Quality Control of the Traditional Patent Medicine Yimu Wan Based on SMRT Sequencing and DNA Barcoding

DNA metabarcoding unveils authenticity and adulteration in commercial Chinese polyherbal preparations: Renshen Jianpi Wan as a critical case study

Objectives

Ensuring quality and authenticity of traditional medicines is crucial, particularly for multi-ingredient formulations like commercial Chinese polyherbal preparations (CCPPs). This study aims to authenticate Renshen Jianpi Wan (RSJPW), a classical CCPP composed of 11 prescribed botanical drugs, using DNA metabarcoding to overcome challenges in species-level identification of processed biological ingredients.

Methods

We analyzed 56 commercial RSJPW products from different manufacturers and production batches, alongside eight laboratory-prepared reference samples serving as authentic controls. A dual-marker protocol combining ITS2 and psbA-trnH regions was employed, with optimized DNA extraction and PCR protocols to mitigate degradation issues.

Results

Detection rates varied across samples, with the highest detection being 10 out of 11 prescribed ingredients in a single sample. The key fungal ingredient Poria cocos () was consistently undetectable, likely due to DNA degradation during processing and challenges in extracting fungal DNA from complex matrices. Multiple high-abundance non-prescribed species from Fabaceae, Apiaceae, Brassicaceae, and other families were frequently detected as potential contaminants.

Conclusions

This study establishes a systematic framework for molecular authentication of complex herbal formulations, providing technical support for reliable identification of botanical drugs. While DNA metabarcoding offers valuable insights into CCPP composition, authentication of heavily processed ingredients remains a significant technical limitation. The integration with complementary analytical methods such as metabolomics could provide more comprehensive quality assessment in future studies, demonstrating the necessity of multi-analytical approaches in ensuring the authenticity of traditional medicine.

Analysis of Whole-Genome for Identification of Seven Penicillium Species with Significant Economic Value

The Penicillium genus exhibits a broad global distribution and holds substantial economic value in sectors including agriculture, industry, and medicine. Particularly in agriculture, Penicillium species significantly impact plants, causing diseases and contamination that adversely affect crop yields and quality. Timely detection of Penicillium species is crucial for controlling disease and preventing mycotoxins from entering the food chain. To tackle this issue, we implement a novel species identification approach called Analysis of whole GEnome (AGE). Here, we initially applied bioinformatics analysis to construct specific target sequence libraries from the whole genomes of seven Penicillium species with significant economic impact: P. canescens, P. citrinum, P. oxalicum, P. polonicum, P. paneum, P. rubens, and P. roqueforti. We successfully identified seven Penicillium species using the target we screened combined with Sanger sequencing and CRISPR-Cas12a technologies. Notably, based on CRISPR-Cas12a technology, AGE can achieve rapid and accurate identification of genomic DNA samples at a concentration as low as 0.01 ng/µL within 30 min. This method features high sensitivity and portability, making it suitable for on-site detection. This robust molecular approach provides precise fungal species identification with broad implications for agricultural control, industrial production, clinical diagnostics, and food safety.

Analysis of Whole-Genome as a Novel Strategy for Animal Species Identification

Survival crises stalk many animals, especially endangered and rare animals. Accurate species identification plays a pivotal role in animal resource conservation. In this study, we developed an animal species identification method called Analysis of whole-GEnome (AGE), which identifies species by finding species-specific sequences through bioinformatics analysis of the whole genome and subsequently recognizing these sequences using experimental technologies. To clearly demonstrate the AGE method, Cervus nippon, a well-known endangered species, and a closely related species, Cervus elaphus, were set as model species, without and with published genomes, respectively. By analyzing the whole genomes of C. nippon and C. elaphus, which were obtained through next-generation sequencing and online databases, we built specific sequence databases containing 7,670,140 and 570,981 sequences, respectively. Then, the species specificities of the sequences were confirmed experimentally using Sanger sequencing and the CRISPR-Cas12a system. Moreover, for 11 fresh animal samples and 35 commercially available products, our results were in complete agreement with those of other authoritative identification methods, demonstrating AGE's precision and potential application. Notably, AGE found a mixture in the 35 commercially available products and successfully identified it. This study broadens the horizons of species identification using the whole genome and sheds light on the potential of AGE for conserving animal resources.

Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review

The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.

