Deep sequencing of plant and animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns

Review: Wildlife forensic genetics-Biological evidence, DNA markers, analytical approaches, and challenges

Wildlife-related crimes are the second most prevalent lawbreaking offense globally. This illicit trade encompasses hunting, breeding and trafficking. Besides diminishing many species and their habitats and ecosystems, hindering the economic development of local communities that depend on them, undermining the rule of law and financing terrorism, various cross-species transmissions (zoonoses) of pathogens, including COVID-19, can be attributed to wildlife crimes. Wildlife forensics applies interdisciplinary scientific analyses to support law enforcement in investigating wildlife crimes. Its main objectives are to identify the taxonomic species in question, determine if a crime has been committed, link a suspect to the crime and support the conviction and prosecution of the perpetrator. This article reviews wildlife crime and its implications, wildlife forensic science investigation, common forms of wildlife biological evidence, including DNA, wildlife DNA techniques and challenges in wildlife forensic genetics. The article also reviews the contributions of genetic markers such as short tandem repeat (STR) and mitochondrial DNA (mtDNA) markers, which provide the probative genetic data representing the bulk of DNA evidence for solving wildlife crime. This review provides an overview of wildlife DNA databases, which are critical for searching and matching forensic DNA profiles and sequences and establishing how frequent forensic DNA profiles and sequences are in a particular population or geographic region. As such, this review will contain an in-depth analysis of the current status of wildlife forensic genetics, and it will be of general interest to wildlife and conservation biologists, law enforcement officers, and academics interested in combating crimes against wildlife using animal forensic DNA methods.

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.

Three-tiered authentication of herbal traditional Chinese medicine ingredients used in women's health provides progressive qualitative and quantitative insight

Traditional Chinese Medicine (TCM) herbal products are increasingly used in Europe, but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients.

Mechanisms of multi-omics and network pharmacology to explain traditional chinese medicine for vascular cognitive impairment: A narrative review

BACKGROUND

The term "vascular cognitive impairment" (VCI) describes various cognitive conditions that include vascular elements. It increases the risk of morbidity and mortality in the elderly population and is the most common cognitive impairment associated with cerebrovascular disease. Understanding the etiology of VCI may aid in identifying approaches to target its possible therapy for the condition. Treatment of VCI has focused on vascular risk factors. There are no authorized conventional therapies available right now. The medications used to treat VCI are solely approved for symptomatic relief and are not intended to prevent or slow the development of VCI.

PURPOSE

The function of Chinese medicine in treating VCI has not yet been thoroughly examined. This review evaluates the preclinical and limited clinical evidence to comprehend the "multi-component, multi-target, multi-pathway" mechanism of Traditional Chinese medicine (TCM). It investigates the various multi-omics approaches in the search for the pathological mechanisms of VCI, as well as the new research strategies, in the hopes of supplying supportive evidence for the clinical treatment of VCI.

METHODS

This review used the Preferred Reporting Items for Preferred reporting items for systematic reviews and meta-analyses (PRISMA) statements. Using integrated bioinformatics and network pharmacology approaches, a thorough evaluation and analysis of 25 preclinical studies published up to July 1, 2023, were conducted to shed light on the mechanisms of TCM for vascular cognitive impairment. The studies for the systematic review were located using the following databases: PubMed, Web of Science, Scopus, Cochrane, and ScienceDirect.

RESULTS

We discovered that the multi-omics analysis approach would hasten the discovery of the role of TCM in the treatment of VCI. It will explore components, compounds, targets, and pathways, slowing the progression of VCI from the perspective of inhibiting oxidative stress, stifling neuroinflammation, increasing cerebral blood flow, and inhibiting iron deposition by a variety of molecular mechanisms, which have significant implications for the treatment of VCI.

CONCLUSION

TCM is a valuable tool for developing dementia therapies, and further research is needed to determine how TCM components may affect the operation of the neurovascular unit. There are still some limitations, although several research have offered invaluable resources for searching for possible anti-dementia medicines and treatments. To gain new insights into the molecular mechanisms that precisely modulate the key molecules at different levels during pharmacological interventions-a prerequisite for comprehending the mechanism of action and determining the potential therapeutic value of the drugs-further research should employ more standardized experimental methods as well as more sophisticated science and technology. Given the results of this review, we advocate integrating chemical and biological component analysis approaches in future research on VCI to provide a more full and objective assessment of the standard of TCM. With the help of bioinformatics, a multi-omics analysis approach will hasten the discovery of the role of TCM in the treatment of VCI, which has significant implications for the treatment of VCI.

Complementary authentication of Chinese herbal products to treat endometriosis using DNA metabarcoding and HPTLC shows a high level of variability

Traditional Chinese Medicine (TCM) is popular for the treatment of endometriosis, a complex gynecological disease that affects 10% of women globally. The growing market for TCMs has yielded a significant incentive for product adulteration, and although emerging technologies show promise to improve their quality control, many challenges remain. We tested the authenticity of two traditional Chinese herbal formulae used in women's healthcare for the treatment of endometriosis, known as Gui Zhi Fu Ling Wan (FL) and Ge Xia Zhu Yu Tang (GX). Dual-locus DNA metabarcoding analysis coupled with high-performance thin-layer chromatography (HPTLC) were used to authenticate 19 FL and six GX commercial herbal products, as well as three ad hoc prepared artificial mixtures. HPTLC was able to detect most of the expected ingredients via comparative component analysis. DNA metabarcoding was able to detect an unexpected species diversity in the products, including 38 unexpected taxa. Chromatography has a resolution for all species indirectly through the identification of marker compounds for the different species ingredients. Metabarcoding on the other hand yields an overview of species diversity in each sample, but interpretation of the results can be challenging. Detected species might not be present in quantities that matter, and without validated quantification, some detected species can be hard to interpret. Comparative analysis of the two analytical approaches also reveals that DNA for species might be absent or too fragmented to amplify as the relevant chemical marker compounds can be detected but no amplicons are assigned to the same species. Our study emphasizes that integrating DNA metabarcoding with phytochemical analysis brings valuable data for the comprehensive authentication of Traditional Chinese Medicines ensuring their quality and safe use.

