Strain identifier
BacDive ID: 162650
Type strain: 
Species: Paenibacillus yonginensis
Strain history: D.-C. Yang and Y.-J. Kim DCY84.
NCBI tax ID(s): 1462996 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 162650
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Paenibacillus yonginensis JCM 19885 is a spore-forming, mesophilic bacterium that was isolated from Humus soil of Yongin forest.
NCBI tax id
- NCBI tax id: 1462996
- Matching level: species
strain history
- @ref: 67770
- history: D.-C. Yang and Y.-J. Kim DCY84.
doi: 10.13145/bacdive162650.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Paenibacillaceae
- genus: Paenibacillus
- species: Paenibacillus yonginensis
- full scientific name: Paenibacillus yonginensis Sukweenadhi et al. 2016
@ref: 67770
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Caryophanales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus yonginensis
full scientific name: Paenibacillus yonginensis Sukweenadhi et al. 2016
type strain: yes
Morphology
cell morphology
- @ref: 125439
- motility: yes
- confidence: 93
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | yes | 93.224 |
| 125439 | yes | 96.7 |
observation
- @ref: 67770
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Humus soil of Yongin forest
- geographic location: Gyeonggi Province
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
taxonmaps
- @ref: 69479
- File name: preview.99_1378.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_796;97_927;98_1087;99_1378&stattab=map
- Last taxonomy: Paenibacillus yonginensis subclade
- 16S sequence: KF915796
- Sequence Identity:
- Total samples: 36
- soil counts: 9
- aquatic counts: 6
- animal counts: 17
- plant counts: 4
Sequence information
16S sequences
- @ref: 67770
- description: Paenibacillus yonginensis strain DCY84 16S ribosomal RNA gene, partial sequence
- accession: KF915796
- length: 1474
- database: nuccore
- NCBI tax ID: 1462996
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paenibacillus sp. DCY84 | 1462996.4 | complete | patric | 1462996 |
| 67770 | Paenibacillus yonginensis DCY84 | GCA_001685395 | complete | ncbi | 1462996 |
GC content
- @ref: 67770
- GC-content: 62.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 69.129 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 94.806 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 93.224 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 59.302 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 91.328 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 81.739 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 96.7 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 93 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 82.8 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 88.2 |
External links
@ref: 67770
culture collection no.: JCM 19885, KCTC 33428
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25169799 | Paenibacillus yonginensis sp. nov., a potential plant growth promoting bacterium isolated from humus soil of Yongin forest. | Sukweenadhi J, Kim YJ, Lee KJ, Koh SC, Hoang VA, Nguyen NL, Yang DC | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0263-8 | 2014 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Forests, Hydrogen-Ion Concentration, Korea, Locomotion, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, Vitamin K 2/analysis | Genetics |
| Genetics | 29046742 | Complete genome sequence of Paenibacillus yonginensis DCY84(T), a novel plant Symbiont that promotes growth via induced systemic resistance. | Kim YJ, Sukweenadhi J, Seok JW, Kang CH, Choi ES, Subramaniyam S, Yang DC | Stand Genomic Sci | 10.1186/s40793-017-0277-8 | 2017 | ||
| Phylogeny | 29458522 | Paenibacillus mobilis sp. nov., a Gram-stain-negative bacterium isolated from soil. | Yang D, Cha S, Choi J, Seo T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002643 | 2018 | Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 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/ | |
| 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/ |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |