Strain identifier
BacDive ID: 14117
Type strain: 
Species: Sphingobacterium versatilis
Strain Designation: KM 2138
Strain history: <- ATCC <- E. Yabuuchi, KM 2138 (GIFU 2138) <- W. Minamide (Flavobacterium sp. No. 6)
NCBI tax ID(s): 525372 (strain), 258 (species)
version 9.1 (current version)
General
@ref: 1132
BacDive-ID: 14117
DSM-Number: 2582
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Sphingobacterium versatilis KM 2138 is a Gram-negative bacterium that was isolated from vaginal secretion.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 258 | species |
| 525372 | strain |
strain history
- @ref: 1132
- history: <- ATCC <- E. Yabuuchi, KM 2138 (GIFU 2138) <- W. Minamide (Flavobacterium sp. No. 6)
doi: 10.13145/bacdive14117.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Sphingobacterium
- species: Sphingobacterium versatilis
- full scientific name: Sphingobacterium versatilis Yabuuchi et al. 1981
@ref: 1132
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Sphingobacterium
species: Sphingobacterium spiritivorum
full scientific name: Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 emend. Lai et al. 2016
strain designation: KM 2138
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.604
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 1132 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
| 1132 | CY-AGAR (DSMZ Medium 67) | yes | https://mediadive.dsmz.de/medium/67 | Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 1132 | positive | growth | 28 |
| 1132 | positive | growth | 30 |
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 1132
- sample type: vaginal secretion
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host Body-Site | #Urogenital tract | #Vagina |
| #Host Body Product | #Urogenital tract | #Vaginal secretion |
taxonmaps
- @ref: 69479
- File name: preview.99_3331.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_1738;97_2079;98_2555;99_3331&stattab=map
- Last taxonomy: Sphingobacterium spiritivorum subclade
- 16S sequence: AJ459411
- Sequence Identity:
- Total samples: 7762
- soil counts: 926
- aquatic counts: 1560
- animal counts: 4723
- plant counts: 553
Safety information
risk assessment
- @ref: 1132
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Sphingobacterium spiritivorum partial 16S rRNA gene, strain DSM 2582
- accession: AJ459411
- length: 1476
- database: nuccore
- NCBI tax ID: 258
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingobacterium spiritivorum ATCC 33300 | GCA_000159515 | scaffold | ncbi | 525372 |
| 66792 | Sphingobacterium spiritivorum ATCC 33300 | 525372.3 | wgs | patric | 525372 |
| 66792 | Sphingobacterium spiritivorum strain FDAARGOS_1146 | 258.9 | complete | patric | 258 |
| 66792 | Sphingobacterium spiritivorum ATCC 33300 | 643886135 | draft | img | 525372 |
GC content
- @ref: 1132
- GC-content: 39.9
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 | 99.604 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.641 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.812 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 84.592 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 98 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 86.5 | no |
External links
@ref: 1132
culture collection no.: DSM 2582, ATCC 33300, GIFU 2138
straininfo link
- @ref: 83284
- straininfo: 311050
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1132 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2582) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2582 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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 | |||
| 83284 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID311050.1 | StrainInfo: A central database for resolving microbial strain identifiers |