Comprehensive analysis using DNA metabarcoding, SCAR marker based PCR assay, and HPLC unveils the adulteration in Brahmi herbal products

BACKGROUND

Brahmi is one of the important nootropic botanicals, widely sold in the market, with the name "Brahmi'' being used to describe both Bacopa monnieri and Centella asiatica species. The Brahmi herbal products market is expanding; hence, economically motivated adulteration is highly prevalent.

METHODS AND RESULTS

This study aimed to develop DNA-based methods, including SCAR marker-based PCR and metabarcoding, to authenticate Brahmi herbal products and compare these methods with HPLC. These methods have been validated using mock controls (in-house blended formulations). All targeted plant species in mock controls were detected successfully with all three methods, whereas, in market samples, only 22.2%, 55.6%, and 50.0% were found positive for Brahmi by PCR assay, DNA metabarcoding, and HPLC, respectively. Metabarcoding can detect the presence of non-labeled plants together with targeted species, which is an advantage over PCR assay or HPLC.

CONCLUSION

SCAR marker-based PCR is a rapid and cost-effective method for detecting the presence of B. monnieri and C. asiatica. However, in this study, the success rate of PCR amplification was relatively low because the primers targeted either RAPD or ITS-based SCAR markers. HPLC assay, although an alternative, was unable to detect the presence of other botanicals, just like the SCAR marker-based PCR assay. On the other hand, metabarcoding can be utilized to identify the target plants, even in very small quantities, while also providing simulated identification of other botanicals. This study successfully addressed the need for quality control of Brahmi herbal products and provided the first-time report of DNA metabarcoding for such products.

Authentication of milk thistle commercial products using UHPLC-QTOF-ESI + MS metabolomics and DNA metabarcoding

BACKGROUND

Milk thistle is one of the most popular hepatoprotectants, and is often sold in combination with other ingredients. Botanical supplements are known to be vulnerable to contamination and adulteration, and emerging technologies show promise to improve their quality control.

METHODS

Untargeted and semi-targeted metabolomics based on UHPLC-QTOF-ESI⁺MS techniques, UV spectrometry, and DNA metabarcoding using Illumina MiSeq were used to authenticate eighteen milk thistle botanical formulations (teas, capsules, tablets, emulsion).

RESULTS

Untargeted metabolomics separated 217 molecules and by multivariate analysis the discrimination between the different preparations was established. The semi-targeted metabolomics focused on 63 phytochemicals, mainly silymarin flavonolignans and flavonoids, that may be considered as putative biomarkers of authenticity. All formulations contained molecules from silymarin complexes at different levels. The quantitative evaluation of silybins was done using in parallel UV spectrometry and UHPLC-QTOF-ESI⁺MS and their correlations were compared. DNA metabarcoding detected milk thistle in eleven out of sixteen retained preparations, whereas two others had incomplete evidence of milk thistle despite metabolomics validating specific metabolites, e.g., silymarin complex, identified and quantified in all samples. Meanwhile, the DNA metabarcoding provided insights into the total species composition allowing the interpretation of the results in a broad context.

CONCLUSION

Our study emphasizes that combining spectroscopic, chromatographic, and genetic techniques bring complementary information to guarantee the quality of the botanical formulations.

A combined approach of DNA metabarcoding collectively enhances the detection efficiency of medicinal plants in single and polyherbal formulations

Introduction

Empirical research has refined traditional herbal medicinal systems. The traditional market is expanding globally, but inadequate regulatory guidelines, taxonomic knowledge, and resources are causing herbal product adulteration. With the widespread adoption of barcoding and next-generation sequencing, metabarcoding is emerging as a potential tool for detecting labeled and unlabeled plant species in herbal products.

Methods

This study validated newly designed rbcL and ITS2 metabarcode primers for metabarcoding using in-house mock controls of medicinal plant gDNA pools and biomass pools. The applicability of the multi-barcode sequencing approach was evaluated on 17 single drugs and 15 polyherbal formulations procured from the Indian market.

Results

The rbcL metabarcode demonstrated 86.7% and 71.7% detection efficiencies in gDNA plant pools and biomass mock controls, respectively, while the ITS2 metabarcode demonstrated 82.2% and 69.4%. In the gDNA plant pool and biomass pool mock controls, the cumulative detection efficiency increased by 100% and 90%, respectively. A 79% cumulative detection efficiency of both metabarcodes was observed in single drugs, while 76.3% was observed in polyherbal formulations. An average fidelity of 83.6% was observed for targeted plant species present within mock controls and in herbal formulations.

Discussion

In the present study, we achieved increasing cumulative detection efficiency by combining the high universality of the rbcL locus with the high-resolution power of the ITS2 locus in medicinal plants, which shows applicability of multilocus strategies in metabarcoding as a potential tool for the Pharmacovigilance of labeled and unlabeled plant species in herbal formulations.

Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations

Herbal medicines and preparations are widely used in healthcare systems globally, but concerns remain about their quality and safety. New herbal products are constantly being introduced to the market under varying regulatory frameworks, with no global consensus on their definition or characterization. These biologically active mixtures are sold through complex globalized value chains, which create concerns around contamination and profit-driven adulteration. Industry, academia, and regulatory bodies must collaborate to develop innovative strategies for the identification and authentication of botanicals and their preparations to ensure quality control. High-throughput sequencing (HTS) has significantly improved our understanding of the total species diversity within DNA mixtures. The standard concept of DNA barcoding has evolved over the last two decades to encompass genomic data more broadly. Recent research in DNA metabarcoding has focused on developing methods for quantifying herbal product ingredients, yielding meaningful results in a regulatory framework. Techniques, such as loop-mediated isothermal amplification (LAMP), DNA barcode-based Recombinase Polymerase Amplification (BAR-RPA), DNA barcoding coupled with High-Resolution Melting (Bar-HRM), and microfluidics-based methods, offer more affordable tests for the detection of target species. While target capture sequencing and genome skimming are considerably increasing the species identification resolution in challenging plant clades, ddPCR enables the quantification of DNA in samples and could be used to detect intended and unwanted ingredients in herbal medicines. Here, we explore the latest advances in emerging DNA-based technologies and the opportunities they provide as taxa detection tools for evaluating the safety and quality of dietary supplements and herbal medicines.

