Strain identifier
BacDive ID: 2743
Type strain:
Species: Clostridium methylpentosum
Strain Designation: R2
Strain history: <- ATCC <- B.H. Himelbloom and E. Canale-Parola, R2
NCBI tax ID(s): 537013 (strain), 84026 (species)
General
@ref: 2178
BacDive-ID: 2743
DSM-Number: 5476
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Clostridium methylpentosum R2 is an anaerobe, mesophilic bacterium that was isolated from human faeces.
NCBI tax id
NCBI tax id | Matching level |
---|---|
537013 | strain |
84026 | species |
strain history
- @ref: 2178
- history: <- ATCC <- B.H. Himelbloom and E. Canale-Parola, R2
doi: 10.13145/bacdive2743.20230509.8.1
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 methylpentosum
- full scientific name: Clostridium methylpentosum Himelbloom and Canale-Parola 1989
@ref: 2178
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium methylpentosum
full scientific name: Clostridium methylpentosum Himelbloom and Canale-Parola 1989
strain designation: R2
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 92.848 | |
69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 2178
- name: CLOSTRIDIUM METHYLPENTOSUM MEDIUM (DSMZ Medium 492)
- growth: yes
- link: https://mediadive.dsmz.de/medium/492
- composition: Name: CLOSTRIDIUM METHYLPENTOSUM MEDIUM (DSMZ Medium 492) Composition: L-Rhamnose 1.99005 g/l L-Cysteine HCl x H2O 0.995025 g/l NaHCO3 0.995025 g/l NaCl 0.895522 g/l KH2PO4 0.895522 g/l NH4Cl 0.895522 g/l CaCl2 x 2 H2O 0.0199005 g/l MnCl2 x 4 H2O 0.0199005 g/l MgSO4 x 7 H2O 0.0199005 g/l CoCl2 x 6 H2O 0.00497512 g/l FeSO4 x 7 H2O 0.00497512 g/l ZnSO4 x 7 H2O 0.00199005 g/l CuSO4 x H2O 0.00199005 g/l Sodium resazurin 0.000497512 g/l Pyridoxine hydrochloride 9.95025e-05 g/l (DL)-alpha-Lipoic acid 4.97512e-05 g/l p-Aminobenzoic acid 4.97512e-05 g/l Calcium D-(+)-pantothenate 4.97512e-05 g/l Nicotinic acid 4.97512e-05 g/l Riboflavin 4.97512e-05 g/l Thiamine HCl 4.97512e-05 g/l Folic acid 1.99005e-05 g/l Biotin 1.99005e-05 g/l Vitamin B12 9.95025e-07 g/l Distilled water
culture temp
- @ref: 2178
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
2178 | anaerobe | |
69480 | anaerobe | 100 |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 98.605
Isolation, sampling and environmental information
isolation
- @ref: 2178
- sample type: human faeces
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_2767.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_349;96_1471;97_1755;98_2147;99_2767&stattab=map
- Last taxonomy: [Clostridium] methylpentosum subclade
- 16S sequence: Y18181
- Sequence Identity:
- Total samples: 37435
- soil counts: 154
- aquatic counts: 270
- animal counts: 36917
- plant counts: 94
Safety information
risk assessment
- @ref: 2178
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 2178
- description: Clostridium methylpentosum 16S rRNA gene, partial, strain DSM 5476
- accession: Y18181
- length: 1435
- database: ena
- NCBI tax ID: 537013
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | [Clostridium] methylpentosum DSM 5476 | GCA_000158655 | scaffold | ncbi | 537013 |
66792 | Clostridium methylpentosum DSM 5476 | 537013.3 | wgs | patric | 537013 |
66792 | Clostridium methylpentosum R2, DSM 5476 | 643886206 | draft | img | 537013 |
GC content
- @ref: 2178
- GC-content: 46.0
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 77 | no |
motile | no | 89.588 | no |
flagellated | no | 96.755 | no |
gram-positive | yes | 90.186 | no |
anaerobic | yes | 99.671 | no |
aerobic | no | 99.028 | no |
halophile | no | 90.452 | no |
spore-forming | no | 70.906 | no |
thermophile | no | 96.014 | no |
glucose-util | yes | 83.041 | no |
glucose-ferment | yes | 65.804 | no |
External links
@ref: 2178
culture collection no.: DSM 5476, ATCC 43829
straininfo link
- @ref: 72273
- straininfo: 42073
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 2742449 | Clostridium methylpentosum sp. nov.: a ring-shaped intestinal bacterium that ferments only methylpentoses and pentoses. | Himelbloom BH, Canale-Parola E | Arch Microbiol | 10.1007/BF00406553 | 1989 | Arabinose/metabolism, Clostridium/*metabolism/ultrastructure, Fermentation, Fucose/metabolism, Humans, Intestines/*microbiology, Microscopy, Electron, Microscopy, Electron, Scanning, Pentoses/*metabolism, Rhamnose/metabolism, Spores, Bacterial/ultrastructure | Pathogenicity |
Phylogeny | 28901896 | Paludicola psychrotolerans gen. nov., sp. nov., a novel psychrotolerant chitinolytic anaerobe of the family Ruminococcaceae. | Li Y, Zhang LL, Liu L, Tian YQ, Liu XF, Li WJ, Dai YM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002260 | 2017 | Bacterial Typing Techniques, Base Composition, China, Chitin/metabolism, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Wetlands | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2178 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5476) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-5476 | |||
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 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
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) | |||
72273 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42073.1 | StrainInfo: A central database for resolving microbial strain identifiers |