Strain identifier
BacDive ID: 24548
Type strain: 
Species: Daejeonella lutea
Strain Designation: N7d-4, P-2
Strain history: <- KS Bae, KRIBB
NCBI tax ID(s): 572036 (species)
version 8.1 (current version)
General
@ref: 20726
BacDive-ID: 24548
DSM-Number: 22385
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, rod-shaped
description: Daejeonella lutea N7d-4 is an aerobe, mesophilic, motile bacterium that was isolated from soil of a potato field.
NCBI tax id
- NCBI tax id: 572036
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20726 | <- K. S. Bae, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; N7d-4 <- W.-J. Jeong |
| 67770 | K.-S. Bae N7d-4 <-- W.-J. Jeong P-2. |
| 67771 | <- KS Bae, KRIBB |
doi: 10.13145/bacdive24548.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Daejeonella
- species: Daejeonella lutea
- full scientific name: Daejeonella lutea (Oh et al. 2013) García-López et al. 2020
synonyms
- @ref: 20215
- synonym: Pedobacter luteus
@ref: 20726
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Daejeonella
species: Daejeonella lutea
full scientific name: Daejeonella lutea (Oh et al. 2013) García-López et al. 2020
strain designation: N7d-4, P-2
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | flagellum arrangement | gram stain | confidence |
|---|---|---|---|---|---|
| 67771 | rod-shaped | yes | gliding | ||
| 67771 | negative | ||||
| 69480 | negative | 99.992 |
Culture and growth conditions
culture medium
- @ref: 20726
- 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 |
|---|---|---|---|---|
| 20726 | positive | growth | 25-30 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
| 67771 | positive | growth | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.987 |
observation
| @ref | observation |
|---|---|
| 67770 | quinones: MK-7 |
| 67771 | quinones: MK-7 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 20726 | soil of a potato field | Chungcheongbuk-do (36° 43' 00'' N 127° 26' 12'' E) | Republic of Korea | KOR | Asia | 36.7167 | 127.437 |
| 67770 | Soil of a potato field | Republic of Korea | KOR | Asia | |||
| 67771 | From soil cultivating potatoes | Ochang | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_3402.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1777;97_2127;98_2607;99_3402&stattab=map
- Last taxonomy: Daejeonella lutea
- 16S sequence: FJ377314
- Sequence Identity:
- Total samples: 437
- soil counts: 220
- aquatic counts: 159
- animal counts: 40
- plant counts: 18
Safety information
risk assessment
- @ref: 20726
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20726
- description: Pedobacter luteus strain N7d-4 16S ribosomal RNA gene, partial sequence
- accession: FJ377314
- length: 1403
- database: ena
- NCBI tax ID: 572036
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pedobacter luteus strain DSM 22385 | 572036.3 | wgs | patric | 572036 |
| 66792 | Pedobacter luteus DSM 22385 | 2595698248 | draft | img | 572036 |
| 67770 | Daejeonella lutea DSM 22385 | GCA_900168015 | scaffold | ncbi | 572036 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 20726 | 48.5 | high performance liquid chromatography (HPLC) |
| 67770 | 42.3 | genome sequence analysis |
| 67771 | 48.5 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.511 | yes |
| anaerobic | no | 99.198 | no |
| halophile | no | 94.384 | no |
| spore-forming | no | 94.903 | no |
| glucose-util | yes | 81.892 | no |
| flagellated | no | 97.532 | yes |
| aerobic | yes | 85.193 | no |
| thermophile | no | 96.023 | yes |
| motile | no | 90.883 | no |
| glucose-ferment | no | 89.701 | no |
External links
@ref: 20726
culture collection no.: DSM 22385, KCTC 22699, JCM 16318
straininfo link
- @ref: 88403
- straininfo: 402387
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22798651 | Pedobacter luteus sp. nov., isolated from soil. | Oh HW, Kim BC, Park DS, Jeong WJ, Kim H, Lee KH, Kim SU | Int J Syst Evol Microbiol | 10.1099/ijs.0.033134-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Solanum tuberosum/microbiology, Sphingolipids/analysis, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Phylogeny | 29461180 | Pedobacter mongoliensis sp. nov., isolated from grassland soil. | Yuan K, Cao M, Li J, Wang G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002637 | 2018 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Grassland, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 20726 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22385 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22385) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | |||
| 88403 | 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-ID402387.1 |