Pragmatic applications of DNA barcoding markers in identification of fish species – a review

DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.

MRTCM: A comprehensive dataset for probabilistic risk assessment of metals and metalloids in traditional Chinese medicine

Traditional Chinese medicine (TCM) is still considered a global complementary or alternative medical system, but exogenous hazardous contaminants remain in TCM even after decocting. Besides, it is time-consuming to conduct a risk assessment of trace elements in TCMs with a non-automatic approach due to the wide variety of TCMs. Here, we present MRTCM, a cloud-computing infrastructure for automating the probabilistic risk assessment of metals and metalloids in TCM. MRTCM includes a consumption database and a pollutant database involving forty million rows of consumption data and fourteen types of TCM potentially toxic elements concentrations. The algorithm of probabilistic risk assessment was also packaged in MRTCM to assess the risks of eight elements with Monte Carlo simulation. The results demonstrated that 96.64% and 99.46% had no non-carcinogenic risk (hazard indices (HI) were < 1.0) for animal and herbal medicines consumers, respectively. After twenty years of exposure, less than 1% of the total carcinogenic risk (CR_t) was > 10^-4 for TCM consumers, indicating that they are at potential risk for carcinogenicity. Sensitivity analysis revealed that annual consumption and concentration were the main variables affecting the assessment results. Ultimately, a priority management list of TCMs was also generated, indicating that more attention should be paid to the non-carcinogenic risks of As, Mn, and Hg and the carcinogenic risks of As and Cr in Pheretima and Cr in Arcae Conch. In general, MRTCM could significantly enhance the efficiency of risk assessment in TCM and provide reasonable guidance for policymakers to optimize risk management.

Current Trends in Toxicity Assessment of Herbal Medicines: A Narrative Review

Even in modern times, the popularity level of medicinal plants and herbal medicines in therapy is still high. The World Health Organization estimates that 80% of the population in developing countries uses these types of remedies. Even though herbal medicine products are usually perceived as low risk, their potential health risks should be carefully assessed. Several factors can cause the toxicity of herbal medicine products: plant components or metabolites with a toxic potential, adulteration, environmental pollutants (heavy metals, pesticides), or contamination of microorganisms (toxigenic fungi). Their correct evaluation is essential for the patient’s safety. The toxicity assessment of herbal medicine combines in vitro and in vivo methods, but in the past decades, several new techniques emerged besides conventional methods. The use of omics has become a valuable research tool for prediction and toxicity evaluation, while DNA sequencing can be used successfully to detect contaminants and adulteration. The use of invertebrate models (Danio renio or Galleria mellonella) became popular due to the ethical issues associated with vertebrate models. The aim of the present article is to provide an overview of the current trends and methods used to investigate the toxic potential of herbal medicinal products and the challenges in this research field.

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.

Antihypertensive effect of Equisetum arvense L.: a double-blind, randomized efficacy and safety clinical trial

BACKGROUND

Equisetum arvense L. (EA) is a traditional phytomedicine used as a diuretic agent worldwide and regulated strictly by European Medicine Agency (EMA) and Brazilian National Health Surveillance Agency (ANVISA). However, few studies evaluating its efficacy and safety have been published and no clinical trial assessing its antihypertensive effect has been reported to date.

PURPOSE

To assess antihypertensive effect, safety and tolerability of EA compared to hydrochlorothiazide (HCTZ).

METHODS

This is a double-blind randomized clinical trial, allocating 58 systemic arterial hypertension (SAH) stage I patients (both sexes, 25-65 years old) into two groups (EA and HCTZ). All patients underwent biochemical and cardiologic checkup prior to and during interventions. The EA standardized dry extract (900 mg/day) or HCTZ (25 mg/day) were administered for 3 months and follow-up visits were conducted every 30 days. Efficacy established goals were systolic blood pressure (SBP) and/or diastolic blood pressure (DBP) decreases ≥ 10.0 mmHg and/or casual blood pressure (CBP) < 140/90 mmHg.

RESULTS

EA treatment demonstrated a significant antihypertensive effect, promoting a mean decrease of SBP and DBP by 12.6 and 8.1 mmHg, respectively, and resulting a CBP mean of 134.0/84.5 mmHg at the end of intervention on the SAH stage I patients (CBP mean of 148.5/95.7 mmHg). There were no significant statistical differences between EA and HCTZ interventions on blood pressure decrease, and before-after treatments regarding to biochemical tests and signs of acute toxicity, renal, hepatic and hematologic alterations. A slight trend but no significant difference were observed between adverse events from EA (3.58%) and HCTZ (4.68%) groups.

CONCLUSION

EA standardized dry extract was successfully applied to the SAH stage I patient treatment, decreasing effectively SBP ad DBP values to the reference normal ranges, and demonstrating a well-tolerability profile similar to HCTZ intervention.

Strategies for sample labelling and library preparation in DNA metabarcoding studies

Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample-specific nucleotide identifiers are added to the amplicons prior to sequencing. The latter enables assignment of the sequences back to the samples they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and during "library preparation", that is, when amplicons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, ensuring that data generation is robust and fit for the chosen purpose is critically important for practitioners seeking to employ metabarcoding for biodiversity assessments. Here, we present an overview of the three main workflows for sample-specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms; one-step PCR, two-step PCR, and tagged PCR. Further, we distill the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess biodiversity across a range of applications.

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.

Heavy Metals and Probabilistic Risk Assessment via Pheretima (a Traditional Chinese Medicine) Consumption in China

Earthworms are known to accumulate inorganic contaminants from the soil; they are also used as a traditional Chinese medicine (TCM) called Pheretima, which might cause safety problems with long-term exposure. Here, this study was conducted to determine and analyze the level of heavy metal contamination such as arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), manganese (Mn), nickel (Ni), and lead (Pb) in Pheretima and then explore the probabilistic health risks caused by 8 heavy metals in 98 batches of Pheretima using Monte Carlo simulation. A risk assessment strategy was conducted to assess heavy metal-associated health risk of Pheretima based on consumption data. For random consumption sampling, the results found that the non-carcinogenic risk of As is higher than the acceptable level, and the carcinogenic risk levels of As and Cr exceeded the acceptable risk recommended by the USEPA. Cr and As were regarded as the priority metals for risk control in the present study. Finally, it was recommended that the dosing frequency should be less than 24 d/y. In general, this study conducted a probabilistic risk assessment of heavy metals in Pheretima, which would be of significance for policy makers to take effective strategies to improve the quality and safety of Pheretima.

