Strain identifier
BacDive ID: 2665
Type strain: 
Species: Clostridium scatologenes
Strain history: ATCC 25775 <-- L. DS. Smith VPI 5393.
NCBI tax ID(s): 1548 (species)
version 8.1 (current version)
General
@ref: 429
BacDive-ID: 2665
DSM-Number: 757
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile, human pathogen
description: Clostridium scatologenes DSM 757 is an anaerobe, spore-forming, mesophilic human pathogen of the family Clostridiaceae.
NCBI tax id
- NCBI tax id: 1548
- Matching level: species
strain history
| @ref | history |
|---|---|
| 429 | <- NCIB <- H. Rosenberger, University of Sheffield, U.K. |
| 67770 | ATCC 25775 <-- L. DS. Smith VPI 5393. |
doi: 10.13145/bacdive2665.20230509.8.1
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 scatologenes
- full scientific name: Clostridium scatologenes (Weinberg and Ginsbourg 1927) Prévot 1948 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Bacillus scatologenes
@ref: 429
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium scatologenes
full scientific name: Clostridium scatologenes (Weinberg and Ginsbourg 1927) Prévot 1948
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 95.219 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 429
- 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 |
|---|---|---|---|---|
| 429 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 429 | anaerobe | |
| 69480 | anaerobe | 99.579 |
spore formation
- @ref: 69480
- spore formation: yes
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 429
- geographic location: Country of origin unknown
taxonmaps
- @ref: 69479
- File name: preview.99_3450.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_1801;97_2159;98_2649;99_3450&stattab=map
- Last taxonomy: Clostridium
- 16S sequence: LC007109
- Sequence Identity:
- Total samples: 12042
- soil counts: 5169
- aquatic counts: 4051
- animal counts: 2029
- plant counts: 793
Safety information
risk assessment
- @ref: 429
- 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 scatologenes strain ATCC 25775 16S ribosomal RNA gene, complete sequence | M59104 | 1460 | ena | 1548 |
| 20218 | Clostridium scatologenes strain DSM 757 16S ribosomal RNA gene, partial sequence | DQ911270 | 320 | ena | 1548 |
| 429 | Clostridium scatologenes strain ATCC 25775 16S ribosomal RNA, partial sequence | NR_118727 | 1460 | nuccore | 1548 |
| 67770 | Clostridium scatologenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 1414 | LC007109 | 1473 | ena | 1548 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium scatologenes ATCC 25775 | GCA_000968375 | complete | ncbi | 1548 |
| 66792 | Clostridium scatologenes strain ATCC 25775 | 1548.3 | wgs | patric | 1548 |
| 66792 | Clostridium scatologenes ATCC 25775 | 2627854033 | complete | img | 1548 |
| 66792 | Clostridium scatologenes ATCC 25775 | 2579778644 | draft | img | 1548 |
| 67770 | Clostridium scatologenes ATCC 25775 | GCA_000632785 | scaffold | ncbi | 1548 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 429 | 27.0 | |
| 67770 | 27 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 89 | no |
| motile | yes | 81.705 | no |
| flagellated | no | 62.368 | no |
| gram-positive | no | 55.567 | no |
| anaerobic | yes | 97.8 | yes |
| aerobic | no | 97.919 | yes |
| halophile | no | 96.405 | no |
| spore-forming | yes | 93.939 | no |
| thermophile | no | 96.713 | yes |
| glucose-util | yes | 89.984 | no |
| glucose-ferment | yes | 60.938 | no |
External links
@ref: 429
culture collection no.: DSM 757, ATCC 25775, NCIMB 8855, VPI 5393, JCM 1414, BCRC 14540, CCUG 9283, NCTC 12992
straininfo link
- @ref: 72194
- straininfo: 44728
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 10758858 | Clostridium scatologenes strain SL1 isolated as an acetogenic bacterium from acidic sediments. | Kusel K, Dorsch T, Acker G, Stackebrandt E, Drake HL | Int J Syst Evol Microbiol | 10.1099/00207713-50-2-537 | 2000 | Acetates/*metabolism, Aldehyde Oxidoreductases/metabolism, Base Composition, Carbon Monoxide/metabolism, Clostridium/*classification/cytology/isolation & purification/physiology, Culture Media, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fermentation, Genes, rRNA, Geologic Sediments/*microbiology, Hydrogen/metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Multienzyme Complexes/metabolism, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water Microbiology | Phylogeny |
