Strain identifier
BacDive ID: 14102
Type strain: 
Species: Pedobacter soli
Strain Designation: 15-51
Variant: Isotype of BacDive ID 131129
Strain history: <- H.-Y. Weon, KACC; 15-51
NCBI tax ID(s): 390242 (species)
version 8.1 (current version)
General
@ref: 7623
BacDive-ID: 14102
DSM-Number: 18609
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Pedobacter soli 15-51 is a mesophilic, Gram-negative bacterium that was isolated from rhizosphere soil of Chinese cabbage .
NCBI tax id
- NCBI tax id: 390242
- Matching level: species
strain history
- @ref: 7623
- history: <- H.-Y. Weon, KACC; 15-51
doi: 10.13145/bacdive14102.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Pedobacter
- species: Pedobacter soli
- full scientific name: Pedobacter soli Kwon et al. 2011
@ref: 7623
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter soli
full scientific name: Pedobacter soli Kwon et al. 2011
strain designation: 15-51
variant: Isotype of BacDive ID 131129
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.982
Culture and growth conditions
culture medium
- @ref: 7623
- name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
- growth: yes
- link: https://mediadive.dsmz.de/medium/545
- composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
culture temp
- @ref: 7623
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.987 |
Isolation, sampling and environmental information
isolation
- @ref: 7623
- sample type: rhizosphere soil of Chinese cabbage (Brassica campestris L.)
- host species: Brassica campestris
- geographic location: Suwon (37° 16' 38.50'' N 126° 58' 59.60'' E)
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
- latitude: 37.2774
- longitude: 126.983
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Rhizosphere |
Safety information
risk assessment
- @ref: 7623
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7623
- description: Pedobacter soli partial 16S rRNA gene, type strain 15-51T
- accession: AM279215
- length: 1487
- database: ena
- NCBI tax ID: 390242
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pedobacter soli DSM 18609 | GCA_900101435 | scaffold | ncbi | 390242 |
| 66792 | Pedobacter soli strain DSM 18609 | 390242.6 | wgs | patric | 390242 |
| 66792 | Pedobacter soli DSM 18609 | 2622736512 | draft | img | 390242 |
GC content
- @ref: 7623
- GC-content: 38.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 88.537 | no |
| flagellated | no | 96.266 | no |
| gram-positive | no | 97.664 | no |
| anaerobic | no | 99.63 | no |
| aerobic | yes | 87.399 | no |
| halophile | no | 96.616 | no |
| spore-forming | no | 93.735 | no |
| glucose-ferment | no | 89.973 | no |
| thermophile | no | 99.184 | yes |
| glucose-util | yes | 89.629 | no |
External links
@ref: 7623
culture collection no.: DSM 18609, KACC 14939, NBRC 107691
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21257686 | Pedobacter rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris). | Kwon SW, Son JA, Kim SJ, Kim YS, Park IC, Bok JI, Weon HY | Int J Syst Evol Microbiol | 10.1099/ijs.0.026781-0 | 2011 | Base Composition, Brassica/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Pedobacter/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Soil Microbiology | Metabolism |
| Phylogeny | 22990491 | Pedobacter kyungheensis sp. nov., with ginsenoside converting activity. | Yang JE, Shin JY, Park SY, T Mavlonov G, Yi EJ, Lee EH, Lee JM, Yi TH | J Gen Appl Microbiol | 10.2323/jgam.58.309 | 2012 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Biotransformation, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Ginsenosides/*metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/growth & development, Pedobacter/*classification/*isolation & purification/metabolism/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, Soil Microbiology, Temperature, beta-Glucosidase/metabolism | Metabolism |
| Phylogeny | 27600161 | Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine. | Wang Z, Tan Y, Xu D, Wang G, Yuan J, Zheng S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001480 | 2016 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Mining, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Vanadium, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 30540241 | Pedobacter miscanthi sp. nov., isolated from Miscanthus sinensis. | Chen Z, Tian W, Sun F, Chen Y, Han H, Yao L, Zhang Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003161 | 2019 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pedobacter/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, Plant Stems/microbiology, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 34590995 | Pedobacter riviphilus sp. nov., isolated from stream sediment. | Im HS, Joung Y, Lee SS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004989 | 2021 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Pedobacter/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2 | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 7623 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18609) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18609 | |
| 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) | |
| 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 |