Molecular quantification, a new strategy for quality control of Chinese patent medicine containing animal-derived crude drug: Qi She in Jinlong capsule as an example

Quality control for Chinese patent medicine (CPM) containing animal-derived crude drug(s) is rather difficult. The methods based on chemical composition analysis, which are commonly used in CPM consisted of plant-derived crude drugs, are often not applicable for CPM containing animal-derived crude drug, because the effective constituents of most animal-derived crude drugs remain unknown. Even if there are such methods, they are usually qualitative rather than quantitative, and the specificity is generally poor. Here we proposed a molecular quantification method for CPM containing animal-derived crude drug, based upon the hypothesis that the amount of remnant DNA fragments could reflect feeding quantity of the crude drugs and thus ensure the quality of the CPM. Take Jinlong capsule [a hepatocellular carcinoma-resisting Chinese patent medicine comprising of three fresh animal drugs, i.e. Shougong (Peking gecko, Gekko swinhonis), Qi She (sharp-snouted pitviper, Deinagkistrodon acutus), and Jinqian Baihua She (many-banded krait, Bungarus multicinctus)] as an example, we established a qPCR assay for Qi She in the capsule, which verified the feasibility of the quality control method based on molecular quantification. Species-specific primers and TaqMan probe for Qi She were designed, and the qPCR assay system was then established. The assay exhibited a good specificity; there's a good linearity between Ct values and logarithm of the target amplicon copy numbers within the range of 8.8 × 10¹ to 8.8 × 10⁶ copies/μL, and the limit of detection was 88 copies/μL. The method was validated through reproducibility, stability assessment. Recovery of spiked samples was between 91.59% and 101.69%. It was verified that the copy numbers reflected the original feeding amount of an animal-derived crude drug by self-made Jinlong capsules. The assay was successfully applied in Qi She-specific amplicon determination in 20 batches of Jinlong capsule. The study was expected to provide a new strategy for quality control of CPM containing animal-derived crude drug.

Quantification of adulteration in traded ayurvedic raw drugs employing machine learning approaches with DNA barcode database

Adulteration of expensive raw drugs with inferior taxa has become a routine practice, conceding the quality and safety of derived herbal products. In this regard, the study addresses the development of an integrated approach encompassing DNA barcode and HPTLC fingerprinting to authenticate chiefly traded ayurvedic raw drugs in south India [viz. Saraca asoca (Roxb.) Willd., Terminalia arjuna (Roxb. ex DC.) Wight and Arn., Sida alnifolia L. and Desmodium gangeticum (L.) DC.] from its adulterants. Consortium of Barcode of Life (CBOL) recommended DNA barcode gene regions viz. nuclear ribosomal-Internal Transcribed Spacer (nrDNA-ITS), maturase K (matK), ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) and psbA-trnH spacer regions along with HPTLC profiling were experimented and a reference database was created. Further, an integrated analytical approach employing genetic distance-based Maximum Likelihood phylogenetic tree and Artificial Intelligence (AI)based Machine Learning Algorithms (MLA)-Waikato Environment for Knowledge Analysis (WEKA) and Barcoding with Logic (BLOG) were employed to prove efficacy of DNA barcode tool. Even though, among the four barcodes, psbA-trnH (S. alnifolia and its adulterants, T. arjuna and its adulterants) or ITS region (S. asoca and its adulterants, D. gangeticum and its adulterants) showed highest inter specific divergences in the selected Biological Reference Materials (BRMs), rbcL or matK barcode regions alone were successful for authentication of traded samples. The automated species identification techniques, WEKA and BLOG, experimented for the first time in India for raw drug validation, could achieve rapid and precise identification. A national certification agency for raw drug authentication employing an integrated approach involving a DNA barcoding tool along with standard organoleptic and analytical methods can strengthen and ensure safety and quality of herbal medicines in India.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03001-5.

Next-Generation Food Research: Use of Meta-Omic Approaches for Characterizing Microbial Communities Along the Food Chain

Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread of antimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Development and validation of simultaneous identification of 26 mammalian and poultry species by a multiplex assay

A multiplex PCR assay was developed to simultaneously identify 22 mammalian species (alpaca, Asiatic black bear, Bactrian camel, brown rat, cat, cattle, common raccoon, dog, European rabbit, goat, horse, house mouse, human, Japanese badger, Japanese wild boar, masked palm civet, pig, raccoon dog, red fox, sheep, Siberian weasel, and sika deer) and four poultry species (chicken, domestic turkey, Japanese quail, and mallard), even from a biological sample containing a DNA mixture of multiple species. The assay was designed to identify species through multiplex PCR and capillary electrophoresis, with a combination of amplification of a partial region of the mitochondrial D-loop by universal primer sets and a partial region of the cytochrome b (cyt b) gene by species-specific primer sets. The assay was highly sensitive, with a detection limit of 100 copies of mitochondrial DNA. The assay's ability to identify species from complex DNA mixtures was demonstrated using an experimental sample consisting of 10 species. Efficacy, accuracy, and reliability of the assay were validated for use in forensic analysis with the guidelines of Scientific Working Group on DNA Analysis Methods (SWGDAM). The multiplex PCR assay developed in this study enables cost-effective, highly sensitive, and simultaneous species identification without massively parallel sequencing (MPS) platforms. Thus, the technique described is straightforward and suitable for routine forensic investigations.

