Strain identifier
BacDive ID: 2819
Type strain:
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)
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
@ref | history |
---|---|
5799 | <- H. Biebl, GBF; SH1 <- H. Biebl {1987} |
116775 | CIP <- 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
@ref | name | growth | link | composition |
---|---|---|---|---|
5799 | 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 |
33170 | 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) | |
116775 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5799 | positive | growth | 37 | mesophilic |
33170 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 5799
- oxygen tolerance: anaerobe
spore formation
- @ref: 116775
- spore formation: yes
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
116775 | 17108 | D-arabinose | + | degradation |
116775 | 15824 | D-fructose | + | degradation |
116775 | 17634 | D-glucose | + | degradation |
116775 | 65327 | D-xylose | + | degradation |
116775 | 17057 | cellobiose | + | degradation |
116775 | 17716 | lactose | + | degradation |
116775 | 17306 | maltose | + | degradation |
116775 | 17814 | salicin | + | degradation |
116775 | 17992 | sucrose | + | degradation |
116775 | 4853 | esculin | + | hydrolysis |
116775 | 17632 | nitrate | - | reduction |
116775 | 16301 | nitrite | - | reduction |
116775 | 17632 | nitrate | + | respiration |
metabolite production
- @ref: 116775
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
116775 | oxidase | - | |
116775 | beta-galactosidase | - | 3.2.1.23 |
116775 | gelatinase | - | |
116775 | amylase | + | |
116775 | DNase | - | |
116775 | caseinase | - | 3.4.21.50 |
116775 | catalase | - | 1.11.1.6 |
116775 | tween esterase | - | |
116775 | lecithinase | - | |
116775 | lipase | - | |
116775 | protease | - | |
116775 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116775 | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
5799 | decaying straw | Braunschweig | Germany | DEU | Europe | |
116775 | Decaying straw | Northern | Germany | DEU | Europe | 1987 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
5799 | 1 | Risk group (German classification) |
116775 | 2 | Risk 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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clostridium diolis DSM 15410 | GCA_008705175 | complete | ncbi | 223919 |
66792 | Clostridium diolis DSM 15410 | GCA_008580445 | scaffold | ncbi | 223919 |
66792 | Clostridium diolis DSM 15410 | GCA_000409695 | contig | ncbi | 1316937 |
66792 | Clostridium diolis DSM 15410 | 1316937.3 | wgs | patric | 1316937 |
66792 | Clostridium diolis strain DSM 15410 | 223919.11 | complete | patric | 223919 |
66792 | Clostridium diolis strain DSM 15410 | 223919.10 | wgs | patric | 223919 |
66792 | Clostridium diolis DSM 15410 | 2554235113 | draft | img | 1316937 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 85.926 | no |
flagellated | yes | 66.763 | no |
gram-positive | yes | 54.696 | no |
anaerobic | yes | 97.18 | yes |
aerobic | no | 97.298 | yes |
halophile | no | 98.355 | no |
spore-forming | yes | 95.996 | no |
thermophile | no | 99.444 | yes |
glucose-util | yes | 90.181 | no |
glucose-ferment | yes | 65.308 | no |
External links
@ref: 5799
culture collection no.: DSM 15410, ATCC BAA 557, DSM 5431, CIP 107836
straininfo link
- @ref: 72343
- straininfo: 87981
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12583708 | Taxonomy of the glycerol fermenting clostridia and description of Clostridium diolis sp. nov. | Biebl H, Sproer C | Syst Appl Microbiol | 10.1078/07232020260517616 | 2002 | Base Sequence, Clostridium/*classification/genetics/*metabolism, Fatty Acids/analysis, Fermentation, Glycerol/*metabolism, Nucleic Acid Hybridization, Phylogeny, Propylene Glycols/metabolism, RNA, Ribosomal, 16S | Metabolism |
Biotechnology | 19854917 | Genome shuffling in Clostridium diolis DSM 15410 for improved 1,3-propanediol production. | Otte B, Grunwaldt E, Mahmoud O, Jennewein S | Appl Environ Microbiol | 10.1128/AEM.01774-09 | 2009 | Clostridium/*genetics, Culture Media, Gene Expression Regulation, Bacterial, Genetic Engineering, Genetic Enhancement, Genome, Bacterial, Glycerol, *Industrial Microbiology, *Mutagenesis, Propylene Glycols/*metabolism | Cultivation |
Genetics | 23908285 | Genome Sequence of Clostridium diolis Strain DSM 15410, a Promising Natural Producer of 1,3-Propanediol. | Wang Y, Tao F, Tang H, Xu P | Genome Announc | 10.1128/genomeA.00542-13 | 2013 | ||
Metabolism | 26750307 | Co-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 P | Sci Rep | 10.1038/srep19044 | 2016 | Anaerobiosis/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/metabolism | Biotechnology |
Phylogeny | 32068529 | Reclassification 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 M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004059 | 2020 | Bacterial 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, DNA | Transcriptome |
Biotechnology | 32915256 | Milling 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 V | Appl Microbiol Biotechnol | 10.1007/s00253-020-10882-8 | 2020 | *Acetone, *Butanols, Clostridium, Ethanol, Fermentation | |
Metabolism | 33166602 | Phenotypic 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 P | Genomics | 10.1016/j.ygeno.2020.11.007 | 2020 | 2-Propanol/*metabolism, Biofuels, Clostridium/classification/*genetics/metabolism, *Genome, Bacterial, Industrial Microbiology, Phenotype, *Phylogeny, Propylene Glycols/*metabolism | Phylogeny |
Genetics | 33927028 | Draft Genome Sequence of Clostridium beijerinckii Strain mbf-VZ-132, Isolated from an Environmental Soil Sample. | Thieme N, Liebl W, Zverlov VV | Microbiol Resour Announc | 10.1128/MRA.00131-21 | 2021 | Phylogeny |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
5799 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15410) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15410 | |
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 | |
33170 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5391 | ||
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) | |
68382 | Automatically annotated from API zym | |||
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 | |
72343 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID87981.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
116775 | Curators of the CIP | Collection of Institut Pasteur (CIP 107836) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107836 |