Strain identifier
BacDive ID: 17756
Type strain:
Species: Niastella koreensis
Strain Designation: GR20-10
Strain history: <- S. W. Kwon, KACC; GR20-10
NCBI tax ID(s): 700598 (strain), 354356 (species)
General
@ref: 7091
BacDive-ID: 17756
DSM-Number: 17620
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Niastella koreensis GR20-10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil cultivated with Korean ginseng.
NCBI tax id
NCBI tax id | Matching level |
---|---|
700598 | strain |
354356 | species |
strain history
- @ref: 7091
- history: <- S. W. Kwon, KACC; GR20-10
doi: 10.13145/bacdive17756.20230509.8.1
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 koreensis
- full scientific name: Niastella koreensis Weon et al. 2006
@ref: 7091
domain: Bacteria
phylum: Bacteroidetes
class: Chitinophagia
order: Sphingobacteriales
family: Chitinophagaceae
genus: Niastella
species: Niastella koreensis
full scientific name: Niastella koreensis Weon et al. 2006
strain designation: GR20-10
type strain: yes
Morphology
cell morphology
- @ref: 31772
- gram stain: negative
- cell length: 10-50 µm
- cell width: 0.5-0.5 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 31772
- production: yes
multimedia
- @ref: 66793
- multimedia content: EM_DSM_17620_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 7091
- 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 |
---|---|---|---|---|
7091 | positive | growth | 28 | mesophilic |
31772 | positive | growth | 10-37 | |
31772 | positive | optimum | 30-37 | 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: 31772
- spore formation: no
observation
- @ref: 31772
- observation: aggregates in chains
enzymes
@ref | value | activity | ec |
---|---|---|---|
31772 | alkaline phosphatase | + | 3.1.3.1 |
31772 | alpha-galactosidase | + | 3.2.1.22 |
Isolation, sampling and environmental information
isolation
- @ref: 7091
- 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_3008.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_1581;97_1887;98_2317;99_3008&stattab=map
- Last taxonomy: Niastella koreensis
- 16S sequence: DQ244077
- Sequence Identity:
- Total samples: 697
- soil counts: 506
- aquatic counts: 22
- animal counts: 7
- plant counts: 162
Safety information
risk assessment
- @ref: 7091
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7091
- description: Niastella koreensis strain GR20-10 16S ribosomal RNA gene, partial sequence
- accession: DQ244077
- length: 1468
- database: ena
- NCBI tax ID: 700598
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Niastella koreensis GR20-10 | GCA_000246855 | complete | ncbi | 700598 |
66792 | Niastella koreensis DSM 17620 | GCA_002077985 | contig | ncbi | 354356 |
66792 | Niastella koreensis GR20-10 | 700598.3 | complete | patric | 700598 |
66792 | Niastella koreensis DSM 17620 | 2802429642 | draft | img | 700598 |
66792 | Niastella koreensis GR20-10, DSM 17620 | 2506520016 | complete | img | 700598 |
GC content
@ref | GC-content | method |
---|---|---|
7091 | 45.8 | high performance liquid chromatography (HPLC) |
31772 | 45.8 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 89.898 | yes |
flagellated | no | 95.915 | no |
gram-positive | no | 97.023 | no |
anaerobic | no | 99.195 | no |
aerobic | yes | 88.144 | yes |
halophile | no | 97.47 | no |
spore-forming | no | 88.014 | yes |
glucose-util | yes | 89.961 | no |
thermophile | no | 98.503 | yes |
glucose-ferment | no | 85.074 | no |
External links
@ref: 7091
culture collection no.: DSM 17620, KACC 11465
straininfo link
- @ref: 86747
- straininfo: 406708
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 | 19654358 | Niastella populi sp. nov., isolated from soil of Euphrates poplar (Populus euphratica) forest, and emended description of the genus Niastella. | Zhang K, Wang Y, Tang Y, Dai J, Zhang L, An H, Luo G, Rahman E, Fang C | Int J Syst Evol Microbiol | 10.1099/ijs.0.012112-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, Populus/*microbiology, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingobacterium/*classification/genetics/*isolation & purification/metabolism | Metabolism |
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 | 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 | journal |
---|---|---|---|---|---|---|---|
7091 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17620) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17620 | ||||
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) | ||||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||
86747 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID406708.1 | StrainInfo: A central database for resolving microbial strain identifiers |