Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing

Abstract

Global concerns have been paid to the potential hazard of traditional herbal medicinal products (THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, real-time (SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan (JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing (CCS) reads belonging to the ITS2 and psbA-trnH regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs.

Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

“…Due to lack of proper monitoring and regulatory systems, there is a risk that many medicinal plants and their products sold on the market will be taxonomically misidentified, mislabeled, or contaminated [90]. Globally, the focus has been on the potential hazards of traditional herbal medicinal products [91]. It is hoped that our study will aid in the development of DNA-barcoding markers to clarify the taxonomic identity of Withania species in medicinal plant production.…”

Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?

“…To allow direct comparison with the results obtained in Meiklejohn et al [20], the same traditional barcoding loci were targeted: cytochrome oxidase subunit I ( COI ) for animals, and maturase K ( matK ) and ribulose biphosphate carboxylase ( rbcL ) for plants. While alternative barcode loci that permit discrimination and can be more straightforwardly sequenced on MPS platforms have been identified and assessed (e.g., trnL , ITS2 , and psbA-trnH in plants [25,26,27,28,29,30,31,32,33,34]), these were not targeted in this study. For clarity, amplifications of plant barcoding loci matK and rbcL were completed using the KAPA3G Plant DNA polymerase (KAPA Biosystems, Wilmington, MA, USA) and the COI barcode region was amplified using the Q5 ® Hot Start High-Fidelity DNA polymerase (New England BioLabs Inc, Ipswich, MA, USA).…”

DNA Mini-Barcoding: A Derived Barcoding Method for Herbal Molecular Identification

“…In meta-barcoding studies on CPMs, ITS2 or other plant barcodes are frequently chosen because these sequences can produce high identification efficiency among many species. As sequencing technologies have developed, next-generation sequencing (NGS) has been widely used for NHP quality control and analysis (de Boer et al, 2017; Raclariu et al, 2017; Xin et al, 2018a,b). Most CPM prescriptions are very complex; hence, universal primer pairs for DNA barcode amplification may not be feasible for the identification of herbal products using Sanger sequencing.…”