DNA-Based Authentication and Metabolomics Analysis of Medicinal Plants Samples by DNA Barcoding and Ultra-High-Performance Liquid Chromatography/Triple Quadrupole Mass Spectrometry (UHPLC-MS)

Relevance of Indian Traditional Herbal Brews for Gut Microbiota Balance

The considerable changes in lifestyle patterns primarily affect the human gut microbiota and result in obesity, diabetes, dyslipidemia, renal complications, etc. though there are few traditional safeguards such as herbal brews to maintain the ecological stability under intestinal dysbiosis. The present article is designed to collect all the scientific facts in a place to decipher the role of the Indian traditional herbal brews used to balance gut health for centuries. Computerized databases, commercial search engines, research papers, articles, and books were used to search by using different keywords to select the most appropriate published articles from 2000 onward to September 2023. A total of 1907 articles were scrutinized, 46 articles were finally selected from the 254 screened, and targeted information was compiled. Interaction of herbal brews to the gut microflora and resulting metabolites act as prebiotics due to antimicrobial, anti-inflammatory, and antioxidant properties, and modulate the pH of the gut. The effect of brews on gut microbiota has a drastic impact on various gut-related diseases and has gained popularity as an alternative to antibiotics against bacteria, fungi, viruses, parasites, and boosting the immune system and strengthening the intestinal barrier. Berberine, kaempferol, piperine, and quercetin have been found in more than one brew discussed in the present article. Practically, these brews balance the gut microbiota, prevent chronic and degenerative diseases, and reduce organ inflammation, though, there is a knowledge gap on the molecular mechanism to explain their efficacy. Indian traditional herbal brews used to reboot and heal the gut microbiota since centuries-old practice with successful history without toxicity. The systematic consumption of these brews under specific dietary prescriptions has a hope of arrays for a healthy human gut microbiome in the present hasty lifestyle with overall health and well-being.

Graphical Abstract

Systematic review on fingerprinting development to determine adulteration of Chinese herbal medicines

BACKGROUND

It has been a current research hospots using fingerprinting technology for quality control of Chinese herbal medicines (CHMs), which provides a scientific basis for establishment of overall quality control in accordance with the characteristics of CHMs. The fingerprinting technology for CHMs is diverse, and the research field covers many disciplines, such as analytical chemistry, pharmacology, pharmaceutics, biochemistry, and molecular biology.

PURPOSE

To effectively understand the key areas and future directions of research regarding the fingerprint and adulteration of CHMs.

METHODS/RESULTS

this paper analyzed 879 articles in this field in the Web of Science Core Collection from 2000 to 2023 with CiteSpace and VOSviewer, and systematically assessed the research process, hotspots, topic distribution among disciplines, etc. The most prominent contributors of fingerprint and adulteration of CHMs research are mainly from China, India, the United States, England, and Brazil. The knowledge domains of fingerprint and adulteration of CHMs research focus mainly on the topics of molecular authentication, DNA barcoding, HPLC, near-infrared spectroscopy, manage data, chemometrics, and electrochemical fingerprinting. Most countries have recognized the pharmaceutical potential of natural products, and have paid more attention to the fingerprint and adulteration of CHMs in the past decade. Future the research tends to focus more on molecular identification and authentication, and electrochemical and chromatographic fingerprinting in controlling the adulteration of CHMs.

CONCLUSION

This research provides a valuable reference for scholars in related fields to analyze existing research results, understand the development trend, and explore new research directions.

Identification strategy of Fructus Gardeniae and its adulterant based on UHPLC/Q-orbitrap-MS and UHPLC-QTRAP-MS/MS combined with PLS regression model

