Strain identifier
BacDive ID: 2848
Type strain: 
Species: Ruminiclostridium sufflavum
Strain Designation: CDT-1
Strain history: A. Ueki CDT-1.
NCBI tax ID(s): 1121337 (strain), 396504 (species)
version 9.1 (current version)
General
@ref: 8187
BacDive-ID: 2848
DSM-Number: 19573
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, Gram-negative, motile, rod-shaped
description: Ruminiclostridium sufflavum CDT-1 is an anaerobe, spore-forming, Gram-negative bacterium that was isolated from rice-straw residue from a methanogenic reactor treating cattle waste.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 396504 | species |
| 1121337 | strain |
strain history
| @ref | history |
|---|---|
| 8187 | <- A. Ueki, Yamagata Univ., Tsuruoka, Japan; CDT-1 |
| 67770 | A. Ueki CDT-1. |
doi: 10.13145/bacdive2848.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Ruminiclostridium
- species: Ruminiclostridium sufflavum
- full scientific name: Ruminiclostridium sufflavum (Nishiyama et al. 2009) Zhang et al. 2018
synonyms
- @ref: 20215
- synonym: Clostridium sufflavum
@ref: 8187
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Oscillospiraceae
genus: Ruminiclostridium
species: Ruminiclostridium sufflavum
full scientific name: Ruminiclostridium sufflavum (Nishiyama et al. 2009) Zhang et al. 2018
strain designation: CDT-1
type strain: yes
Morphology
cell morphology
- @ref: 28926
- gram stain: negative
- cell length: 3.5 µm
- cell width: 0.55 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 28926
- production: yes
Culture and growth conditions
culture medium
- @ref: 8187
- 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 | growth | type | temperature |
|---|---|---|---|
| 8187 | positive | growth | 30 |
| 28926 | positive | growth | 20-33 |
| 28926 | positive | optimum | 33 |
| 67770 | positive | growth | 30 |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 28926 | positive | growth | 5.9-8.2 |
| 28926 | positive | optimum | 7.4 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 8187 | anaerobe | |
| 28926 | anaerobe | |
| 69480 | anaerobe | 90.141 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 28926 | yes | |
| 69481 | yes | 100 |
observation
- @ref: 28926
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28926 | 30089 | acetate | + | carbon source |
| 28926 | 17057 | cellobiose | + | carbon source |
| 28926 | 16236 | ethanol | + | carbon source |
| 28926 | 28757 | fructose | + | carbon source |
| 28926 | 17234 | glucose | + | carbon source |
| 28926 | 33942 | ribose | + | carbon source |
| 28926 | 30911 | sorbitol | + | carbon source |
| 28926 | 18222 | xylose | + | carbon source |
metabolite production
- @ref: 28926
- Chebi-ID: 16183
- metabolite: methane
- production: yes
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 8187 | rice-straw residue from a methanogenic reactor treating cattle waste | Hokkaido, Betsukai-machi | Japan | JPN | Asia |
| 67770 | Methanogenic reactor treating cattle waste |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Bioreactor | |
| #Engineered | #Waste | |
| #Host | #Mammals | #Bovinae (Cow, Cattle) |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_69092.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_196;96_1460;97_1742;98_40502;99_69092&stattab=map
- Last taxonomy: Ruminiclostridium sufflavum
- 16S sequence: AB267266
- Sequence Identity:
- Total samples: 2019
- soil counts: 1497
- aquatic counts: 321
- animal counts: 107
- plant counts: 94
Safety information
risk assessment
- @ref: 8187
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8187
- description: [Clostridium] sufflavum gene for 16S ribosomal RNA, partial sequence
- accession: AB267266
- length: 1436
- database: nuccore
- NCBI tax ID: 396504
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Ruminiclostridium sufflavum DSM 19573 | GCA_003208175 | scaffold | ncbi | 1121337 |
| 66792 | [Clostridium] sufflavum DSM 19573 | 1121337.3 | wgs | patric | 1121337 |
| 66792 | Ruminiclostridium sufflavum DSM 19573 | 2599185205 | draft | img | 1121337 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8187 | 40.7 | high performance liquid chromatography (HPLC) |
| 28926 | 40.7 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 56.397 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 90.141 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 95.402 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 83.015 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 70.884 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 78.387 | no |
External links
@ref: 8187
culture collection no.: DSM 19573, JCM 14807
straininfo link
- @ref: 72372
- straininfo: 401866
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19406778 | Clostridium sufflavum sp. nov., isolated from a methanogenic reactor treating cattle waste. | Nishiyama T, Ueki A, Kaku N, Ueki K | Int J Syst Evol Microbiol | 10.1099/ijs.0.001719-0 | 2009 | Anaerobiosis, Animal Husbandry/*methods, Animals, Bacterial Typing Techniques, Base Composition, *Bioreactors, Cattle, Clostridium/*classification/genetics/isolation & purification/physiology, Fatty Acids/analysis, Genes, rRNA, Japan, Methane/*metabolism, Molecular Sequence Data, Oryza/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Refuse Disposal/*methods, Sequence Analysis, DNA, Species Specificity | Genetics |
| Phylogeny | 33555241 | Ruminiclostridium herbifermentans sp. nov., a mesophilic and moderately thermophilic cellulolytic and xylanolytic bacterium isolated from a lab-scale biogas fermenter fed with maize silage. | Rettenmaier R, Kowollik ML, Klingl A, Liebl W, Zverlov V | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004692 | 2021 |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 8187 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19573) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19573 | ||||
| 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 | ||||
| 28926 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25365 | 28776041 | ||
| 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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
| 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 | ||||
| 72372 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401866.1 | StrainInfo: A central database for resolving microbial strain identifiers |