The serum lipidomics reveal the action mechanism of Danggui-Yimucao herbal pair in abortion mice

Medical abortion is a common medical procedure that women choose to terminate an unwanted pregnancy, but it often brings post-abortion complications. Danggui (Angelica sinensis Radix)-Yimucao (Leonuri Herba), as a herbal pair (DY) in clinical prescriptions of traditional Chinese medicine, is often used in the treatment of gynecological diseases and has the traditional functions of tonifying the blood, promoting blood circulation, removing blood stasis and regulating menstruation. In this study, serum lipidomics were adopted to dissect the mechanism of DY in promoting recovery after medical abortion. A total of 152 differential metabolites were screened by lipidomics. All metabolites were imported into MetaboAnalyst for analysis, and finally key metabolic pathways such as glycerophospholipid metabolism, linoleic acid metabolism and pentose and glucuronate interconversions were enriched. Our results indicated that metabolic disorders in abortion mice were alleviated by DY through glycerophospholipid metabolism, while prostaglandin and leukotriene metabolites might be the key targets of DY to promote post-abortion recovery.

Application of third-generation sequencing to herbal genomics

There is a long history of traditional medicine use. However, little genetic information is available for the plants used in traditional medicine, which limits the exploitation of these natural resources. Third-generation sequencing (TGS) techniques have made it possible to gather invaluable genetic information and develop herbal genomics. In this review, we introduce two main TGS techniques, PacBio SMRT technology and Oxford Nanopore technology, and compare the two techniques against Illumina, the predominant next-generation sequencing technique. In addition, we summarize the nuclear and organelle genome assemblies of commonly used medicinal plants, choose several examples from genomics, transcriptomics, and molecular identification studies to dissect the specific processes and summarize the advantages and disadvantages of the two TGS techniques when applied to medicinal organisms. Finally, we describe how we expect that TGS techniques will be widely utilized to assemble telomere-to-telomere (T2T) genomes and in epigenomics research involving medicinal plants.

Multi-omics approaches for in-depth understanding of therapeutic mechanism for Traditional Chinese Medicine

Traditional Chinese Medicine (TCM) is extensively utilized in clinical practice due to its therapeutic and preventative treatments for various diseases. With the development of high-throughput sequencing and systems biology, TCM research was transformed from traditional experiment-based approaches to a combination of experiment-based and omics-based approaches. Numerous academics have explored the therapeutic mechanism of TCM formula by omics approaches, shifting TCM research from the "one-target, one-drug" to "multi-targets, multi-components" paradigm, which has greatly boosted the digitalization and internationalization of TCM. In this review, we concentrated on multi-omics approaches in principles and applications to gain a better understanding of TCM formulas against various diseases from several aspects. We first summarized frequently used TCM quality assessment methods, and suggested that incorporating both chemical and biological ingredients analytical methods could lead to a more comprehensive assessment of TCM. Secondly, we emphasized the significance of multi-omics approaches in deciphering the therapeutic mechanism of TCM formulas. Thirdly, we focused on TCM network analysis, which plays a vital role in TCM-diseases interaction, and serves for new drug discovery. Finally, as an essential source for storing multi-omics data, we evaluated and compared several TCM databases in terms of completeness and reliability. In summary, multi-omics approaches have infiltrated many aspects of TCM research. With the accumulation of omics data and data-mining resources, deeper understandings of the therapeutic mechanism of TCM have been acquired or will be gained in the future.

Advancements and future prospective of DNA barcodes in the herbal drug industry

Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology. Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations. Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification. Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.

DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances

Traditional Chinese medicine (TCM) plays an important role in the global traditional health systems. However, adulterated and counterfeit TCM is on the rise. DNA barcoding is an effective, rapid, and accurate technique for identifying plant species. In this study, we collected manuscripts on DNA barcoding published in the last decade and summarized the use of this technique in identifying 50 common Chinese herbs listed in the Chinese pharmacopoeia. Based on the dataset of the major seven DNA barcodes of plants in the NCBI database, the strengths and limitations of the barcodes and their derivative barcoding technology, including single-locus barcode, multi-locus barcoding, super-barcoding, meta-barcoding, and mini-barcoding, were illustrated. In addition, the advances in DNA barcoding, particularly identifying plant species for TCM using machine learning technology, are also reviewed. Finally, the selection process of an ideal DNA barcoding technique for accurate identification of a given TCM plant species was also outlined.

TaqMan Probe-Based Quantitative Real-Time PCR to Detect Panax notoginseng in Traditional Chinese Patent Medicines

Background: There has been global concern about the safety and accuracy of traditional Chinese patent medicines (TCPMs). Panax notoginseng, also known as sanqi, is an important constituent of TCPMs. However, identifying the species contained in TCPMs is challenging due to the presence of multiple ingredients and the use of various preparation processes.

Objective: To detect P. notoginseng in TCPMs.