Fructus Gardeniae (FG) is the desiccative and ripe fruits of Gardenia jasminoides Ellis in the Rubiaceae family, which is a commonly used in traditional Chinese medicine (TCM) for clearing away heat, detoxification, relieving restlessness, and eliminating blood stasis. At the same time, it has also been announced as the first batch of TCM with homology of medicine and food. Fructus Gardeniae Grandiflorae (FGG), the fruit of Gardenia jasminoides Ellis var. grandiflora Nakai (Rubiaceae), is a common counterfeit herbal medicine of FG, which still appears in the TCM market, and causes a certain degree of confusion. In order to effectively distinguish FG and its adulterant, the compounds in these two species were thoroughly characterized firstly by ultrahigh-performance liquid chromatography/quadrupole-orbitrap mass spectrometry (UHPLC/Q-Orbitrap MS). Furthermore, a pseudo-targeted metabonomics method with 60 targeted ion pairs was established based on UHPLC-triple quadrupole-linear ion trap mass spectrometry (UHPLC-QTRAP-MS) for discrimination. Multivariate statistical analysis showed that FG and FGG were clustered obviously, and 13 significantly differential markers were screened out by variable importance for projection (VIP) > 1 and p < 0.05 for the construction of the partial least squares (PLS) regression prediction model. The validation of the model proved that its prediction ability was quite satisfactory. Moreover, based on the absolute quantitative analysis of these 13 characteristics, the quality control standards of FG and FFG were established. In summary, an integral method of pseudo-targeted metabonomics combined with chemometrics analysis and a PLS regression model was proposed to provide an effective identification strategy for discrimination FG and FGG.

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.

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.

Deoxyribonucleic Acid Barcoding for the Identification of Botanicals

The Natural Herbal Products industry uses botanicals or herbs as raw materials for production of herbal products or dietary supplements. Recently, the demand for natural herbal products has increased tremendously and this has led to adulteration and to counterfeit herbal products. The present chapter deals with currently used molecular methods from "simple" single genomic regions to high-throughput whole genome or transcriptome sequencing methods used in the identification of botanicals.

ITS1 Barcode and Phytochemical Analysis by Gas Chromatography-Mass Spectrometry of Corynaea crassa Hook. f (Balanophoraceae) from Ecuador and Peru

The use of medicinal plants is the basis of traditional healthcare. Recently, the use of herbal medicine has been increasing among consumers due to availability, economy, and less side effect. For instance, the hemiparasite plant Corynaea crassa has medicinal properties and could be found in some regions of America, from Costa Rica to Bolivia. Phytochemical and genetic characterization of medicinal plants is needed for proper identification of metabolites responsible for medicinal properties and for genotyping, respectively. Moreover, characterization of medicinal plants through the use of DNA barcodes is an important tool for phylogenetic analysis and identification of species; furthermore, complemented with phytochemical analysis, both are useful for identification of plant species and quality control of medicinal products. The objective of this study was to analyze the species of C. crassa collected in Ecuador and Peru from the phylogenetic and phytochemical point of view. Polymerase chain reaction (PCR) was performed for amplification of the internal transcribed spacer 1 (ITS1) region after DNA extraction of samples of C. crassa. Blast analysis was performed in the GenBank database with the ITS1 sequences obtained from two accessions of C. crassa from Ecuador (GenBank accession numbers OM471920 and OM471919 for isolates CIBE-17 and CIBE-18, respectively) and three from Peru (GenBank accession numbers OM471921, OM471922, and OM471923 for isolates CIBE-13, CIBE-14, and CIBE-15, respectively). The accessions available in the GenBank were used for phylogenetic analysis. For the phytochemical analysis, hydroalcoholic extracts were obtained by maceration using 80% ethanol as solvent, followed by a derivatization process and analysis by gas chromatography-mass spectrometry. Based on the phylogenetic analysis of the C. crassa samples, the ITS1 sequence could be used to differentiate C. crassa of different locations. The samples of C. crassa from Ecuador and Peru are more similar between them than with other clades including Helosis spp. The phytochemical study revealed differences in the presence and relative abundance of some metabolites; mainly eugenol, 1,4-lactone arabinonic acid, dimethoxyrabelomycin and azelaic acid, which are reported for the first time for the species under study and the genus Corynaea. These results are the first findings on the combined analysis using genetic and phytochemical analysis for C. crassa, which could be used as a useful tool for quality control of the C. crassa species in medicinal products.

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.

