Strain identifier
BacDive ID: 2774
Type strain:
Species: Clostridium thermoalcaliphilum
Strain Designation: JW/YL23-2
Strain history: <- J. Wiegel, JW/YL23-2
NCBI tax ID(s): 29349 (species)
General
@ref: 3111
BacDive-ID: 2774
DSM-Number: 7309
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, motile
description: Clostridium thermoalcaliphilum JW/YL23-2 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from sewage sludge.
NCBI tax id
- NCBI tax id: 29349
- Matching level: species
strain history
- @ref: 3111
- history: <- J. Wiegel, JW/YL23-2
doi: 10.13145/bacdive2774.20230509.8.1
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 thermoalcaliphilum
- full scientific name: Clostridium thermoalcaliphilum Li et al. 1994
@ref: 3111
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium thermoalcaliphilum
full scientific name: Clostridium thermoalcaliphilum Li et al. 1994
strain designation: JW/YL23-2
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 91.721 | |
69480 | 99.719 | positive |
Culture and growth conditions
culture medium
- @ref: 3111
- name: YTG MEDIUM (DSMZ Medium 616)
- growth: yes
- link: https://mediadive.dsmz.de/medium/616
- composition: Name: CLOSTRIDIUM (YTG) MEDIUM (DSMZ Medium 616) Composition: Tryptone 10.0 g/l Na2CO3 5.3 g/l Yeast extract 5.0 g/l D-Glucose 3.0 g/l Na2HPO4 x 2 H2O 0.36 g/l Na2S x 9 H2O 0.2 g/l L-Cysteine HCl x H2O 0.2 g/l KCl 0.08 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
@ref | growth | type | temperature | range | confidence |
---|---|---|---|---|---|
3111 | positive | growth | 50 | thermophilic | |
69480 | thermophilic | 96.809 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
3111 | anaerobe | |
69480 | anaerobe | 100 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 99.539 |
murein
- @ref: 3111
- murein short key: A21.04
- type: A4ß L-Orn-D-Asp
Isolation, sampling and environmental information
isolation
- @ref: 3111
- sample type: sewage sludge
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Sewage sludge
taxonmaps
- @ref: 69479
- File name: preview.99_17231.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2;96_1875;97_2252;98_13052;99_17231&stattab=map
- Last taxonomy: [Clostridium] thermoalcaliphilum subclade
- 16S sequence: FR749954
- Sequence Identity:
- Total samples: 422
- soil counts: 101
- aquatic counts: 156
- animal counts: 155
- plant counts: 10
Safety information
risk assessment
- @ref: 3111
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
3111 | Clostridium thermoalcaliphilum partial 16S rRNA gene, type strain DSM 7309T, clone 1 | FR749953 | 1581 | ena | 29349 |
3111 | Clostridium thermoalcaliphilum partial 16S rRNA gene, type strain DSM 7309T, clone 2 | FR749954 | 1546 | ena | 29349 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | [Clostridium] thermoalcaliphilum DSM 7309 | GCA_002029295 | contig | ncbi | 29349 |
66792 | [Clostridium] thermoalcaliphilum strain DSM 7309 | 29349.3 | wgs | patric | 29349 |
66792 | Clostridium thermoalcaliphilum DSM 7309 | 2833455180 | draft | img | 29349 |
66792 | Clostridium thermoalcaliphilum JW/YL23-2 | 2711768657 | draft | img | 29349 |
GC content
- @ref: 3111
- GC-content: 32.0
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 75.608 | no |
anaerobic | yes | 99.045 | yes |
halophile | no | 75.304 | no |
spore-forming | yes | 88.119 | no |
glucose-util | yes | 88.894 | no |
motile | yes | 85.779 | no |
flagellated | no | 64.146 | no |
thermophile | yes | 99.251 | yes |
aerobic | no | 96.481 | yes |
glucose-ferment | yes | 59.92 | no |
External links
@ref: 3111
culture collection no.: DSM 7309, ATCC 51508, CIP 105528
straininfo link
- @ref: 72304
- straininfo: 46154
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 8123553 | Clostridium thermoalcaliphilum sp. nov., an anaerobic and thermotolerant facultative alkaliphile. | Li Y, Engle M, Weiss N, Mandelco L, Wiegel J | Int J Syst Bacteriol | 10.1099/00207713-44-1-111 | 1994 | Base Sequence, Clostridium/genetics/*isolation & purification/physiology, Fermentation, Hydrogen-Ion Concentration, Molecular Sequence Data, RNA, Ribosomal, 16S/chemistry, Sewage, Sodium Chloride/pharmacology, Temperature | Genetics |
Genetics | 28522721 | First Insights into the Genome Sequence of the Alkaliphilic Thermotolerant Bacterium Clostridium thermoalcaliphilum JW/YL23-2(T). | Poehlein A, Berg A, Welsing G, Daniel R | Genome Announc | 10.1128/genomeA.00368-17 | 2017 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3111 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7309) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-7309 | |||
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 | |||
72304 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46154.1 | StrainInfo: A central database for resolving microbial strain identifiers |