Detecting Plant-Based Food Fraud Using Nanopore Metabarcoding: A Proof-of-Concept Study

Area of Science:

• Food Science
• Molecular Biology
• Genetics

Background:

• Economically motivated adulteration (EMA) is a significant threat to food safety, consumer trust, and regulatory compliance, particularly in plant-based food products.
• Traditional detection methods often fail with processed foods and complex mixtures, necessitating advanced analytical techniques.
• DNA metabarcoding presents a powerful, non-targeted, high-throughput alternative for identifying adulterants in food matrices.

Purpose of the Study:

• To develop and evaluate a cost-effective, user-friendly nanopore sequencing-based DNA metabarcoding workflow for detecting economically motivated adulteration (EMA) in food products.
• To assess the sensitivity and reliability of the proposed method using spices and herbal teas as model systems.
• To compare the efficacy of multi-marker (ITS2 + matK + trnH-psbA) versus single-marker approaches for improved detection.

Main Methods:

• Development of a nanopore sequencing workflow for DNA extraction and metabarcoding analysis.
• Utilized a combination of three DNA markers (ITS2, matK, trnH-psbA) for enhanced species identification.
• Validated the method using eight single-species reference samples and five commercial multi-ingredient food products.

Main Results:

• The nanopore sequencing method successfully detected undeclared plant ingredients and species substitutions in commercial food samples, such as mint in oregano.
• The combined ITS2 + matK + trnH-psbA marker set demonstrated higher sensitivity compared to single-barcode methods.
• The workflow achieved a 2-4 day turnaround time with minimal infrastructure requirements.

Conclusions:

• The developed DNA metabarcoding workflow is a sensitive, cost-effective, and rapid screening tool for assessing food authenticity and detecting economically motivated adulteration (EMA).
• The method shows potential for compliance with food labelling regulations (e.g., EU 1169/2011) and food safety programs (e.g., FDA EMA).
• Further research is needed to validate against regulatory limits and expand application to diverse species and processed food matrices, addressing DNA degradation and database limitations.