Species Identification of Biological Ingredients in Herbal Product, Gurigumu-7, Based on DNA Barcoding and Shotgun Metagenomics

Overview

Journal Front Plant Sci

Date 2024 Jun 6

PMID 38841282

Authors

Miaojie Wei

Yu Tian

Erhuan Zang

Battseren Tsambaa

Jinxin Liu

Linchun Shi

Almaz Borjigidai

Affiliations

Soon will be listed here.

Abstract

Accurate identification the species composition in mixtures poses a significant challenge, especially in processed mixtures comprising multiple species, such as those found in food and pharmaceuticals. Therefore, we have attempted to utilize shotgun metabarcoding technology to tackle this issue. In this study, the method was initially established using two mock samples of the Mongolian compound preparation Gurigumu-7 (G-7), which was then applied to three pharmaceutical products and 12 hospital-made preparations. A total of 119.72 Gb of raw data sets were obtained through shotgun metagenomic sequencing. By combining ITS2, , and , all the labeled bio-ingredients specified in the G-7 prescription can be detected, although some species may not be detectable in all samples. The prevalent substitution of can be found in all the pharmaceutical and hospital samples, except for YN02 and YN12. The toxic alternative to , , was exclusively identified in the YN02 sample. To further confirm this result, we validated it in YN02 using HPLC and real-time PCR with TaqMan probes. The results showed that aristolochic acid A (AAA) was detected in YN02 using HPLC, and the ITS2 sequence of has been validated in YN02 through qPCR and the use of a TaqMan probe. This study confirms that shotgun metabarcoding can effectively identify the biological components in Mongolian medicine compound preparation G-7. It also demonstrates the method's potential to be utilized as a general identification technique for mixtures containing a variety of plants.

References

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

Liu J, Shi M, Zhao Q, Kong W, Mu W, Xie H . Precise Species Detection in Traditional Herbal Patent Medicine, Qingguo Wan, Using Shotgun Metabarcoding. Front Pharmacol. 2021; 12:607210. PMC: 8113863. DOI: 10.3389/fphar.2021.607210. View

Ding M, Zhou F, Li Y, Liu C, Gu Y, Wu J . improves non-alcoholic fatty liver disease through autophagy-related pathway. Chin Herb Med. 2023; 15(3):421-429. PMC: 10394324. DOI: 10.1016/j.chmed.2022.09.006. View

Li D, Liu C, Luo R, Sadakane K, Lam T . MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015; 31(10):1674-6. DOI: 10.1093/bioinformatics/btv033. View

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

Liu J, Mu W, Shi M, Zhao Q, Kong W, Xie H . The Species Identification in Traditional Herbal Patent Medicine, Wuhu San, Based on Shotgun Metabarcoding. Front Pharmacol. 2021; 12:607200. PMC: 7921783. DOI: 10.3389/fphar.2021.607200. View

Xu H, Ma Q, Ma J, Wu Z, Wang Y, Ma C . Hepato-protective effects and chemical constituents of a bioactive fraction of the traditional compound medicine-Gurigumu-7. BMC Complement Altern Med. 2016; 16:179. PMC: 4906903. DOI: 10.1186/s12906-016-1156-3. View

de Boer H, Ichim M, Newmaster S . DNA Barcoding and Pharmacovigilance of Herbal Medicines. Drug Saf. 2015; 38(7):611-20. DOI: 10.1007/s40264-015-0306-8. View

Nurk S, Meleshko D, Korobeynikov A, Pevzner P . metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017; 27(5):824-834. PMC: 5411777. DOI: 10.1101/gr.213959.116. View

10.

Etherington G, Ramirez-Gonzalez R, MacLean D . bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby. Bioinformatics. 2015; 31(15):2565-7. DOI: 10.1093/bioinformatics/btv178. View

11.

Huson D, Auch A, Qi J, Schuster S . MEGAN analysis of metagenomic data. Genome Res. 2007; 17(3):377-86. PMC: 1800929. DOI: 10.1101/gr.5969107. View

12.

Edgar R, Haas B, Clemente J, Quince C, Knight R . UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011; 27(16):2194-200. PMC: 3150044. DOI: 10.1093/bioinformatics/btr381. View

13.

Devarbhavi H, Asrani S, Arab J, Nartey Y, Pose E, Kamath P . Global burden of liver disease: 2023 update. J Hepatol. 2023; 79(2):516-537. DOI: 10.1016/j.jhep.2023.03.017. View

14.

Xie H, Zhao Q, Shi M, Kong W, Mu W, Li B . Biological Ingredient Analysis of Traditional Herbal Patent Medicine Fuke Desheng Wan Using the Shotgun Metabarcoding Approach. Front Pharmacol. 2021; 12:607197. PMC: 8416078. DOI: 10.3389/fphar.2021.607197. View

15.

Zhang Z, Mu W, Kong W, Liu J, Zhao J, Zhao Q . Validation of the shotgun metabarcoding approach for comprehensively identifying herbal products containing plant, fungal, and animal ingredients. PLoS One. 2023; 18(7):e0286069. PMC: 10317219. DOI: 10.1371/journal.pone.0286069. View

16.

Xin T, Su C, Lin Y, Wang S, Xu Z, Song J . Precise species detection of traditional Chinese patent medicine by shotgun metagenomic sequencing. Phytomedicine. 2018; 47:40-47. DOI: 10.1016/j.phymed.2018.04.048. View

17.

Vanherweghem J, Depierreux M, Tielemans C, Abramowicz D, Dratwa M, Jadoul M . Rapidly progressive interstitial renal fibrosis in young women: association with slimming regimen including Chinese herbs. Lancet. 1993; 341(8842):387-91. DOI: 10.1016/0140-6736(93)92984-2. View

18.

Xin T, Xu Z, Jia J, Leon C, Hu S, Lin Y . Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing. Acta Pharm Sin B. 2018; 8(3):488-497. PMC: 5990340. DOI: 10.1016/j.apsb.2017.10.001. View

19.

Vanhaelen M, Vanhaelen-Fastre R, But P, Vanherweghem J . Identification of aristolochic acid in Chinese herbs. Lancet. 1994; 343(8890):174. DOI: 10.1016/s0140-6736(94)90964-4. View

20.

Lo Y, Shaw P . Application of next-generation sequencing for the identification of herbal products. Biotechnol Adv. 2019; 37(8):107450. DOI: 10.1016/j.biotechadv.2019.107450. View