Strain identifier
BacDive ID: 2652
Type strain: 
Species: Clostridium putrefaciens
Strain history: ATCC 25786 <-- L. DS. Smith VPI 5395 <-- NCTC 9836 <-- E. M. Barnes.
NCBI tax ID(s): 99675 (species)
version 8.1 (current version)
General
@ref: 622
BacDive-ID: 2652
DSM-Number: 1291
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile, human pathogen
description: Clostridium putrefaciens DSM 1291 is an anaerobe, spore-forming, mesophilic human pathogen that was isolated from ham.
NCBI tax id
- NCBI tax id: 99675
- Matching level: species
strain history
| @ref | history |
|---|---|
| 622 | <- ATCC <- L. DS. Smith, Virginia Polytechnical Institute and State University, Blacksburg, V., USA; VPI 5395 <- NCTC <- E. M. Barnes, Low Temperature Research Station, Cambridge, England, U.K. {1956} |
| 67770 | ATCC 25786 <-- L. DS. Smith VPI 5395 <-- NCTC 9836 <-- E. M. Barnes. |
doi: 10.13145/bacdive2652.20230509.8.1
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 putrefaciens
- full scientific name: Clostridium putrefaciens (McBryde 1911) Sturges and Drake 1927 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Bacillus putrefaciens
@ref: 622
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium putrefaciens
full scientific name: Clostridium putrefaciens (McBryde 1911) Sturges and Drake 1927
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 93.709 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 622
- name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
- growth: yes
- link: https://mediadive.dsmz.de/medium/110
- composition: 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
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 622 | positive | growth | 26 | mesophilic |
| 50134 | positive | growth | 26 | mesophilic |
| 50134 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 26 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 622 | anaerobe | |
| 50134 | anaerobe | |
| 69480 | anaerobe | 99.3 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 99.647 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 622 | ham | United Kingdom | GBR | Europe |
| 50134 | Spoiled cured ham | |||
| 67770 | Spoiled ham |
isolation source categories
- Cat1: #Engineered
- Cat2: #Food production
- Cat3: #Meat
taxonmaps
- @ref: 69479
- File name: preview.99_2592.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_899;97_1048;98_2008;99_2592&stattab=map
- Last taxonomy: Clostridium
- 16S sequence: Y18177
- Sequence Identity:
- Total samples: 19709
- soil counts: 4363
- aquatic counts: 3822
- animal counts: 10663
- plant counts: 861
Safety information
risk assessment
- @ref: 622
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Clostridium putrifaciens 16S rRNA gene, partial, strain DSM 1291 | Y18177 | 1480 | ena | 99675 |
| 20218 | Clostridium putrefaciens gene for 16S ribosomal RNA, partial cds, strain: JCM 1431 | AB618788 | 1473 | ena | 99675 |
| 622 | Clostridium putrefaciens 16S ribosomal RNA gene, partial sequence | AF127024 | 1487 | ena | 99675 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium putrefaciens strain NCTC9836 | 99675.3 | wgs | patric | 99675 |
| 66792 | Clostridium putrefaciens NCTC 9836 | 2808606539 | draft | img | 99675 |
| 67770 | Clostridium putrefaciens NCTC9836 | GCA_900461105 | contig | ncbi | 99675 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 83.226 | no |
| flagellated | yes | 59.124 | no |
| gram-positive | yes | 93.057 | no |
| anaerobic | yes | 97.537 | yes |
| halophile | no | 83.363 | no |
| spore-forming | yes | 96.047 | no |
| thermophile | no | 99.679 | yes |
| glucose-util | yes | 88.513 | no |
| aerobic | no | 93.987 | no |
| glucose-ferment | yes | 64.764 | no |
External links
@ref: 622
culture collection no.: DSM 1291, ATCC 25786, NCTC 9836, CCUG 30534, VPI 5395, JCM 1431, BCRC 14480, NCIMB 11406
straininfo link
- @ref: 72183
- straininfo: 92909
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 622 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1291) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1291 | |||
| 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 | |
| 50134 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 30534) | https://www.ccug.se/strain?id=30534 | |||
| 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) | |||
| 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 | |||
| 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 | |||
| 72183 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92909.1 | StrainInfo: A central database for resolving microbial strain identifiers |