Improved Protocols of ITS1-Based Metabarcoding and Their Application in the Analysis of Plant-Containing Products

• Main Authors: Denis O. Omelchenko, Anna S. Speranskaya, Andrey A. Ayginin, Kamil Khafizov, Anastasia A. Krinitsina, Anna V. Fedotova, Denis V. Pozdyshev, Viktoria Y. Shtratnikova, Evgenia V. Kupriyanova, German A. Shipulin, Maria D. Logacheva
• Format: Article
• Language: English
• Published: MDPI AG 2019-02-01
• Series: Genes
• Subjects: metabarcoding; ITS1; high-throughput sequencing; food safety; herbal medicine; tea; spice
• Online Access: https://www.mdpi.com/2073-4425/10/2/122

Plants are widely used for food and beverage preparation, most often in the form of complex mixtures of dried and ground parts, such as teas, spices or herbal medicines. Quality control of such products is important due to the potential health risks from the presence of unlabelled components or absence of claimed ones. A promising approach to analyse such products is DNA metabarcoding due to its high resolution and sensitivity. However, this method’s application in food analysis requires several methodology optimizations in DNA extraction, amplification and library preparation. In this study, we present such optimizations. The most important methodological outcomes are the following: (1) the DNA extraction method greatly influences amplification success; (2) the main problem for the application of metabarcoding is DNA purity, not integrity or quantity; and (3) the “non-amplifiable„ samples can be amplified with polymerases resistant to inhibitors. Using this optimized workflow, we analysed a broad set of plant products (teas, spices and herbal remedies) using two NGS platforms. The analysis revealed the problem of both the presence of extraneous components and the absence of labelled ones. Notably, for teas, no correlation was found between the price and either the absence of labelled components or presence of unlabelled ones; for spices, a negative correlation was found between the price and presence of unlabelled components.