Strain identifier

BacDive ID: 131500

Type strain: Yes

Species: Clostridium jeddahense

Strain Designation: JCD

Strain history: <- J.-C. Lagier, Timone Hospital, Marseille, France; JCD

NCBI tax ID(s): 1414721 (species)

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General

@ref: 22727

BacDive-ID: 131500

DSM-Number: 27834

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Clostridium jeddahense JCD is an anaerobe, mesophilic bacterium that was isolated from feces from an obese 24-year-old male volunteer.

NCBI tax id

  • NCBI tax id: 1414721
  • Matching level: species

strain history

  • @ref: 22727
  • history: <- J.-C. Lagier, Timone Hospital, Marseille, France; JCD

doi: 10.13145/bacdive131500.20230509.8.1

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 jeddahense
  • full scientific name: Clostridium jeddahense Lagier et al. 2016

@ref: 22727

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium jeddahense

full scientific name: Clostridium jeddahense Lagier et al. 2016

strain designation: JCD

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 22727
  • name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/110
  • composition: Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

culture temp

  • @ref: 22727
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 22727
  • oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

  • @ref: 22727
  • sample type: feces from an obese 24-year-old male volunteer
  • country: Saudi Arabia
  • origin.country: SAU
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_3826.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_229;96_1964;97_2361;98_2915;99_3826&stattab=map
  • Last taxonomy: Clostridium
  • 16S sequence: HG726040
  • Sequence Identity:
  • Total samples: 3765
  • soil counts: 262
  • aquatic counts: 422
  • animal counts: 2985
  • plant counts: 96

Safety information

risk assessment

  • @ref: 22727
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22727
  • description: Clostridium jeddahense partial 16S rRNA gene, isolate JCD
  • accession: HG726040
  • length: 1387
  • database: ena
  • NCBI tax ID: 1414721

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium jeddahense JCDGCA_000577335contigncbi1414721
66792Clostridium jeddahense JCD2619619242draftimg1414721

GC content

  • @ref: 22727
  • GC-content: 52
  • method: sequence analysis

External links

@ref: 22727

culture collection no.: DSM 27834, CSUR P693

straininfo link

  • @ref: 89916
  • straininfo: 398660

literature

  • topic: Genetics
  • Pubmed-ID: 25197479
  • title: Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov.
  • authors: Lagier JC, Bibi F, Ramasamy D, Azhar EI, Robert C, Yasir M, Jiman-Fatani AA, Alshali KZ, Fournier PE, Raoult D
  • journal: Stand Genomic Sci
  • DOI: 10.4056/sigs.5571026
  • year: 2014
  • topic2: Phylogeny

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
22727Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27834Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27834)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
89916Reimer, 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 identifiers10.60712/SI-ID398660.1