Strain identifier
BacDive ID: 3825
Type strain: 
Species: Spirosoma spitsbergense
Strain Designation: RODSPM9, SPM-9
Strain history: <- K. Finster, Århus Univ., Denmark; SPM 9 <- R. A. Herbert
NCBI tax ID(s): 1123278 (strain), 431554 (species)
version 9.1 (current version)
General
@ref: 8279
BacDive-ID: 3825
DSM-Number: 19989
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Spirosoma spitsbergense RODSPM9 is a Gram-negative bacterium that was isolated from permafrost soil.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 431554 | species |
| 1123278 | strain |
strain history
- @ref: 8279
- history: <- K. Finster, Århus Univ., Denmark; SPM 9 <- R. A. Herbert
doi: 10.13145/bacdive3825.20240916.9.1
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 spitsbergense
- full scientific name: Spirosoma spitsbergense Finster et al. 2009
@ref: 8279
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Spirosomaceae
genus: Spirosoma
species: Spirosoma spitsbergense
full scientific name: Spirosoma spitsbergense Finster et al. 2009 emend. Hahnke et al. 2016
strain designation: RODSPM9, SPM-9
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 96.833
Culture and growth conditions
culture medium
- @ref: 8279
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
- @ref: 8279
- growth: positive
- type: growth
- temperature: 20
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 8279
- sample type: permafrost soil
- geographic location: Spitsbergen, Adventdalen valley
- country: Norway
- origin.country: NOR
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Permafrost |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_1781.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_148;96_1011;97_1177;98_1407;99_1781&stattab=map
- Last taxonomy: Spirosoma spitsbergense subclade
- 16S sequence: EF451725
- Sequence Identity:
- Total samples: 995
- soil counts: 323
- aquatic counts: 361
- animal counts: 274
- plant counts: 37
Safety information
risk assessment
- @ref: 8279
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8279
- description: Spirosoma spitsbergense strain SPM-9 16S ribosomal RNA gene, partial sequence
- accession: EF451725
- length: 1296
- database: nuccore
- NCBI tax ID: 431554
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Spirosoma spitsbergense DSM 19989 | GCA_000374085 | scaffold | ncbi | 1123278 |
| 66792 | Spirosoma spitsbergense DSM 19989 | 1123278.3 | wgs | patric | 1123278 |
| 66792 | Spirosoma spitsbergense DSM 19989 | 2515154151 | draft | img | 1123278 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8279 | 49.1 | high performance liquid chromatography (HPLC) |
| 8279 | 50.4 | sequence analysis |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.833 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.491 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.228 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.528 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 94.469 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 83 | no |
External links
@ref: 8279
culture collection no.: DSM 19989, NCIMB 14407
straininfo link
- @ref: 73336
- straininfo: 398184
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19329617 | Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma. | Finster KW, Herbert RA, Lomstein BA | Int J Syst Evol Microbiol | 10.1099/ijs.0.002725-0 | 2009 | Arctic Regions, Bacterial Typing Techniques, Cluster Analysis, Cytophagaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Norway, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology | 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 | 28698912 | Spirosoma areae sp. nov., Isolated from Soil. | Jang JH, Cha S, Lee D, Srinivasan S, Jheong W, Hwang HS, Kim MK, Seo T | Curr Microbiol | 10.1007/s00284-017-1297-8 | 2017 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification/metabolism, DNA Barcoding, Taxonomic, Metabolomics/methods, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Transcriptome |
| Phylogeny | 29058653 | Spirosoma koreense sp. nov., a species of the family Cytophagaceae isolated from beach soil. | Ten LN, Okiria J, Lee JJ, Lee SY, Kang IK, Lee DS, Jung HY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002440 | 2017 | Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 8279 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19989) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19989 | |
| 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) | |
| 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 | |
| 73336 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398184.1 | StrainInfo: A central database for resolving microbial strain identifiers |