Strain identifier
BacDive ID: 2834
Type strain: 
Species: Thomasclavelia saccharogumia
Strain Designation: SDG-Mt85-3Db
Strain history: <- T. Clavel, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany; SDG-Mt85-3Db
NCBI tax ID(s): 1121333 (strain), 341225 (species)
version 8.1 (current version)
General
@ref: 6999
BacDive-ID: 2834
DSM-Number: 17460
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive
description: Thomasclavelia saccharogumia SDG-Mt85-3Db is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from faecal sample of a healthy male adult.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 341225 | species |
| 1121333 | strain |
strain history
- @ref: 6999
- history: <- T. Clavel, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany; SDG-Mt85-3Db
doi: 10.13145/bacdive2834.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Erysipelotrichia
- order: Erysipelotrichales
- family: Coprobacillaceae
- genus: Thomasclavelia
- species: Thomasclavelia saccharogumia
- full scientific name: Thomasclavelia saccharogumia (Clavel et al. 2007) Lawson et al. 2023
synonyms
- @ref: 20215
- synonym: Clostridium saccharogumia
@ref: 6999
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium saccharogumia
full scientific name: Clostridium saccharogumia Clavel et al. 2007
strain designation: SDG-Mt85-3Db
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
- @ref: 59205
- incubation period: 1 day
Culture and growth conditions
culture medium
- @ref: 6999
- name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104c
- composition: Name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c) 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 Na2CO3 1.0 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 | range |
|---|---|---|---|---|
| 6999 | positive | growth | 37 | mesophilic |
| 59205 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 6999 | anaerobe | |
| 59205 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.727
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 6999 | faecal sample of a healthy male adult | Berlin | Germany | DEU | Europe | |
| 59205 | Human feces,26-yr-old healthy man | Germany | DEU | Europe | 2005-01-20 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Patient | |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
| #Host | #Human | #Male |
taxonmaps
- @ref: 69479
- File name: preview.99_6729.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15821;96_590;97_3900;98_4958;99_6729&stattab=map
- Last taxonomy: [Clostridium] saccharogumia subclade
- 16S sequence: DQ100445
- Sequence Identity:
- Total samples: 35392
- soil counts: 124
- aquatic counts: 784
- animal counts: 34442
- plant counts: 42
Safety information
risk assessment
- @ref: 6999
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 6999
- description: Clostridium sp. SDG-Mt85-3Db 16S ribosomal RNA gene, partial sequence
- accession: DQ100445
- length: 1484
- database: ena
- NCBI tax ID: 341225
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thomasclavelia saccharogumia DSM 17460 | GCA_000686665 | scaffold | ncbi | 1121333 |
| 66792 | [Clostridium] saccharogumia DSM 17460 | 1121333.3 | wgs | patric | 1121333 |
| 66792 | Clostridium saccharogumia DSM 17460 | 2563366727 | draft | img | 1121333 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 51 | no |
| motile | no | 91.914 | no |
| flagellated | no | 95.451 | no |
| gram-positive | yes | 96.482 | no |
| anaerobic | yes | 98.171 | yes |
| halophile | no | 77.248 | no |
| spore-forming | no | 74.702 | no |
| glucose-util | yes | 87.62 | no |
| aerobic | no | 98.885 | no |
| thermophile | no | 98.103 | no |
| glucose-ferment | yes | 70.524 | no |
External links
@ref: 6999
culture collection no.: DSM 17460, CCUG 51486
straininfo link
- @ref: 72358
- straininfo: 297635
literature
- topic: Phylogeny
- Pubmed-ID: 17196483
- title: Clostridium saccharogumia sp. nov. and Lactonifactor longoviformis gen. nov., sp. nov., two novel human faecal bacteria involved in the conversion of the dietary phytoestrogen secoisolariciresinol diglucoside.
- authors: Clavel T, Lippman R, Gavini F, Dore J, Blaut M
- journal: Syst Appl Microbiol
- DOI: 10.1016/j.syapm.2006.02.003
- year: 2007
- mesh: 4-Butyrolactone/analogs & derivatives/metabolism, Adult, Base Composition, Butylene Glycols/*metabolism, Clostridium/*classification/genetics/growth & development/metabolism, Colon/microbiology, Culture Media, DNA/chemistry, DNA, Ribosomal/genetics, Dietary Carbohydrates/*metabolism, Feces/*microbiology, Genotype, Glucosides/*metabolism, Gram-Positive Rods/*classification/genetics/growth & development/metabolism, Humans, Lignans/metabolism, Male, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Phytoestrogens/*metabolism, RNA, Ribosomal, 16S/genetics
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 6999 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17460) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17460 | |
| 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 | |
| 59205 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 51486) | https://www.ccug.se/strain?id=51486 | |
| 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 | |
| 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) | |
| 72358 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297635.1 | StrainInfo: A central database for resolving microbial strain identifiers |