| Phylogeny | 16166714 | Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov. | Liou JS, Balkwill DL, Drake GR, Tanner RS | Int J Syst Evol Microbiol | 10.1099/ijs.0.63482-0 | 2005 | Acetic Acid/*metabolism, *Agriculture, Bacterial Typing Techniques, Carbon Monoxide/*metabolism, Clostridium/*classification/genetics/growth & development/isolation & purification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Solvents/*metabolism, *Water Microbiology | Metabolism |
| Phylogeny | 17684276 | Clostridium nitrophenolicum sp. nov., a novel anaerobic p-nitrophenol-degrading bacterium, isolated from a subsurface soil sample. | Suresh K, Prakash D, Rastogi N, Jain RK | Int J Syst Evol Microbiol | 10.1099/ijs.0.64604-0 | 2007 | Base Composition, Clostridium/chemistry/classification/*isolation & purification/*physiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nitrophenols/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Genetics |
| Metabolism | 19055631 | 3-Methylindole production is regulated in Clostridium scatologenes ATCC 25775. | Doerner KC, Cook KL, Mason BP | Lett Appl Microbiol | 10.1111/j.1472-765X.2008.02502.x | 2008 | Clostridium/*metabolism/physiology, Culture Media/chemistry, Hydrogen-Ion Concentration, Skatole/*metabolism, Temperature, Up-Regulation | Biotechnology |
| Metabolism | 19055633 | Fe(III) stimulates 3-methylindole and 4-methylphenol production in swine lagoon enrichments and Clostridium scatologenes ATCC 25775. | Doerner KC, Mason BP, Kridelbaugh D, Loughrin J | Lett Appl Microbiol | 10.1111/j.1472-765X.2008.02500.x | 2008 | Anaerobiosis, Clostridium/*drug effects/*metabolism, Cresols/*metabolism, Culture Media/chemistry, Ferric Compounds/*metabolism, Geologic Sediments/*microbiology, Skatole/*metabolism | Biotechnology |
| Metabolism | 19187496 | Development of a defined medium for Clostridium scatologenes ATCC 25775. | Kridelbaugh D, Doerner KC | Lett Appl Microbiol | 10.1111/j.1472-765X.2008.02546.x | 2009 | Animals, Bacteriological Techniques, Clostridium/*growth & development/metabolism, Cresols/*metabolism, Culture Media/*chemistry, Fructose/metabolism, Glucose/metabolism, Glutamic Acid/metabolism, Glutamine/metabolism, Ketoglutaric Acids/metabolism, Skatole/*metabolism | Cultivation |
| Genetics | 24831152 | Draft Genome Sequence of Clostridium scatologenes ATCC 25775, a Chemolithoautotrophic Acetogenic Bacterium Producing 3-Methylindole and 4-Methylphenol. | Song Y, Jeong Y, Shin HS, Cho BK | Genome Announc | 10.1128/genomeA.00459-14 | 2014 | ||
| Genetics | 26210291 | Complete genome sequence of a malodorant-producing acetogen, Clostridium scatologenes ATCC 25775(T). | Zhu Z, Guo T, Zheng H, Song T, Ouyang P, Xie J | J Biotechnol | 10.1016/j.jbiotec.2015.07.013 | 2015 | Acetates/metabolism, Base Sequence, Clostridium/*genetics/metabolism, *Genome, Bacterial, Molecular Sequence Data, Odorants, RNA, Bacterial/genetics, Skatole/metabolism | Metabolism |
| Phylogeny | 35353674 | Clostridium muellerianum sp. nov., a carbon monoxide-oxidizing acetogen isolated from old hay. | Doyle DA, Smith PR, Lawson PA, Tanner RS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005297 | 2022 | Bacterial Typing Techniques, Base Composition, *Carbon Monoxide, Clostridium, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 429 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 757) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-757 | |||
| 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 | |
| 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) | |||
| 72194 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44728.1 | StrainInfo: A central database for resolving microbial strain identifiers |