Strain identifier

BacDive ID: 2770

Type strain: Yes

Species: Clostridium paradoxum

Strain Designation: JW-YL-7

Strain history: <- J. Wiegel, JW-YL-7

NCBI tax ID(s): 1121328 (strain), 29346 (species)

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General

@ref: 3110

BacDive-ID: 2770

DSM-Number: 7308

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, Gram-positive

description: Clostridium paradoxum JW-YL-7 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from aeration pool, sewage plant.

NCBI tax id

NCBI tax idMatching level
29346species
1121328strain

strain history

  • @ref: 3110
  • history: <- J. Wiegel, JW-YL-7

doi: 10.13145/bacdive2770.20230509.8.1

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 paradoxum
  • full scientific name: Clostridium paradoxum Li et al. 1993

@ref: 3110

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium paradoxum

full scientific name: Clostridium paradoxum Li et al. 1993

strain designation: JW-YL-7

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 99.719

Culture and growth conditions

culture medium

  • @ref: 3110
  • name: YTG MEDIUM (DSMZ Medium 616)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/616
  • composition: Name: CLOSTRIDIUM (YTG) MEDIUM (DSMZ Medium 616) Composition: Tryptone 10.0 g/l Na2CO3 5.3 g/l Yeast extract 5.0 g/l D-Glucose 3.0 g/l Na2HPO4 x 2 H2O 0.36 g/l Na2S x 9 H2O 0.2 g/l L-Cysteine HCl x H2O 0.2 g/l KCl 0.08 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
3110positivegrowth55thermophilic
69480thermophilic98.984

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
3110anaerobe
69480anaerobe99.999

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 99.998

Isolation, sampling and environmental information

isolation

  • @ref: 3110
  • sample type: aeration pool, sewage plant
  • geographic location: Georgia, Athens
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Wastewater
#Engineered#Waste#Water treatment plant

Safety information

risk assessment

  • @ref: 3110
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.paradoxum 16S rRNA gene (clone para1)Z699271567ena29346
20218C.paradoxum 16S rRNA gene (clone para11)Z699281566ena29346
20218C.paradoxum 16S rRNA gene (clone para25)Z699301572ena29346
20218C.paradoxum 16S rRNA gene (clone para27)Z699311571ena29346
20218C.paradoxum 16S rRNA gene (clone para39)Z699321589ena29346
20218C.paradoxum 16S rRNA gene (clone para83)Z699331574ena29346
20218C.paradoxum 16S rRNA gene (clone para89)Z699341574ena29346
20218C.paradoxum 16S rRNA gene (clone para32)Z699351547ena29346
20218C.paradoxum 16S rRNA gene (clone para78)Z699361547ena29346
20218C.paradoxum 16S rRNA gene (clone para82)Z699371564ena29346
20218C.paradoxum 16S rRNA gene (clone para85)Z699381548ena29346
20218C.paradoxum 16S rRNA gene (clone para99)Z699391573ena29346
20218C.paradoxum 16S rRNA gene (clone para23)Z699401452ena29346
20218C.paradoxum 16S rRNA gene (clone para2)Z699411449ena29346
20218C.paradoxum 16S rRNA geneZ699421410ena29346
20218Clostridium paradoxum small subunit ribosomal RNAL068381467ena29346
3110C.paradoxum 16S rRNA gene (clone para24)Z699291553ena1121328

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792[Clostridium] paradoxum JW-YL-7 = DSM 7308GCA_001584565contigncbi1121328
66792[Clostridium] paradoxum JW-YL-7 = DSM 7308GCA_900142555scaffoldncbi1121328
66792[Clostridium] paradoxum JW-YL-7 = DSM 73081121328.3wgspatric1121328
66792[Clostridium] paradoxum JW-YL-7 = DSM 73081121328.12wgspatric1121328
66792Clostridium paradoxum DSM 73082599185174draftimg1121328
66792Clostridium paradoxum JW-YL-72690315891draftimg1121328

GC content

  • @ref: 3110
  • GC-content: 30.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes81no
motileyes81.868no
flagellatedno77.153no
gram-positiveyes66.229no
anaerobicyes99.056yes
aerobicno97.472no
halophileno68.209no
spore-formingyes82.35no
thermophileyes99.499yes
glucose-utilyes88.84no
glucose-fermentyes60.104no

External links

@ref: 3110

culture collection no.: DSM 7308, ATCC 51510, CIP 105527

straininfo link

  • @ref: 72300
  • straininfo: 43026

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8760921Clostridium paradoxum DSM 7308T contains multiple 16S rRNA genes with heterogeneous intervening sequences.Rainey FA, Ward-Rainey NL, Janssen PH, Hippe H, Stackebrandt EMicrobiology (Reading)10.1099/13500872-142-8-20871996Base Sequence, Cloning, Molecular, Clostridium/*genetics, DNA Primers, DNA Probes, Escherichia coli/genetics, Genes, Bacterial, Genetic Variation, *Introns, Molecular Sequence Data, *Multigene Family, Polymerase Chain Reaction, RNA, RNA, Ribosomal, 16S/*genetics, Sequence Homology, Nucleic AcidEnzymology
Genetics27151784Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7.Lancaster WA, Utturkar SM, Poole FL, Klingeman DM, Elias DA, Adams MW, Brown SDGenome Announc10.1128/genomeA.00229-162016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3110Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7308)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7308
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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)
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)
72300Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43026.1StrainInfo: A central database for resolving microbial strain identifiers