Strain identifier
BacDive ID: 2789
Type strain: 
Species: Clostridium vincentii
Strain Designation: lac-1
Strain history: <- D. O. Mountfort, Cawthron Institute, Private Bag 2, Nelson, New Zealand; lac-1 <- D. O. Mountfort {1994}
NCBI tax ID(s): 52704 (species)
version 8.1 (current version)
General
@ref: 3853
BacDive-ID: 2789
DSM-Number: 10228
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, psychrophilic, motile
description: Clostridium vincentii lac-1 is an anaerobe, spore-forming, psychrophilic bacterium that was isolated from anaerobic sediment.
NCBI tax id
- NCBI tax id: 52704
- Matching level: species
strain history
- @ref: 3853
- history: <- D. O. Mountfort, Cawthron Institute, Private Bag 2, Nelson, New Zealand; lac-1 <- D. O. Mountfort {1994}
doi: 10.13145/bacdive2789.20230509.8.1
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 vincentii
- full scientific name: Clostridium vincentii Mountfort et al. 1997
@ref: 3853
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium vincentii
full scientific name: Clostridium vincentii Mountfort et al. 1997
strain designation: lac-1
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 97.189 | |
| 69480 | 99.719 | positive |
Culture and growth conditions
culture medium
- @ref: 3853
- name: CLOSTRIDIUM VINCENTII MEDIUM (DSMZ Medium 769)
- growth: yes
- link: https://mediadive.dsmz.de/medium/769
- composition: Name: CLOSTRIDIUM VINCENTII MEDIUM (DSMZ Medium 769) Composition: Sea Salt 11.988 g/l Lactose 1.998 g/l Yeast extract 0.999001 g/l NaHCO3 0.999001 g/l Trypticase peptone 0.3996 g/l Na2S x 9 H2O 0.2997 g/l L-Cysteine HCl x H2O 0.2997 g/l NH4NO3 0.0999001 g/l Sodium resazurin 0.0004995 g/l Pyridoxine hydrochloride 9.99001e-05 g/l Riboflavin 4.995e-05 g/l Thiamine HCl 4.995e-05 g/l Nicotinic acid 4.995e-05 g/l Calcium D-(+)-pantothenate 4.995e-05 g/l (DL)-alpha-Lipoic acid 4.995e-05 g/l p-Aminobenzoic acid 4.995e-05 g/l Folic acid 1.998e-05 g/l Biotin 1.998e-05 g/l Vitamin B12 9.99001e-07 g/l Na-phosphate buffer Distilled water
culture temp
- @ref: 3853
- growth: positive
- type: growth
- temperature: 12
- range: psychrophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 3853 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 97.976 |
Isolation, sampling and environmental information
isolation
- @ref: 3853
- sample type: anaerobic sediment
- geographic location: McMurdo Ice Shelf
- continent: Australia and Oceania
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_41681.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_1253;97_2106;98_30306;99_41681&stattab=map
- Last taxonomy: Clostridium vincentii subclade
- 16S sequence: X97432
- Sequence Identity:
- Total samples: 3349
- soil counts: 696
- aquatic counts: 807
- animal counts: 1724
- plant counts: 122
Safety information
risk assessment
- @ref: 3853
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 3853
- description: C.vincentii 16S rRNA gene
- accession: X97432
- length: 1464
- database: ena
- NCBI tax ID: 52704
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium vincentii DSM 10228 | GCA_002995745 | contig | ncbi | 52704 |
| 66792 | Clostridium vincentii strain DSM 10228 | 52704.3 | wgs | patric | 52704 |
| 66792 | Clostridium vincentii DSM 10228 | 2916606478 | draft | img | 52704 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| gram-positive | yes | 66.559 | no |
| anaerobic | yes | 98.976 | yes |
| halophile | no | 94.503 | no |
| spore-forming | yes | 96.995 | no |
| glucose-util | yes | 85.668 | no |
| motile | yes | 85.049 | no |
| aerobic | no | 99.231 | no |
| thermophile | no | 98.355 | no |
| flagellated | yes | 85.243 | no |
| glucose-ferment | yes | 55.717 | no |
External links
@ref: 3853
culture collection no.: DSM 10228
straininfo link
- @ref: 72316
- straininfo: 48781
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 9000342 | Clostridium vincentii sp. nov., a new obligately anaerobic, saccharolytic, psychrophilic bacterium isolated from low-salinity pond sediment of the McMurdo Ice Shelf, Antarctica. | Mountfort DO, Rainey FA, Burghardt J, Kaspar HF, Stackebrandt E | Arch Microbiol | 10.1007/s002030050416 | 1997 | Clostridium/classification/*isolation & purification/metabolism, DNA, Bacterial/analysis, Fermentation, Geologic Sediments, Glucose/metabolism, Lactose/metabolism, RNA, Ribosomal, 16S/genetics, Substrate Specificity, *Water Microbiology | Metabolism |
| Genetics | 29650586 | First Insight into the Genome Sequence of Clostridium vincentii DSM 10228, Isolated from Sediment of the McMurdo Ice Shelf, Antarctica. | Poehlein A, Bolz S, Fischer B, Daniel R | Genome Announc | 10.1128/genomeA.00334-18 | 2018 | Phylogeny |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3853 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10228) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10228 | |||
| 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 | |||
| 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 | |||
| 72316 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48781.1 | StrainInfo: A central database for resolving microbial strain identifiers |