Strain identifier
BacDive ID: 17757
Type strain: 
Species: Niastella yeongjuensis
Strain Designation: GR20-13
Strain history: <- S. W. Kwon, KACC; GR20-13
NCBI tax ID(s): 1122606 (strain), 354355 (species)
version 8.1 (current version)
General
@ref: 7092
BacDive-ID: 17757
DSM-Number: 17621
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Niastella yeongjuensis GR20-13 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil cultivated with Korean ginseng.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 354355 | species |
| 1122606 | strain |
strain history
- @ref: 7092
- history: <- S. W. Kwon, KACC; GR20-13
doi: 10.13145/bacdive17757.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Chitinophagia
- order: Chitinophagales
- family: Chitinophagaceae
- genus: Niastella
- species: Niastella yeongjuensis
- full scientific name: Niastella yeongjuensis Weon et al. 2006
@ref: 7092
domain: Bacteria
phylum: Bacteroidetes
class: Chitinophagia
order: Sphingobacteriales
family: Chitinophagaceae
genus: Niastella
species: Niastella yeongjuensis
full scientific name: Niastella yeongjuensis Weon et al. 2006
strain designation: GR20-13
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31772 | negative | 10-40 µm | 0.4-0.6 µm | rod-shaped | no | |
| 69480 | negative | 99.992 |
pigmentation
- @ref: 31772
- production: yes
Culture and growth conditions
culture medium
- @ref: 7092
- 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 |
|---|---|---|---|---|
| 7092 | positive | growth | 28 | mesophilic |
| 31772 | positive | growth | 15-33 | |
| 31772 | positive | optimum | 30-33 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 31772 | positive | growth | 05-08 |
| 31772 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 31772
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31772 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.902 |
observation
- @ref: 31772
- observation: aggregates in chains
metabolite utilization
- @ref: 31772
- Chebi-ID: 4853
- metabolite: esculin
- utilization activity: +
- kind of utilization tested: hydrolysis
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31772 | alkaline phosphatase | + | 3.1.3.1 |
| 31772 | alpha-galactosidase | + | 3.2.1.22 |
| 31772 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 7092
- sample type: soil cultivated with Korean ginseng
- geographic location: Yeongju region of Korea
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_7944.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_1581;97_1887;98_2317;99_7944&stattab=map
- Last taxonomy: Niastella yeongjuensis
- 16S sequence: DQ244076
- Sequence Identity:
- Total samples: 656
- soil counts: 458
- aquatic counts: 13
- animal counts: 12
- plant counts: 173
Safety information
risk assessment
- @ref: 7092
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7092
- description: Niastella yeongjuensis strain GR20-13 16S ribosomal RNA gene, partial sequence
- accession: DQ244076
- length: 1468
- database: ena
- NCBI tax ID: 354355
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Niastella yeongjuensis DSM 17621 | GCA_900110245 | scaffold | ncbi | 354355 |
| 66792 | Niastella yeongjuensis DSM 17621 | GCA_002077935 | contig | ncbi | 354355 |
| 66792 | Niastella yeongjuensis strain DSM 17621 | 354355.6 | wgs | patric | 354355 |
| 66792 | Niastella yeongjuensis DSM 17621 | 2599185237 | draft | img | 354355 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 7092 | 44.3 | high performance liquid chromatography (HPLC) |
| 31772 | 44.3 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| glucose-ferment | no | 85.309 | no |
| motile | no | 90.781 | yes |
| flagellated | no | 97.197 | yes |
| gram-positive | no | 96.569 | yes |
| anaerobic | no | 99.291 | yes |
| aerobic | yes | 86.141 | no |
| halophile | no | 96.366 | no |
| spore-forming | no | 90.261 | no |
| thermophile | no | 98.179 | yes |
| glucose-util | yes | 90.794 | no |
External links
@ref: 7092
culture collection no.: DSM 17621, KACC 11466
straininfo link
- @ref: 86748
- straininfo: 401957
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16902007 | Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng. | Weon HY, Kim BY, Yoo SH, Lee SY, Kwon SW, Go SJ, Stackebrandt E | Int J Syst Evol Microbiol | 10.1099/ijs.0.64242-0 | 2006 | Agriculture, Bacteroidetes/chemistry/*classification/genetics/isolation & purification, Base Composition, Cyanoacrylates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Panax, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity | Genetics |
| Phylogeny | 17329780 | Niabella aurantiaca gen. nov., sp. nov., isolated from a greenhouse soil in Korea. | Kim BY, Weon HY, Yoo SH, Hong SB, Kwon SW, Stackebrandt E, Go SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.64614-0 | 2007 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Flavobacterium/*classification/cytology/genetics/isolation & purification, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Genetics |
| Phylogeny | 19406810 | Lacibacter cauensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from sediment of a eutrophic lake. | Qu JH, Yuan HL, Yang JS, Li HF, Chen N | Int J Syst Evol Microbiol | 10.1099/ijs.0.003475-0 | 2009 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/physiology, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Eutrophication, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
| Phylogeny | 26296587 | Niastella gongjuensis sp. nov., isolated from greenhouse soil. | Kim SJ, Ahn JH, Weon HY, Hong SB, Seok SJ, Kim JS, Kwon SW | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000387 | 2015 | Bacterial Typing Techniques, *Bacteroidetes/classification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization/genetics, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil, Soil Microbiology | Genetics |
| Phylogeny | 27638144 | Niastellahibisci sp. nov., isolated from rhizosphere soil of mugunghwa, the Korean national flower. | Yan ZF, Lin P, Wang YS, Gao W, Li CT, Kook MC, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001498 | 2016 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hibiscus/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 29072559 | Rurimicrobium arvi gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from farmland soil. | Dahal RH, Chaudhary DK, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002452 | 2017 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, *Farms, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry | Transcriptome |
| Phylogeny | 34252019 | Niastella soli sp. nov., isolated from rhizospheric soil of a persimmon tree. | Akter S, Park JH, Rahman MM, Huq MA | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004870 | 2021 | Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Diospyros/*microbiology, Fatty Acids/metabolism, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Rhizosphere, *Soil Microbiology, Trees/microbiology, Vitamin K 2/analogs & derivatives/chemistry | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7092 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17621) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17621 | |||
| 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 | |||
| 31772 | 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 | 28045 | 28776041 | |
| 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) | |||
| 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 | |||
| 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 | |||
| 86748 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401957.1 | StrainInfo: A central database for resolving microbial strain identifiers |