Strain identifier
BacDive ID: 2783
Type strain:
Species: Clostridium pascui
Strain Designation: Cm19, Cm 19
Strain history: CIP <- 1997, H. Hippe, Germany: strain Cm 19 <- N. Tosunoglu
NCBI tax ID(s): 46609 (species)
General
@ref: 3918
BacDive-ID: 2783
DSM-Number: 10365
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile
description: Clostridium pascui Cm19 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from soil, donkey pasture.
NCBI tax id
- NCBI tax id: 46609
- Matching level: species
strain history
@ref | history |
---|---|
3918 | <- E. Wilde and H. Hippe; Cm19 <- N. Tosunoglu {1981} |
121616 | CIP <- 1997, H. Hippe, Germany: strain Cm 19 <- N. Tosunoglu |
doi: 10.13145/bacdive2783.20230509.8.1
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 pascui
- full scientific name: Clostridium pascui Wilde et al. 1997
@ref: 3918
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium pascui
full scientific name: Clostridium pascui Wilde et al. 1997
strain designation: Cm19, Cm 19
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 91.303 | ||
69480 | 100 | positive | ||
121616 | no | positive | rod-shaped |
colony morphology
- @ref: 121616
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3918 | WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) | yes | https://mediadive.dsmz.de/medium/339 | Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water |
3918 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water |
39214 | 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) | |
121616 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3918 | positive | growth | 37 | mesophilic |
39214 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
3918 | anaerobe | |
69480 | anaerobe | 99.251 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
121616 | yes |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
121616 | 15824 | D-fructose | - | degradation |
121616 | 17634 | D-glucose | - | degradation |
121616 | 65327 | D-xylose | - | degradation |
121616 | 17057 | cellobiose | - | degradation |
121616 | 17716 | lactose | - | degradation |
121616 | 17306 | maltose | - | degradation |
121616 | 17814 | salicin | - | degradation |
121616 | 17992 | sucrose | - | degradation |
121616 | 4853 | esculin | - | hydrolysis |
121616 | 17632 | nitrate | - | reduction |
121616 | 16301 | nitrite | - | reduction |
121616 | 17632 | nitrate | + | respiration |
metabolite production
- @ref: 121616
- Chebi-ID: 35581
- metabolite: indole
- production: yes
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 |
121616 | oxidase | - | |
121616 | beta-galactosidase | + | 3.2.1.23 |
121616 | gelatinase | - | |
121616 | catalase | - | 1.11.1.6 |
121616 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121616 | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121616 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | isolation date |
---|---|---|---|---|---|
3918 | soil, donkey pasture | Pakistan | PAK | Asia | |
121616 | Environment, Donkey, pasture soil | Pakistan | PAK | Asia | 1981 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Grassland |
#Environmental | #Terrestrial | #Soil |
#Host | #Mammals | #Equidae (Horse) |
taxonmaps
- @ref: 69479
- File name: preview.99_5428.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_2632;97_3224;98_4051;99_5428&stattab=map
- Last taxonomy: Clostridium pascui
- 16S sequence: NR_026322
- Sequence Identity:
- Total samples: 1907
- soil counts: 839
- aquatic counts: 543
- animal counts: 469
- plant counts: 56
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
3918 | 1 | Risk group (German classification) |
121616 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | C.pascui 16S rRNA gene | X96736 | 1471 | ena | 46609 |
3918 | Clostridium pascui strain DSM 10365 16S ribosomal RNA, partial sequence | NR_026322 | 1471 | nuccore | 46609 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clostridium pascui DSM 10365 | GCA_016908015 | contig | ncbi | 46609 |
66792 | Clostridium pascui strain DSM 10365 | 46609.3 | wgs | patric | 46609 |
66792 | Clostridium pascui DSM 10365 | 2901044109 | draft | img | 46609 |
GC content
- @ref: 3918
- GC-content: 27
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | no | 52.644 | no |
anaerobic | yes | 98.892 | yes |
halophile | no | 94.092 | no |
spore-forming | yes | 94.428 | no |
glucose-util | yes | 86.208 | no |
aerobic | no | 97.432 | no |
flagellated | yes | 66.417 | no |
thermophile | no | 94.123 | no |
motile | yes | 84.984 | no |
glucose-ferment | yes | 52.814 | no |
External links
@ref: 3918
culture collection no.: DSM 10365, CIP 105172, JCM 11012
straininfo link
- @ref: 72310
- straininfo: 48820
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 8995820 | Clostridium pascui sp. nov., a new glutamate-fermenting sporeformer from a pasture in Pakistan. | Wilde E, Collins MD, Hippe H | Int J Syst Bacteriol | 10.1099/00207713-47-1-164 | 1997 | Acetates/metabolism, Bacterial Proteins/analysis, Bacteriological Techniques, Base Composition, Butyrates/metabolism, Carbon Dioxide/metabolism, Clostridium/chemistry/*classification/genetics/metabolism, Culture Media/metabolism, Ethanol/metabolism, Fatty Acids/analysis, Fermentation, Glutamates/metabolism, Histidine/metabolism, Hydrogen/metabolism, Indoles/metabolism, Microbial Sensitivity Tests, Molecular Sequence Data, Nucleic Acid Hybridization, Pakistan, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Soil Microbiology | Phylogeny |
Phylogeny | 16514039 | Clostridium lundense sp. nov., a novel anaerobic lipolytic bacterium isolated from bovine rumen. | Cirne DG, Delgado OD, Marichamy S, Mattiasson B | Int J Syst Evol Microbiol | 10.1099/ijs.0.63730-0 | 2006 | Animals, Cattle/*microbiology, Clostridium/*classification/genetics/isolation & purification/physiology, DNA, Ribosomal/chemistry, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sequence Analysis, DNA | Phenotype |
Phylogeny | 16957104 | Gracilibacter thermotolerans gen. nov., sp. nov., an anaerobic, thermotolerant bacterium from a constructed wetland receiving acid sulfate water. | Lee YJ, Romanek CS, Mills GL, Davis RC, Whitman WB, Wiegel J | Int J Syst Evol Microbiol | 10.1099/ijs.0.64040-0 | 2006 | Bacteria, Anaerobic/classification/metabolism, Clostridium/classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, RNA, Ribosomal, 16S/analysis/genetics, Sulfates/*metabolism, Water Microbiology | Metabolism |
Phylogeny | 26597830 | Clostridium liquoris sp. nov., isolated from a fermentation pit used for the production of Chinese strong-flavoured liquor. | Yin Q, Tao Y, Zhu X, Zhou Y, He X, Cheng L, Huang Y, Li D | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000787 | 2015 | Biotechnology | |
Phylogeny | 31199222 | Clostridium prolinivorans sp. nov., a thermophilic bacterium isolated from an anaerobic reactor degrading propionate. | Huang Y, Wei Z, Cong L, Qiu Z, Chen R, Deng Y, Zhang Y, Fan H, Ma S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003523 | 2019 | Anaerobiosis, Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Clostridium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Propionates/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3918 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10365) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10365 | |||
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 | |
39214 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17162 | ||||
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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
72310 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48820.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121616 | Curators of the CIP | Collection of Institut Pasteur (CIP 105172) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105172 |