Strain identifier
BacDive ID: 17691
Type strain: 
Species: Oscillibacter valericigenes
Strain Designation: Sjm 18-20
Strain history: <- T. Iino, NBRC; Sjm 18-20 <- T. Iino {2005}
NCBI tax ID(s): 693746 (strain), 351091 (species)
version 8.1 (current version)
General
@ref: 7351
BacDive-ID: 17691
DSM-Number: 18026
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Oscillibacter valericigenes Sjm 18-20 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from clam, alimentary canal of Corbicula japonica.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 693746 | strain |
| 351091 | species |
strain history
- @ref: 7351
- history: <- T. Iino, NBRC; Sjm 18-20 <- T. Iino {2005}
doi: 10.13145/bacdive17691.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Oscillibacter
- species: Oscillibacter valericigenes
- full scientific name: Oscillibacter valericigenes Iino et al. 2007
@ref: 7351
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Oscillospiraceae
genus: Oscillibacter
species: Oscillibacter valericigenes
full scientific name: Oscillibacter valericigenes Iino et al. 2007
strain designation: Sjm 18-20
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31960 | negative | 2.5-6.0 µm | 0.5 µm | rod-shaped | yes | |
| 69480 | positive | 100 |
Culture and growth conditions
culture medium
- @ref: 7351
- 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 | range |
|---|---|---|---|---|
| 7351 | positive | growth | 30 | mesophilic |
| 31960 | positive | growth | 15-35 | |
| 31960 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31960 | positive | growth | 5.0-8.5 | alkaliphile |
| 31960 | positive | optimum | 6.25 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 7351 | anaerobe | |
| 31960 | anaerobe | |
| 69480 | anaerobe | 99.998 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31960 | no | |
| 69481 | no | 91 |
| 69480 | no | 99.092 |
halophily
- @ref: 31960
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-4 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31960 | 22599 | arabinose | + | carbon source |
| 31960 | 17234 | glucose | + | carbon source |
| 31960 | 33942 | ribose | + | carbon source |
| 31960 | 18222 | xylose | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 7351
- sample type: clam, alimentary canal of Corbicula japonica
- host species: Corbicula japonica
- geographic location: sea coast in Shimane
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Invertebrates (Other) | #Mollusca |
| #Host Body-Site | #Gastrointestinal tract |
taxonmaps
- @ref: 69479
- File name: preview.99_329.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_91;96_229;97_251;98_280;99_329&stattab=map
- Last taxonomy: Oscillibacter valericigenes subclade
- 16S sequence: AB238598
- Sequence Identity:
- Total samples: 17056
- soil counts: 86
- aquatic counts: 509
- animal counts: 16381
- plant counts: 80
Safety information
risk assessment
- @ref: 7351
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7351
- description: Oscillibacter valericigenes gene for 16S rRNA, partial sequence
- accession: AB238598
- length: 1453
- database: ena
- NCBI tax ID: 351091
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Oscillibacter valericigenes Sjm18-20 | 693746.10 | plasmid | patric | 693746 |
| 66792 | Oscillibacter valericigenes Sjm18-20 | 693746.9 | complete | patric | 693746 |
GC content
- @ref: 7351
- GC-content: 52.9
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 91 | no |
| gram-positive | no | 64.736 | yes |
| anaerobic | yes | 98.62 | yes |
| halophile | no | 74.833 | no |
| spore-forming | no | 67.653 | yes |
| glucose-util | yes | 84.637 | yes |
| thermophile | no | 99.404 | no |
| flagellated | no | 76.857 | no |
| motile | yes | 87.711 | yes |
| aerobic | no | 98.735 | no |
| glucose-ferment | yes | 61.892 | no |
External links
@ref: 7351
culture collection no.: DSM 18026, NBRC 101213
straininfo link
- @ref: 86682
- straininfo: 404955
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17684268 | Oscillibacter valericigenes gen. nov., sp. nov., a valerate-producing anaerobic bacterium isolated from the alimentary canal of a Japanese corbicula clam. | Iino T, Mori K, Tanaka K, Suzuki KI, Harayama S | Int J Syst Evol Microbiol | 10.1099/ijs.0.64717-0 | 2007 | 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 | Metabolism |
| Phylogeny | 23024142 | Oscillibacter ruminantium sp. nov., isolated from the rumen of Korean native cattle. | Lee GH, Rhee MS, Chang DH, Lee J, Kim S, Yoon MH, Kim BC | Int J Syst Evol Microbiol | 10.1099/ijs.0.041749-0 | 2012 | Animals, Bacterial Typing Techniques, Base Composition, Cattle/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Gram-Negative Bacteria/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rumen/*microbiology, Sequence Analysis, DNA | Genetics |
| Genetics | 23408234 | Complete genome sequence of Oscillibacter valericigenes Sjm18-20(T) (=NBRC 101213(T)). | Katano Y, Fujinami S, Kawakoshi A, Nakazawa H, Oji S, Iino T, Oguchi A, Ankai A, Fukui S, Terui Y, Kamata S, Harada T, Tanikawa S, Suzuki K, Fujita N | Stand Genomic Sci | 10.4056/sigs.2826118 | 2012 |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 7351 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18026) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18026 | ||||
| 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 | ||||
| 31960 | 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 | 28216 | 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 | ||
| 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 | ||||
| 86682 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404955.1 | StrainInfo: A central database for resolving microbial strain identifiers |