Essential Oil Chemotypes and Genetic Variability of Cinnamomum verum Leaf Samples Commercialized and Cultivated in the Amazon

Cinnamomum verum (Lauraceae), also known as "true cinnamon" or "Ceylon cinnamon" has been widely used in traditional folk medicine and cuisine for a long time. The systematics of C. verum presents some difficulties due to genetic variation and morphological similarity between other Cinnamomum species. The present work aimed to find chemical and molecular markers of C. verum samples from the Amazon region of Brazil. The leaf EOs and the genetic material (DNA) were extracted from samples cultivated and commercial samples. The chemical composition of the essential oils from samples of C. verum cultivated (Cve1-Cve5) and commercial (Cve6-c-Cv9-c) was grouped by multivariate statistical analysis of Principal Component Analysis (PCA). The major compounds were rich in benzenoids and phenylpropanoids, such as eugenol (0.7-91.0%), benzyl benzoate (0.28-76.51%), (E)-cinnamyl acetate (0.36-32.1%), and (E)-cinnamaldehyde (1.0-19.73%). DNA barcodes were developed for phylogenetic analysis using the chloroplastic regions of the matK and rbcL genes, and psbA-trnH intergenic spacer. The psbA-trnH sequences provided greater diversity of nucleotides, and matK confirmed the identity of C. verum. The combination of DNA barcode and volatile profile was found to be an important tool for the discrimination of C. verum varieties and to examine the authenticity of industrial sources.

Exploring the potential of paper-based analytical sensors for tea geographical origin authentication

Tea (Camellia sinensis (L.) Kuntze-surname of German origin) is a popular beverage consumed worldwide due to its health benefits. Its quality depends on measuring features that may discriminate teas from distinct provenances. Protected designation of origin (PDO) is therefore a very useful label for tea quality evaluation. In the present work, antioxidant activity profiles obtained from microfluidic paper-based analytical devices (µPADs) were analyzed by chemometrics to determine the tea geographic origin. Based on the existing literature, we constructed a database containing chemical data from 26 samples and evaluated it by principal component analysis (PCA) coupled to linear discriminant analysis (LDA). Antioxidant activity was an effective LDA predictor for sample discrimination accomplishing accuracies from 75 to 82%. Modeling performance was favored by an external validation method. The best classification model was found using the first nine PCs as input variables. Training samples achieved a perfect success rate, while the test ones were predicted with 83% specificity, 100% sensitivity, and 90% overall accuracy. The modeling robustness was verified by integrating AUC (0.943) from ROC curve. The PCA-LDA approach taken here demonstrated that the teas coming from different countries can be correctly authenticated through µPADs, thus contributing to certificate samples PDO.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-022-05440-1.

Authentication of Zingiber Species Based on Analysis of Metabolite Profiles

Zingiber corallinum and Zingiber montanum, which belong to the Zingiberaceae family, are traditional Chinese folk medicinal herbs in Guizhou and Yunnan Province of China. They share great similarities in morphology, chemical constituent, and DNA barcoding sequence. The taxonomy of the two Zingiber species is controversial and discrimination of traditional Chinese medicines directly affects the pharmacological and clinical effects. In the present study, we performed a systemic analysis of "super-barcode" and untargeted metabolomics between Z. corallinum and Z. montanum using chloroplast (cp) genome sequencing and gas chromatography-mass spectrometry (GC-MS) analysis. Comparison and phylogenetic analysis of cp genomes of the two Zingiber species showed that the cp genome could not guarantee the accuracy of identification. An untargeted metabolomics strategy combining GC-MS with chemometric methods was proposed to distinguish the Zingiber samples of known variety. A total of 51 volatile compounds extracted from Z. corallinum and Z. montanum were identified, and nine compounds were selected as candidate metabolic markers to reveal the significant difference between Z. corallinum and Z. montanum. The performance of the untargeted metabolomic approach was verified with unknown Zingiber samples. Although the cp genomes could not be used to identify Zingiber species in this study, it will still provide a valuable genomics resource for population studies in the Zingiberaceae family, and the GC-MS based metabolic fingerprint is more promising for species identification and safe application of Z. corallinum and Z. montanum.