Methods: A TaqMan probe-based qPCR assay was constructed and validated with DNA extracted from P. notoginseng and adulterants. In total, 75 samples derived from 25 batches of TCPMs were tested using the constructed qPCR method.

Results: A TaqMan probe-based qPCR assay targeting P. notoginseng was established. The constructed qPCR assay could specifically discriminate P. notoginseng from Panax ginseng, Panax quinquefolium and Curcuma aromatica Salisb. cv. Wenyujin. The sensitivity study showed that the detectable DNA template concentration of P. notoginseng for this qPCR assay was 0.001 ng/μl. All 75 samples from TCPMs were confirmed to contain P. notoginseng by the qPCR assay.

Conclusions: The qPCR method can accurately identify P. notoginseng in TCPMs and is promising as a powerful tool for quality control and market regulation.

Decoding herbal materials of TCM preparations with the multi-barcode sequencing approach

With the rapid development of high-throughput sequencing technology, approaches for assessing biological ingredients in Traditional Chinese Medicine (TCM) preparations have also advanced. Using a multi-barcode sequencing approach, all biological ingredients could be identified from TCM preparations in theory, as long as their DNA is present. The biological ingredients of several classical TCM preparations were analyzed successfully based on this approach in previous studies. However, the universality, sensitivity and reliability of this approach on a diverse set of TCM preparations remain unclear. In this study, we selected four representative TCM preparations, namely Bazhen Yimu Wan, Da Huoluo Wan, Niuhuang Jiangya Wan, and You Gui Wan, for concrete assessment of the multi-barcode sequencing approach. Based on ITS2 and trnL biomarkers, we have successfully detected the prescribed herbal materials (PHMs) in these representative TCM preparations (minimum sensitivity: 77.8%, maximum sensitivity: 100%). The results based on ITS2 have also shown higher reliability than trnL at species level, while their combination could provide higher sensitivity and reliability. The multi-barcode sequencing approach has shown good universality, sensitivity and reliability in decoding these four representative TCM preparations. In the omics big-data era, this work has undoubtedly made one step forward for applying multi-barcode sequencing approach in PHMs analysis of TCM preparation, towards better digitization and modernization of drug quality control.

Strategies for molecular authentication of herbal products: from experimental design to data analysis

Molecular herbal authentication has gained worldwide popularity in the past decade. DNA-based methods, including DNA barcoding and species-specific amplification, have been adopted for herbal identification by various pharmacopoeias. Development of next-generating sequencing (NGS) drastically increased the throughput of sequencing process and has sped up sequence collection and assembly of organelle genomes, making more and more reference sequences/genomes available. NGS allows simultaneous sequencing of multiple reads, opening up the opportunity of identifying multiple species from one sample in one go. Two major experimental approaches have been applied in recent publications of identification of herbal products by NGS, the PCR-dependent DNA metabarcoding and PCR-free genome skimming/shotgun metagenomics. This review provides a brief introduction of the use of DNA metabarcoding and genome skimming/shotgun metagenomics in authentication of herbal products and discusses some important considerations in experimental design for botanical identification by NGS, with a specific focus on quality control, reference sequence database and different taxon assignment programs. The potential of quantification or abundance estimation by NGS is discussed and new scientific findings that could potentially interfere with accurate taxon assignment and/or quantification is presented.

Network pharmacology-based study on immunomodulatory mechanism of danggui-yimucao herb pair for the treatment of RU486-induced abortion

ETHNOPHARMACOLOGICAL RELEVANCE

The Danggui-Yimucao herb pair (DY) is a classic combination in Chinese herbal formulas, consisting of the root of Angelica sinensis (Oliv.) Diels and the aerial parts of Leonurus japonicus Houtt. DY first appeared in "Zhulinsi fuke mifang" in the Jin Dynasty, and it has a long history as a drug for the treatment of abortion. However, its underlying immunomodulatory mechanisms involved are still unclear.

AIM OF THE STUDY

In this study, network pharmacology and pharmacological experiments were used to explore the role and mechanism of DY in the treatment of medical abortion.

MATERIALS AND METHODS

Network pharmacology was used to establish the relationship between the components of DY and abortion-related targets, and to enrich important pathways and biological process for verification. ELISA was used to assess progesterone levels. Flow cytometry was used to detect the degree of differentiation of Th1/Th2 cells. Immunohistochemical methods and qPCR were used to measure the expression levels of T-bet, GATA-3 and IL-4.

