006742065 | complete | ncbi | 1492 |
66792 | Clostridium butyricum NBRC 13949 | GCA_007992895 | contig | ncbi | 1492 |
66792 | Clostridium butyricum DSM 10702 | 1316931.3 | wgs | patric | 1316931 |
66792 | Clostridium butyricum strain DSM 10702 | 1492.204 | complete | patric | 1492 |
66792 | Clostridium butyricum strain NBRC 13949 | 1492.174 | wgs | patric | 1492 |
66792 | Clostridium butyricum strain NBRC 13949 | 1492.171 | wgs | patric | 1492 |
66792 | Clostridium butyricum DSM 10702 | 2554235109 | draft | img | 1316931 |
67770 | Clostridium butyricum DSM 10702 | GCA_000409755 | contig | ncbi | 1316931 |
GC content
- @ref: 4045
- GC-content: 28
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 84.869 | no |
flagellated | yes | 66.269 | no |
gram-positive | yes | 73.809 | no |
anaerobic | yes | 96.975 | yes |
aerobic | no | 96.624 | yes |
halophile | no | 91.758 | no |
spore-forming | yes | 94.624 | no |
glucose-util | yes | 89.786 | no |
thermophile | no | 97.369 | yes |
glucose-ferment | yes | 71.328 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 4020299 | Phosphatidylserine decarboxylase from Clostridium butyricum. | Verma JN, Goldfine H | J Lipid Res | S0022-2275(20)34348-0 | 1985 | Carboxy-Lyases/antagonists & inhibitors/*metabolism, Chromatography, Thin Layer, Clostridium/*enzymology/growth & development, Decarboxylation, Detergents/pharmacology, Phosphatidylserines/metabolism, Plasmalogens/metabolism, Protoplasts/enzymology | Enzymology |
Enzymology | 9353929 | Molecular 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 NP | Microbiology (Reading) | 10.1099/00221287-143-10-3287 | 1997 | Amino 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 Acid | Metabolism |
Enzymology | 9711857 | Molecular 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 NP | FEMS Microbiol Lett | 10.1111/j.1574-6968.1998.tb13146.x | 1998 | Amino 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, Bacterial | Genetics |
Metabolism | 11160107 | Regulation 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 P | J Bacteriol | 10.1128/JB.183.5.1748-1754.2001 | 2001 | Carbon/*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 Force | Cultivation |
Metabolism | 15378388 | Production of 1,3-propanediol by Clostridium butyricum VPI 3266 using a synthetic medium and raw glycerol. | Gonzalez-Pajuelo M, Andrade JC, Vasconcelos I | J Ind Microbiol Biotechnol | 10.1007/s10295-004-0168-z | 2004 | Clostridium butyricum/drug effects/growth & development/*metabolism, Culture Media/*metabolism/pharmacology, Fermentation, Glycerol/*metabolism/pharmacology, Propylene Glycols/*metabolism | Biotechnology |
Biotechnology | 16044292 | Production of 1,3-Propanediol by Clostridium butyricum VPI 3266 in continuous cultures with high yield and productivity. | Gonzalez-Pajuelo M, Andrade JC, Vasconcelos I | J Ind Microbiol Biotechnol | 10.1007/s10295-005-0012-0 | 2005 | Acetates/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/*metabolism | Metabolism |
Metabolism | 16095939 | Metabolic 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 P | Metab Eng | 10.1016/j.ymben.2005.06.001 | 2005 | Cell Culture Techniques/methods, Clostridium acetobutylicum/*genetics/*metabolism, Escherichia coli/*genetics/metabolism, Genetic Enhancement/*methods, Glycerol/*metabolism, Industrial Microbiology/*methods, Propylene Glycols/*metabolism | Biotechnology |
Metabolism | 16321068 | Hydrogen production from glucose by anaerobes. | Ogino H, Miura T, Ishimi K, Seki M, Yoshida H | Biotechnol Prog | 10.1021/bp050224r | 2005 | Bacteria, Anaerobic/*metabolism, Biotechnology, Carbohydrate Metabolism, Clostridium acetobutylicum/metabolism, Clostridium butyricum/metabolism, Culture Media, Enterobacter aerogenes/metabolism, Glucose/*metabolism, Hydrogen/*metabolism, Reducing Agents | Biotechnology |
Metabolism | 16391030 | Microbial 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 I | Appl Environ Microbiol | 10.1128/AEM.72.1.96-101.2006 | 2006 | Clostridium 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/*metabolism | Enzymology |
Genetics | 23908293 | Genome 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 P | Genome Announc | 10.1128/genomeA.00563-13 | 2013 | ||
25401066 | Reduced 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 DB | AMB Express | 10.1186/s13568-014-0063-6 | 2014 | |||
Phylogeny | 28754474 | Description 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 YH | Anaerobe | 10.1016/j.anaerobe.2017.07.006 | 2017 | Animals, 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, DNA | Enzymology |
Metabolism | 29580783 | Enhancement 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 P | J Biosci Bioeng | 10.1016/j.jbiosc.2018.02.017 | 2018 | Biodegradation, 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/*metabolism | Biotechnology |
Pathogenicity | 32066216 | Effect of Probiotic Clostridium butyricum NCTC 7423 Supernatant on Biofilm Formation and Gene Expression of Bacteroides fragilis. | Shin DS, Rhee KJ, Eom YB | J Microbiol Biotechnol | 10.4014/jmb.2001.01027 | 2020 | Anti-Bacterial Agents/pharmacology, Bacteroides fragilis/drug effects/*physiology, *Biofilms, *Clostridium butyricum, Gene Expression, Gene Expression Regulation, Bacterial/*drug effects, Probiotics/*pharmacology | |
Phylogeny | 33555251 | Clostridium vitabionis sp. nov., isolated from the large intestine of a mini-pig. | Shin Y, Paek J, Kim H, Kook JK, Chang YH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004694 | 2021 | ||
Metabolism | 36265075 | Heterologous Gene Regulation in Clostridia: Rationally Designed Gene Regulation for Industrial and Medical Applications. | Zhang Y, Bailey TS, Kubiak AM, Lambin P, Theys J | ACS Synth Biol | 10.1021/acssynbio.2c00401 | 2022 | *Escherichia coli/genetics/metabolism, Codon, Initiator/metabolism, *Escherichia coli K12/genetics, Clostridium/genetics, Promoter Regions, Genetic/genetics, 5' Untranslated Regions | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4045 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10702) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10702 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
33296 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7134 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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 | |||
72096 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92601.1 | StrainInfo: A central database for resolving microbial strain identifiers |