Strain identifier
BacDive ID: 2780
Type strain:
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}
NCBI tax ID(s): 1121344 (strain), 47246 (species)
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 id | Matching level |
---|---|
47246 | species |
1121344 | strain |
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
@ref | oxygen tolerance | confidence |
---|---|---|
2846 | anaerobe | |
69480 | anaerobe | 99.998 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 98.805 |
compound production
@ref | compound |
---|---|
2846 | 5 hydroxyvalerate-CoA transferase |
2846 | 5 hydroxyvaleryl-CoA dehydratase |
2846 | 2,4 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | [Clostridium] viride DSM 6836 | GCA_000620945 | scaffold | ncbi | 1121344 |
66792 | Clostridium viride DSM 6836 | 1121344.3 | wgs | patric | 1121344 |
66792 | Clostridium viride DSM 6836 | 2558309036 | draft | img | 1121344 |
GC content
- @ref: 2846
- GC-content: 41.5
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | yes | 83.379 | no |
flagellated | no | 81.732 | no |
gram-positive | yes | 71.161 | no |
anaerobic | yes | 99.291 | yes |
halophile | no | 86.73 | no |
spore-forming | yes | 60.929 | no |
glucose-util | yes | 68.68 | no |
aerobic | no | 98.12 | no |
thermophile | no | 97.646 | no |
glucose-ferment | no | 59.73 | no |
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
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
2846 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6836) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6836 | |
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
69479 | João 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 | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |
72308 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42160.1 | StrainInfo: A central database for resolving microbial strain identifiers |