RESULTS

Through the prediction analysis of network pharmacology, we found that key pathway for DY treatment of abortion, such as anemia, pelvic infection, immune disorders, and coagulation disorders, was Th1/Th2 cell differentiation pathway. The pharmacological results revealed that DY greatly corrected the imbalance of Th cell subsets in abortion mice, significantly inhibited the differentiation of Th2 cells, and resulted in an increase in the Th1/Th2 ratio. In addition, the concentration of progesterone in the serum of mice after abortion was significantly reduced. We also found that DY upregulated spleen T-bet and downregulated IL-4 gene expression in mice. Besides, immunohistochemical results showed that DYE could up-regulate T-bet but inhibit GATA-3 expression.

CONCLUSIONS

Our results showed that after RU486-induced abortion, progesterone and Th1/Th2 paradigm were disordered in mice, but DY could make mice recover more quickly, which indicated that DY had great development value in immunoregulation.

Danggui-Yimucao Herb Pair Can Protect Mice From the Immune Imbalance Caused by Medical Abortion and Stabilize the Level of Serum Metabolites

Unintended pregnancy is a situation that every woman may encounter, and medical abortion is the first choice for women, but abortion often brings many sequelae. Angelica sinensis Radix (Danggui) and Leonuri Herba (Yimucao) are widely used in the treatment of gynecological diseases, which can regulate menstrual disorders, amenorrhea, dysmenorrhea, and promote blood circulation and remove blood stasis, but the mechanism for the treatment of abortion is not clear. We determined the ability of Danggui and Yimucao herb pair (DY) to regulate the Th1/Th2 paradigm by detecting the level of progesterone in the serum and the expression of T-bet and GATA-3 in the spleen and uterus. Then, we detected the level of metabolites in the serum and enriched multiple metabolic pathways. The arachidonic acid pathway can directly regulate the differentiation of Th1/Th2 cells. This may be one of the potential mechanisms of DY in the treatment of abortion.

Biological Ingredient Analysis of Traditional Herbal Patent Medicine Fuke Desheng Wan Using the Shotgun Metabarcoding Approach

With the widespread use of traditional medicine around the world, the safety and efficacy of traditional herbal patent medicine have become an increasing concern to the public. However, it is difficult to supervise the authenticity of herbal materials in mixed herbal products according to the current quality standards, especially for traditional herbal patent medicine, with a distinct variance in the dosage of herbal materials. This study utilized the shotgun metabarcoding approach to analyze the biological ingredients of Fuke Desheng Wan (FKDSW), which is an effective traditional herbal product for the treatment of dysmenorrhea. Six herbal materials were collected, and a lab-made mock FKDSW sample was produced to establish a method for the authentication assessment of biological ingredients in traditional herbal patent medicine based on shotgun metabarcoding. Furthermore, four commercial FKDSW samples were collected to verify the practicality of the shotgun metabarcoding approach. Then, a total of 52.16 Gb raw data for 174 million paired-end reads was generated using the Illumina NovaSeq sequencing platform. Meanwhile, 228, 23, and 14 operational taxonomic units (OTUs) were obtained for the ITS2, matK, and rbcL regions, respectively, after bioinformatic analysis. Moreover, no differences were evident between the assembly sequences obtained via shotgun metabarcoding and their corresponding reference sequences of the same species obtained via Sanger sequencing, except for part of the ITS2 and matK assembly sequences of Paeonia lactiflora Pall., Saussurea costus (Falc.) Lipsch. and Bupleurum chinense DC. with 1–6 different bases. The identification results showed that all six prescribed ingredients were successfully detected and that the non-authentic ingredient of Bupleuri Radix (Chaihu, Bupleurum chinense DC. or Bupleurum scorzonerifolium Willd.) was found in all the commercial samples, namely Bupleurum falcatum L. Here, 25 weed species representing 16 genera of ten families were detected. Moreover, 26 fungal genera belonging to 17 families were found in both lab-made and commercial FKDSW samples. This study demonstrated that the shotgun metabarcoding approach could overcome the biased PCR amplification and authenticate the biological ingredients of traditional herbal patent medicine with a distinct variance in the dosage of the herbal materials. Therefore, this provides an appropriate evaluation method for improving the safety and efficacy of traditional herbal patent medicine.

Validation and Optimization of qPCR Method for Identification of Actaea racemosa (Black Cohosh) NHPs

BACKGROUND

Actaea racemosa (black cohosh) herbal dietary supplements are commonly used to treat menopausal symptoms in women. However, there is a considerable risk of contamination of A. racemosa herbal products in the natural health product (NHP) industry, impacting potential efficacy. Authentication of A. racemosa products is challenging because of the standard, multi-part analytical chemistry methods that may be too costly and not appropriate for both raw and finished products.

