Strain identifier
BacDive ID: 2858
Type strain: 
Species: Clostridium chromiireducens
Strain Designation: GCAF-1
Strain history: <- A. Ogram, Univ. Florida, USA; GCAF-1 <- K. Sharma {2001}
NCBI tax ID(s): 225345 (species)
version 9.3 (current version)
General
@ref: 16787
BacDive-ID: 2858
DSM-Number: 23318
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Clostridium chromiireducens GCAF-1 is an anaerobe, mesophilic bacterium that was isolated from chromium-contaminated wetland soil.
NCBI tax id
- NCBI tax id: 225345
- Matching level: species
strain history
- @ref: 16787
- history: <- A. Ogram, Univ. Florida, USA; GCAF-1 <- K. Sharma {2001}
doi: 10.13145/bacdive2858.20250331.9.3
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 chromiireducens
- full scientific name: Clostridium chromiireducens Inglett et al. 2011
@ref: 16787
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium chromiireducens
full scientific name: Clostridium chromiireducens Inglett et al. 2011
strain designation: GCAF-1
type strain: yes
Culture and growth conditions
culture medium
- @ref: 16787
- 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
- @ref: 16787
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 16787 | anaerobe | |
| 125439 | facultative anaerobe | 97.1 |
Isolation, sampling and environmental information
isolation
- @ref: 16787
- sample type: chromium-contaminated wetland soil
- geographic location: Michigan
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | #Heavy metal |
| #Environmental | #Terrestrial | #Soil |
| #Environmental | #Terrestrial | #Wetland (Swamp) |
taxonmaps
- @ref: 69479
- File name: preview.99_59826.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_149;97_160;98_179;99_59826&stattab=map
- Last taxonomy: Clostridium
- 16S sequence: AY228334
- Sequence Identity:
- Total samples: 3219
- soil counts: 736
- aquatic counts: 700
- animal counts: 1552
- plant counts: 231
Safety information
risk assessment
- @ref: 16787
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16787
- description: Clostridium chromiireducens strain GCAF-1 16S ribosomal RNA gene, partial sequence
- accession: AY228334
- length: 1474
- database: nuccore
- NCBI tax ID: 225345
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium chromiireducens DSM 23318 | GCA_002029255 | contig | ncbi | 225345 |
| 66792 | Clostridium chromiireducens strain DSM 23318 | 225345.3 | wgs | patric | 225345 |
| 66792 | Clostridium chromiireducens DSM 23318 | 2711768655 | draft | img | 225345 |
GC content
- @ref: 16787
- GC-content: 30.7
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 56.257 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 87.29 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 74.077 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 92.345 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 93.795 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 77.008 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 84.5 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 82.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 75.7 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | facultative anaerobe | 97.1 |
External links
@ref: 16787
culture collection no.: DSM 23318, KCTC 5935
straininfo link
- @ref: 72382
- straininfo: 400406
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21148674 | Clostridium chromiireducens sp. nov., isolated from Cr(VI)-contaminated soil. | Inglett KS, Bae HS, Aldrich HC, Hatfield K, Ogram AV | Int J Syst Evol Microbiol | 10.1099/ijs.0.024554-0 | 2010 | Base Composition, Chromium/*metabolism, Clostridium/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Soil Pollutants/metabolism | Metabolism |
| 28572314 | First Insights into the Genome of the Cr(VI)-Reducing Bacterium Clostridium chromiireducens DSM 23318. | Poehlein A, Hoche N, Mehr A, Daniel R | Genome Announc | 10.1128/genomeA.00420-17 | 2017 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 16787 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23318) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23318 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 72382 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400406.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |