Strain identifier
BacDive ID: 160948
Type strain: 
Species: Clostridium scindens
Strain history: F. Takamine <-- P. B. Hylemon <-- VPI 12708.
NCBI tax ID(s): 29347 (species)
version 8.1 (current version)
General
@ref: 67770
BacDive-ID: 160948
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Clostridium scindens JCM 10418 is a mesophilic bacterium that was isolated from Feces of colon-cancer patient.
NCBI tax id
- NCBI tax id: 29347
- Matching level: species
strain history
- @ref: 67770
- history: F. Takamine <-- P. B. Hylemon <-- VPI 12708.
doi: 10.13145/bacdive160948.20230509.8.1
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: 67770
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Clostridiaceae
genus: Clostridium
species: Clostridium scindens
full scientific name: Clostridium scindens Morris et al. 1985
type strain: no
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Feces of colon-cancer patient
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: AB971816
- Sequence Identity:
- Total samples: 80205
- soil counts: 346
- aquatic counts: 837
- animal counts: 78797
- plant counts: 225
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | Clostridium scindens 16S rRNA, partial sequence, strain:JCM 10418 | AB020727 | 1453 | ena | 29347 |
| 67770 | [Clostridium] scindens gene for 16S ribosomal RNA, partial sequence, strain: JCM 10418 | AB971816 | 1399 | ena | 29347 |
Genome sequences
- @ref: 66792
- description: [Clostridium] scindens VPI12708
- accession: GCA_027941655
- assembly level: complete
- database: ncbi
- NCBI tax ID: 29347
GC content
- @ref: 67770
- GC-content: 47.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 85.07 | no |
| flagellated | no | 92.915 | no |
| gram-positive | yes | 91.799 | no |
| anaerobic | yes | 99.003 | no |
| aerobic | no | 98.035 | no |
| halophile | no | 81.086 | no |
| spore-forming | yes | 61.35 | no |
| glucose-ferment | yes | 65.588 | no |
| thermophile | no | 99.342 | no |
| glucose-util | yes | 91.808 | no |
External links
@ref: 67770
culture collection no.: JCM 10418, VPI 12708
straininfo link
- @ref: 113113
- straininfo: 88187
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 10843034 | Assignment of Eubacterium sp. VPI 12708 and related strains with high bile acid 7alpha-dehydroxylating activity to Clostridium scindens and proposal of Clostridium hylemonae sp. nov., isolated from human faeces. | Kitahara M, Takamine F, Imamura T, Benno Y | Int J Syst Evol Microbiol | 10.1099/00207713-50-3-971 | 2000 | Base Composition, Bile Acids and Salts/metabolism, Clostridium/*classification/enzymology/isolation & purification, DNA, Ribosomal/chemistry/genetics, Eubacterium/*classification/*enzymology, Feces/*microbiology, Genes, rRNA, Humans, *Hydroxysteroid Dehydrogenases, Molecular Sequence Data, *Oxidoreductases, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Steroid Hydroxylases/*metabolism | Enzymology |
| Phylogeny | 12691873 | Development and application of a polymerase chain reaction assay for the detection and enumeration of bile acid 7alpha-dehydroxylating bacteria in human feces. | Wells JE, Williams KB, Whitehead TR, Heuman DM, Hylemon PB | Clin Chim Acta | 10.1016/s0009-8981(03)00115-3 | 2003 | Cholic Acids/*metabolism, Clostridium/*genetics/*isolation & purification/metabolism, DNA Primers/genetics, Feces/*microbiology, Humans, Hydroxylation, Phylogeny, Polymerase Chain Reaction/*methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid | Metabolism |
| Enzymology | 23836456 | Structural and functional characterization of BaiA, an enzyme involved in secondary bile acid synthesis in human gut microbe. | Bhowmik S, Jones DH, Chiu HP, Park IH, Chiu HJ, Axelrod HL, Farr CL, Tien HJ, Agarwalla S, Lesley SA | Proteins | 10.1002/prot.24353 | 2013 | Apoenzymes/chemistry, Bacterial Proteins/*chemistry, Bile Acids and Salts/*biosynthesis, Catalytic Domain, Clostridium/*enzymology, Crystallography, X-Ray, Humans, Hydrogen-Ion Concentration, Hydroxysteroid Dehydrogenases/*chemistry, Kinetics, Models, Molecular, NAD/chemistry | Pathogenicity |
| Enzymology | 26650892 | Structure and functional characterization of a bile acid 7alpha dehydratase BaiE in secondary bile acid synthesis. | Bhowmik S, Chiu HP, Jones DH, Chiu HJ, Miller MD, Xu Q, Farr CL, Ridlon JM, Wells JE, Elsliger MA, Wilson IA, Hylemon PB, Lesley SA | Proteins | 10.1002/prot.24971 | 2016 | Amino Acid Substitution, Bacterial Proteins/*chemistry/genetics, Catalytic Domain, Cholic Acids/biosynthesis/*chemistry, Clostridium/*enzymology, Crystallography, X-Ray, Humans, Hydro-Lyases/*chemistry/genetics, Hydrogen Bonding, Hydroxylation, Kinetics, Molecular Docking Simulation, Mutagenesis, Site-Directed, Protein Binding, Protein Structure, Secondary, Structural Homology, Protein | Pathogenicity |
| Metabolism | 29617190 | Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243(T). | Harris SC, Devendran S, Mendez-Garcia C, Mythen SM, Wright CL, Fields CJ, Hernandez AG, Cann I, Hylemon PB, Ridlon JM | Gut Microbes | 10.1080/19490976.2018.1458180 | 2018 | Actinobacteria/classification/enzymology/genetics/*metabolism, Bile Acids and Salts/*metabolism, Clostridium/metabolism, Feces/microbiology, Genome, Bacterial/genetics, Humans, Hydrogen, Hydroxysteroid Dehydrogenases/chemistry/genetics/isolation & purification/*metabolism, Metabolic Networks and Pathways/genetics, Nitrogen/metabolism, Oxidation-Reduction, Recombinant Proteins/isolation & purification/metabolism, Substrate Specificity | Enzymology |
| Metabolism | 32179626 | Strain-Dependent Inhibition of Clostridioides difficile by Commensal Clostridia Carrying the Bile Acid-Inducible (bai) Operon. | Reed AD, Nethery MA, Stewart A, Barrangou R, Theriot CM | J Bacteriol | 10.1128/JB.00039-20 | 2020 | Antibiosis, Bacterial Proteins/genetics/metabolism, Bile Acids and Salts/*metabolism, Clostridiales/genetics/*physiology, Clostridioides difficile/growth & development/*physiology, Clostridium Infections/metabolism/*microbiology, Clostridium histolyticum/genetics/*physiology, Humans, Operon, Species Specificity, Symbiosis | Pathogenicity |
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 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 |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |
| 113113 | 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-ID88187.1 |