OBJECTIVE

In this paper, we discuss developing and validating quick alternative biotechnology methods to authenticate A. racemosa herbal dietary supplements, based on the use of a species-specific hydrolysis PCR probe assay.

METHODS

A qPCR-based species-specific hydrolysis probe assay was designed, validated, and optimized for precisely identifying the species of interest using the following analytical validation criteria: (1) specificity (accuracy) in determining the target species ingredient, while not identifying other non-target species; (2) sensitivity in detecting the smallest amount of the target material; and (3) reliability (repeatability and reproducibility) in detecting the target species in raw materials on a real-time PCR platform.

RESULTS

The results show that the species-specific hydrolysis probe assay was successfully developed for the raw materials and powders of A. racemosa. The specificity of the test was 100% to the target species. The efficiency of the assay was observed to be 99%, and the reliability of the assay was 100% for the raw/starting and powder materials.

CONCLUSION

The method developed in this study can be used to authenticate and perform qualitative analysis of A. racemosa supplements.

The Species Identification in Traditional Herbal Patent Medicine, Wuhu San, Based on Shotgun Metabarcoding

Traditional herbal patent medicine typically consists of multiple ingredients, making it challenging to supervise contamination by impurities and the improper use of raw materials. This study employed shotgun metabarcoding for the species identification of biological ingredients in traditional herbal patent medicine, Wuhu San. The five prescribed herbal materials found in Wuhu San were collected, and their reference sequences were obtained by traditional DNA barcoding using Sanger sequencing. Two lab-made and three commercial Wuhu San samples were collected, and a total of 37.14 Gb of shotgun sequencing data was obtained for these five samples using the Illumina sequencing platform. A total of 1,421,013 paired-end reads were enriched for the Internal Transcribed Spacer 2 (ITS2), psbA and trnH intergenic spacer region (psbA-trnH), maturase k (matK), and ribulose-1, 5-bisphosphate carboxylase (rbcL) regions. Furthermore, 80, 11, 9, and 8 operational taxonomic units were obtained for the ITS2, psbA-trnH, matK, and rbcL regions, respectively, after metagenomic assembly, annotation, and chimeric detection. In the two lab-made mock samples, all labeled ingredients in the Wuhu San prescription were successfully detected, and the positive control, Panax quinquefolius L., was detected in the HSZY172 mock sample. Three species, namely Angelica sinensis (Oliv.) Diels, Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk., and Carthamus tinctorius L., belonging to three labeled ingredients, Angelicae Sinensis Radix (Danggui), Saposhnikoviae Radix (Fangfeng), and Carthami Flos (Honghua), were detected in the three commercial samples. Angelica dahurica (Hoffm.) Benth. & Hook. f. ex Franch. & Sav., the original Angelicae Dahuricae Radix (Baizhi) species, was only detected in WHS003. Arisaema erubescens (Wall.) Schott, Arisaema heterophyllum Blume, or Arisaema amurense Maxim., the original Arisaematis Rhizoma (Tiannanxing) species, were not detected in any of the commercial samples, which could be attributed to the fact that this medicinal material underwent extensive processing. In addition, the Saposhnikovia divaricata adulterant was detected in all the commercial samples, while 24 fungal genera, including Aspergillus, were identified in both the lab-made and commercial samples. This study showed that shotgun metabarcoding provided alternative strategy and technical means for identifying prescribed ingredients in traditional herbal patent medicine and displayed the potential to effectively complement traditional methods.

Identification of medicinal plants within the Apocynaceae family using ITS2 and psbA-trnH barcodes

To ensure the safety of medications, it is vital to accurately authenticate species of the Apocynaceae family, which is rich in poisonous medicinal plants. We identified Apocynaceae species by using nuclear internal transcribed spacer 2 (ITS2) and psbA-trnH based on experimental data. The identification ability of ITS2 and psbA-trnH was assessed using specific genetic divergence, BLAST1, and neighbor-joining trees. For DNA barcoding, ITS2 and psbA-trnH regions of 122 plant samples of 31 species from 19 genera in the Apocynaceae family were amplified. The PCR amplification for ITS2 and psbA-trnH sequences was 100%. The sequencing success rates for ITS2 and psbA-trnH sequences were 81% and 61%, respectively. Additional data involved 53 sequences of the ITS2 region and 38 sequences of the psbA-trnH region were downloaded from GenBank. Moreover, the analysis showed that the inter-specific divergence of Apocynaceae species was greater than its intra-specific variations. The results indicated that, using the BLAST1 method, ITS2 showed a high identification efficiency of 97% and 100% of the samples at the species and genus levels, respectively, via BLAST1, and psbA-trnH successfully identified 95% and 100% of the samples at the species and genus levels, respectively. The barcode combination of ITS2/psbA-trnH successfully identified 98% and 100% of samples at the species and genus levels, respectively. Subsequently, the neighbor joining tree method also showed that barcode ITS2 and psbA-trnH could distinguish among the species within the Apocynaceae family. ITS2 is a core barcode and psbA-trnH is a supplementary barcode for identifying species in the Apocynaceae family. These results will help to improve DNA barcoding reference databases for herbal drugs and other herbal raw materials.

