Strain identifier

BacDive ID: 2743

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
537013strain
84026species

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

@refmotilityconfidencegram stain
69480no92.848
69480100positive

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

@refoxygen toleranceconfidence
2178anaerobe
69480anaerobe100

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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792[Clostridium] methylpentosum DSM 5476GCA_000158655scaffoldncbi537013
66792Clostridium methylpentosum DSM 5476537013.3wgspatric537013
66792Clostridium methylpentosum R2, DSM 5476643886206draftimg537013

GC content

  • @ref: 2178
  • GC-content: 46.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno77no
motileno89.588no
flagellatedno96.755no
gram-positiveyes90.186no
anaerobicyes99.671no
aerobicno99.028no
halophileno90.452no
spore-formingno70.906no
thermophileno96.014no
glucose-utilyes83.041no
glucose-fermentyes65.804no

External links

@ref: 2178

culture collection no.: DSM 5476, ATCC 43829

straininfo link

  • @ref: 72273
  • straininfo: 42073

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism2742449Clostridium methylpentosum sp. nov.: a ring-shaped intestinal bacterium that ferments only methylpentoses and pentoses.Himelbloom BH, Canale-Parola EArch Microbiol10.1007/BF004065531989Arabinose/metabolism, Clostridium/*metabolism/ultrastructure, Fermentation, Fucose/metabolism, Humans, Intestines/*microbiology, Microscopy, Electron, Microscopy, Electron, Scanning, Pentoses/*metabolism, Rhamnose/metabolism, Spores, Bacterial/ultrastructurePathogenicity
Phylogeny28901896Paludicola 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 YMInt J Syst Evol Microbiol10.1099/ijsem.0.0022602017Bacterial 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, *WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2178Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5476)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5476
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
72273Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42073.1StrainInfo: A central database for resolving microbial strain identifiers