Strain identifier

BacDive ID: 2753

Type strain: Yes

Species: Clostridium homopropionicum

Strain Designation: LuHBu1

Strain history: <- C. Dörner, LuHBu1

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2336

BacDive-ID: 2753

DSM-Number: 5847

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

description: Clostridium homopropionicum LuHBu1 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from anoxic sewage sludge.

NCBI tax id

NCBI tax idMatching level
1121318strain
36844species

strain history

  • @ref: 2336
  • history: <- C. Dörner, LuHBu1

doi: 10.13145/bacdive2753.20230509.8.1

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 homopropionicum
  • full scientific name: Clostridium homopropionicum Dörner and Schink 1991

@ref: 2336

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium homopropionicum

full scientific name: Clostridium homopropionicum Dörner and Schink 1991

strain designation: LuHBu1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes98.27
69480100positive

Culture and growth conditions

culture medium

  • @ref: 2336
  • name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/503
  • composition: Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: Na-3-hydroxybutyrate 1.49551 g/l Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

culture temp

  • @ref: 2336
  • growth: positive
  • type: growth
  • temperature: 35
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2336anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481yes99
69480yes100

Isolation, sampling and environmental information

isolation

  • @ref: 2336
  • sample type: anoxic sewage sludge
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Sewage sludge
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7942.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_3674;97_4513;98_5796;99_7942&stattab=map
  • Last taxonomy: Clostridium homopropionicum
  • 16S sequence: X76744
  • Sequence Identity:
  • Total samples: 8577
  • soil counts: 172
  • aquatic counts: 329
  • animal counts: 8049
  • plant counts: 27

Safety information

risk assessment

  • @ref: 2336
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 2336
  • description: Clostridium homopropionicum 16S rRNA gene type strain DSM 5847T
  • accession: X76744
  • length: 1461
  • database: ena
  • NCBI tax ID: 36844

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium homopropionicum DSM 5847GCA_900113195scaffoldncbi36844
66792Clostridium homopropionicum DSM 5847GCA_001263795contigncbi1121318
66792Clostridium homopropionicum DSM 58471121318.3wgspatric1121318
66792Clostridium homopropionicum strain DSM 584736844.3wgspatric36844
66792Clostridium homopropionicum DSM 58472622736521draftimg1121318
66792Clostridium homopropionicum DSM 58472645727554draftimg1121318

GC content

  • @ref: 2336
  • GC-content: 32.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes99no
motileyes79.298no
flagellatedyes60.277no
gram-positiveyes53.299no
anaerobicyes99.683yes
aerobicno98.608no
halophileno92.627no
spore-formingyes93.255no
glucose-utilyes82.065no
thermophileno91.524no
glucose-fermentno57.685no

External links

@ref: 2336

culture collection no.: DSM 5847, ATCC 51426

straininfo link

  • @ref: 72283
  • straininfo: 42977

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism2244786Clostridium homopropionicum sp. nov., a new strict anaerobe growing with 2-, 3-, or 4-hydroxybutyrate.Dorner C, Schink BArch Microbiol10.1007/BF002765291990Acetates/metabolism, Acrylates/metabolism, Anaerobiosis, Biodegradation, Environmental, Butyrates/metabolism, Clostridium/enzymology/*growth & development/metabolism, Fermentation, Fresh Water, Fructose/metabolism, Hydroxybutyrates/*metabolism, Lactates/metabolism, Propionates/metabolism, Seawater, *Sewage, *Water MicrobiologyPhylogeny
Genetics26430034Draft Genome Sequence of the Strict Anaerobe Clostridium homopropionicum LuHBu1 (DSM 5847).Beck MH, Poehlein A, Bengelsdorf FR, Schiel-Bengelsdorf B, Daniel R, Durre PGenome Announc10.1128/genomeA.01112-152015

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2336Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5847)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5847
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
72283Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42977.1StrainInfo: A central database for resolving microbial strain identifiers