Authentication of garlic (Allium sativum L.) supplements using a trnLUAA mini-barcode

Garlic (Allium sativum), a widely distributed plant with great cultural and medicinal significance, is one of the most popular herbal dietary supplements in Europe and North America. Garlic supplements are consumed for a variety of reasons, including for their purported antihypertensive, antibacterial, and anticarcinogenic effects. The steady increase in the global herbal dietary supplement market paired with a global patchwork of regulatory frameworks makes the development of assays for authentication of these products increasingly important. A DNA mini-barcode assay was developed using the P6 loop of the plastid trnL^UAA intron to positively identify A. sativum products. Analysis of 43 commercially available garlic herbal dietary supplements produced mini-barcode sequences for 33 supplements, all of which contained detectable amounts of A. sativum. The trnL^UAA P6 mini-barcode can be highly useful for specimen identification, particularly for samples that may contain degraded DNA.

Quality Control of Herbal Medicines: From Traditional Techniques to State-of-the-art Approaches

Herbal medicines are important options for the treatment of several illnesses. Although their therapeutic applicability has been demonstrated throughout history, several concerns about their safety and efficacy are raised regularly. Quality control of articles of botanical origin, including plant materials, plant extracts, and herbal medicines, remains a challenge. Traditionally, qualitative (e.g., identification and chromatographic profile) and quantitative (e.g., content analyses) markers are applied for this purpose. The compound-oriented approach may stand alone in some cases (e.g., atropine in Atropa belladonna). However, for most plant materials, plant extracts, and herbal medicines, it is not possible to assure quality based only on the content or presence/absence of one (sometimes randomly selected) compound. In this sense, pattern-oriented approaches have been extensively studied, introducing the use of multivariate data analysis on chromatographic/spectroscopic fingerprints. The use of genetic methods for plant material/plant extract authentication has also been proposed. In this study, traditional approaches are reviewed, although the focus is on the applicability of fingerprints for quality control, highlighting the most used approaches, as well as demonstrating their usefulness. The literature review shows that a pattern-oriented approach may be successfully applied to the quality assessment of articles of botanical origin, while also providing directions for a compound-oriented approach and a rational marker selection. These observations indicate that it may be worth considering to include fingerprints and their data analysis in the regulatory framework for herbal medicines concerning quality control since this is the foundation of the holistic view that these complex products demand.

Microbiomes in forensic botany: a review

Fragments of botanical material can often be found at crime scenes (on live and dead bodies, or on incriminating objects) and can provide circumstantial evidence on various aspects of forensic investigations such as determining crime scene locations, times of death or possession of illegal species. Morphological and genetic analysis are the most commonly applied methods to analyze plant fragment evidence but are limited by their low capacity to differentiate between potential source locations, especially at local scales. Here, we review the current applications and limitations of current plant fragment analysis for forensic investigations and introduce the potential of microbiome analysis to complement the existing forensic plant fragment analysis toolkit. The potential for plant fragment provenance identification at geographic scales meaningful to forensic investigations warrants further investigation of the phyllosphere microbiome in this context. To that end we identify three key areas of future research: 1) Retrieval of microbial DNA of sufficient quality and quantity from botanical material; 2) Variability of the phyllosphere microbiome at different taxonomic and spatial scales, with explicit reference to assignment capacity; 3) Impacts on assignment capacity of time, seasonality and movement of fragments between locations. The development of robust microbiome analysis tools for forensic purposes in botanical material could increase the evidentiary value of the botanical evidence commonly encountered in casework, aiding in the identification of crime scene locations.

Animal Forensic Genetics

Animal forensic genetics, where the focus is on non-human species, is broadly divided in two: domestic species and wildlife. When traces of a domestic species are relevant to a forensic investigation the question of species identification is less important, as the material comes from either a dog or a cat for instance, but more relevant may be the identification of the actual pet. Identification of a specific animal draws on similar methods to those used in human identification by using microsatellite markers. The use of cat short tandem repeats to link a cat hair to a particular cat paved the way for similar identification of dogs. Wildlife forensic science is becoming accepted as a recognised discipline. There is growing acceptance that the illegal trade in wildlife is having devasting effects on the numbers of iconic species. Loci on the mitochondrial genome are used to identify the most likely species present. Sequencing the whole locus may not be needed if specific bases can be targeted. There can be benefits of increased sensitivity using mitochondrial loci for species testing, but occasionally there is an issue if hybrids are present. The use of massively parallel DNA sequencing has a role in the identification of the ingredients of traditional medicines where studies found protected species to be present, and a potential role in future species assignments. Non-human animal forensic testing can play a key role in investigations provided that it is performed to the same standards as all other DNA profiling processes.

Estimating included animal species in mixed crude drugs derived from animals using massively parallel sequencing

We developed a method that can detect each animal species of origin for crude drugs derived from multiple animal species based on massively parallel sequencing analysis of mitochondrial genes. The crude drugs derived from animals investigated in this study were Cervi Parvum Cornu and Trogopterorum feces, which are derived from a mix of different animal species, two chopped cicada sloughs, and two commercial Kampo drugs. The mitochondrial 12S rRNA, 16S rRNA, and cytochrome oxidase subunit I gene regions were amplified and sequenced using MiSeq. The ratios of haplotype to total number of sequences reads were calculated after sequence extraction and trimming. Haplotypes that exceeded the threshold were defined as positive haplotypes, which were compared with all available sequences using BLAST. In the Cervi Parvum Cornu and Trogopterorum feces samples, the haplotype ratios corresponded roughly to the mixture ratios, although there was a slight difference from mixture ratios depending on the gene examined. This method could also roughly estimate the compositions of chopped cicada sloughs and Kampo drugs. This analysis, whereby the sequences of several genes are elucidated, is better for identifying the included animal species. This method should be useful for quality control of crude drugs and Kampo drugs.

Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification

Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification.

A combination index and glycoproteomics-based approach revealed synergistic anticancer effects of curcuminoids of turmeric against prostate cancer PC3 cells

ETHNOPHARMACOLOGICAL RELEVANCE

Herbal medicines (HMs) often exert integration effects, including synergistic, additive and antagonistic effects, in such ways that they act on multiple targets and multiple pathways on account of their multiple components. Turmeric, made from the rhizome of Curcuma longa L., is a well-known HM prescribed in the polyherbal formulas for cancer treatment in traditional Chinese medicines (TCMs). However, neither the multiple anticancer compounds of turmeric nor the integration effects of these components are fully known.

