Strain identifier
BacDive ID: 130250
Type strain: 
Species: Clostridium oryzae
Strain Designation: KC3
Strain history: <- A. Tonouchi, Faculty Agriculture and Life Sci., Hirosaki Univ., Japan; KC3 <- A. Tonouchi {2011}
NCBI tax ID(s): 1450648 (species)
version 8.1 (current version)
General
@ref: 21884
BacDive-ID: 130250
DSM-Number: 28571
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive
description: Clostridium oryzae KC3 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from rice field soil.
NCBI tax id
- NCBI tax id: 1450648
- Matching level: species
strain history
- @ref: 21884
- history: <- A. Tonouchi, Faculty Agriculture and Life Sci., Hirosaki Univ., Japan; KC3 <- A. Tonouchi {2011}
doi: 10.13145/bacdive130250.20230509.8.1
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 oryzae
- full scientific name: Clostridium oryzae Horino et al. 2015
@ref: 21884
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium oryzae
full scientific name: Clostridium oryzae Horino et al. 2015
strain designation: KC3
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 21884
- name: PY + X MEDIUM (DSMZ Medium 104b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104b
- composition: Name: PY + X MEDIUM (DSMZ Medium 104b; with strain-specific modifications) Composition: Yeast extract 10.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l Cellobiose 1.0 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: 21884
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 21884 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 99.999 |
Isolation, sampling and environmental information
isolation
- @ref: 21884
- sample type: rice field soil
- geographic location: Aomori Prefecture, Goshogawara city, Kanagi
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_6064.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16488;96_2893;97_3555;98_4498;99_6064&stattab=map
- Last taxonomy: Clostridium oryzae subclade
- 16S sequence: AB904755
- Sequence Identity:
- Total samples: 6843
- soil counts: 3427
- aquatic counts: 1863
- animal counts: 1263
- plant counts: 290
Safety information
risk assessment
- @ref: 21884
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21884
- description: Clostridium oryzae gene for 16S ribosomal RNA, partial sequence
- accession: AB904755
- length: 1458
- database: ena
- NCBI tax ID: 1450648
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium oryzae DSM 28571 | GCA_002029235 | contig | ncbi | 1450648 |
| 66792 | Clostridium oryzae strain DSM 28571 | 1450648.3 | wgs | patric | 1450648 |
| 66792 | Clostridium oryzae DSM 28571 | 2711768656 | draft | img | 1450648 |
GC content
- @ref: 21884
- GC-content: 37.5
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 82.65 | no |
| gram-positive | yes | 68.719 | no |
| anaerobic | yes | 97.584 | yes |
| halophile | no | 91.924 | no |
| spore-forming | yes | 95.745 | no |
| glucose-util | yes | 93.606 | no |
| thermophile | no | 89.068 | yes |
| aerobic | no | 98.06 | no |
| flagellated | yes | 60.613 | no |
| glucose-ferment | yes | 65.087 | no |
External links
@ref: 21884
culture collection no.: DSM 28571, NBRC 110163
straininfo link
- @ref: 88789
- straininfo: 407839
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25563913 | Clostridium oryzae sp. nov., from soil of a Japanese rice field. | Horino H, Ito M, Tonouchi A | Int J Syst Evol Microbiol | 10.1099/ijs.0.000042 | 2015 | Amino Acid Sequence, Bacterial Typing Techniques, Base Composition, Bioreactors/microbiology, Clostridium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
| Genetics | 28619808 | First Insights into the Genome Sequence of Clostridium oryzae DSM 28571, Isolated from the Soil of a Japanese Rice Field. | Poehlein A, Gippert AL, Bierenbroodspot MJ, Daniel R | Genome Announc | 10.1128/genomeA.00539-17 | 2017 | Phylogeny | |
| Phylogeny | 30358527 | Clostridium composti sp. nov., a new anaerobic bacteria isolated from compost. | Shin Y, Paek J, Son AY, Kim H, Kook JK, Paek WK, Chang YH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003074 | 2018 | Bacterial Typing Techniques, Base Composition, Clostridium/*classification/genetics/isolation & purification, *Composting, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 21884 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28571 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28571) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 88789 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID407839.1 |