Strain identifier

BacDive ID: 2548

Type strain: Yes

Species: Clostridium beijerinckii

Strain Designation: E. McCoy A-67, L.S. McClung 1671, 10026

Strain history: CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10026 <- ATCC <- L.D.S. Smith: strain VPI 5481

NCBI tax ID(s): 1520 (species)

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General

@ref: 448

BacDive-ID: 2548

DSM-Number: 791

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

description: Clostridium beijerinckii E. McCoy A-67 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 1520
  • Matching level: species

strain history

@refhistory
448<- ATCC <- L. DS. Smith, Virginia Polytechnical Institute and State University, Blacksburg, V., USA; VPI 5481
67770ATCC 25752 <-- L. DS. Smith VPI 5481.
116776CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10026 <- ATCC <- L.D.S. Smith: strain VPI 5481

doi: 10.13145/bacdive2548.20230509.8.1

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 beijerinckii
  • full scientific name: Clostridium beijerinckii Donker 1926 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Clostridium diolis

@ref: 448

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium beijerinckii

full scientific name: Clostridium beijerinckii Donker 1926 emend. Keis et al. 2001

strain designation: E. McCoy A-67, L.S. McClung 1671, 10026

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes93.956
69480100positive
116776yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
448CHOPPED 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
39664MEDIUM 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)
116776CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
448positivegrowth37mesophilic
39664positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
448anaerobe
69480anaerobe99.156
116776anaerobe

spore formation

@refspore formationconfidence
69481yes99
69480yes100
116776yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11677617632nitrate-reduction
11677616301nitrite-reduction

metabolite production

@refmetaboliteproductionChebi-ID
67770butanolyes
116776indoleno35581

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
116776oxidase-
116776catalase-1.11.1.6
116776urease-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
116776-----------+--------

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_378.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_149;97_160;98_179;99_378&stattab=map
  • Last taxonomy: Clostridium
  • 16S sequence: AB643462
  • Sequence Identity:
  • Total samples: 10335
  • soil counts: 1985
  • aquatic counts: 1977
  • animal counts: 5931
  • plant counts: 442

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
4481Risk group (German classification)
1167762Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium beijerinckii strain DSM 791 16S ribosomal RNA gene, partial sequenceHM245931837ena1520
448C.beijerinckii (DSM791) rrn gene for 16S rRNAX681791510ena1520
67770Clostridium beijerinckii gene for 16S ribosomal RNA, partial sequence, strain: JCM 1390AB6434621473ena1520

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium beijerinckii DSM 791GCA_018223745completencbi1520
66792Clostridium beijerinckii NCTC13035GCA_900447025contigncbi1520
66792Clostridium beijerinckii NBRC 109359GCA_007992515contigncbi1520
66792Clostridium beijerinckii strain DSM 7911520.584completepatric1520
66792Clostridium beijerinckii strain DSM 7911520.98wgspatric1520
66792Clostridium beijerinckii strain NBRC 1093591520.326wgspatric1520
66792Clostridium beijerinckii strain NCTC130351520.300wgspatric1520
66792Clostridium beijernckii VPI 54812703719315draftimg1520
67770Clostridium beijerinckii DSM 791GCA_002006445contigncbi1520

GC content

@refGC-contentmethod
44828.0
6777028thermal denaturation, midpoint method (Tm)
6777031.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
flagellatedyes68.655no
gram-positiveyes65.22no
anaerobicyes98.175yes
aerobicno97.087yes
halophileno98.41no
spore-formingyes95.39no
thermophileno99.13no
glucose-utilyes89.032no
motileyes85.104no
glucose-fermentyes64.547no

External links

@ref: 448

culture collection no.: DSM 791, ATCC 25752, NCIMB 9362, CCUG 56442, CIP 104308, NCTC 13035, LMG 5716, JCM 1390, VPI 5481, ATCC 17778, BCRC 14488, NBRC 109359, VTT E-91425

