Strain identifier
BacDive ID: 2833
Type strain: 
Species: Clostridium aciditolerans
Strain Designation: JW/4JL B3
Strain history: <- J. Wiegel and Y.-J. Lee, Univ. of Georgia, Athens, USA; JW/4JL B3
NCBI tax ID(s): 339861 (species)
version 9.3 (current version)
General
@ref: 6960
BacDive-ID: 2833
DSM-Number: 17425
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped
description: Clostridium aciditolerans JW/4JL B3 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from sediment sample.
NCBI tax id
- NCBI tax id: 339861
- Matching level: species
strain history
- @ref: 6960
- history: <- J. Wiegel and Y.-J. Lee, Univ. of Georgia, Athens, USA; JW/4JL B3
doi: 10.13145/bacdive2833.20250331.9.3
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 aciditolerans
- full scientific name: Clostridium aciditolerans Lee et al. 2007
@ref: 6960
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium aciditolerans
full scientific name: Clostridium aciditolerans Lee et al. 2007
strain designation: JW/4JL B3
type strain: yes
Morphology
cell morphology
- @ref: 31879
- gram stain: positive
- cell length: 6 µm
- cell width: 0.75 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 31879
- production: no
Culture and growth conditions
culture medium
- @ref: 6960
- name: PY + X MEDIUM (DSMZ Medium 104b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104b
- composition: 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
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 6960 | positive | growth | 37 |
| 31879 | positive | growth | 20-45 |
| 31879 | positive | optimum | 35 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31879 | positive | growth | 3.8-8.9 | alkaliphile |
| 31879 | positive | optimum | 7.25 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 6960 | anaerobe | |
| 31879 | anaerobe | |
| 125439 | anaerobe | 90.6 |
spore formation
- @ref: 31879
- spore formation: yes
halophily
- @ref: 31879
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1.5 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31879 | 17057 | cellobiose | + | carbon source |
| 31879 | 28757 | fructose | + | carbon source |
| 31879 | 28260 | galactose | + | carbon source |
| 31879 | 5291 | gelatin | + | carbon source |
| 31879 | 17234 | glucose | + | carbon source |
| 31879 | 29987 | glutamate | + | carbon source |
| 31879 | 17716 | lactose | + | carbon source |
| 31879 | 17306 | maltose | + | carbon source |
| 31879 | 37684 | mannose | + | carbon source |
| 31879 | 15361 | pyruvate | + | carbon source |
| 31879 | 16634 | raffinose | + | carbon source |
| 31879 | 33942 | ribose | + | carbon source |
| 31879 | 17992 | sucrose | + | carbon source |
| 31879 | 18222 | xylose | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31879 | acid phosphatase | + | 3.1.3.2 |
| 31879 | alkaline phosphatase | + | 3.1.3.1 |
| 31879 | gelatinase | + |
Isolation, sampling and environmental information
isolation
- @ref: 6960
- sample type: sediment sample
- geographic location: Aiken
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Sediment |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_76067.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_7260;97_8707;98_10675;99_76067&stattab=map
- Last taxonomy: Clostridium
- 16S sequence: DQ114945
- Sequence Identity:
- Total samples: 1856
- soil counts: 1133
- aquatic counts: 317
- animal counts: 289
- plant counts: 117
Safety information
risk assessment
- @ref: 6960
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6960
- description: Clostridium aciditolerans strain JW/YJL-B3 16S ribosomal RNA gene, partial sequence
- accession: DQ114945
- length: 1391
- database: nuccore
- NCBI tax ID: 339861
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium aciditolerans DSM 17425 | GCA_016316925 | scaffold | ncbi | 339861 |
| 66792 | Clostridium aciditolerans strain DSM 17425 | 339861.3 | wgs | patric | 339861 |
GC content
- @ref: 31879
- GC-content: 30.8
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 65.133 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 86.246 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 93.779 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 85.965 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 90.401 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 72.05 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 78.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 79 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 69.3 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 90.6 |
External links
@ref: 6960
culture collection no.: DSM 17425, ATCC BAA-1220
straininfo link
- @ref: 72357
- straininfo: 297144
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17267970 | Clostridium aciditolerans sp. nov., an acid-tolerant spore-forming anaerobic bacterium from constructed wetland sediment. | Lee YJ, Romanek CS, Wiegel J | Int J Syst Evol Microbiol | 10.1099/ijs.0.64583-0 | 2007 | Acetic Acid/metabolism, Anaerobiosis, Anti-Bacterial Agents/pharmacology, Base Composition, Butyrates/metabolism, Carbohydrate Metabolism, Clostridium/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Ethanol/metabolism, Genes, rRNA/genetics, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, Proteins/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Soil Microbiology, Spores, Bacterial, Temperature, Water Microbiology, *Wetlands | Metabolism |
| Phylogeny | 35188883 | Clostridium thailandense sp. nov., a novel CO2-reducing acetogenic bacterium isolated from peatland soil. | Chaikitkaew S, In-Chan S, Singkhala A, Tukanghan W, Mamimin C, Reungsang A, Birkeland NK, O-Thong S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005254 | 2022 | Bacterial Typing Techniques, Base Composition, *Carbon Dioxide/metabolism, Clostridium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphagnopsida/*microbiology | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 6960 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17425) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17425 | |||
| 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 | |||
| 31879 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28139 | 28776041 | |
| 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) | |||
| 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 | |||
| 72357 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297144.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |