3 Biotech

, 9:300 | Cite as

Metagenomic analysis of bacterial endophyte community structure and functions in Panax ginseng at different ages

  • Chi Eun Hong
  • Jang Uk Kim
  • Jung Woo Lee
  • Kyong Hwan Bang
  • Ick Hyun JoEmail author
Short Reports


This study investigated the root-associated bacterial endophytes of Panax ginseng at different ages by shotgun metagenomic analysis. After mapping metagenome data to the complete ginseng genome to identify unmapped sequences, we predicted the structure and functions of ginseng bacterial endophytes by metagenomic rapid annotation using subsystems technology analysis. While Proteobacteria and Actinobacteria were the predominant phyla in all samples (2–6-year-old roots), class Alphaproteobacteria was most abundant in 3-, 4-, and 5-year-old plants. We found that 3-year-old P. ginseng had a 0.66% unmapped rate against the whole ginseng genome and showed the greatest diversity of endophytic bacteria (α diversity = 299). Prediction of endophytic bacterial functions at different ages by SEED subsystem analysis revealed that siderophore and auxin-related traits—which are known to promote plant growth—were most highly represented in 3-year-old plants. This was supported by a gene frequency analysis of plant growth-promoting genes, including those responsible for solubilization of phosphate and nitrogen metabolism, using BLASTn. These results suggest that endophytic bacteria of the P. ginseng root affect plant growth. Furthermore, the isolation and purification of plant growth-promoting endophytes identified in this study could promote sustainable cultivation of ginseng in the future.


Panax ginseng Bacterial endophyte Shotgun metagenomics Siderophore 



This work was supported by the Cooperative Research Program for Agriculture Science & Technology Development (Project no. PJ 01312412019), Rural Development Administration, Republic of Korea; and by the 2019 Postdoctoral Fellowship Program of National Institute of Horticultural and Herbal Science, Rural Development Administration, Republic of Korea.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.


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Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  1. 1.Department of Herbal Crop ResearchNational Institute of Horticultural and Herbal Science, Rural Development AdministrationEumseongSouth Korea

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