Strain identifier
BacDive ID: 23278
Type strain: 
Species: Sphingomonas sediminicola
Strain history: <- S.-T. Lee, KAIST; Dae 20 ("Kaistobacter terrae") <- D.-S. An, KAIST (Korean Advanced Insititute of Science and Technology)
NCBI tax ID(s): 386874 (species)
version 8.1 (current version)
General
@ref: 18851
BacDive-ID: 23278
DSM-Number: 18106
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Sphingomonas sediminicola DSM 18106 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater sediment.
NCBI tax id
- NCBI tax id: 386874
- Matching level: species
strain history
- @ref: 18851
- history: <- S.-T. Lee, KAIST; Dae 20 ("Kaistobacter terrae") <- D.-S. An, KAIST (Korean Advanced Insititute of Science and Technology)
doi: 10.13145/bacdive23278.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingomonas
- species: Sphingomonas sediminicola
- full scientific name: Sphingomonas sediminicola An et al. 2013
@ref: 18851
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas sediminicola
full scientific name: Sphingomonas sediminicola An et al. 2013
type strain: yes
Morphology
cell morphology
- @ref: 30596
- gram stain: negative
- cell length: 1.5 µm
- cell width: 0.55 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 30596
- production: yes
Culture and growth conditions
culture medium
- @ref: 18851
- 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 | growth | type | temperature | range |
|---|---|---|---|---|
| 18851 | positive | growth | 30 | mesophilic |
| 30596 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 30596 | positive | growth | 6.5-7.5 |
| 30596 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30596
- oxygen tolerance: aerobe
spore formation
- @ref: 30596
- spore formation: no
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30596 | 22599 | arabinose | + | carbon source |
| 30596 | 17992 | sucrose | + | carbon source |
| 30596 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30596 | acid phosphatase | + | 3.1.3.2 |
| 30596 | catalase | + | 1.11.1.6 |
| 30596 | gelatinase | + | |
| 30596 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 18851
- sample type: freshwater sediment
- geographic location: Daecheong Bank, near Daejeon City
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Aquatic | #Freshwater |
Safety information
risk assessment
- @ref: 18851
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18851
- description: Sphingomonas sediminicola gene for 16S rRNA, partial sequence
- accession: AB258386
- length: 1440
- database: ena
- NCBI tax ID: 386874
GC content
| @ref | GC-content | method |
|---|---|---|
| 18851 | 67.9 | high performance liquid chromatography (HPLC) |
| 18851 | 66.84 | |
| 30596 | 67.9 |
External links
@ref: 18851
culture collection no.: DSM 18106, KCTC 12629, LMG 23592, Dae 20
straininfo link
- @ref: 87500
- straininfo: 397177
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22505600 | Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov. | An DS, Liu QM, Lee HG, Jung MS, Kim SC, Lee ST, Im WT | Int J Syst Evol Microbiol | 10.1099/ijs.0.039578-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Glycosphingolipids/analysis, Molecular Sequence Data, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analysis | Genetics |
| Phylogeny | 24449789 | Sphingomonas daechungensis sp. nov., isolated from sediment of a eutrophic reservoir. | Huy H, Jin L, Lee KC, Kim SG, Lee JS, Ahn CY, Oh HM | Int J Syst Evol Microbiol | 10.1099/ijs.0.054510-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Eutrophication, Fatty Acids/chemistry, Geologic Sediments/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, *Water Microbiology | Genetics |
| Phylogeny | 26428917 | Sphingomonas parvus sp. nov. isolated from a ginseng-cultivated soil. | Ahn JH, Kim BC, Kim SJ, Lee GH, Song J, Kwon SW, Weon HY | J Microbiol | 10.1007/s12275-015-5132-2 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/genetics, Fatty Acids/analysis, Molecular Sequence Data, Panax/*microbiology, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Republic of Korea, *Soil Microbiology, Sphingomonas/chemistry/*classification/genetics/*isolation & purification, Ubiquinone/analogs & derivatives/analysis | Genetics |
| Phylogeny | 27902188 | Sphingomonas lutea sp. nov., isolated from freshwater of an artificial reservoir. | Lee JH, Kim DI, Kang JW, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001546 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 33877575 | Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish). | Hyun DW, Jeong YS, Lee JY, Sung H, Lee SY, Choi JW, Kim HS, Kim PS, Bae JW | J Microbiol | 10.1007/s12275-021-1036-5 | 2021 | Animals, Base Composition, DNA, Bacterial/genetics/metabolism, Fishes/microbiology, Intestines/microbiology, Nocardioides/*classification/genetics/*isolation & purification/metabolism, Phospholipids/metabolism, Phylogeny, Republic of Korea, Sphingomonas/*classification/genetics/*isolation & purification/metabolism | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 18851 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18106) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18106 | |||
| 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 | |||
| 30596 | 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 | 26927 | 28776041 | |
| 87500 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397177.1 | StrainInfo: A central database for resolving microbial strain identifiers |