Strain identifier
BacDive ID: 2812
Type strain: 
Species: Clostridium isatidis
Strain Designation: Wv6, Vv6
Strain history: CIP <- 2001, NCIMB <- V. Dillon, Reading University, UK: strain Vv6
NCBI tax ID(s): 182773 (species)
version 8.1 (current version)
General
@ref: 5710
BacDive-ID: 2812
DSM-Number: 15098
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive
description: Clostridium isatidis Wv6 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from fermenting woad vat.
NCBI tax id
- NCBI tax id: 182773
- Matching level: species
strain history
| @ref | history |
|---|---|
| 5710 | <- NCIMB <- V. M. Dillon; Wv6 |
| 120283 | CIP <- 2001, NCIMB <- V. Dillon, Reading University, UK: strain Vv6 |
doi: 10.13145/bacdive2812.20230509.8.1
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 isatidis
- full scientific name: Clostridium isatidis Padden et al. 1999
@ref: 5710
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium isatidis
full scientific name: Clostridium isatidis Padden et al. 1999
strain designation: Wv6, Vv6
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence | cell shape | motility |
|---|---|---|---|---|
| 69480 | positive | 100 | ||
| 120283 | positive | rod-shaped | yes |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 5710 | 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 |
| 33606 | MEDIUM 417 - for Clostridium isotidis | yes | Distilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Glucose (2.000 g);Brain heart infusion (17.500 g);Cysteine hydrochloride (0.500 g);Di Sodium hydrogen phosphate (2.500 g);Tryptose (10.000 g) | |
| 120283 | CIP Medium 417 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=417 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 5710 | positive | growth | 37 | mesophilic |
| 33606 | positive | growth | 37 | mesophilic |
| 120283 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 5710 | anaerobe | |
| 69480 | anaerobe | 98.648 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 96.328 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 5710 | fermenting woad vat | Reading | United Kingdom | GBR | Europe |
| 120283 | Woad vat | United Kingdom | GBR | Europe |
isolation source categories
- Cat1: #Engineered
- Cat2: #Industrial
- Cat3: #Engineered product
taxonmaps
- @ref: 69479
- File name: preview.99_84349.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_1253;97_32225;98_41313;99_84349&stattab=map
- Last taxonomy: Clostridium
- 16S sequence: X98395
- Sequence Identity:
- Total samples: 415
- soil counts: 58
- aquatic counts: 34
- animal counts: 300
- plant counts: 23
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 5710 | 1 | Risk group (German classification) |
| 120283 | 2 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 5710
- description: Clostridium sp. 16S rRNA gene
- accession: X98395
- length: 1332
- database: ena
- NCBI tax ID: 1506
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium isatidis DSM 15098 | GCA_002285495 | complete | ncbi | 182773 |
| 66792 | Clostridium isatidis strain DSM 15098 | 182773.3 | complete | patric | 182773 |
| 66792 | Clostridium isatidis DSM 15098 | 2877451605 | complete | img | 182773 |
GC content
- @ref: 5710
- GC-content: 27
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| flagellated | no | 50.809 | no |
| gram-positive | yes | 82.711 | no |
| anaerobic | yes | 98.152 | yes |
| aerobic | no | 99.463 | yes |
| halophile | no | 85.812 | no |
| spore-forming | yes | 93.776 | no |
| glucose-util | yes | 85.844 | no |
| thermophile | no | 91.489 | yes |
| motile | yes | 79.801 | no |
| glucose-ferment | yes | 72.092 | no |
External links
@ref: 5710
culture collection no.: DSM 15098, NCFB 3071, NCIMB 703071, CIP 107118
straininfo link
- @ref: 72338
- straininfo: 62136
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 10425759 | An indigo-reducing moderate thermophile from a woad vat, Clostridium isatidis sp. nov. | Padden AN, Dillon VM, Edmonds J, Collins MD, Alvarez N, John P | Int J Syst Bacteriol | 10.1099/00207713-49-3-1025 | 1999 | Bacterial Typing Techniques, Clostridium/*classification/cytology/genetics/*isolation & purification/physiology, Coloring Agents/*metabolism, DNA, Bacterial/chemistry/genetics, Genes, rRNA, Hydrogen-Ion Concentration, Indigo Carmine, Indoles/*metabolism, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Plant Leaves/chemistry/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature | Metabolism |
| Metabolism | 22581408 | Implementation of a biotechnological process for vat dyeing with woad. | Osimani A, Aquilanti L, Baldini G, Silvestri G, Butta A, Clementi F | J Ind Microbiol Biotechnol | 10.1007/s10295-012-1139-4 | 2012 | Anaerobiosis, *Bioreactors, Clostridium/drug effects/*metabolism, Coloring Agents/*chemistry/*metabolism, Fermentation, Indigo Carmine, Indoles/*chemistry/metabolism, Isatis/*chemistry, Yeasts/chemistry, Zea mays/chemistry | Pathogenicity |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5710 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15098) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15098 | |||
| 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 | |||
| 33606 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/4519 | ||||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 72338 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID62136.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 120283 | Curators of the CIP | Collection of Institut Pasteur (CIP 107118) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107118 |