DNA metabarcoding to unravel plant species composition in selected herbal medicines on the National List of Essential Medicines (NLEM) of Thailand

Traditional medicines are widely traded across the globe and have received considerable attention in the recent past, with expectations of heightened demand in the future. However, there are increasing global concerns over admixture, which can affect the quality, safety, and efficacy of herbal medicinal products. In this study, we aimed to use DNA metabarcoding to identify 39 Thai herbal products on the Thai National List of Essential Medicines (NLEM) and assess species composition and admixture. Among the products, 24 samples were in-house-prepared formulations, and 15 samples were registered formulations. In our study, DNA metabarcoding analysis using ITS2 and rbcL barcode regions were employed to identify herbal ingredients mentioned in the products. The nuclear region, ITS2, was able to identify herbal ingredients in the products at the genus- and family-levels in 55% and 63% of cases, respectively. The chloroplast gene, rbcL, enabled genus- and family-level identifications in 58% and 73% of cases, respectively. In addition, plant species were detected in larger numbers (Family identified, absolute %) in registered herbal products than in in-house-prepared formulations. The level of fidelity increases concerns about the reliability of the products. This study highlights that DNA metabarcoding is a useful analytical tool when combined with advanced chemical techniques for the identification of plant species in highly processed, multi-ingredient herbal products.

Full-Length Multi-Barcoding: DNA Barcoding from Single Ingredient to Complex Mixtures

DNA barcoding has been used for decades, although it has mostly been applied to somesingle-species. Traditional Chinese medicine (TCM), which is mainly used in the form ofcombination-one type of the multi-species, identification is crucial for clinical usage.Next-generation Sequencing (NGS) has been used to address this authentication issue for the pastfew years, but conventional NGS technology is hampered in application due to its short sequencingreads and systematic errors. Here, a novel method, Full-length multi-barcoding (FLMB) vialong-read sequencing, is employed for the identification of biological compositions in herbalcompound formulas in adequate and well controlled studies. By directly sequencing the full-lengthamplicons of ITS2 and psbA-trnH through single-molecule real-time (SMRT) technology, thebiological composition of a classical prescription Sheng-Mai-San (SMS) was analyzed. At the sametime, clone-dependent Sanger sequencing was carried out as a parallel control. Further, anotherformula-Sanwei-Jili-San (SJS)-was analyzed with genes of ITS2 and CO1. All the ingredients inthe samples of SMS and SJS were successfully authenticated at the species level, and 11 exogenousspecies were also checked, some of which were considered as common contaminations in theseproducts. Methodology analysis demonstrated that this method was sensitive, accurate andreliable. FLMB, a superior but feasible approach for the identification of biological complexmixture, was established and elucidated, which shows perfect interpretation for DNA barcodingthat could lead its application in multi-species mixtures.

Biological ingredient complement chemical ingredient in the assessment of the quality of TCM preparations

Traditional Chinese Medicine (TCM) preparations have been used in China for thousands of years. Quality evaluation for TCM preparations could be conducted based on chemical ingredients or biological ingredients. To date, the overwhelming majority of researches have focused on chemical ingredients while few studies were reported for biological ingredients. It is only recently that the assessments based on biological ingredients have drawn broader attentions. In this work, we have established a method for quality evaluation of TCM preparations by combination of chemical ingredients determined by HPLC fingerprint and biological ingredients obtained by high-throughput sequencing. This proof-of-concept method has been evaluated and compared with existing methods on Liuwei Dihuang Wan, a classical TCM preparation in China. By comparison of this method with those only based on chemical or biological ingredients, it is suggested that (1) Biological ingredient could complement chemical ingredient in separating TCM preparation from different manufacturers and batches with high accuracy; (2) classification of samples based on selected features would always out-perform those based on all features (either chemical or biological or both). By rationally selecting representative biological and chemical features, we have proven that these two types of features could complement each other for the assessment of ingredient consistencies and differences among various TCM samples, which is helpful to ensure the effectiveness, safety and legality of TCM preparations.

