Strain identifier
BacDive ID: 2624
Type strain:
Species: Clostridium paraputrificum
Strain history: ATCC 25780 <-- L. DS. Smith VPI 1584.
NCBI tax ID(s): 29363 (species)
General
@ref: 1176
BacDive-ID: 2624
DSM-Number: 2630
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Clostridium paraputrificum DSM 2630 is an anaerobe, mesophilic bacterium of the family Clostridiaceae.
NCBI tax id
- NCBI tax id: 29363
- Matching level: species
strain history
@ref | history |
---|---|
1176 | <- ATCC <- L.DS. Smith, VPI 1584 |
67770 | ATCC 25780 <-- L. DS. Smith VPI 1584. |
doi: 10.13145/bacdive2624.20230509.8.1
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 paraputrificum
- full scientific name: Clostridium paraputrificum (Bienstock 1906) Snyder 1936 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Bacillus paraputrificus
@ref: 1176
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium paraputrificum
full scientific name: Clostridium paraputrificum (Bienstock 1906) Snyder 1936
type strain: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1176 | 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 |
1176 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1176 | positive | growth | 37 | mesophilic |
51161 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
1176 | anaerobe |
51161 | anaerobe |
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_3373.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_1253;97_2106;98_2586;99_3373&stattab=map
- Last taxonomy: Clostridium paraputrificum subclade
- 16S sequence: AB536771
- Sequence Identity:
- Total samples: 61941
- soil counts: 2219
- aquatic counts: 4616
- animal counts: 54761
- plant counts: 345
Safety information
risk assessment
- @ref: 1176
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Clostridium paraputrificum strain DSM 2630 16S ribosomal RNA gene, partial sequence | HM245948 | 836 | ena | 29363 |
20218 | Clostridium paraputrificum 16S rRNA gene, strain DSM 2630 | X73445 | 1511 | ena | 29363 |
20218 | Clostridium paraputrificum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1293 | AB536771 | 1476 | ena | 29363 |
1176 | C.paraputrificum 16S rRNA gene | X75907 | 1467 | ena | 29363 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Clostridium paraputrificum strain NCTC11833 | 29363.20 | wgs | patric | 29363 |
67770 | Clostridium paraputrificum NCTC11833 | GCA_900447045 | contig | ncbi | 29363 |
GC content
@ref | GC-content | method |
---|---|---|
1176 | 27.0 | |
67770 | 27 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | yes | 81.675 | no |
anaerobic | yes | 98.399 | yes |
halophile | no | 84.564 | no |
spore-forming | yes | 93.606 | no |
glucose-util | yes | 88.506 | no |
motile | yes | 81.069 | no |
flagellated | yes | 60.005 | no |
aerobic | no | 98.435 | yes |
thermophile | no | 95.024 | no |
glucose-ferment | yes | 63.563 | no |
External links
@ref: 1176
culture collection no.: DSM 2630, ATCC 25780, NCIB 10671, CCUG 32755, NCTC 11833, VPI 1584, JCM 1293, BCRC 14550, NCIMB 10671
straininfo link
- @ref: 72155
- straininfo: 265463
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Pathogenicity | 24083511 | Growth-Inhibiting and morphostructural effects of constituents identified in Asarum heterotropoides root on human intestinal bacteria. | Perumalsamy H, Jung MY, Hong SM, Ahn YJ | BMC Complement Altern Med | 10.1186/1472-6882-13-245 | 2013 | Asarum/*chemistry, Bacteria/*drug effects, Cell Shape/drug effects, Gastrointestinal Tract/drug effects/*microbiology, Humans, Microbial Sensitivity Tests, Microbiota/*drug effects, Plant Extracts/chemistry/*pharmacology, Plant Roots/chemistry | |
Metabolism | 33938389 | Completion of the gut microbial epi-bile acid pathway. | Doden HL, Wolf PG, Gaskins HR, Anantharaman K, Alves JMP, Ridlon JM | Gut Microbes | 10.1080/19490976.2021.1907271 | 2021 | Actinobacteria/genetics, Bacterial Proteins/genetics/metabolism, Bile Acids and Salts/*metabolism, Clostridium/*enzymology/*genetics/*metabolism, Clostridium Infections/microbiology, DNA, Bacterial, Gastrointestinal Microbiome, Humans, Hydroxysteroid Dehydrogenases/*genetics/*metabolism, Lithocholic Acid/metabolism, NADP/metabolism, Phylogeny, Recombinant Proteins/genetics/metabolism | Enzymology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1176 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2630) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2630 | |||
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 | |
51161 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 32755) | https://www.ccug.se/strain?id=32755 | |||
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 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | |||
72155 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265463.1 | StrainInfo: A central database for resolving microbial strain identifiers |