Strain identifier
BacDive ID: 130435
Type strain: 
Species: Nesterenkonia populi
Strain Designation: GP10-3
Strain history: <- Cheng-hang Sun, Institute of Medicinal Biotechnology, China
NCBI tax ID(s): 1591087 (species)
version 8.1 (current version)
General
@ref: 21687
BacDive-ID: 130435
DSM-Number: 27959
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive
description: Nesterenkonia populi GP10-3 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from plant, bark sample of Populus euphratica.
NCBI tax id
- NCBI tax id: 1591087
- Matching level: species
strain history
| @ref | history |
|---|---|
| 21687 | <- C.-H. Sun, Chinese Acad. Med. Sciences & Peking Union Medical College; GP10-3 <- J. Liu |
| 67770 | DSM 27959 <-- C.-H. Sun; Inst. of Med. Biotechnol., Chin. Acad. Med. Sci. & Peking Union Med. Coll., China; GP10-3. |
| 67771 | <- Cheng-hang Sun, Institute of Medicinal Biotechnology, China |
doi: 10.13145/bacdive130435.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Micrococcaceae
- genus: Nesterenkonia
- species: Nesterenkonia populi
- full scientific name: Nesterenkonia populi Liu et al. 2015
@ref: 21687
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micrococcaceae
genus: Nesterenkonia
species: Nesterenkonia populi
full scientific name: Nesterenkonia populi Liu et al. 2015
strain designation: GP10-3
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 21687
- name: MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514d
- composition: Name: MODIFIED BACTO MARINE BROTH (DSMZ Medium 514d) Composition: Difco marine broth 37.4 g/l Agar 15.0 g/l Malt extract 1.0 g/l Soy peptone 1.0 g/l Pancreatic digest of casein 1.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 21687 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.999 |
observation
- @ref: 67770
- observation: quinones: MK-8, MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 21687 | plant, bark sample of Populus euphratica | Populus euphratica | Xinjiang, Taklimakan desert | China | CHN | Asia |
| 67770 | Bark of Populus euphratica on the southern edge of the Taklimakan Desert | Populus euphratica | Xinjiang | China | CHN | Asia |
| 67771 | From Plant | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Tree |
| #Host Body-Site | #Plant | #Bark |
taxonmaps
- @ref: 69479
- File name: preview.99_75098.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2198;97_40303;98_52510;99_75098&stattab=map
- Last taxonomy: Nesterenkonia populi subclade
- 16S sequence: KP057085
- Sequence Identity:
- Total samples: 212
- soil counts: 18
- aquatic counts: 13
- animal counts: 158
- plant counts: 23
Safety information
risk assessment
- @ref: 21687
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21687
- description: Nesterenkonia populi strain GP10-3 16S ribosomal RNA gene, partial sequence
- accession: KP057085
- length: 1481
- database: ena
- NCBI tax ID: 1591087
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Nesterenkonia populi DSM 27959 | GCA_007994735 | contig | ncbi | 1591087 |
| 66792 | Nesterenkonia populi strain DSM 27959 | 1591087.3 | wgs | patric | 1591087 |
GC content
- @ref: 21687
- GC-content: 67.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 54.635 | no |
| gram-positive | yes | 91.601 | no |
| anaerobic | no | 99.128 | yes |
| aerobic | yes | 93.807 | yes |
| halophile | yes | 77.588 | no |
| spore-forming | no | 93.895 | no |
| thermophile | no | 95.721 | yes |
| glucose-util | yes | 85.302 | no |
| flagellated | no | 92.106 | no |
| glucose-ferment | no | 88.342 | no |
External links
@ref: 21687
culture collection no.: DSM 27959, JCM 31979, KCTC 29119
straininfo link
- @ref: 88965
- straininfo: 400528
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25701851 | Nesterenkonia populi sp. nov., an actinobacterium isolated from Populus euphratica. | Liu JM, Tuo L, Habden X, Guo L, Jiang ZK, Liu XF, Chen L, Zhang YQ, Sun CH | Int J Syst Evol Microbiol | 10.1099/ijs.0.000123 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Bark/microbiology, Populus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry | Genetics |
| Phylogeny | 34468853 | Nesterenkonia ebinurensis sp. nov., a Novel Actinobacterium Isolated From Populus euphratica. | Anwar N, Ye Y, Chen C, Mamtimin T, Wang R, Rahman E, Wu M | Curr Microbiol | 10.1007/s00284-021-02597-4 | 2021 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Micrococcaceae, Nucleic Acid Hybridization, Peptidoglycan, Phospholipids/analysis, Phylogeny, *Populus, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
| Phylogeny | 34609528 | Nesterenkonia sedimenti sp. nov., isolated from marine sediment. | Xie F, Pei S, Zhang Y, Tian Y, Zhang G | Arch Microbiol | 10.1007/s00203-021-02596-w | 2021 | Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/analysis, *Geologic Sediments, Micrococcaceae, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2 | 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 | |
| 21687 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27959 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27959) | |
| 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 | |
| 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 | |
| 88965 | 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-ID400528.1 |