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

In recent years, the demand for natural herbal products (NHP) has increased; however, the quality of these products is difficult to confirm due to the lack of a comprehensive quality control system. Traditional methods are not effective in detecting processed ingredients. DNA barcoding is an established technique that has been used for more than 10 years. This technique uses short standard sequences (generally 200-600 bp) to identify species. While a complete DNA barcode is difficult to obtain from NHP due to DNA degradation, mini-barcoding is a complementary tool to identify species in NHP. DNA mini-barcoding uses smaller DNA segments for polymerase chain reaction amplification and can be applied to identify species rapidly. The present review summarizes the development and application of DNA mini-barcodes over recent years and discusses the limitations of this technique. This review also compares mini-barcoding and meta-barcoding, a technique using universal polymerase chain reaction primers to simultaneously amplify multiple DNA barcodes and identify many species in a single environmental sample. Additionally, other detection methods that can be combined with mini-barcodes, such as nucleotide signatures, high-resolution DNA melting analysis, and gold nanoparticles, are discussed. DNA mini-barcoding can fill the gaps left by other methods in the field of herbal molecular identification.

Quality control of goji (fruits of Lycium barbarum L. and L. chinense Mill.): A value chain analysis perspective

ETHNOPHARMACOLOGICAL RELEVANCE

Goji (fruits of Lycium barbarum L. and L. chinense Mill., Solanaceae) have been used as a traditional food and medicine for hundreds of years in Asian countries and are now consumed globally. Quality of herbal medicines is critical for safe use and has been shown to be affected by value chains.

AIM OF THE STUDY

Using a value chain (VC) framework, we aim at understanding the influence of different VC types on goji quality and revenue of stakeholders.

MATERIALS AND METHODS

Participant observation and semi-structured interviews were conducted during five months of fieldwork in the main production areas in China with a total of 65 stakeholders. Quality of goji, behaviour and financial performance of stakeholders was documented and analysed for different VCs.

RESULTS

Ten different types of VCs were identified. VCs with vertical integration and horizontal collaboration were found to have a more coherent quality control and better goji quality as well as improved stakeholders' financial performance. Vertical integration at different levels was found for independent farmer-based VCs, horizontal collaboration was found in the cooperative-based VCs. Full vertically integrated VCs were found in large-scale production.

CONCLUSIONS

Goji quality and stakeholders' revenues are linked with different types of VCs which mirror stakeholders' behaviour driven by target markets. Considering their positive influence on quality and revenues, well-developed vertically integrated value chains are likely to become more important in the near future.

Trends in herbgenomics

From Shen Nong's Herbal Classic (Shennong Bencao Jing) to the Compendium of Materia Medica (Bencao Gangmu) and the first scientific Nobel Prize for the mainland of China, each milestone in the historical process of the development of traditional Chinese medicine (TCM) involves screening, testing and integrating. After thousands of years of inheritance and development, herbgenomics (bencaogenomics) has bridged the gap between TCM and international advanced omics studies, promoting the application of frontier technologies in TCM. It is a discipline that uncovers the genetic information and regulatory networks of herbs to clarify their molecular mechanism in the prevention and treatment of human diseases. The main theoretical system includes genomics, functional genomics, proteomics, transcriptomics, metabolomics, epigenomics, metagenomics, synthetic biology, pharmacogenomics of TCM, and bioinformatics, among other fields. Herbgenomics is mainly applicable to the study of medicinal model plants, genomic-assisted breeding, herbal synthetic biology, protection and utilization of gene resources, TCM quality evaluation and control, and TCM drug development. Such studies will accelerate the application of cutting-edge technologies, revitalize herbal research, and strongly promote the development and modernization of TCM.

Precise species detection of traditional Chinese patent medicine by shotgun metagenomic sequencing

BACKGROUND

Current quality control methods for traditional Chinese patent medicines (TCPMs), e.g., microscopy, thin-layer chromatography (TLC), and high-performance liquid chromatography (HPLC), cannot detect herbal species composition with adequate precision. To address this issue, more effective detection methods should be explored.

HYPOTHESIS/PURPOSE

We hypothesized that shotgun metagenomic sequencing can fulfill the requirements for the species detection of multi-ingredient TCPMs.

METHODS

Longdan Xiegan Wan (LDXGW), once thought to be the chief culprit in aristolochic acid nephropathy (AAN), was selected to establish the method. It was used for both reference and commercial LDXGW samples. The precision authentication of herbal species contained in multi-ingredient TCPM is based on the shotgun metagenomic sequencing of genomic DNA without PCR amplification. Chemical analyses were also conducted as a contrast test.

