Project's information

Project's title Genome sequencing and identification of genomic features related to antibiotic activity, cytotoxicity of endophytic actinomycetes from Litsea cubeba (Lour.) Pers.
Project’s code ĐLTE00.03/21-22
Research hosting institution Institute of Biotechnology
Project leader’s name Dr. Quach Ngoc Tung
Project duration 01/01/2021 - 31/12/2022
Project’s budget 500 million VND
Classify Grade B
Main results
- Theoretical results: The research has achieved the following results: 
Of the 63 endophytic actinomycete strains from the plant Litsea cubeba (Lour.) Pers. in the VAST-Culture Collection of Microorganisms (VCCM), strain LCP02, LCP06 and LCP18 were the most potential strains with antibacterial activity against 8 tested pathogens. Besides, crude extract of the 3 strains at 100 μg/mL displayed strong inhibition against lung cancer A549, breast cancer MCF7 and hepatic cancer Hep-3B. 
 Based on morphological, biochemical characteristics and 16S rRNA sequence analysis, strain LCP02 was identified as S. cacaoi LCP02; strain LCP06 as S. albus LCP06; and strain LCP18 as S. variabilis LCP18. 
In order to explore genomic features relating to antibacterial and anticancer activities, whole genomes of S. cacaoi LCP02, S. albus LCP06 and S. variabilis LCP18 were sequenced using Illumina platform. Three strains had large genome sizes varying between 7.39-8.44 Mb, of which functional genes comprised of 6830-7359 sequences. 
Comparison of chemical and gene cluster analyses revealed a putative biosynthesis pathway of two plant-derived compounds such as daidzein and genistein in the genome of S. variabilis LCP18. UPLC-HR-MS/MS analysis resulted in 8 compounds from the crude extract of S. cacaoi LCP02, among which albonoursin and griseorhodin had the corresponding predicted gene clusters in LCP02 genome. Regarding S. albus LCP06, evaluation of genomic features and crude extract chemical compositions showed a gene cluster encoding the biosynthesis pathway of two isomers (3Z,6E)-1-N-methylalbonoursin and (3Z(E),6E(Z))-1-N-methylalbonoursin.
- Applied results: This project has contributed to the application of genome sequencing technology in research to further explore compounds with antibacterial and anticancer activity. The identified compounds from 03 strains possess the potential to be developed to be therapeutic compounds in pharmacology and medicine. 
Products of the project

- Scientific papers in referred journals (list): 
01 SCIE publications
Ngoc Tung Quach, Quang Huy Nguyen, Thi Hanh Nguyen Vu, Thi Thu Hang Le, Thi Thu Thuy Ta, Tien Dat Nguyen, Van Thuoc Doan, Van The Nguyen, Tat Thanh Dang, Xuan Canh Nguyen, Hoang Ha Chu, Quyet Tien Phi (2021). Plant-derived bioactive compounds produced by Streptomyces variabilis LCP18 associated with Litsea cubeba (Lour.) Pers as potential target to combat human pathogenic bacteria and human cancer cell lines. Brazilian Journal of Microbiology, 1-10 (Q3; IF 2,2)
02 publications on National Journal/Conference proceedings 
Quach Ngoc Tung, Thi Hanh Nguyen Vu, Nguyen Thi Thu An, Bui Thi Lien, Le Thi Thanh Xuan, Quyet Tien Phi (2022) Exploring antibacterial and cytotoxic potential of endophytic Streptomyces isolated from the medicinal plant Litsea cubeba (Lour.) Pers. Vietnam Journal of Science and Technology 60 (5): 756-766.
Quach Ngoc Tung, Thi Hanh Nguyen Vu, Bui Thi Lien, Le Phuong Chi, Phi Quyet Tien (2021) Identification and evaluation of antibacterial and anticancer activities of Streptomyces cavourensis LCP14 from Litsea cubeba (Lour.) Pers. National Biotechnology Conference 2021: 507-512. ISBN 978-604-9987-88-5.
01 book 
Phí Quyết Tiến, Vũ Thị Hạnh Nguyên, Quách Ngọc Tùng (2022) Appications of endophytic actinomycetes from Vietnamese plants. Vietnam plants. Natural Science and Technology Publishing House.
- Education and training (list):
Le Phuong Chi defended successfully the master thesis at the Graduate University of Science and Technology on 18th May, 2023.  
- Technological products (describe in details: technical characteristics, place):
A collection of 12 endophytic actinomycete strains with antibacterial and anticancer activities. 
A genomic database of 03 potential actinomycete strains.
A list of predicted gene clusters relating to biosynthesis pathway of antibiotics and anticancer compounds from the genomes of 03 actinomycete strains. 
A chemical profile database identified from chemical analysis of 03 actinomycete strains. 

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