Strain identifier

BacDive ID: 2780

Type strain: Yes

Species: Clostridium viride

Strain Designation: T2-7

Strain history: <- W. Buckel, Philipps-Univ. Marburg, Germany; T2-7 <- H. A. Barker, University of California, Berkeley, USA {1985}

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: 2846

BacDive-ID: 2780

DSM-Number: 6836

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Clostridium viride T2-7 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from anaerobic sewage sludge.

NCBI tax id

NCBI tax idMatching level
47246species
1121344strain

strain history

  • @ref: 2846
  • history: <- W. Buckel, Philipps-Univ. Marburg, Germany; T2-7 <- H. A. Barker, University of California, Berkeley, USA {1985}

doi: 10.13145/bacdive2780.20230509.8.1

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 viride
  • full scientific name: Clostridium viride Buckel et al. 1995

@ref: 2846

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium viride

full scientific name: Clostridium viride Buckel et al. 1995

strain designation: T2-7

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

  • @ref: 2846
  • name: CLOSTRIDIUM VIRIDE MEDIUM (DSMZ Medium 526)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/526
  • composition: Name: CLOSTRIDIUM VIRIDE MEDIUM (DSMZ Medium 526) Composition: 5-Aminovaleric acid 15.0 g/l K2HPO4 8.7 g/l Yeast extract 7.5 g/l NaHCO3 2.5 g/l L-Cysteine HCl x H2O 0.25 g/l MgSO4 x 7 H2O 0.096 g/l Nitrilotriacetic acid 0.02 g/l CaCl2 x 2 H2O 0.002 g/l FeSO4 x 7 H2O 0.002 g/l ZnSO4 x 7 H2O 0.00176 g/l NiCl2 x 6 H2O 0.001 g/l MnSO4 x H2O 0.001 g/l CoCl2 x 6 H2O 0.001 g/l VOSO4 x 5 H2O 0.001 g/l Na2MoO4 x 2 H2O 0.001 g/l Sodium resazurin 0.0005 g/l CuSO4 x 5 H2O 0.00048 g/l Distilled water

culture temp

  • @ref: 2846
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2846anaerobe
69480anaerobe99.998

spore formation

@refspore formationconfidence
69481no99
69480no98.805

compound production

@refcompound
28465 hydroxyvalerate-CoA transferase
28465 hydroxyvaleryl-CoA dehydratase
28462,4 pentadienoyl-CoA reductase

Isolation, sampling and environmental information

isolation

  • @ref: 2846
  • sample type: anaerobic sewage sludge
  • geographic location: California
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4305.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_91;96_2161;97_2616;98_3240;99_4305&stattab=map
  • Last taxonomy: [Clostridium] viride subclade
  • 16S sequence: X81125
  • Sequence Identity:
  • Total samples: 6043
  • soil counts: 127
  • aquatic counts: 150
  • animal counts: 5722
  • plant counts: 44

Safety information

risk assessment

  • @ref: 2846
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 2846
  • description: C.viride 16S rRNA gene
  • accession: X81125
  • length: 1482
  • database: ena
  • NCBI tax ID: 47246

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792[Clostridium] viride DSM 6836GCA_000620945scaffoldncbi1121344
66792Clostridium viride DSM 68361121344.3wgspatric1121344
66792Clostridium viride DSM 68362558309036draftimg1121344

GC content

  • @ref: 2846
  • GC-content: 41.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes83.379no
flagellatedno81.732no
gram-positiveyes71.161no
anaerobicyes99.291yes
halophileno86.73no
spore-formingyes60.929no
glucose-utilyes68.68no
aerobicno98.12no
thermophileno97.646no
glucose-fermentno59.73no

External links

@ref: 2846

culture collection no.: DSM 6836, ATCC 43977

straininfo link

  • @ref: 72308
  • straininfo: 42160

literature

  • topic: Phylogeny
  • Pubmed-ID: 17684268
  • title: Oscillibacter valericigenes gen. nov., sp. nov., a valerate-producing anaerobic bacterium isolated from the alimentary canal of a Japanese corbicula clam.
  • authors: Iino T, Mori K, Tanaka K, Suzuki KI, Harayama S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64717-0
  • year: 2007
  • mesh: Anaerobiosis, Animals, Base Composition, Bivalvia/*microbiology, Clostridium/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gastrointestinal Tract/microbiology, Japan, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Valerates/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
2846Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6836)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6836
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)
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
72308Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42160.1StrainInfo: A central database for resolving microbial strain identifiers