Strain identifier
BacDive ID: 131280
Type strain: 
Species: Sphingomonas oligoaromativorans
Strain Designation: SY-6
Strain history: <- NBRC <- K.-S. Whang, Mokwon Univ., Institute of Microbial Ecology and Resources, Daejeon, Korea; SY-6
NCBI tax ID(s): 575322 (species)
version 8.1 (current version)
General
@ref: 22507
BacDive-ID: 131280
DSM-Number: 102246
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Sphingomonas oligoaromativorans SY-6 is a mesophilic, Gram-negative bacterium that was isolated from humus forest soil.
NCBI tax id
- NCBI tax id: 575322
- Matching level: species
strain history
- @ref: 22507
- history: <- NBRC <- K.-S. Whang, Mokwon Univ., Institute of Microbial Ecology and Resources, Daejeon, Korea; SY-6
doi: 10.13145/bacdive131280.20230509.8.1
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 oligoaromativorans
- full scientific name: Sphingomonas oligoaromativorans Han et al. 2014
@ref: 22507
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Pseudomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas oligoaromativorans
full scientific name: Sphingomonas oligoaromativorans Han et al. 2014
strain designation: SY-6
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.903
Culture and growth conditions
culture medium
- @ref: 22507
- 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: 22507
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.952 |
Isolation, sampling and environmental information
isolation
- @ref: 22507
- sample type: humus forest soil
- geographic location: Gyeryong Mountain National Park
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
- latitude: 36.3641
- longitude: 127.193
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | |
| #Environmental | #Terrestrial | #Forest |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_6588.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_3122;97_3825;98_4859;99_6588&stattab=map
- Last taxonomy: Sphingomonas oligoaromativorans
- 16S sequence: FJ434127
- Sequence Identity:
- Total samples: 1035
- soil counts: 337
- aquatic counts: 484
- animal counts: 143
- plant counts: 71
Safety information
risk assessment
- @ref: 22507
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22507
- description: Sphingomonas oligoaromativorans strain IMER-A1-28 16S ribosomal RNA gene, partial sequence
- accession: FJ434127
- length: 1402
- database: ena
- NCBI tax ID: 575322
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingomonas oligoaromativorans DSM 102246 | GCA_011762195 | contig | ncbi | 575322 |
| 66792 | Sphingomonas oligoaromativorans strain DSM 102246 | 575322.3 | wgs | patric | 575322 |
| 66792 | Sphingomonas oligoaromativorans DSM 102246 | 2828446230 | draft | img | 575322 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.046 | no |
| anaerobic | no | 99.247 | no |
| halophile | no | 95.636 | no |
| spore-forming | no | 93.229 | no |
| glucose-util | yes | 90.764 | no |
| thermophile | no | 94.644 | no |
| flagellated | no | 87.93 | no |
| aerobic | yes | 93.669 | no |
| motile | yes | 83.373 | no |
| glucose-ferment | no | 91.299 | no |
External links
@ref: 22507
culture collection no.: DSM 102246, KACC 12948, NBRC 105508
straininfo link
- @ref: 89724
- straininfo: 397150
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24523444 | Sphingomonas oligoaromativorans sp. nov., an oligotrophic bacterium isolated from a forest soil. | Han SI, Lee JC, Ohta H, Whang KS | Int J Syst Evol Microbiol | 10.1099/ijs.0.052894-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Trees/microbiology, Ubiquinone/chemistry | Genetics |
| Phylogeny | 25985831 | Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch. | Liu Y, Yao S, Lee YJ, Cao Y, Zhai L, Zhang X, Su J, Ge Y, Kim SG, Cheng C | Int J Syst Evol Microbiol | 10.1099/ijs.0.000340 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Morinda/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Enzymology |
| Phylogeny | 26286474 | Sphingomonas hylomeconis sp. nov., isolated from the stem of Hylomecon japonica. | Akbar A, Chen C, Zhu L, Xin K, Cheng J, Yang Q, Zhao L, Zhang L, Shen X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000532 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Papaveraceae/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 29091024 | Sphingomonas difficilis sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead-zinc mine. | Feng GD, Xiong X, Zhu HH, Li HP | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002461 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Mining, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, *Zinc | Transcriptome |
| Phylogeny | 32515726 | Sphingomonas chungangi sp. nov., a bacterium isolated from garden soil sample. | Akter S, Huq MA | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004267 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gardens, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22507 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102246 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102246) | |
| 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 | |
| 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 | |
| 89724 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID397150.1 |