Strain identifier
BacDive ID: 14199
Type strain: 
Species: Sphingobium mellinum
Strain Designation: WI4
Strain history: <- LMG <- A. van Bruggen Univ. California, USA (Rhizomonas sp.)
NCBI tax ID(s): 1387166 (species)
version 8.1 (current version)
General
@ref: 3163
BacDive-ID: 14199
DSM-Number: 7458
keywords: 16S sequence, Bacteria, mesophilic, plant pathogen
description: Sphingobium mellinum WI4 is a mesophilic plant pathogen that was isolated from soil using lettuce seedlings as bait.
NCBI tax id
- NCBI tax id: 1387166
- Matching level: species
strain history
- @ref: 3163
- history: <- LMG <- A. van Bruggen Univ. California, USA (Rhizomonas sp.)
doi: 10.13145/bacdive14199.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingobium
- species: Sphingobium mellinum
- full scientific name: Sphingobium mellinum Francis et al. 2014
@ref: 3163
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingobium
species: Sphingobium mellinum
full scientific name: Sphingobium mellinum Francis et al. 2014
strain designation: WI4
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 3163 | RHIZOMONAS SUBERIFACIENS MEDIUM (DSMZ Medium 726) | yes | https://mediadive.dsmz.de/medium/726 | Name: RHIZOMONAS SUBERIFACIENS MEDIUM (DSMZ Medium 726) Composition: Agar 11.0 g/l Enzymatic digest of casein 5.0 g/l Glucose 2.5 g/l K2HPO4 x 3 H2O 1.3 g/l MgSO4 x 7 H2O 0.5 g/l KNO3 0.5 g/l Ca(NO3)2 x 4 H2O 0.06 g/l Distilled water |
| 3163 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | 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: 3163
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Isolation, sampling and environmental information
isolation
- @ref: 3163
- sample type: soil using lettuce seedlings as bait
- geographic location: Wisconsin
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_79484.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_32;97_33;98_3875;99_79484&stattab=map
- Last taxonomy: Sphingobium
- 16S sequence: KF437546
- Sequence Identity:
- Total samples: 218
- soil counts: 32
- aquatic counts: 93
- animal counts: 28
- plant counts: 65
Safety information
risk assessment
- @ref: 3163
- pathogenicity plant: yes
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Sphingomonas sp. WI4 16S ribosomal RNA, partial sequence | S57491 | 267 | ena | 106806 |
| 3163 | Sphingobium mellinum strain WI4 16S ribosomal RNA gene, partial sequence | KF437546 | 1451 | ena | 1387166 |
GC content
- @ref: 3163
- GC-content: 63.0
- method: thermal denaturation, midpoint method (Tm)
External links
@ref: 3163
culture collection no.: DSM 7458, ATCC 51292, LMG 11032
straininfo link
- @ref: 83358
- straininfo: 4813
literature
- topic: Phylogeny
- Pubmed-ID: 24436067
- title: Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov.
- authors: Francis IM, Jochimsen KN, De Vos P, van Bruggen AHC
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.058909-0
- year: 2014
- mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lettuce/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Diseases/*microbiology, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3163 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7458) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-7458 | |||
| 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 | |
| 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 | |||
| 83358 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID4813.1 | StrainInfo: A central database for resolving microbial strain identifiers |