Strain identifier

BacDive ID: 2774

Type strain: Yes

Species: Clostridium thermoalcaliphilum

Strain Designation: JW/YL23-2

Strain history: <- J. Wiegel, JW/YL23-2

NCBI tax ID(s): 29349 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 3111

BacDive-ID: 2774

DSM-Number: 7309

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

description: Clostridium thermoalcaliphilum JW/YL23-2 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from sewage sludge.

NCBI tax id

  • NCBI tax id: 29349
  • Matching level: species

strain history

  • @ref: 3111
  • history: <- J. Wiegel, JW/YL23-2

doi: 10.13145/bacdive2774.20230509.8.1

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 thermoalcaliphilum
  • full scientific name: Clostridium thermoalcaliphilum Li et al. 1994

@ref: 3111

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium thermoalcaliphilum

full scientific name: Clostridium thermoalcaliphilum Li et al. 1994

strain designation: JW/YL23-2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes91.721
6948099.719positive

Culture and growth conditions

culture medium

  • @ref: 3111
  • 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
3111positivegrowth50thermophilic
69480thermophilic96.809

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
3111anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
69481yes100
69480yes99.539

murein

  • @ref: 3111
  • murein short key: A21.04
  • type: A4ß L-Orn-D-Asp

Isolation, sampling and environmental information

isolation

  • @ref: 3111
  • sample type: sewage sludge
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Sewage sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_17231.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2;96_1875;97_2252;98_13052;99_17231&stattab=map
  • Last taxonomy: [Clostridium] thermoalcaliphilum subclade
  • 16S sequence: FR749954
  • Sequence Identity:
  • Total samples: 422
  • soil counts: 101
  • aquatic counts: 156
  • animal counts: 155
  • plant counts: 10

Safety information

risk assessment

  • @ref: 3111
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
3111Clostridium thermoalcaliphilum partial 16S rRNA gene, type strain DSM 7309T, clone 1FR7499531581ena29349
3111Clostridium thermoalcaliphilum partial 16S rRNA gene, type strain DSM 7309T, clone 2FR7499541546ena29349

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792[Clostridium] thermoalcaliphilum DSM 7309GCA_002029295contigncbi29349
66792[Clostridium] thermoalcaliphilum strain DSM 730929349.3wgspatric29349
66792Clostridium thermoalcaliphilum DSM 73092833455180draftimg29349
66792Clostridium thermoalcaliphilum JW/YL23-22711768657draftimg29349

GC content

  • @ref: 3111
  • GC-content: 32.0
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes75.608no
anaerobicyes99.045yes
halophileno75.304no
spore-formingyes88.119no
glucose-utilyes88.894no
motileyes85.779no
flagellatedno64.146no
thermophileyes99.251yes
aerobicno96.481yes
glucose-fermentyes59.92no

External links

@ref: 3111

culture collection no.: DSM 7309, ATCC 51508, CIP 105528

straininfo link

  • @ref: 72304
  • straininfo: 46154

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8123553Clostridium thermoalcaliphilum sp. nov., an anaerobic and thermotolerant facultative alkaliphile.Li Y, Engle M, Weiss N, Mandelco L, Wiegel JInt J Syst Bacteriol10.1099/00207713-44-1-1111994Base Sequence, Clostridium/genetics/*isolation & purification/physiology, Fermentation, Hydrogen-Ion Concentration, Molecular Sequence Data, RNA, Ribosomal, 16S/chemistry, Sewage, Sodium Chloride/pharmacology, TemperatureGenetics
Genetics28522721First Insights into the Genome Sequence of the Alkaliphilic Thermotolerant Bacterium Clostridium thermoalcaliphilum JW/YL23-2(T).Poehlein A, Berg A, Welsing G, Daniel RGenome Announc10.1128/genomeA.00368-172017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3111Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7309)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7309
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72304Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46154.1StrainInfo: A central database for resolving microbial strain identifiers