Strain identifier

BacDive ID: 2819

Type strain: No

Species: Clostridium beijerinckii

Strain Designation: 88-273, SH1

Strain history: CIP <- 2003, H. Biebl, GBF, Braunschweig, Germany: strain SH1 <- DSMZ

NCBI tax ID(s): 223919 (species)

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

@ref: 5799

BacDive-ID: 2819

DSM-Number: 15410

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Clostridium beijerinckii 88-273 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from decaying straw.

NCBI tax id

  • NCBI tax id: 223919
  • Matching level: species

strain history

@refhistory
5799<- H. Biebl, GBF; SH1 <- H. Biebl {1987}
116775CIP <- 2003, H. Biebl, GBF, Braunschweig, Germany: strain SH1 <- DSMZ

doi: 10.13145/bacdive2819.20230509.8.1

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: 5799

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: 88-273, SH1

type strain: no

Morphology

cell morphology

  • @ref: 116775
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 116775

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5799PY + 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
33170MEDIUM 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)
116775CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
5799positivegrowth37mesophilic
33170positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 5799
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 116775
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11677517108D-arabinose+degradation
11677515824D-fructose+degradation
11677517634D-glucose+degradation
11677565327D-xylose+degradation
11677517057cellobiose+degradation
11677517716lactose+degradation
11677517306maltose+degradation
11677517814salicin+degradation
11677517992sucrose+degradation
1167754853esculin+hydrolysis
11677517632nitrate-reduction
11677516301nitrite-reduction
11677517632nitrate+respiration

metabolite production

  • @ref: 116775
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
116775oxidase-
116775beta-galactosidase-3.2.1.23
116775gelatinase-
116775amylase+
116775DNase-
116775caseinase-3.4.21.50
116775catalase-1.11.1.6
116775tween esterase-
116775lecithinase-
116775lipase-
116775protease-
116775urease-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
116775-----------+---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5799decaying strawBraunschweigGermanyDEUEurope
116775Decaying strawNorthernGermanyDEUEurope1987

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Decomposing plant
#Host#Plants#Herbaceous plants (Grass,Crops)

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: AJ458418
  • 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
57991Risk group (German classification)
1167752Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5799
  • description: Clostridium diolis partial 16S rRNA gene, strain DSM 5431
  • accession: AJ458418
  • length: 1483
  • database: ena
  • NCBI tax ID: 223919

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium diolis DSM 15410GCA_008705175completencbi223919
66792Clostridium diolis DSM 15410GCA_008580445scaffoldncbi223919
66792Clostridium diolis DSM 15410GCA_000409695contigncbi1316937
66792Clostridium diolis DSM 154101316937.3wgspatric1316937
66792Clostridium diolis strain DSM 15410223919.11completepatric223919
66792Clostridium diolis strain DSM 15410223919.10wgspatric223919
66792Clostridium diolis DSM 154102554235113draftimg1316937

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes85.926no
flagellatedyes66.763no
gram-positiveyes54.696no
anaerobicyes97.18yes
aerobicno97.298yes
halophileno98.355no
spore-formingyes95.996no
thermophileno99.444yes
glucose-utilyes90.181no
glucose-fermentyes65.308no

External links

@ref: 5799

culture collection no.: DSM 15410, ATCC BAA 557, DSM 5431, CIP 107836

straininfo link

  • @ref: 72343
  • straininfo: 87981

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Biotechnology19854917Genome shuffling in Clostridium diolis DSM 15410 for improved 1,3-propanediol production.Otte B, Grunwaldt E, Mahmoud O, Jennewein SAppl Environ Microbiol10.1128/AEM.01774-092009Clostridium/*genetics, Culture Media, Gene Expression Regulation, Bacterial, Genetic Engineering, Genetic Enhancement, Genome, Bacterial, Glycerol, *Industrial Microbiology, *Mutagenesis, Propylene Glycols/*metabolismCultivation
Genetics23908285Genome Sequence of Clostridium diolis Strain DSM 15410, a Promising Natural Producer of 1,3-Propanediol.Wang Y, Tao F, Tang H, Xu PGenome Announc10.1128/genomeA.00542-132013
Metabolism26750307Co-utilization of glycerol and lignocellulosic hydrolysates enhances anaerobic 1,3-propanediol production by Clostridium diolis.Xin B, Wang Y, Tao F, Li L, Ma C, Xu PSci Rep10.1038/srep190442016Anaerobiosis/physiology, Arabinose/metabolism, Bioreactors, Clostridium/*metabolism, Fermentation, Glucose/metabolism, Glycerol/*metabolism, Hydrolysis, Industrial Microbiology, Kinetics, Lignin/chemistry/*metabolism, Molasses/microbiology, NAD/metabolism, Propylene Glycols/*metabolism, Xylose/metabolismBiotechnology
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
Biotechnology32915256Milling byproducts are an economically viable substrate for butanol production using clostridial ABE fermentation.Thieme N, Panitz JC, Held C, Lewandowski B, Schwarz WH, Liebl W, Zverlov VAppl Microbiol Biotechnol10.1007/s00253-020-10882-82020*Acetone, *Butanols, Clostridium, Ethanol, Fermentation
Metabolism33166602Phenotypic and genomic analysis of isopropanol and 1,3-propanediol producer Clostridium diolis DSM 15410.Sedlar K, Vasylkivska M, Musilova J, Branska B, Provaznik I, Patakova PGenomics10.1016/j.ygeno.2020.11.00720202-Propanol/*metabolism, Biofuels, Clostridium/classification/*genetics/metabolism, *Genome, Bacterial, Industrial Microbiology, Phenotype, *Phylogeny, Propylene Glycols/*metabolismPhylogeny
Genetics33927028Draft Genome Sequence of Clostridium beijerinckii Strain mbf-VZ-132, Isolated from an Environmental Soil Sample.Thieme N, Liebl W, Zverlov VVMicrobiol Resour Announc10.1128/MRA.00131-212021Phylogeny

Reference

@idauthorscataloguedoi/urltitle
5799Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15410)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15410
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
33170Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5391
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
72343Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87981.1StrainInfo: A central database for resolving microbial strain identifiers
116775Curators of the CIPCollection of Institut Pasteur (CIP 107836)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107836