Strain identifier
BacDive ID: 2840
Type strain: 
Species: Ruminiclostridium josui
Strain history: K. Sakka <-- K. Ohmiya strain III.
NCBI tax ID(s): 1291050 (strain), 1499 (species)
version 8.1 (current version)
General
@ref: 18098
BacDive-ID: 2840
DSM-Number: 25723
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, motile
description: Ruminiclostridium josui DSM 25723 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from Thai compost.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1499 | species |
| 1291050 | strain |
strain history
| @ref | history |
|---|---|
| 18098 | <- K. Sakka, Mie Univ., Grad. School of Bioresources, Tsu City, Japan <- K. Ohmiya, Nagoya Univ., School of Agric., Japan |
| 67770 | K. Sakka <-- K. Ohmiya strain III. |
doi: 10.13145/bacdive2840.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Ruminiclostridium
- species: Ruminiclostridium josui
- full scientific name: Ruminiclostridium josui (Sukhumavasi et al. 1988) Zhang et al. 2018
synonyms
- @ref: 20215
- synonym: Clostridium josui
@ref: 18098
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Oscillospiraceae
genus: Ruminiclostridium
species: Ruminiclostridium josui
full scientific name: Ruminiclostridium josui (Sukhumavasi et al. 1988) Zhang et al. 2018
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 93.058 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 18098
- name: ACETIVIBRIO MEDIUM (DSMZ Medium 122)
- growth: yes
- link: https://mediadive.dsmz.de/medium/122
- composition: Name: ACETIVIBRIO MEDIUM (DSMZ Medium 122) Composition: Cellulose 10.0 g/l (optional) Na2-ß-glycerophosphate x 5 H2O 6.0 g/l K2HPO4 5.5 g/l Cellobiose 5.0 g/l Yeast extract 4.5 g/l MgCl2 x 6 H2O 2.6 g/l KH2PO4 1.43 g/l (NH4)2SO4 1.3 g/l L-Glutathione 0.25 g/l CaCl2 x 2 H2O 0.13 g/l FeSO4 x 7 H2O 0.0011 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 18098 | positive | growth | 45 | thermophilic |
| 67770 | positive | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 18098 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 95 |
| 69480 | yes | 99.644 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 18098 | Thai compost | Thailand | THA | Asia |
| 67770 | Compost | Thailand | THA | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Biodegradation
- Cat3: #Composting
taxonmaps
- @ref: 69479
- File name: preview.99_3811.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_196;96_1460;97_1742;98_2903;99_3811&stattab=map
- Last taxonomy: Ruminiclostridium
- 16S sequence: AB011057
- Sequence Identity:
- Total samples: 18647
- soil counts: 10142
- aquatic counts: 5182
- animal counts: 1933
- plant counts: 1390
Safety information
risk assessment
- @ref: 18098
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 18098 | Clostridium josui gene for 16S rRNA, partial sequence | AB011057 | 1565 | ena | 1499 |
| 67770 | Clostridium josui gene for 16S ribosomal RNA, partial sequence, strain: JCM 17888 | AB675738 | 1537 | ena | 1291050 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | [Clostridium] josui JCM 17888 | 1291050.6 | wgs | patric | 1291050 |
| 66792 | Clostridium josui JCM 17888 | 1291050.4 | wgs | patric | 1291050 |
| 66792 | Clostridium josui JCM 17888 | 2541046955 | draft | img | 1291050 |
| 66792 | Ruminiclostridium josui JCM 17888 | 2728369667 | draft | img | 1291050 |
| 67770 | Ruminiclostridium josui JCM 17888 | GCA_001311015 | contig | ncbi | 1291050 |
| 67770 | Ruminiclostridium josui JCM 17888 | GCA_000526495 | contig | ncbi | 1291050 |
GC content
- @ref: 18098
- GC-content: 40
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 95 | no |
| motile | yes | 75.835 | no |
| gram-positive | yes | 56.384 | no |
| anaerobic | yes | 99.193 | yes |
| aerobic | no | 98.514 | yes |
| halophile | no | 96.794 | no |
| spore-forming | yes | 95.908 | no |
| glucose-util | yes | 85.211 | no |
| flagellated | no | 61.001 | no |
| thermophile | yes | 80.482 | no |
| glucose-ferment | yes | 53.008 | no |
External links
@ref: 18098
culture collection no.: DSM 25723, FERM P-9684, JCM 17888, KCTC 15379
straininfo link
- @ref: 72364
- straininfo: 399265
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 2679386 | Cloning of an endo-1,4-beta-D-glucanase gene from Clostridium josui and its expression in Escherichia coli. | Ohmiya K, Fujino T, Sukhumavasi J, Shimizu S | Appl Environ Microbiol | 10.1128/aem.55.9.2399-2402.1989 | 1989 | Bacterial Proteins/biosynthesis/*genetics, Cellulase/biosynthesis/*genetics/metabolism, Cloning, Molecular, Clostridium/enzymology/*genetics/growth & development, DNA, Bacterial/isolation & purification, Escherichia coli/*genetics, *Genes, Bacterial, Plasmids, Restriction Mapping, Transformation, Bacterial | Metabolism |
| Enzymology | 11210125 | Cloning, sequencing, and expression of the gene encoding a cell-bound multi-domain xylanase from Clostridium josui, and characterization of the translated product. | Feng JX, Karita S, Fujino E, Fujino T, Kimura T, Sakka K, Ohmiya K | Biosci Biotechnol Biochem | 10.1271/bbb.64.2614 | 2000 | Amino Acid Sequence, Animals, Base Sequence, Catalytic Domain, Cellulose/metabolism, Cloning, Molecular, Clostridium/enzymology/*genetics, Escherichia coli/genetics, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic, Mice, Mice, Inbred BALB C, Molecular Sequence Data, Protein Biosynthesis, Protein Structure, Tertiary, Recombinant Proteins/genetics/isolation & purification/metabolism, Sequence Analysis, Sequence Homology, Amino Acid, Xylan Endo-1,3-beta-Xylosidase, Xylosidases/*genetics/immunology/*metabolism | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 18098 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25723) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25723 | |
| 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) | |
| 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 | |
| 72364 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399265.1 | StrainInfo: A central database for resolving microbial strain identifiers |