AIM OF THE STUDY

This work aims to develop a systematic approach to reveal the integration effect mechanisms of multiple anticancer compounds in turmeric against prostate cancer PC3 cells.

MATERIALS AND METHODS

Combination index and omics technologies were applied to profile the integration effect mechanisms of bioactive compounds in proportions naturally found in turmeric. PC3 cell line (a prostate cancer cell line) fishing and high resolution mass spectrometry were employed to screen and identify the anticancer compounds from turmeric. The combinations which contain different cell-bound compounds in natural proportions were prepared for further evaluation of anti-cancer activity by using cell viability assays, and assessment of cell apoptosis and cell cycle analysis. Combination index analysis was applied to study the integration effects of the anticancer compounds in their natural proportions. Finally, quantitative glycoproteomics/proteomics and Western blot were implemented to reveal the potential synergistic effect mechanisms of the anticancer compounds based on their natural proportions in turmeric.

RESULTS

Three curcuminoids (curcumin, CUR; demethoxycurcumin, DMC; bisdemethoxycurcumin, BDMC) in turmeric were discovered and shown to possess significant synergistic anticancer activities. Combination index analysis revealed an additive effect of CUR combined with DMC or BDMC and a slight synergistic effect of DMC combined with BDMC in natural proportions in turmeric, while a combination of all three curcuminoids (CUR, DMC and BDMC) at a ratio of 1:1:1 yielded superior synergistic effects. Interestingly, the presence of BDMC and DMC are essential for synergistic effect. Glycoproteomics and proteomics demonstrated that different curcuminoids regulate various protein pathways, such as ribosome, glycolysis/gluconeogenesis, biosynthesis of amino acids, and combination of CUR + DMC + BDMC showed the most powerful effects on down-regulation of protein expression.

CONCLUSIONS

Our analytical approach provides a systematic understanding of the holistic activity and integration effects of the anti-cancer compounds in turmeric and three curcuminoids of turmeric showed a synergistic effect on PC3 cells.

Wildlife crime in Australia

Wildlife crime is on a massive scale by whatever metric is used. The illegal trade in wildlife and related products is leading to the decline and extinction of many iconic species from rhino to tigers. Almost all countries are signatures to CITES and therefore should enforce national legislation if alleged infringements of trade of wildlife occur. No country is immune from this illegal trade although countries like Australia have their own specific wildlife crimes. Australia is home to many reptilian, amphibian and avian species that are highly prized, predominantly as pets. Collection of protected species from the wild is illegal in all jurisdictions yet policing remote areas of the outback, where so much of the native endemic fauna and flora lives, is nearly impossible. The illegal international trade in these species is highlighted by two case studies provided in this review. A further case highlights the issues of each of the six states of Australia having separate legislation, which is compounded when wildlife crime can be inter-state crime. Australia is one of the few countries having an institute, based at the Australian Museum, with an accredited wildlife forensic science laboratory and therefore the capability to undertake forensic testing of seized samples. One way to reduce wildlife crime may be by educating those who buy illegally seized products that there is a direct connection between the dead animal from which it came and the devasting effect this purchase has on the environment.

Efficient COI barcoding using high throughput single-end 400 bp sequencing

BACKGROUND

Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current high-throughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (e.g. a maximum read length of 300 bp for the Illumina's MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio's SEQUEL II system).

RESULTS

Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5' and 3' ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%.

CONCLUSIONS

The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications.

Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia magna

This is the first study in which the Daphnia magna (D. magna) nuclear genome (nDNA) obtained from the GenBank database was analyzed for pseudogene sequences of mitochondrial origin. To date, there is no information about pseudogenes localized in D. magna genome. This study aimed to identify NUMTs, their length, homology, and location for potential use in evolutionary studies and to check whether their occurrence causes co-amplification during mitochondrial genome (mtDNA) analyses. Bioinformatic analysis showed 1909 fragments of the mtDNA of D. magna, of which 1630 were located in ten linkage groups (LG) of the nDNA. The best-matched NUMTs covering >90% of the gene sequence have been identified for two mt-tRNA genes, and they may be functional nuclear RNA molecules. Isolating the total DNA in mtDNA studies, co-amplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes. It was observed that TRNA-MET fragments had the highest level of sequence homology, thus they could be evolutionarily the youngest. The lowest homology was found in the D-loop-derived pseudogene. It may probably be the oldest NUMT incorporated into the nDNA; however, further analysis is necessary.

Pitfalls and promises of raw drug identification techniques in the ayurvedic industry: an overview

India, with a rich heritage of floral diversity, is well-known for its medicinal plant wealth and is the largest producer of medicinal herbs in the world. Ethnobiological Survey of Ministry of Environment and Forests (MOEF) could identify 8000 plant species utilized in various systems of medicine with approximately 25,000 effective herbal formulations. The extensive consumption to meet demand-supply ratio exerts a heavy strain on the existing resources. This subsequently led to the adulteration and substitution of medicinal plants with look-alike species. The consumer's faith on herbal medicine is in the phase of decline due to the extremities in adulteration/substitution and ensuing consequences. It is imperative to bring forth universally acceptable standard tools to authenticate raw drugs before being processed further into formulations. A vast array of techniques such as physical, chemical (analytical), biochemical, anatomical, organoleptic, and recently emerged DNA based molecular methods are widely used for plant species authentication. In recent years, DNA barcoding has made remarkable progress in the field of medicinal plants research. DNA metabarcoding is the latest development for qualitative evaluation of the herbal formulations, whereas for quantitative analysis, combination of pharmacognostic, pharmacovigilance and analytical methods are inevitable for authentication. This review addresses the overall strengths and shortcomings of the existing as well as recently emerged techniques in authenticating ayurvedic raw drugs.

Is there a role for botanical medicines in the twenty-first century?: Promotion of untested traditional therapies by the World Health Organization and China endangers global public health

China and the WHO's promotion of herbal and traditional medicines, most of which were not tested for safety and efficacy, have raised public health concerns.

