Assessing the Identity of Commercial Herbs From a Cambodian Market Using DNA Barcoding

Existing status and future advancements of adulteration detection techniques in herbal products

BACKGROUND

Herbal products have been commonly used all over the world for centuries. Its products have gained remarkable acceptance as therapeutic agents for a variety of disorders. However, following recent research disclosing discrepancies between labeling and actual components of herbal products, there is growing concern about the efficacy, quality and safety of the products. The admixture and adulteration of herbal medicinal products pose a risk of serious health compromise and the well-being of the consumers. To prevent adulteration in raw ingredients and final herbal products, it is necessary to use approaches to assess both genomes as well as metabolomics of the products; this offers quality assurance in terms of product identification and purity. The combinations of molecular and analytical methods are inevitable for thorough verification and quality control of herbal medicine.

METHODS AND RESULTS

This review discusses the combination of DNA barcoding, DNA metabarcoding, mass spectroscopy as well as HPLC for the authentication of herbal medicine and determination of the level of adulteration. It also discusses the roles of PCR and real-time PCR techniques in validating and ensuring the quality, purity and identity of the herbal products.

CONCLUSIONS

In conclusion, each technique has its own pros and cons, but the cumulative of both the chemical and molecular methods is proven to be the best strategy for adulteration detection. Moreover, CRISPR diagnosis tools equipped with multiplexing techniques may be implemented for screening adulteration from herbal drugs, this will play a crucial role in herbal product authentication in the future.

DNA Barcoding and Metabarcoding Protocols for Species Identification

The article presents the several steps to be performed on a plant, fungal, insect, or soil sample to obtain DNA sequences for DNA barcode analysis. The chapter begins with a description of sample preparation including procedures for cleaning and proceeds to DNA extraction with methods adapted for the specific type of sample. Next, DNA quantification is described so the proper amount is used for the amplification of the selected barcode regions. Information is provided for reaction mixes and amplification conditions for several referenced barcode primer pairs tuned for the individual sample of interest. This is followed by a description of procedures to access the success of amplification, cleanup, and quantification of the product ready for either Sanger sequencing or library preparation for massive parallel sequencing (MPS). Finally, procedures are provided for Sanger sequencing, library preparation, and MPS sequencing. The chapter provides several references of barcode regions for different sample types.

A nucleotide signature for the identification of Pinelliae Rhizoma (Banxia) and its products

Background

Ensuring the authenticity of raw materials is a key step prior to producing Chinese patent medicines. Pinelliaternata (Thunb.) Breit. is the botanical origin of Pinelliae Rhizoma (Banxia), a traditional Chinese medicine used to treat cough, insomnia, nausea, inflammation, epilepsy, and so on. Unfortunately, authentic Pinelliae Rhizoma is often adulterated by morphologically indistinguishable plant material due to the insufficient regulatory procedures of processed medicinal plant products. Thus, it is important to develop a molecular assay based on species-specific nucleotide signatures and primers to efficiently distinguish authentic Pinelliae Rhizoma from its adulterants.

Methods and results

The ITS2 region of 67 Pinelliae Rhizoma and its common adulterants were sequenced. Eight single nucleotide polymorphisms within a 28–43 bp stretch of ITS2 were used to develop six primer pairs to amplify these species-specific regions. We assayed 56 Pinelliae Rhizoma products sold on the Chinese market, including medicinal slices, powder and Chinese patent medicines, which revealed that about 66% of products were adulterated. The most common adulterants were Pinelliapedatisecta (found in 57% of the assayed products), Arisaemaerubescens (9%), Typhoniumgiganteum (2%) and Typhoniumflagelliforme (2%).

Conclusions

A severe adulteration condition was revealed in the traditional medicine market. The species-specific nucleotide assays developed in this study can be applied to reliably identify Pinelliae Rhizoma and its adulterants, aiding in the authentication and quality control of processed products on the herbal market.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11033-022-07600-0.

Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks

Integrative taxonomy is central to modern taxonomy and systematic biology, including behaviour, niche preference, distribution, morphological analysis and DNA barcoding. However, decades of use demonstrate that these methods can face challenges when used in isolation, for instance, potential misidentifications due to phenotypic plasticity for morphological methods, and incorrect identifications because of introgression, incomplete lineage sorting and horizontal gene transfer for DNA barcoding. Although researchers have advocated the use of integrative taxonomy, few detailed algorithms have been proposed. Here, we develop a convolutional neural network method (morphology-molecule network (MMNet)) that integrates morphological and molecular data for species identification. The newly proposed method (MMNet) worked better than four currently-available alternative methods when tested with 10 independent datasets representing varying genetic diversity from different taxa. High accuracies were achieved for all groups, including beetles (98.1% of 123 species), butterflies (98.8% of 24 species), fishes (96.3% of 214 species) and moths (96.4% of 150 total species). Further, MMNet demonstrated a high degree of accuracy (>98%) in four datasets including closely related species from the same genus. The average accuracy of two modest sub-genomic (single nucleotide polymorphism) datasets, comprising eight putative subspecies respectively, is 90%. Additional tests show that the success rate of species identification under this method most strongly depends on the amount of training data, and is robust to sequence length and image size. Analyses on the contribution of different data types (image versus gene) indicate that both morphological and genetic data are important to the model, and that genetic data contribute slightly more. The approaches developed here serve as a foundation for the future integration of multi-modal information for integrative taxonomy, such as image, audio, video, 3D scanning and biosensor data, to characterize organisms more comprehensively as a basis for improved investigation, monitoring and conservation of biodiversity.

Wild food plants and fungi sold in the markets of Luang Prabang, Lao PDR

BACKGROUND

Open air markets hold an important position for ethnobiologists. In Southeast Asia, they are seriously understudied, in spite of their incredible biocultural diversity. In order to fill this gap we recorded plants and fungi sold in the open air markets of Luang Prabang, Lao PDR.

METHODS

The markets were visited 38 times in four seasons: the dry season, early monsoon, mid-monsoon, and end-of-monsoon, at least 8 times per season. All items were photographed and voucher specimens were collected. Fungi were identified using DNA barcoding techniques.

RESULTS

We recorded 110 species of wild edible plants and 54 species of fungi, including 49 wild-collected species. The sold plants included 86 species of green vegetables, 18 species of fruits and 3 species of flowers. Products from woody species constitute around half of all taxa sold. These include the young shoots of tree leaves, which are used for salads-an interesting feature of Lao cuisine. A large number of extremely rare Russula, with no reference sequences represented in databases or even species unknown to science is present on sale in the markets.

CONCLUSIONS

Luang Prabang markets are some of the richest in species of wild edible plants and fungi in Asia, and indeed in the whole world. It is worth pointing out the exceptionally long list of wild edible mushrooms which are sold in Luang Prabang (and probably elsewhere in Laos). We view the Morning Market of Luang Prabang as a cultural treasure that unites the traditions of eating a large number of living species with very diverse flora and fauna. Measures should be taken to strike a balance between local foraging traditions and nature conservation priorities.