straininfo link

  • @ref: 72081
  • straininfo: 92210

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9103631Cultures of "Clostridium acetobutylicum" from various collections comprise Clostridium acetobutylicum, Clostridium beijerinckii, and two other distinct types based on DNA-DNA reassociation.Johnson JL, Toth J, Santiwatanakul S, Chen JSInt J Syst Bacteriol10.1099/00207713-47-2-42019971-Butanol, Acetone/metabolism, Butanols/metabolism, Clostridium/*classification/*genetics/metabolism, DNA, Bacterial/*genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Riboflavin/biosynthesis, Species SpecificityMetabolism
Phylogeny12583708Taxonomy of the glycerol fermenting clostridia and description of Clostridium diolis sp. nov.Biebl H, Sproer CSyst Appl Microbiol10.1078/072320202605176162002Base Sequence, Clostridium/*classification/genetics/*metabolism, Fatty Acids/analysis, Fermentation, Glycerol/*metabolism, Nucleic Acid Hybridization, Phylogeny, Propylene Glycols/metabolism, RNA, Ribosomal, 16SMetabolism
Metabolism12620847Identification and characterization of two novel clostridial bacteriocins, circularin A and closticin 574.Kemperman R, Kuipers A, Karsens H, Nauta A, Kuipers O, Kok JAppl Environ Microbiol10.1128/AEM.69.3.1589-1597.20032003Amino Acid Sequence, Bacteria/drug effects, Bacterial Proteins/genetics/isolation & purification/metabolism/pharmacology, *Bacteriocins/genetics/isolation & purification/metabolism/pharmacology, Base Sequence, Clostridium/growth & development/*metabolism, Genes, Bacterial, Microbial Sensitivity Tests, Molecular Sequence DataEnzymology
Metabolism14532033Functional analysis of the gene cluster involved in production of the bacteriocin circularin A by Clostridium beijerinckii ATCC 25752.Kemperman R, Jonker M, Nauta A, Kuipers OP, Kok JAppl Environ Microbiol10.1128/AEM.69.10.5839-5848.20032003Amino Acid Sequence, Bacterial Proteins/*biosynthesis/chemistry/genetics, Bacteriocins/*biosynthesis/genetics/pharmacology, Base Sequence, Clostridium/drug effects/genetics/growth & development/*metabolism, Drug Resistance, Bacterial/genetics, Enterococcus faecalis/genetics/metabolism, Lactococcus lactis/genetics/metabolism, Microbial Sensitivity Tests, Molecular Sequence Data, *Multigene Family, Open Reading Frames, Sequence Analysis, DNAGenetics
Metabolism15544534The circular bacteriocins gassericin A and circularin A.Kawai Y, Kemperman R, Kok J, Saito TCurr Protein Pept Sci10.2174/13892030433795492004Animals, Bacteriocins/*biosynthesis/*chemistry/genetics/isolation & purification, Clostridium beijerinckii/chemistry/genetics/metabolism, Gene Expression, Humans, Lactobacillus/chemistry/genetics, Peptide Hydrolases/metabolismPathogenicity
Transcriptome18034824Genetic features of circular bacteriocins produced by Gram-positive bacteria.Maqueda M, Sanchez-Hidalgo M, Fernandez M, Montalban-Lopez M, Valdivia E, Martinez-Bueno MFEMS Microbiol Rev10.1111/j.1574-6976.2007.00087.x2007Amino Acid Sequence, Bacteriocins/chemistry/*genetics, Base Sequence, Drug Resistance, Bacterial/genetics, Gene Expression Profiling, Gene Expression Regulation, Bacterial/genetics, Gram-Positive Bacteria/*genetics, Multigene Family/genetics, Sequence Analysis, DNA
Phylogeny21148674Clostridium chromiireducens sp. nov., isolated from Cr(VI)-contaminated soil.Inglett KS, Bae HS, Aldrich HC, Hatfield K, Ogram AVInt J Syst Evol Microbiol10.1099/ijs.0.024554-02010Base Composition, Chromium/*metabolism, Clostridium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Soil Pollutants/metabolismMetabolism
Metabolism27085150Production of 1,3-propanediol by Clostridium beijerinckii DSM 791 from crude glycerol and corn steep liquor: Process optimization and metabolic engineering.Wischral D, Zhang J, Cheng C, Lin M, De Souza LMG, Pessoa FLP, Pereira N Jr, Yang STBioresour Technol10.1016/j.biortech.2016.04.0202016Acetates/metabolism, Batch Cell Culture Techniques, Bioreactors/microbiology, Butyrates/metabolism, Clostridium beijerinckii/*metabolism, Fermentation, Glycerol/*metabolism, Hydrogen-Ion Concentration, Kinetics, Metabolic Engineering/*methods, Metabolic Networks and Pathways, Plasmids/metabolism, Propylene Glycols/*metabolism, Sugar Alcohol Dehydrogenases/metabolism, *Waste Disposal, Fluid, Zea mays/*chemistryEnzymology
Phylogeny32068529Reclassification of Clostridium diolis Biebl and Sproer 2003 as a later heterotypic synonym of Clostridium beijerinckii Donker 1926 (Approved Lists 1980) emend. Keis et al. 2001.Kobayashi H, Tanizawa Y, Sakamoto M, Nakamura Y, Ohkuma M, Tohno MInt J Syst Evol Microbiol10.1099/ijsem.0.0040592020Bacterial Typing Techniques, Base Composition, Clostridium/*classification, Clostridium beijerinckii/*classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Biotechnology33254466Augmented biohydrogen production from rice mill wastewater through nano-metal oxides assisted dark fermentation.Rambabu K, Bharath G, Thanigaivelan A, Das DB, Show PL, Banat FBioresour Technol10.1016/j.biortech.2020.1242432020Fermentation, Hydrogen/analysis, *Oryza, Oxides, *Waste Water

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
448Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 791)https://www.dsmz.de/collection/catalogue/details/culture/DSM-791
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
39664Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16203
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/
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
72081Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92210.1StrainInfo: A central database for resolving microbial strain identifiers
116776Curators of the CIPCollection of Institut Pasteur (CIP 104308)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104308