Strain identifier
BacDive ID: 159178
Type strain:
Species: Clostridium scindens
Strain Designation: BL-389-WT-3D
Strain history: <- D. Wylensek, TU Munich, Freising-Weihenstephan, Germany; BL-389-WT-3D
NCBI tax ID(s): 29347 (species)
General
@ref: 66001
BacDive-ID: 159178
DSM-Number: 100975
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Clostridium scindens BL-389-WT-3D is a mesophilic bacterium that was isolated from feces; pig, 8 weeks old, wild type.
NCBI tax id
- NCBI tax id: 29347
- Matching level: species
strain history
- @ref: 66001
- history: <- D. Wylensek, TU Munich, Freising-Weihenstephan, Germany; BL-389-WT-3D
doi: 10.13145/bacdive159178.20230509.8.1
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 scindens
- full scientific name: Clostridium scindens Morris et al. 1985
@ref: 66001
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Clostridiaceae
genus: Clostridium
species: Clostridium scindens
full scientific name: Clostridium scindens Morris et al. 1985
strain designation: BL-389-WT-3D
type strain: no
Culture and growth conditions
culture medium
- @ref: 66001
- name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104
- composition: Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
culture temp
- @ref: 66001
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | + | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | - | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
66001 | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 66001
- sample type: feces; pig, 8 weeks old, wild type
- geographic location: Kranzberg (Bavaria)
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
#Host | #Mammals | #Suidae (Pig,Swine) |
taxonmaps
- @ref: 69479
- File name: preview.99_1033.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_592;97_693;98_808;99_1033&stattab=map
- Last taxonomy: [Clostridium] scindens subclade
- 16S sequence: MN537450
- Sequence Identity:
- Total samples: 80205
- soil counts: 346
- aquatic counts: 837
- animal counts: 78797
- plant counts: 225
Safety information
risk assessment
- @ref: 66001
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 66001
- description: [Clostridium] scindens strain DSM 100975 16S ribosomal RNA gene, partial sequence
- accession: MN537450
- length: 1487
- database: ena
- NCBI tax ID: 29347
Genome sequences
- @ref: 66792
- description: [Clostridium] scindens strain BL-389-WT-3D
- accession: 29347.24
- assembly level: wgs
- database: patric
- NCBI tax ID: 29347
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | yes | 94.547 | no |
anaerobic | yes | 99.598 | no |
halophile | no | 81.912 | no |
spore-forming | yes | 54.479 | no |
glucose-util | yes | 90.125 | no |
motile | no | 89.729 | no |
flagellated | no | 95.233 | no |
aerobic | no | 98.297 | no |
thermophile | no | 99.496 | yes |
glucose-ferment | yes | 70.677 | no |
External links
@ref: 66001
culture collection no.: DSM 100975
straininfo link
- @ref: 111681
- straininfo: 406717
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
66001 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100975 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100975) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
68380 | Automatically annotated from API rID32A | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
111681 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID406717.1 |