Combined Liquid Chromatography-mass Spectrometry and Next-generation DNA Sequencing Detection of Adulterants and Contaminants in Analgesic and Anti-inflammatory Herbal Medicines

INTRODUCTION

Methods for assessing the quality of herbal medicine preparations have advanced significantly in recent years in conjunction with increases in herbal medicine use and reports of adulteration and contamination.

OBJECTIVE

This study examined the quality of analgesic and anti-inflammatory herbal medicine preparations available on the Australian market by detecting the presence of listed ingredients, adulterants and contaminants.

METHODS

Forty-nine analgesic and anti-inflammatory herbal medicine preparations were randomly sourced from Australian capital cities. They were audited using a dual approach of liquid chromatography-mass spectrometry (LC-MS) combined with next-generation DNA sequencing. Once screened, a comparison of listed ingredients with verified ingredients was conducted to determine the accuracy of labelling, and the extent of adulteration and contamination.

RESULTS

Twenty-six of 49 (53%) herbal medicines were adulterated or contaminated with undeclared ingredients. LC-MS revealed the presence of pharmaceutical adulterants including atropine and ephedrine. DNA sequencing uncovered concerning levels of herbal substitution, adulteration and contamination, including the use of fillers (alfalfa, wheat and soy), as well as pharmacologically relevant species (Centella asiatica, Panax ginseng, Bupleurum and Passiflora). Pig/boar and bird DNA was found in some preparations, inferring substandard manufacturing practices. Of the 26 contaminated samples, 19 (73%) were manufactured in Australia, and 7 (27%) were imported from other countries (6 from China, 1 from New Zealand). In 23 of 49 (47%) herbal medicine samples, no biological ingredients were detected at all. These were predominantly pain and anti-inflammatory preparations such as glucosamine and eicosapentaenoic and docosahexaenoic acids found in krill and fish oils, so DNA would not be expected to survive the manufacturing process.

CONCLUSION

The high level of contamination and substitution of herbal medicine preparations sourced from Australian dispensaries supports the need for more stringent pharmacovigilance measures in Australia and abroad.

Massively parallel sequencing is unlocking the potential of environmental trace evidence

Massively parallel sequencing (MPS) has revolutionised the field of genomics enabling substantial advances in human DNA profiling. Further, the advent of MPS now allows biological signatures to be obtained from complex DNA mixtures and trace amounts of low biomass samples. Environmental samples serve as ideal forms of contact trace evidence as detection at a scene can establish a link between a suspect, location and victim. Many studies have applied MPS technology to characterise the biodiversity within high biomass environmental samples (such as soil and water) to address questions related to ecology, conservation, climate change and human health. However, translation of these tools to forensic science remains in its infancy, due in part to the merging of traditional forensic ecology practices with unfamiliar DNA technologies and complex datasets. In addition, people and objects also carry low biomass environmental signals which have recently been shown to reflect a specific individual or location. The sensitivity, and reducing cost, of MPS is now unlocking the power of both high and low biomass environmental DNA (eDNA) samples as useful sources of genetic information in forensic science. This paper discusses the potential of eDNA to forensic science by reviewing the most explored applications that are leading the integration of this technology into the field. We introduce novel areas of forensic ecology that could also benefit from these tools with a focus on linking a suspect to a scene or establishing provenance of an unknown sample and discuss the current limitations and validation recommendations to achieve translation of eDNA into casework.

Integrative transcriptomics and metabolomics analyses provide hepatotoxicity mechanisms of asarum

Asarum is frequently applied in combination with other agents for prescriptions in practices of Traditional Chinese Medicine. A number of studies have previously indicated that asarum treatment induces lung toxicity by triggering inflammation. However, the potential effects of asarum in the liver and the underlying mechanisms have remained largely elusive. Therefore, transcriptomics and metabolomics approaches were used in the present study to examine the mechanisms of the hepatotoxicity of asarum. Specifically, mRNA and metabolites were obtained from rat liver samples following intragastric administration of asarum powder. RNA sequencing analysis was subsequently performed to screen for differentially expressed genes (DEGs), and a total of 434 DEGs were identified in liver tissue samples, 214 of which were upregulated and 220 were downregulated. Pathway enrichment analysis found that these genes were particularly enriched in processes including the regulation of p53 signaling, metabolic pathways and bile secretion. To investigate potential changes to the metabolic profile as a result of asarum treatment, a metabolomics analysis was performed, which detected 14 significantly altered metabolites in rat liver samples by gas chromatography-mass spectrometry. These metabolites were predominantly members of the taurine, hypotaurine and amino acid metabolic pathways. Metscape network analyses were subsequently performed to integrate the transcriptomics and metabolomics data. Integrative analyis revealed that the DEGs and metabolites were primarily associated with bile acid biosynthesis, amino acid metabolism and the p53 signaling pathway. Taken together, these results provide novel insight into the mechanism of asarum-mediated hepatotoxicity, which may potentially aid the clinical diagnosis and future therapeutic intervention of asarum poisoning.

Current issues for mammalian species identification in forensic science: a review

Mammalian species identification is one of the important issues in forensic science. Determining the origins of non-human biological material found at crime scenes can increase the possibility of identifying the true culprit by narrowing down the range of suspects. Although many techniques based on mitochondrial DNA (mtDNA) have been developed, challenges remain to cost-effectively identify species from degraded samples containing a mixture of DNA from multiple species and to standardize procedures for mammalian species identification. This review evaluates the reliability and versatility of mtDNA-based techniques to reveal obstacles to the establishment of standard analytical methods, with a particular focus on DNA mixtures. When samples contain a mixture of DNA from multiple species, the interpretation of sequencing analysis results is difficult. Although DNA metabarcoding using next-generation sequencing (NGS) technologies can overcome the DNA mixture problem, DNA metabarcoding is not suitable for the type of small-scale analysis routinely performed by local forensic laboratories, primarily because it is costly and time-consuming. By contrast, fluorescent multiplex PCR analysis enables cost-effective and simultaneous species identification from suboptimal samples, although the number of identifiable species is currently limited in comparison with sequencing techniques. The advantages and limitations of current techniques presented in this review indicate that multiplex PCR analysis will continue to be important for mammalian species identification in forensic casework analysis. Further developments in multiplex PCR analysis that enable the identification of an increased number of species will play a key step for standardization efforts among forensic laboratories.

