Strain identifier
BacDive ID: 134302
Type strain: 
Species: Spirosoma rigui
Strain Designation: WPCB118
Strain history: <- KS Baik, MicroID, Co. Ltd.
NCBI tax ID(s): 564064 (species)
version 8.1 (current version)
General
@ref: 32316
BacDive-ID: 134302
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped
description: Spirosoma rigui WPCB118 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from freshwater .
NCBI tax id
- NCBI tax id: 564064
- Matching level: species
strain history
- @ref: 67771
- history: <- KS Baik, MicroID, Co. Ltd.
doi: 10.13145/bacdive134302.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Cytophagia
- order: Cytophagales
- family: Spirosomataceae
- genus: Spirosoma
- species: Spirosoma rigui
- full scientific name: Spirosoma rigui Baik et al. 2007
@ref: 32316
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Cytophagaceae
genus: Spirosoma
species: Spirosoma rigui
strain designation: WPCB118
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
|---|---|---|---|---|---|---|---|
| 32316 | negative | 6.15 µm | 0.9 µm | rod-shaped | yes | gliding | |
| 67771 | rod-shaped | yes | gliding | ||||
| 67771 | negative | ||||||
| 69480 | negative | 99.994 |
pigmentation
- @ref: 32316
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 32316 | positive | growth | 04-37 | |
| 32316 | positive | optimum | 30 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32316 | positive | growth | 06-11 | alkaliphile |
| 32316 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 32316 | facultative anaerobe |
| 67771 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32316 | no | |
| 67771 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.975 |
halophily
- @ref: 32316
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %
observation
- @ref: 67771
- observation: quinones: MK-7
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32316 | 17234 | glucose | + | carbon source |
| 32316 | 4853 | esculin | + | hydrolysis |
enzymes
- @ref: 32316
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 32316 | freshwater (river, lake, pond) | ||||
| 67771 | From freshwater | Woopo wetland | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Lake (large) |
| #Environmental | #Aquatic | #Pond (small) |
| #Environmental | #Aquatic | #River (Creek) |
taxonmaps
- @ref: 69479
- File name: preview.99_788.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_148;96_478;97_546;98_629;99_788&stattab=map
- Last taxonomy: Spirosoma rigui subclade
- 16S sequence: EF507900
- Sequence Identity:
- Total samples: 3439
- soil counts: 639
- aquatic counts: 613
- animal counts: 1274
- plant counts: 913
Sequence information
16S sequences
- @ref: 32316
- description: Spirosoma rigui strain WPCB118 16S ribosomal RNA gene, partial sequence
- accession: EF507900
- length: 1407
- database: nuccore
- NCBI tax ID: 564064
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Spirosoma rigui KCTC 12531 | GCA_002067135 | complete | ncbi | 564064 |
| 66792 | Spirosoma rigui strain KCTC 12531 | 564064.4 | complete | patric | 564064 |
GC content
- @ref: 32316
- GC-content: 53.3
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 97.212 | yes |
| gram-positive | no | 97.345 | no |
| anaerobic | no | 99.103 | no |
| halophile | no | 93.871 | no |
| spore-forming | no | 93.846 | yes |
| glucose-util | yes | 85.077 | yes |
| aerobic | yes | 89.02 | no |
| thermophile | no | 97.887 | no |
| glucose-ferment | no | 87.379 | no |
| motile | no | 92.875 | no |
External links
@ref: 32316
culture collection no.: KCTC 12531, NBRC 101117
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18048741 | Spirosoma rigui sp. nov., isolated from fresh water. | Baik KS, Kim MS, Park SC, Lee DW, Lee SD, Ka JO, Choi SK, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijs.0.65302-0 | 2007 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Korea, Locomotion/physiology, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysis | Genetics |
| Phylogeny | 19196773 | Spirosoma panaciterrae sp. nov., isolated from soil. | Ten LN, Xu JL, Jin FX, Im WT, Oh HM, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.002436-0 | 2009 | Cytophagaceae/chemistry/*classification/genetics/isolation & purification, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity | Genetics |
| Phylogeny | 24748440 | Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil. | Lee JJ, Srinivasan S, Lim S, Joe M, Im S, Bae SI, Park KR, Han JH, Park SH, Joo BM, Park SJ, Kim MK | Curr Microbiol | 10.1007/s00284-014-0584-x | 2014 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytophagaceae/*classification/*isolation & purification/physiology/radiation effects, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, *Gamma Rays, Korea, Locomotion, Microbial Viability/*radiation effects, Microscopy, Electron, Transmission, Molecular Sequence Data, Oryza, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ultraviolet Rays | Genetics |
| Phylogeny | 26115990 | Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil. | Lee JJ, Kang MS, Joo ES, Kim MK, Im WT, Jung HY, Srinivasan S | J Microbiol | 10.1007/s12275-015-5008-5 | 2015 | Altitude, Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/growth & development/*isolation & purification/radiation effects, DNA, Ribosomal/genetics, *Gamma Rays, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Radiation Tolerance, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, *Ultraviolet Rays, Vitamin K 2/analogs & derivatives/chemistry | Phenotype |
| Phylogeny | 29362880 | Spirosoma agri sp. nov., Isolated from Apple Orchard Soil. | Li W, Lee SY, Kang IK, Ten LN, Jung HY | Curr Microbiol | 10.1007/s00284-018-1434-z | 2018 | Base Composition/genetics, Cytophagaceae/classification/*genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, *Malus, Phenotype, Phospholipids/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Metabolism |
| Phylogeny | 33729126 | Spirosoma utsteinense sp. nov. isolated from Antarctic ice-free soils from the Utsteinen region, East Antarctica. | Tahon G, Lebbe L, Willems A | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004754 | 2021 |
Reference
| @id | authors | title | doi/url | ID_cross_reference | 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 | ||
| 32316 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 28553 | 28776041 |
| 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 | ||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||
| 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 |