Strain identifier

BacDive ID: 2856

Type strain: Yes

Species: Clostridium hydrogeniformans

Strain Designation: BL-20

Strain history: <- W. M. Moe, Louisiana State Univ.; BL-20 <- H.-S. Bae

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: 15920

BacDive-ID: 2856

DSM-Number: 21757

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Clostridium hydrogeniformans BL-20 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from contaminated groundwater.

NCBI tax id

NCBI tax idMatching level
349933species
1121319strain

strain history

  • @ref: 15920
  • history: <- W. M. Moe, Louisiana State Univ.; BL-20 <- H.-S. Bae

doi: 10.13145/bacdive2856.20230509.8.1

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 hydrogeniformans
  • full scientific name: Clostridium hydrogeniformans Bowman et al. 2010

@ref: 15920

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium hydrogeniformans

full scientific name: Clostridium hydrogeniformans Bowman et al. 2010

strain designation: BL-20

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29438positive3.75 µm0.9 µmrod-shapedyes
69480yes93.71
69480positive100

pigmentation

  • @ref: 29438
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15920
  • name: PY + X MEDIUM (DSMZ Medium 104b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104b
  • composition: Name: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15920positivegrowth35mesophilic
29438positivegrowth15-40
29438positiveoptimum35mesophilic

culture pH

@refabilitytypepHPH range
29438positivegrowth05-10alkaliphile
29438positiveoptimum7.9

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
15920anaerobe
29438facultative anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
29438yes
69481yes100
69480yes99.623

halophily

  • @ref: 29438
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2943817814salicin+carbon source
294384853esculin+hydrolysis

metabolite production

  • @ref: 29438
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

  • @ref: 29438
  • value: gelatinase
  • activity: +

Isolation, sampling and environmental information

isolation

  • @ref: 15920
  • sample type: contaminated groundwater
  • geographic location: 10 miles north of Baton Rouge
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Aquatic#Groundwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_21675.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_10969;97_13289;98_16355;99_21675&stattab=map
  • Last taxonomy: Clostridium hydrogeniformans subclade
  • 16S sequence: DQ196623
  • Sequence Identity:
  • Total samples: 2615
  • soil counts: 1225
  • aquatic counts: 916
  • animal counts: 374
  • plant counts: 100

Safety information

risk assessment

  • @ref: 15920
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15920
  • description: Clostridium hydrogeniformans strain BL-20 16S ribosomal RNA gene, partial sequence
  • accession: DQ196623
  • length: 1447
  • database: ena
  • NCBI tax ID: 1121319

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium hydrogeniformans DSM 21757GCA_000686705scaffoldncbi1121319
66792Clostridium hydrogeniformans DSM 217571121319.3wgspatric1121319
66792Clostridium hydrogeniformans DSM 217572563366730draftimg1121319

GC content

@refGC-contentmethod
1592030.4high performance liquid chromatography (HPLC)
2943830.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes83.311no
flagellatedno50no
gram-positiveyes90.186yes
anaerobicyes97.533no
halophileno81.337no
spore-formingyes95.592yes
glucose-utilyes91.902no
aerobicno97.165yes
thermophileno99.505yes
glucose-fermentyes65.698no

External links

@ref: 15920

culture collection no.: DSM 21757, NRRL B-51348

straininfo link

  • @ref: 72380
  • straininfo: 407505

literature

  • topic: Phylogeny
  • Pubmed-ID: 19651721
  • title: Clostridium hydrogeniformans sp. nov. and Clostridium cavendishii sp. nov., hydrogen-producing bacteria from chlorinated solvent-contaminated groundwater.
  • authors: Bowman KS, Dupre RE, Rainey FA, Moe WM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.013169-0
  • year: 2009
  • mesh: Base Composition, Base Sequence, Chlorine/metabolism, Clostridium/*classification/genetics/physiology, DNA, Bacterial/chemistry, Hydrogen/*metabolism, Louisiana, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Solvents/metabolism, *Water Microbiology, *Water Pollution, Chemical
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15920Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21757)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21757
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
29438Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2584428776041
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)
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
72380Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407505.1StrainInfo: A central database for resolving microbial strain identifiers