Simultaneous identification of animal-derived components in meats using high-throughput sequencing in combination with a custom-built mitochondrial genome database

Currently, the inspection and supervision of animal ingredients relies primarily upon specific amplification-dependent methods, whose efficiency and accuracy are being seriously challenged by the increasing diversity and complexity of meat products. High-throughput sequencing (HTS) technology was employed to develop an alternative method to detect animal-derived ingredients in meat products. A custom-built database containing 2,354 complete mitochondrial genomic sequences from animals, an identification analysis pipeline based on short-sequence alignment, and a web-based server were built to facilitate this detection. The entire process, including DNA extraction, gene amplification, and sequencing, was established and optimized for both marker gene (part of the CYTB gene)-based detection and total DNA-based detection. Using simulated samples containing various levels of pig, cattle, sheep, chicken, rabbit, and mice ingredients, the detection capability and accuracy of this method were investigated. The results of this study indicated that the method is capable of detecting animal components in meats that are present at levels as low as 1%. Our method was then tested using 28 batches of real meat products such as raw meat slices, raw meat mince, cooked dried meat, cooked meat sausage, and other supermarket samples, with a traditional qPCR method as the control. The results demonstrated an accuracy of 97.65% for the qualitative detection method, which indicate that the developed method is reliable for the detection of animal components. The method is also effective for the identification of unknown food samples containing mixed animal components, which suggests a good future in application.

Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin

Fast and reliable analytical methods for the identification of plants from metagenomic samples play an important role in identifying the components of complex mixtures of processed biological materials, including food, herbal products, gut contents or environmental samples. Different PCR-based methods that are commonly used for plant identification from metagenomic samples are often inapplicable due to DNA degradation, a low level of successful amplification or a lack of detection power. We introduce a method that combines metagenomic sequencing and an alignment-free k-mer based approach for the identification of plant DNA in processed metagenomic samples. Our method identifies plant DNA directly from metagenomic sequencing reads and does not require mapping or assembly of the reads. We identified more than 31,000 Lupinus-specific 32-mers from assembled chloroplast genome sequences. We demonstrate that lupin DNA can be detected from controlled mixtures of sequences from target species (different Lupinus species) and closely related non-target species (Arachis hypogaea, Glycine max, Pisum sativum, Vicia faba, Phaseolus vulgaris, Lens culinaris, and Cicer arietinum). Moreover, these 32-mers are detectable in the following processed samples: lupin flour, conserved seeds and baked cookies containing different amounts of lupin flour. Under controlled conditions, lupin-specific components are detectable in baked cookies containing a minimum of 0.05% of lupin flour in wheat flour.

Generational Differences in Perceptions of Food Health/Risk and Attitudes toward Organic Food and Game Meat: The Case of the COVID-19 Crisis in China

In December 2019, a novel laboratory-confirmed coronavirus (2019-nCoV) infection, which has caused clusters of severe illnesses, was first reported in Wuhan, the capital of Hubei province, China. This foodborne illness, which reportedly most likely originated in a seafood market where wild animals are sold illegally, has transmitted among humans through close contact, across the world. The aim of this study is to explore health/risk perceptions of and attitudes toward healthy/risky food in the immediate context of food crisis. More specifically, by using the data collected from 1008 respondents in January 2020, the time when China was hit hard by the "Corona Virus Disease 2019" (COVID-19), this study investigates the overall and different generational respondents' health/risk perceptions of and attitudes toward organic food and game meat. The results reveal that, firstly, based on their food health and risk perceptions of healthy and risky food, the respondents' general attitudes are positive toward organic food but relatively negative toward game meat. Secondly, older generations have a more positive attitude and are more committed to organic food. Younger generations' attitude toward game meat is more negative whereas older generations attach more importance to it because of its nutritional and medicinal values. In addition, this research also indicates that the COVID-19 crisis influences the respondents' perceptions of and attitudes toward organic food and game meat consumption. However, the likelihood of its impact on older generations' future change in diets is smaller, which implies that older generations' food beliefs are more stable.

DNA barcoding augments conventional methods for identification of medicinal plant species traded at Tanzanian markets

ETHNOPHARMALOGICAL RELEVANCE

In Africa, traditional medicine is important for local healthcare and plants used for these purposes are commonly traded. Identifying medicinal plants sold on markets is challenging, as leaves, barks and roots are often fragmented or powdered. Vernacular names are often homonymic, and identification of material lacking sufficient morphological characters is time-consuming, season-dependent and might lead to incorrect assessments of commercialised species diversity.

AIM OF THE STUDY

In this study, we identified cases of vernacular heterogeneity of medicinal plants using a tiered approach of literature research, morphology and DNA barcoding.

MATERIAL AND METHODS

A total of 870 single ingredient medicinal plant samples corresponding to 452 local names were purchased from herbal markets in Dar-es-Salaam and Tanga, Tanzania, and identified using conventional methods as well as DNA barcoding using rbcL, matK and nrITS.

RESULTS

Using conventional methods, we could identify 70% of samples to at least family level, while 62% yielded a DNA barcode for at least one of the three markers. Combining conventional methods and DNA barcoding, 76% of the samples could be identified to species level, revealing a diversity of at least 175 species in 65 plant families. Analysis of the market samples revealed 80 cases of multilingualism and over- and under-differentiation. Afzelia quanzensis Welw., Zanthoxylum spp., Allophylus spp. and Albizia anthelmintica Brongn. were the most evident cases of multilingualism and over-differentiation, as they were traded under 8-12 vernacular names in up to five local languages. The most obvious case of under-differentiation was mwingajini (Swahili), which matched to eight scientific species in five different plant families.

CONCLUSIONS

Use of a tiered approach increases the identification success of medicinal plants sold in local market and corroborates findings that DNA barcoding can elucidate the identity of material that is unidentifiable based on morphology and literature as well as verify or disqualify these identifications. Results of this study can be used as a basis for quantitative market surveys of fragmented herbal medicine and to investigate conservation issues associated with this trade.