RESULTS

Over 100 G of raw data was obtained, and this value represented more than 0.75 billion reads. After assembling and filtering all the reads, a total of 261 contigs were obtained, which belonged to the ITS2, psbA-trnH, and matK regions of the reference and commercial samples. Because the homology of the rbcL region was high, it was not analyzed in the HTS data. Bioinformatics analysis indicated that the ITS2 region, as a DNA barcode, showed the highest identification efficiency. It could successfully detect all prescribed species, including four processed herbal ingredients, in the lab-made reference samples. The commercial samples all met the requirements of the Chinese Pharmacopoeia according to the TLC and HPLC tests. However, the shotgun metagenomic sequencing detected the substitution of Akebiae Caulis (Mutong) in the commercial samples, while the chemical analyses could not distinguish.

CONCLUSION

The results highlight that shotgun metagenomic sequencing is a complementary method for the precise species detection of TCPMs.

Quality control of the traditional Chinese medicine Ruyi jinhuang powder based on high-throughput sequencing and real-time PCR

Traditional Chinese medicine (TCM) has been practiced for thousands of years, although concerns about the efficacy, legality, and safety of TCM continue to be raised. Chromatographic studies have detected the presence of heavy metals and plant toxins within some TCM preparations. However, chromatography is not able to identify all of the compounds of TCM, particularly those items that are not clearly labeled on the packaging. The present study aimed to establish a supplemental method that better assesses the ingredient components of TCM preparations.We established an effective approach to screen the biological and toxical composition of TCM based on high-throughput sequencing (HTS), as well as fast detection and validation of the toxical species by real-time PCR, based on ITS2 DNA barcoding. Ruyi jinhuang powder (RHP), a classical herbal prescription containing the toxical herb Arisaematis rhizoma, was chosen to test the method. This method could determine whether the Arisaematis Rhizoma had been replaced by Pinellia pedatisecta in the RHP. The results were validated by real-time PCR. 90% compositions of RHP were identified by ITS2 DNA barcoding, suggesting that more DNA barcoding markers are needed for TCM identification. The strategy of high-throughput sequencing has the potential for comprehensive ingredient profiling for TCM preparations. Real-time PCR provides a expeditious metehod for monitoring the safety and legality of TCM preparations.

Rapid Authentication of Ginkgo biloba Herbal Products Using the Recombinase Polymerase Amplification Assay

Species adulteration in herbal products (HPs) exposes consumers to health risks. Chemical and morphological methods have their own deficiencies when dealing with the detection of species containing the same active compounds in HPs. In this study, we developed a rapid identification method using the recombinase polymerase amplification (RPA) assay to detect two species, Ginkgo biloba and Sophora japonica (as adulteration), in Ginkgo biloba HPs. Among 36 Ginkgo biloba HP samples, 34 were found to have Ginkgo biloba sequences, and 9 were found to have Sophora japonica sequences. During the authentication process, the RPA-LFS assay showed a higher specificity, sensitivity and efficiency than PCR-based methods. We initially applied the RPA-LSF technique to detect plant species in HPs, demonstrating that this assay can be developed into an efficient tool for the rapid on-site authentication of plant species in Ginkgo biloba HPs.

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

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.

A Comprehensive Quality Evaluation System for Complex Herbal Medicine Using PacBio Sequencing, PCR-Denaturing Gradient Gel Electrophoresis, and Several Chemical Approaches

Herbal medicine is a major component of complementary and alternative medicine, contributing significantly to the health of many people and communities. Quality control of herbal medicine is crucial to ensure that it is safe and sound for use. Here, we investigated a comprehensive quality evaluation system for a classic herbal medicine, Danggui Buxue Formula, by applying genetic-based and analytical chemistry approaches to authenticate and evaluate the quality of its samples. For authenticity, we successfully applied two novel technologies, third-generation sequencing and PCR-DGGE (denaturing gradient gel electrophoresis), to analyze the ingredient composition of the tested samples. For quality evaluation, we used high performance liquid chromatography assays to determine the content of chemical markers to help estimate the dosage relationship between its two raw materials, plant roots of Huangqi and Danggui. A series of surveys were then conducted against several exogenous contaminations, aiming to further access the efficacy and safety of the samples. In conclusion, the quality evaluation system demonstrated here can potentially address the authenticity, quality, and safety of herbal medicines, thus providing novel insight for enhancing their overall quality control. Highlight: We established a comprehensive quality evaluation system for herbal medicine, by combining two genetic-based approaches third-generation sequencing and DGGE (denaturing gradient gel electrophoresis) with analytical chemistry approaches to achieve the authentication and quality connotation of the samples.